From c8a7da2cf4ffbddad30d579d1906f343477b41a6 Mon Sep 17 00:00:00 2001 From: GitHubbit <10294502+GitHubbit@users.noreply.github.com> Date: Wed, 31 May 2023 19:31:08 -0400 Subject: [PATCH 1/6] * Addressed Later important tasks of https://github.com/biothings/biothings_explorer/issues/617#issuecomment-1562104578 Made meta-triples in EHR_Risk_parser.ipynb and outputted relevant x-bte sections that go in the yaml to ehr_risk_yaml_xbte_portions.txt. Copied them from the text file to the yaml This effort auto-generates the x-bte operations your changes. Lines starting --- ehr_risk_kp.yaml | 11305 ++++++++++++++++++++++++++------------------- 1 file changed, 6627 insertions(+), 4678 deletions(-) diff --git a/ehr_risk_kp.yaml b/ehr_risk_kp.yaml index ccc8329..604518a 100644 --- a/ehr_risk_kp.yaml +++ b/ehr_risk_kp.yaml @@ -964,4904 +964,6853 @@ components: ## - association.classifier ## - association.original_predicate ## - association.provided_date - DiseaseMONDO_increased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 2963 records - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "MONDO:0005068" ## myocardial infarction (disease) - # oneOutput: "MONDO:0005904" ## pericarditis (disease) - DiseaseMONDO_increased_DiseaseMONDO-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-MONDO" - # testExamples: - # - qInput: "MONDO:0005009" ## congestive heart failure - # oneOutput: "MONDO:0005071" ## nervous system disorder - DiseaseMONDO_increased_DiseaseNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## 9 records - - supportBatch: true - useTemplating: true - inputs: + ChemCHEBI_decreased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 34917 records + -supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "CHEBI:3732" ## clarithromycin + # oneOutput: "MONDO:0004721" ## liver neoplasm + ChemCHEBI_decreased_DiseaseMONDO_rev: + -supportBatch: true + useTemplating: true + inputs: - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "MONDO:0005300" ## chronic kidney disease - # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - DiseaseMONDO_increased_DiseaseNCIT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: CHEBI + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-CHEBI" + # testExamples: + # - qInput: "MONDO:0005090" ## schizophrenia (disease) + # oneOutput: "CHEBI:107736" ## metoclopramide + ChemCHEBI_decreased_DiseaseNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ## 212 records + -supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "CHEBI:7936" ## paroxetine + # oneOutput: "NCIT:C167118" ## Influenza A Virus Positive + ChemCHEBI_decreased_DiseaseNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-MONDO" - # testExamples: - # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - # oneOutput: "MONDO:0005148" ## type 2 diabetes mellitus - DiseaseMONDO_increased_DiseaseSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 200 records - - supportBatch: true - useTemplating: true - inputs: - - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: CHEBI + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-CHEBI" + # testExamples: + # - qInput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission + # oneOutput: "CHEBI:3139" ## bleomycin + ChemCHEBI_decreased_DiseaseSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + ## 2917 records + -supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "CHEBI:9332" ## sulfamethoxazole + # oneOutput: "SNOMEDCT:386033004" ## Neuropathy (disorder) + ChemCHEBI_decreased_DiseaseSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "MONDO:0005090" ## schizophrenia (disease) - # oneOutput: "SNOMEDCT:709073001" ## Neurocognitive disorder (disorder) - DiseaseMONDO_increased_DiseaseSNOMEDCT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: CHEBI + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-CHEBI" + # testExamples: + # - qInput: "SNOMEDCT:2415007" ## Lumbosacral radiculopathy (disorder) + # oneOutput: "CHEBI:4786" ## enalaprilat + ChemCHEBI_decreased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 24505 records + -supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "CHEBI:9123" ## sertraline + # oneOutput: "HP:0031890" ## Increased urine urobilinogen + ChemCHEBI_decreased_PhenoHP_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: HP + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: CHEBI + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-CHEBI" + # testExamples: + # - qInput: "HP:0000964" ## Eczema + # oneOutput: "CHEBI:41423" ## celecoxib + ChemCHEBI_decreased_PhenoNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## 2254 records + -supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "CHEBI:3614" ## chlorhexidine + # oneOutput: "NCIT:C155871" ## Herpes Simplex Virus Infection + ChemCHEBI_decreased_PhenoNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: CHEBI + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-CHEBI" + # testExamples: + # - qInput: "NCIT:C141278" ## Adenovirus Positive + # oneOutput: "CHEBI:8435" ## prochlorperazine + ChemCHEBI_decreased_PhenoSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + ## 244 records + -supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "CHEBI:85264" ## clavulanate + # oneOutput: "SNOMEDCT:191519005" ## Dementia associated with another disease (disorder) + ChemCHEBI_decreased_PhenoSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-MONDO" - # testExamples: - # - qInput: "SNOMEDCT:386033004" ## Neuropathy (disorder) - # oneOutput: "MONDO:0005301" ## multiple sclerosis - DiseaseNCIT_increased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 1 record - - supportBatch: true - useTemplating: true - inputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: CHEBI + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-CHEBI" + # testExamples: + # - qInput: "SNOMEDCT:127295002" ## Traumatic brain injury (disorder) + # oneOutput: "CHEBI:31440" ## copper sulfate + ChemCHEBI_decreased_ProcedureNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT + ## 222 records + -supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "CHEBI:8884" ## rocuronium + # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + ChemCHEBI_decreased_ProcedureNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - # oneOutput: "MONDO:0007140" ## antiphospholipid syndrome - DiseaseNCIT_increased_DiseaseMONDO-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: CHEBI + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-CHEBI" + # testExamples: + # - qInput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission + # oneOutput: "CHEBI:9449" ## terbutaline + ChemCHEBI_increased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 18248 records + -supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "CHEBI:31441" ## fluticasone + # oneOutput: "MONDO:0009410" ## Addison disease + ChemCHEBI_increased_DiseaseMONDO_rev: + -supportBatch: true + useTemplating: true + inputs: - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: CHEBI + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-CHEBI" + # testExamples: + # - qInput: "MONDO:0008315" ## prostate cancer + # oneOutput: "CHEBI:47426" ## furosemide + ChemCHEBI_increased_DiseaseNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ## 131 records + -supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "CHEBI:9449" ## terbutaline + # oneOutput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission + ChemCHEBI_increased_DiseaseNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-NCIT" - # testExamples: - # - qInput: "MONDO:0007140" ## antiphospholipid syndrome - # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - ## no records for DiseaseNCIT_increased_DiseaseNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## no records for DiseaseNCIT_increased_DiseaseSNOMEDCT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## no records for DiseaseSNOMEDCT_increased_DiseaseMONDO - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## no records for DiseaseSNOMEDCT_increased_DiseaseNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## no records for DiseaseSNOMEDCT_increased_DiseaseSNOMEDCT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - DiseaseMONDO_increased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 2107 records - - supportBatch: true - useTemplating: true - inputs: - - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "MONDO:0005002" ## chronic obstructive pulmonary disease - # oneOutput: "HP:0000739" ## Anxiety - DiseaseMONDO_increased_PhenoHP-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: CHEBI + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-CHEBI" + # testExamples: + # - qInput: "NCIT:C159516" ## Liver Lesion + # oneOutput: "CHEBI:9943" ## venlafaxine + ChemCHEBI_increased_DiseaseSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + ## 1542 records + -supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "CHEBI:46632" ## clonidine + # oneOutput: "SNOMEDCT:197352008" ## Toxic hepatitis (disorder) + ChemCHEBI_increased_DiseaseSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: CHEBI + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-CHEBI" + # testExamples: + # - qInput: "SNOMEDCT:191519005" ## Dementia associated with another disease (disorder) + # oneOutput: "CHEBI:44185" ## methotrexate + ChemCHEBI_increased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 13225 records + -supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "CHEBI:135738" ## clevidipine + # oneOutput: "HP:0003077" ## Hyperlipidemia + ChemCHEBI_increased_PhenoHP_rev: + -supportBatch: true + useTemplating: true + inputs: - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-MONDO" - # testExamples: - # - qInput: "HP:0000790" ## Hematuria - # oneOutput: "MONDO:0005002" ## chronic obstructive pulmonary disease - DiseaseMONDO_increased_PhenoNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 42 records - - supportBatch: true - useTemplating: true - inputs: - - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: CHEBI + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-CHEBI" + # testExamples: + # - qInput: "HP:0001397" ## Hepatic steatosis + # oneOutput: "CHEBI:6456" ## lidocaine + ChemCHEBI_increased_PhenoNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## 1176 records + -supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "CHEBI:8499" ## propranolol + # oneOutput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission + ChemCHEBI_increased_PhenoNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "MONDO:0005249" ## pneumonia - # oneOutput: "NCIT:C167118" ## Influenza B Virus Positive (Influenza A Virus Positive?) - DiseaseMONDO_increased_PhenoNCIT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: CHEBI + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-CHEBI" + # testExamples: + # - qInput: "NCIT:C146650" ## Clostridium difficile Positive + # oneOutput: "CHEBI:3207" ## budesonide + ChemCHEBI_increased_PhenoSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + ## 99 records + -supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "CHEBI:9600" ## timolol + # oneOutput: "SNOMEDCT:76571007" ## Septic shock (disorder) + ChemCHEBI_increased_PhenoSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: CHEBI + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-CHEBI" + # testExamples: + # - qInput: "SNOMEDCT:709073001" ## Neurocognitive disorder (disorder) + # oneOutput: "CHEBI:601027" ## aliskiren + ChemCHEBI_increased_ProcedureNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT + ## 121 records + -supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "CHEBI:3515" ## cefuroxime + # oneOutput: "NCIT:C141278" ## Adenovirus Positive + ChemCHEBI_increased_ProcedureNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-MONDO" - # testExamples: - # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - # oneOutput: "MONDO:0005249" ## pneumonia - DiseaseMONDO_increased_PhenoSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ## 18 records - - supportBatch: true - useTemplating: true - inputs: + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: CHEBI + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-CHEBI" + # testExamples: + # - qInput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission + # oneOutput: "CHEBI:33283" ## thiamine + ChemUNII_decreased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 5902 records + -supportBatch: true + useTemplating: true + inputs: + - id: UNII + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "UNII:X85G7936GV" ## abciximab + # oneOutput: "MONDO:0005495" ## adrenal gland disease + ChemUNII_decreased_DiseaseMONDO_rev: + -supportBatch: true + useTemplating: true + inputs: - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: UNII + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-UNII" + # testExamples: + # - qInput: "MONDO:0005090" ## schizophrenia (disease) + # oneOutput: "UNII:2S9ZZM9Q9V" ## bevacizumab + ChemUNII_decreased_DiseaseNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ## 44 records + -supportBatch: true + useTemplating: true + inputs: + - id: UNII + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "UNII:7EV65EAW6H" ## lanolin + # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive + ChemUNII_decreased_DiseaseNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: UNII + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-UNII" + # testExamples: + # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + # oneOutput: "UNII:91X1KLU43E" ## golimumab + ChemUNII_decreased_DiseaseSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + ## 505 records + -supportBatch: true + useTemplating: true + inputs: + - id: UNII + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "UNII:7D0YB67S97" ## abatacept + # oneOutput: "SNOMEDCT:54404000" ## Cervical radiculopathy (disorder) + ChemUNII_decreased_DiseaseSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "MONDO:0004981" ## atrial fibrillation (disease) - # oneOutput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) - DiseaseMONDO_increased_PhenoSNOMEDCT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: UNII + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-UNII" + # testExamples: + # - qInput: "SNOMEDCT:709073001" ## Neurocognitive disorder (disorder) + # oneOutput: "UNII:7EV65EAW6H" ## lanolin + ChemUNII_decreased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 3727 records + -supportBatch: true + useTemplating: true + inputs: + - id: UNII + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "UNII:I031V2H011" ## tocilizumab + # oneOutput: "HP:0000739" ## Anxiety + ChemUNII_decreased_PhenoHP_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: HP + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: UNII + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-UNII" + # testExamples: + # - qInput: "HP:0011897" ## Neutrophilia + # oneOutput: "UNII:9RV78Q2002" ## vedolizumab + ChemUNII_decreased_PhenoNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## 381 records + -supportBatch: true + useTemplating: true + inputs: + - id: UNII + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "UNII:25ADE2236L" ## thrombin + # oneOutput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission + ChemUNII_decreased_PhenoNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: UNII + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-UNII" + # testExamples: + # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + # oneOutput: "UNII:P188ANX8CK" ## trastuzumab + ChemUNII_decreased_PhenoSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + ## 39 records + -supportBatch: true + useTemplating: true + inputs: + - id: UNII + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "UNII:I031V2H011" ## tocilizumab + # oneOutput: "SNOMEDCT:191519005" ## Dementia associated with another disease (disorder) + ChemUNII_decreased_PhenoSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: UNII + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-UNII" + # testExamples: + # - qInput: "SNOMEDCT:239792003" ## Seronegative rheumatoid arthritis (disorder) + # oneOutput: "UNII:I5I8VB78VT" ## erenumab + ChemUNII_decreased_ProcedureNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT + ## 43 records + -supportBatch: true + useTemplating: true + inputs: + - id: UNII + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "UNII:OP401G7OJC" ## etanercept + # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive + ChemUNII_decreased_ProcedureNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: UNII + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-UNII" + # testExamples: + # - qInput: "NCIT:C155871" ## Herpes Simplex Virus Infection + # oneOutput: "UNII:A10SJL62JY" ## ocrelizumab + ChemUNII_increased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 2158 records + -supportBatch: true + useTemplating: true + inputs: + - id: UNII + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "UNII:A10SJL62JY" ## ocrelizumab + # oneOutput: "MONDO:0005090" ## schizophrenia (disease) + ChemUNII_increased_DiseaseMONDO_rev: + -supportBatch: true + useTemplating: true + inputs: - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-MONDO" - # testExamples: - # - qInput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) - # oneOutput: "MONDO:0005044" ## hypertensive disorder - ## no records for DiseaseNCIT_increased_PhenoHP - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## no records for DiseaseNCIT_increased_PhenoNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## no records for DiseaseNCIT_increased_PhenoSNOMEDCT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - DiseaseSNOMEDCT_increased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 52 records - - supportBatch: true - useTemplating: true - inputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: UNII + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-UNII" + # testExamples: + # - qInput: "MONDO:0002447" ## endometrial carcinoma (disease) + # oneOutput: "UNII:O43472U9X8" ## obinutuzumab + ChemUNII_increased_DiseaseNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ## 8 records + -supportBatch: true + useTemplating: true + inputs: + - id: UNII + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "UNII:E47C0NF7LV" ## enoxaparin + # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + ChemUNII_increased_DiseaseNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: UNII + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-UNII" + # testExamples: + # - qInput: "NCIT:C159516" ## Liver Lesion + # oneOutput: "UNII:73B0K5S26A" ## belimumab + ChemUNII_increased_DiseaseSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + ## 171 records + -supportBatch: true + useTemplating: true + inputs: + - id: UNII + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "UNII:DQ448MW7KS" ## palivizumab + # oneOutput: "SNOMEDCT:197352008" ## Toxic hepatitis (disorder) + ChemUNII_increased_DiseaseSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "SNOMEDCT:2415007" ## Lumbosacral radiculopathy (disorder) - # oneOutput: "HP:0001369" ## Arthritis - DiseaseSNOMEDCT_increased_PhenoHP-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: UNII + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-UNII" + # testExamples: + # - qInput: "SNOMEDCT:237519003" ## Autoimmune hypothyroidism (disorder) + # oneOutput: "UNII:4T6H12BN9U" ## petrolatum + ChemUNII_increased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 1993 records + -supportBatch: true + useTemplating: true + inputs: + - id: UNII + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "UNII:K16AIQ8CTM" ## pertuzumab + # oneOutput: "HP:0005518" ## Increased mean corpuscular volume + ChemUNII_increased_PhenoHP_rev: + -supportBatch: true + useTemplating: true + inputs: - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-SNOMEDCT" - # testExamples: - # - qInput: "HP:0002385" ## Paraparesis - # oneOutput: "SNOMEDCT:2415007" ## Lumbosacral radiculopathy (disorder) - ## no records for DiseaseSNOMEDCT_increased_PhenoNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## no records for DiseaseSNOMEDCT_increased_PhenoSNOMEDCT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - DiseaseMONDO_increased_ProcedureNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Procedure - ## 69 records - - supportBatch: true - useTemplating: true - inputs: - - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: UNII + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-UNII" + # testExamples: + # - qInput: "HP:0003124" ## Hypercholesterolemia + # oneOutput: "UNII:FU77B4U5Z0" ## ustekinumab + ChemUNII_increased_PhenoNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## 139 records + -supportBatch: true + useTemplating: true + inputs: + - id: UNII + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "UNII:4F4X42SYQ6" ## rituximab + # oneOutput: "NCIT:C155871" ## Herpes Simplex Virus Infection + ChemUNII_increased_PhenoNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "MONDO:0005300" ## chronic kidney disease - # oneOutput: "NCIT:C15271" ## Liver Transplantation - DiseaseMONDO_increased_ProcedureNCIT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: UNII + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-UNII" + # testExamples: + # - qInput: "NCIT:C15271" ## Liver Transplantation + # oneOutput: "UNII:4Z63YK6E0E" ## daratumumab + ChemUNII_increased_PhenoSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + ## 13 records + -supportBatch: true + useTemplating: true + inputs: + - id: UNII + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "UNII:73B0K5S26A" ## belimumab + # oneOutput: "SNOMEDCT:237519003" ## Autoimmune hypothyroidism (disorder) + ChemUNII_increased_PhenoSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: UNII + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-UNII" + # testExamples: + # - qInput: "SNOMEDCT:386033004" ## Neuropathy (disorder) + # oneOutput: "UNII:DPT0O3T46P" ## pembrolizumab + ChemUNII_increased_ProcedureNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT + ## 9 records + -supportBatch: true + useTemplating: true + inputs: + - id: UNII + - semantic: ChemicalEntity + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "UNII:DPT0O3T46P" ## pembrolizumab + # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive + ChemUNII_increased_ProcedureNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Procedure - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-MONDO" - # testExamples: - # - qInput: "NCIT:C15271" ## Liver Transplantation - # oneOutput: "MONDO:0005155" ## cirrhosis of liver - ## no records for DiseaseNCIT_increased_ProcedureNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Procedure - ## no records for DiseaseSNOMEDCT_increased_ProcedureNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Procedure + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: UNII + semantic: ChemicalEntity + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-UNII" + # testExamples: + # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + # oneOutput: "UNII:I16QD7X297" ## neomycin DiseaseMONDO_decreased_DiseaseMONDO: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 190 records - - supportBatch: true - useTemplating: true - inputs: - - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + ## 13640 records + -supportBatch: true + useTemplating: true + inputs: - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "MONDO:0005148" ## type 2 diabetes mellitus - # oneOutput: "MONDO:0005301" ## multiple sclerosis - DiseaseMONDO_decreased_DiseaseMONDO-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "MONDO:0005010" ## coronary artery disease + # oneOutput: "MONDO:0005626" ## epithelial neoplasm + DiseaseMONDO_decreased_DiseaseMONDO_rev: + -supportBatch: true + useTemplating: true + inputs: - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-MONDO" - # testExamples: - # - qInput: "MONDO:0002039" ## cognitive disorder - # oneOutput: "MONDO:0005178" ## osteoarthritis + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "MONDO:0005154" ## liver disease + # oneOutput: "MONDO:0005009" ## congestive heart failure DiseaseMONDO_decreased_DiseaseNCIT: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## 1 record - - supportBatch: true - useTemplating: true - inputs: + ## 86 records + -supportBatch: true + useTemplating: true + inputs: - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "MONDO:0004981" ## atrial fibrillation (disease) - # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - DiseaseMONDO_decreased_DiseaseNCIT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "MONDO:0004979" ## asthma + # oneOutput: "NCIT:C167118" ## Influenza A Virus Positive + DiseaseMONDO_decreased_DiseaseNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-MONDO" - # testExamples: - # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - # oneOutput: "MONDO:0004981" ## atrial fibrillation (disease) + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "NCIT:C15271" ## Liver Transplantation + # oneOutput: "MONDO:0001150" ## hydrocephalus DiseaseMONDO_decreased_DiseaseSNOMEDCT: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 21 records - - supportBatch: true - useTemplating: true - inputs: - - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "MONDO:0005311" ## atherosclerosis - # oneOutput: "SNOMEDCT:386033004" ## Neuropathy (disorder) - DiseaseMONDO_decreased_DiseaseSNOMEDCT-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-MONDO" - # testExamples: - # - qInput: "SNOMEDCT:2415007" ## Lumbosacral radiculopathy (disorder) - # oneOutput: "MONDO:0005108" ## viral infectious disease - ## no records for DiseaseNCIT_decreased_DiseaseMONDO - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## no records for DiseaseNCIT_decreased_DiseaseNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## no records for DiseaseNCIT_decreased_DiseaseSNOMEDCT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - DiseaseSNOMEDCT_decreased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 6 records - - supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) - # oneOutput: "MONDO:0004670" ## lupus erythematosus - DiseaseSNOMEDCT_decreased_DiseaseMONDO-rev: - - supportBatch: true - useTemplating: true - inputs: + ## 1237 records + -supportBatch: true + useTemplating: true + inputs: - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "MONDO:0002959" ## radiculopathy + # oneOutput: "SNOMEDCT:127295002" ## Traumatic brain injury (disorder) + DiseaseMONDO_decreased_DiseaseSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-SNOMEDCT" - # testExamples: - # - qInput: "MONDO:0005546" ## fibromyalgia - # oneOutput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) - ## no records for DiseaseSNOMEDCT_decreased_DiseaseNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## no records for DiseaseSNOMEDCT_decreased_DiseaseSNOMEDCT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "SNOMEDCT:76571007" ## Septic shock (disorder) + # oneOutput: "MONDO:0005028" ## esophageal adenocarcinoma DiseaseMONDO_decreased_PhenoHP: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 426 records - - supportBatch: true - useTemplating: true - inputs: + ## 10101 records + -supportBatch: true + useTemplating: true + inputs: - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "MONDO:0005002" ## chronic obstructive pulmonary disease - # oneOutput: "HP:0033077" ## Increased circulating free T4 level - DiseaseMONDO_decreased_PhenoHP-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "MONDO:0005340" ## alopecia areata + # oneOutput: "HP:0003119" ## Abnormal circulating lipid concentration + DiseaseMONDO_decreased_PhenoHP_rev: + -supportBatch: true + useTemplating: true + inputs: - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-MONDO" - # testExamples: - # - qInput: "HP:0025066" ## Decreased mean corpuscular volume - # oneOutput: "MONDO:0005071" ## nervous system disorder + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "HP:0001945" ## Fever + # oneOutput: "MONDO:0005155" ## cirrhosis of liver DiseaseMONDO_decreased_PhenoNCIT: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 17 records - - supportBatch: true - useTemplating: true - inputs: + ## 1293 records + -supportBatch: true + useTemplating: true + inputs: - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "MONDO:0005148" ## type 2 diabetes mellitus - # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - DiseaseMONDO_decreased_PhenoNCIT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "MONDO:0005090" ## schizophrenia (disease) + # oneOutput: "NCIT:C3587" ## Chronic Lymphocytic Leukemia in Remission + DiseaseMONDO_decreased_PhenoNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-MONDO" - # testExamples: - # - qInput: "NCIT:C146650" ## Clostridium difficile Positive - # oneOutput: "MONDO:0005249" ## pneumonia - ## no records for DiseaseMONDO_decreased_PhenoSNOMEDCT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "NCIT:C146650" ## Clostridium difficile Positive + # oneOutput: "MONDO:0005180" ## Parkinson disease + DiseaseMONDO_decreased_PhenoSNOMEDCT: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ## no records for DiseaseNCIT_decreased_PhenoHP - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## no records for DiseaseNCIT_decreased_PhenoNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## no records for DiseaseNCIT_decreased_PhenoSNOMEDCT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - DiseaseSNOMEDCT_decreased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 22 records - - supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "SNOMEDCT:76571007" ## Septic shock (disorder) - # oneOutput: "HP:0031963" ## Decreased serum anion gap - DiseaseSNOMEDCT_decreased_PhenoHP-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + ## 88 records + -supportBatch: true + useTemplating: true + inputs: + - id: MONDO + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "MONDO:0011849" ## psoriatic arthritis + # oneOutput: "SNOMEDCT:2415007" ## Lumbosacral radiculopathy (disorder) + DiseaseMONDO_decreased_PhenoSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-SNOMEDCT" - # testExamples: - # - qInput: "HP:0031969" ## Reduced blood urea nitrogen - # oneOutput: "SNOMEDCT:76571007" ## Septic shock (disorder) - ## no records for DiseaseSNOMEDCT_decreased_PhenoNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## no records for DiseaseSNOMEDCT_decreased_PhenoSNOMEDCT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) + # oneOutput: "MONDO:0005485" ## psychotic disorder DiseaseMONDO_decreased_ProcedureNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure - ## 1 record - - supportBatch: true - useTemplating: true - inputs: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT + ## 113 records + -supportBatch: true + useTemplating: true + inputs: - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "MONDO:0007028" ## rotator cuff syndrome + # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + DiseaseMONDO_decreased_ProcedureNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "MONDO:0006011" ## viral hepatitis - # oneOutput: "NCIT:C15271" ## Liver Transplantation - DiseaseMONDO_decreased_ProcedureNCIT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "NCIT:C167118" ## Influenza A Virus Positive + # oneOutput: "MONDO:0001942" ## generalized anxiety disorder + DiseaseMONDO_increased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 14415 records + -supportBatch: true + useTemplating: true + inputs: + - id: MONDO + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "MONDO:0004988" ## breast adenocarcinoma + # oneOutput: "MONDO:0004868" ## biliary tract disease + DiseaseMONDO_increased_DiseaseMONDO_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: MONDO + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "MONDO:0005011" ## Crohn disease + # oneOutput: "MONDO:0042981" ## aortic valve stenosis + DiseaseMONDO_increased_DiseaseNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ## 96 records + -supportBatch: true + useTemplating: true + inputs: + - id: MONDO + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "MONDO:0006763" ## frozen shoulder + # oneOutput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission + DiseaseMONDO_increased_DiseaseNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Procedure - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "NCIT:C146650" ## Clostridium difficile Positive + # oneOutput: "MONDO:0024317" ## chronic pain syndrome + DiseaseMONDO_increased_DiseaseSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + ## 1129 records + -supportBatch: true + useTemplating: true + inputs: - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-MONDO" - # testExamples: - # - qInput: "NCIT:C15271" ## Liver Transplantation - # oneOutput: "MONDO:0006011" ## viral hepatitis - ## no records for DiseaseNCIT_decreased_ProcedureNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure - ## no records for DiseaseSNOMEDCT_decreased_ProcedureNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure - PhenoHP_increased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 3536 records - - supportBatch: true - useTemplating: true - inputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "MONDO:0005344" ## hepatitis B virus infection + # oneOutput: "SNOMEDCT:191519005" ## Dementia associated with another disease (disorder) + DiseaseMONDO_increased_DiseaseSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "SNOMEDCT:54404000" ## Cervical radiculopathy (disorder) + # oneOutput: "MONDO:0005010" ## coronary artery disease + DiseaseMONDO_increased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 9919 records + -supportBatch: true + useTemplating: true + inputs: + - id: MONDO + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "MONDO:0005068" ## myocardial infarction (disease) + # oneOutput: "HP:0002829" ## Arthralgia + DiseaseMONDO_increased_PhenoHP_rev: + -supportBatch: true + useTemplating: true + inputs: - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "HP:0001945" ## Fever + # oneOutput: "MONDO:0005230" ## cellulitis (disease) + DiseaseMONDO_increased_PhenoNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## 527 records + -supportBatch: true + useTemplating: true + inputs: - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "HP:0000093" ## Proteinuria - # oneOutput: "MONDO:0001627" ## dementia (disease) - PhenoHP_increased_DiseaseMONDO-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "MONDO:0005146" ## post-traumatic stress disorder + # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive + DiseaseMONDO_increased_PhenoNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "NCIT:C146650" ## Clostridium difficile Positive + # oneOutput: "MONDO:0005011" ## Crohn disease + DiseaseMONDO_increased_PhenoSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + ## 94 records + -supportBatch: true + useTemplating: true + inputs: - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-HP" - # testExamples: - # - qInput: "MONDO:0001650" ## acute cystitis (disease) - # oneOutput: "HP:0000093" ## Proteinuria - PhenoHP_increased_DiseaseNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## 4 records - - supportBatch: true - useTemplating: true - inputs: - - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "MONDO:0013600" ## insomnia (disease) + # oneOutput: "SNOMEDCT:76571007" ## Septic shock (disorder) + DiseaseMONDO_increased_PhenoSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "SNOMEDCT:127295002" ## Traumatic brain injury (disorder) + # oneOutput: "MONDO:0005300" ## chronic kidney disease + DiseaseMONDO_increased_ProcedureNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT + ## 69 records + -supportBatch: true + useTemplating: true + inputs: + - id: MONDO + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "MONDO:0002959" ## radiculopathy + # oneOutput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission + DiseaseMONDO_increased_ProcedureNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "HP:0003645" ## Prolonged partial thromboplastin time - # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - PhenoHP_increased_DiseaseNCIT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "NCIT:C167118" ## Influenza A Virus Positive + # oneOutput: "MONDO:0007488" ## Lewy body dementia + DiseaseNCIT_decreased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 73 records + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-HP" - # testExamples: - # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - # oneOutput: "HP:0100724" ## Hypercoagulability - PhenoHP_increased_DiseaseSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 253 records - - supportBatch: true - useTemplating: true - inputs: - - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "HP:0000870" ## Increased circulating prolactin concentration - # oneOutput: "SNOMEDCT:127295002" ## Traumatic brain injury (disorder) - PhenoHP_increased_DiseaseSNOMEDCT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "NCIT:C159516" ## Liver Lesion + # oneOutput: "MONDO:0004375" ## end stage renal failure + DiseaseNCIT_decreased_DiseaseMONDO_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: MONDO + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "MONDO:0013662" ## Barrett esophagus + # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + DiseaseNCIT_decreased_DiseaseSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + ## 7 records + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C52007" ## Arthrodesis + # oneOutput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) + DiseaseNCIT_decreased_DiseaseSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:197352008" ## Toxic hepatitis (disorder) + # oneOutput: "NCIT:C155871" ## Herpes Simplex Virus Infection + DiseaseNCIT_decreased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 44 records + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission + # oneOutput: "HP:0002076" ## Migraine + DiseaseNCIT_decreased_PhenoHP_rev: + -supportBatch: true + useTemplating: true + inputs: - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-HP" - # testExamples: - # - qInput: "SNOMEDCT:709073001" ## Neurocognitive disorder (disorder) - # oneOutput: "HP:0000870" ## Increased circulating prolactin concentration - PhenoNCIT_increased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 11 records - - supportBatch: true - useTemplating: true - inputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "HP:0003138" ## Increased blood urea nitrogen + # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive + DiseaseNCIT_decreased_PhenoNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## 9 records + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "NCIT:C159516" ## Liver Lesion - # oneOutput: "MONDO:0005154" ## liver disease - PhenoNCIT_increased_DiseaseMONDO-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C167118" ## Influenza A Virus Positive + # oneOutput: "NCIT:C159516" ## Liver Lesion + DiseaseNCIT_decreased_PhenoNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C155871" ## Herpes Simplex Virus Infection + # oneOutput: "NCIT:C51691" ## Arthroplasty + DiseaseNCIT_decreased_ProcedureNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT + ## 1 records + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C50815" ## Aortic Valve Replacement + # oneOutput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission + DiseaseNCIT_decreased_ProcedureNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + # oneOutput: "NCIT:C50815" ## Aortic Valve Replacement + DiseaseNCIT_increased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 82 records + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "NCIT:C52007" ## Arthrodesis + # oneOutput: "MONDO:0001824" ## polyneuropathy + DiseaseNCIT_increased_DiseaseMONDO_rev: + -supportBatch: true + useTemplating: true + inputs: - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "MONDO:0007256" ## hepatocellular carcinoma + # oneOutput: "NCIT:C50815" ## Aortic Valve Replacement + DiseaseNCIT_increased_DiseaseSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + ## 6 records + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-NCIT" - # testExamples: - # - qInput: "MONDO:0004948" ## B-cell chronic lymphocytic leukemia - # oneOutput: "NCIT:C3587" ## Chronic Lymphocytic Leukemia in Remission - ## no records for PhenoNCIT_increased_DiseaseNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## no records for PhenoNCIT_increased_DiseaseSNOMEDCT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - PhenoSNOMEDCT_increased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 27 records - - supportBatch: true - useTemplating: true - inputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C155871" ## Herpes Simplex Virus Infection + # oneOutput: "SNOMEDCT:127295002" ## Traumatic brain injury (disorder) + DiseaseNCIT_increased_DiseaseSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "SNOMEDCT:166816003" ## Serum lipids high (finding) - # oneOutput: "MONDO:0001356" ## iron deficiency anemia - PhenoSNOMEDCT_increased_DiseaseMONDO-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) + # oneOutput: "NCIT:C15271" ## Liver Transplantation + DiseaseNCIT_increased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 66 records + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "NCIT:C50815" ## Aortic Valve Replacement + # oneOutput: "HP:0100806" ## Sepsis + DiseaseNCIT_increased_PhenoHP_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: HP + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "HP:0001974" ## Leukocytosis + # oneOutput: "NCIT:C15271" ## Liver Transplantation + DiseaseNCIT_increased_PhenoNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## 1 records + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + DiseaseNCIT_increased_PhenoNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C141278" ## Adenovirus Positive + # oneOutput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission + DiseaseNCIT_increased_PhenoSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + ## 1 records + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C38033" ## Arthroscopy + # oneOutput: "SNOMEDCT:237519003" ## Autoimmune hypothyroidism (disorder) + DiseaseNCIT_increased_PhenoSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-SNOMEDCT" - # testExamples: - # - qInput: "MONDO:0006920" ## prediabetes syndrome - # oneOutput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) - ## no records for PhenoSNOMEDCT_increased_DiseaseNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - PhenoSNOMEDCT_increased_DiseaseSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 1 record - - supportBatch: true - useTemplating: true - inputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:709073001" ## Neurocognitive disorder (disorder) + # oneOutput: "NCIT:C3587" ## Chronic Lymphocytic Leukemia in Remission + DiseaseSNOMEDCT_decreased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 1318 records + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "SNOMEDCT:76571007" ## Septic shock (disorder) + # oneOutput: "MONDO:0020696" ## vitamin B12 deficiency + DiseaseSNOMEDCT_decreased_DiseaseMONDO_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: MONDO + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "MONDO:0020108" ## autoimmune hemolytic anemia + # oneOutput: "SNOMEDCT:711150003" ## Long-term current use of anticoagulant (situation) + DiseaseSNOMEDCT_decreased_DiseaseNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ## 10 records + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "SNOMEDCT:166816003" ## Serum lipids high (finding) - # oneOutput: "SNOMEDCT:191519005" ## Dementia associated with another disease (disorder) - PhenoSNOMEDCT_increased_DiseaseSNOMEDCT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) + # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + DiseaseSNOMEDCT_decreased_DiseaseNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C167118" ## Influenza A Virus Positive + # oneOutput: "SNOMEDCT:386033004" ## Neuropathy (disorder) + DiseaseSNOMEDCT_decreased_DiseaseSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + ## 101 records + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "SNOMEDCT:191519005" ## Dementia associated with another disease (disorder) + # oneOutput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) + DiseaseSNOMEDCT_decreased_DiseaseSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-SNOMEDCT" - # testExamples: - # - qInput: "SNOMEDCT:191519005" ## Dementia associated with another disease (disorder) - # oneOutput: "SNOMEDCT:166816003" ## Serum lipids high (finding) - PhenoHP_increased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 5487 records - - supportBatch: true - useTemplating: true - inputs: - - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "HP:0000093" ## Proteinuria - # oneOutput: "HP:0003155" ## Elevated alkaline phosphatase - PhenoHP_increased_PhenoHP-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-HP" - # testExamples: - # - qInput: "HP:0003138" ## Increased blood urea nitrogen - # oneOutput: "HP:0000093" ## Proteinuria - PhenoHP_increased_PhenoNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 244 records - - supportBatch: true - useTemplating: true - inputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "SNOMEDCT:237519003" ## Autoimmune hypothyroidism (disorder) + # oneOutput: "SNOMEDCT:201839001" ## Primary coxarthrosis, bilateral (disorder) + DiseaseSNOMEDCT_decreased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 957 records + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "SNOMEDCT:711150003" ## Long-term current use of anticoagulant (situation) + # oneOutput: "HP:0000870" ## Increased circulating prolactin concentration + DiseaseSNOMEDCT_decreased_PhenoHP_rev: + -supportBatch: true + useTemplating: true + inputs: - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "HP:0000988" ## Skin rash - # oneOutput: "NCIT:C155871" ## Herpes Simplex Virus Infection - PhenoHP_increased_PhenoNCIT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "HP:0003282" ## Low alkaline phosphatase + # oneOutput: "SNOMEDCT:47049007" ## Ankylosis of spine (disorder) + DiseaseSNOMEDCT_decreased_PhenoNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## 116 records + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:2415007" ## Lumbosacral radiculopathy (disorder) + # oneOutput: "NCIT:C141278" ## Adenovirus Positive + DiseaseSNOMEDCT_decreased_PhenoNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-HP" - # testExamples: - # - qInput: "NCIT:C159516" ## Liver Lesion - # oneOutput: "HP:0000870" ## Increased circulating prolactin concentration - PhenoHP_increased_PhenoSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ## 19 records - - supportBatch: true - useTemplating: true - inputs: - - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C15271" ## Liver Transplantation + # oneOutput: "SNOMEDCT:386033004" ## Neuropathy (disorder) + DiseaseSNOMEDCT_decreased_PhenoSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + ## 8 records + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "HP:0001369" ## Arthritis - # oneOutput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) - PhenoHP_increased_PhenoSNOMEDCT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) + # oneOutput: "SNOMEDCT:197352008" ## Toxic hepatitis (disorder) + DiseaseSNOMEDCT_decreased_PhenoSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-HP" - # testExamples: - # - qInput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) - # oneOutput: "HP:0011227" ## Elevated C-reactive protein level - PhenoNCIT_increased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 15 records - - supportBatch: true - useTemplating: true - inputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "SNOMEDCT:711150003" ## Long-term current use of anticoagulant (situation) + # oneOutput: "SNOMEDCT:201839001" ## Primary coxarthrosis, bilateral (disorder) + DiseaseSNOMEDCT_decreased_ProcedureNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT + ## 13 records + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:76571007" ## Septic shock (disorder) + # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + DiseaseSNOMEDCT_decreased_ProcedureNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - # oneOutput: "HP:0003326" ## Myalgia - PhenoNCIT_increased_PhenoHP-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C155871" ## Herpes Simplex Virus Infection + # oneOutput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) + DiseaseSNOMEDCT_increased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 1007 records + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "SNOMEDCT:191519005" ## Dementia associated with another disease (disorder) + # oneOutput: "MONDO:0007147" ## obstructive sleep apnea syndrome + DiseaseSNOMEDCT_increased_DiseaseMONDO_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: MONDO + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "MONDO:0005298" ## osteoporosis + # oneOutput: "SNOMEDCT:202805003" ## Sacroiliac disorder (disorder) + DiseaseSNOMEDCT_increased_DiseaseNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ## 5 records + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:709073001" ## Neurocognitive disorder (disorder) + # oneOutput: "NCIT:C159516" ## Liver Lesion + DiseaseSNOMEDCT_increased_DiseaseNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-NCIT" - # testExamples: - # - qInput: "HP:0001397" ## Hepatic steatosis - # oneOutput: "NCIT:C159516" ## Liver Lesion - ## no records for PhenoNCIT_increased_PhenoNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## no records for PhenoNCIT_increased_PhenoSNOMEDCT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - PhenoSNOMEDCT_increased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 15 records - - supportBatch: true - useTemplating: true - inputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission + # oneOutput: "SNOMEDCT:386033004" ## Neuropathy (disorder) + DiseaseSNOMEDCT_increased_DiseaseSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + ## 81 records + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "SNOMEDCT:166816003" ## Serum lipids high (finding) - # oneOutput: "HP:0000964" ## Eczema - PhenoSNOMEDCT_increased_PhenoHP-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "SNOMEDCT:127295002" ## Traumatic brain injury (disorder) + # oneOutput: "SNOMEDCT:711150003" ## Long-term current use of anticoagulant (situation) + DiseaseSNOMEDCT_increased_DiseaseSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-SNOMEDCT" - # testExamples: - # - qInput: "HP:0002617" ## Vascular dilatation - # oneOutput: "SNOMEDCT:166816003" ## Serum lipids high (finding) - ## no records for PhenoSNOMEDCT_increased_PhenoNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## no records for PhenoSNOMEDCT_increased_PhenoSNOMEDCT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - PhenoHP_increased_ProcedureNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Procedure - ## 15 records - - supportBatch: true - useTemplating: true - inputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "SNOMEDCT:54404000" ## Cervical radiculopathy (disorder) + # oneOutput: "SNOMEDCT:239792003" ## Seronegative rheumatoid arthritis (disorder) + DiseaseSNOMEDCT_increased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 693 records + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "SNOMEDCT:201839001" ## Primary coxarthrosis, bilateral (disorder) + # oneOutput: "HP:0006775" ## Multiple myeloma + DiseaseSNOMEDCT_increased_PhenoHP_rev: + -supportBatch: true + useTemplating: true + inputs: - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "HP:0000787" ## Nephrolithiasis + # oneOutput: "SNOMEDCT:76571007" ## Septic shock (disorder) + DiseaseSNOMEDCT_increased_PhenoNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## 34 records + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:66944004" ## Autoimmune thyroiditis (disorder) + # oneOutput: "NCIT:C141278" ## Adenovirus Positive + DiseaseSNOMEDCT_increased_PhenoNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "HP:0001882" ## Leukopenia - # oneOutput: "NCIT:C15271" ## Liver Transplantation - PhenoHP_increased_ProcedureNCIT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C167118" ## Influenza A Virus Positive + # oneOutput: "SNOMEDCT:201839001" ## Primary coxarthrosis, bilateral (disorder) + DiseaseSNOMEDCT_increased_PhenoSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + ## 7 records + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "SNOMEDCT:197352008" ## Toxic hepatitis (disorder) + # oneOutput: "SNOMEDCT:54404000" ## Cervical radiculopathy (disorder) + DiseaseSNOMEDCT_increased_PhenoSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "SNOMEDCT:127295002" ## Traumatic brain injury (disorder) + # oneOutput: "SNOMEDCT:197352008" ## Toxic hepatitis (disorder) + DiseaseSNOMEDCT_increased_ProcedureNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT + ## 2 records + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:201839001" ## Primary coxarthrosis, bilateral (disorder) + # oneOutput: "NCIT:C3587" ## Chronic Lymphocytic Leukemia in Remission + DiseaseSNOMEDCT_increased_ProcedureNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Procedure - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-HP" - # testExamples: - # - qInput: "NCIT:C15271" ## Liver Transplantation - # oneOutput: "HP:0012213" ## Decreased glomerular filtration rate - ## no records for PhenoNCIT_increased_ProcedureNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Procedure - ## no records for PhenoSNOMEDCT_increased_ProcedureNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Procedure + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission + # oneOutput: "SNOMEDCT:197354009" ## Toxic liver disease (disorder) PhenoHP_decreased_DiseaseMONDO: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 4025 records - - supportBatch: true - useTemplating: true - inputs: + ## 18759 records + -supportBatch: true + useTemplating: true + inputs: - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "HP:0000870" ## Increased circulating prolactin concentration + # oneOutput: "MONDO:0007275" ## carpal tunnel syndrome + PhenoHP_decreased_DiseaseMONDO_rev: + -supportBatch: true + useTemplating: true + inputs: - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "HP:0000093" ## Proteinuria - # oneOutput: "MONDO:0002253" ## spondylosis - PhenoHP_decreased_DiseaseMONDO-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-HP" - # testExamples: - # - qInput: "MONDO:0002050" ## depressive disorder - # oneOutput: "HP:0000093" ## Proteinuria + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "MONDO:0005130" ## celiac disease + # oneOutput: "HP:0002900" ## Hypokalemia PhenoHP_decreased_DiseaseNCIT: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## 1 record - - supportBatch: true - useTemplating: true - inputs: + ## 113 records + -supportBatch: true + useTemplating: true + inputs: - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "HP:0025435" ## Increased lactate dehydrogenase level + # oneOutput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission + PhenoHP_decreased_DiseaseNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "HP:0011991" ## Abnormal neutrophil count - # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - PhenoHP_decreased_DiseaseNCIT-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: NCIT - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-HP" - # testExamples: - # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - # oneOutput: "HP:0011991" ## Abnormal neutrophil count + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "NCIT:C159516" ## Liver Lesion + # oneOutput: "HP:0032237" ## Increased circulating myelocyte count PhenoHP_decreased_DiseaseSNOMEDCT: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 291 records - - supportBatch: true - useTemplating: true - inputs: + ## 1532 records + -supportBatch: true + useTemplating: true + inputs: - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "HP:0012531" ## Pain + # oneOutput: "SNOMEDCT:54404000" ## Cervical radiculopathy (disorder) + PhenoHP_decreased_DiseaseSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "HP:0000870" ## Increased circulating prolactin concentration - # oneOutput: "SNOMEDCT:54404000" ## Cervical radiculopathy (disorder) - PhenoHP_decreased_DiseaseSNOMEDCT-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) + # oneOutput: "HP:0011877" ## Increased mean platelet volume + PhenoHP_decreased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 11425 records + -supportBatch: true + useTemplating: true + inputs: - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-HP" - # testExamples: - # - qInput: "SNOMEDCT:76571007" ## Septic shock (disorder) - # oneOutput: "HP:0000790" ## Hematuria - PhenoNCIT_decreased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 43 records - - supportBatch: true - useTemplating: true - inputs: - - id: NCIT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - # oneOutput: "MONDO:0001711" ## hepatic encephalopathy - PhenoNCIT_decreased_DiseaseMONDO-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-NCIT" - # testExamples: - # - qInput: "MONDO:0005247" ## urinary tract infection (disease) - # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - ## no records for PhenoNCIT_decreased_DiseaseNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - PhenoNCIT_decreased_DiseaseSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 3 records - - supportBatch: true - useTemplating: true - inputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "HP:0012418" ## Hypoxemia + # oneOutput: "HP:0002919" ## Ketonuria + PhenoHP_decreased_PhenoHP_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: HP + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "HP:0012343" ## Decreased circulating ferritin concentration + # oneOutput: "HP:0003077" ## Hyperlipidemia + PhenoHP_decreased_PhenoNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## 1257 records + -supportBatch: true + useTemplating: true + inputs: + - id: HP + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "HP:0011227" ## Elevated C-reactive protein level + # oneOutput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission + PhenoHP_decreased_PhenoNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - # oneOutput: "SNOMEDCT:2415007" ## Lumbosacral radiculopathy (disorder) - PhenoNCIT_decreased_DiseaseSNOMEDCT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "NCIT:C3587" ## Chronic Lymphocytic Leukemia in Remission + # oneOutput: "HP:0031851" ## Reduced hematocrit + PhenoHP_decreased_PhenoSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + ## 121 records + -supportBatch: true + useTemplating: true + inputs: + - id: HP + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "HP:0012378" ## Fatigue + # oneOutput: "SNOMEDCT:54404000" ## Cervical radiculopathy (disorder) + PhenoHP_decreased_PhenoSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) + # oneOutput: "HP:0000023" ## Inguinal hernia + PhenoHP_decreased_ProcedureNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT + ## 132 records + -supportBatch: true + useTemplating: true + inputs: + - id: HP + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "HP:0001899" ## Increased hematocrit + # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + PhenoHP_decreased_ProcedureNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:76571007" ## Septic shock (disorder) - # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - PhenoSNOMEDCT_decreased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 17 records - - supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "SNOMEDCT:166816003" ## Serum lipids high (finding) - # oneOutput: "MONDO:0006920" ## prediabetes syndrome - PhenoSNOMEDCT_decreased_DiseaseMONDO-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "NCIT:C167118" ## Influenza A Virus Positive + # oneOutput: "HP:0001297" ## Stroke + PhenoHP_increased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 12086 records + -supportBatch: true + useTemplating: true + inputs: + - id: HP + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "HP:0002318" ## Cervical myelopathy + # oneOutput: "MONDO:0002471" ## bursitis + PhenoHP_increased_DiseaseMONDO_rev: + -supportBatch: true + useTemplating: true + inputs: - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-SNOMEDCT" - # testExamples: - # - qInput: "MONDO:0005391" ## restless legs syndrome - # oneOutput: "SNOMEDCT:166816003" ## Serum lipids high (finding) - ## no records for PhenoSNOMEDCT_decreased_DiseaseNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - PhenoSNOMEDCT_decreased_DiseaseSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 1 record - - supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "SNOMEDCT:166816003" ## Serum lipids high (finding) - # oneOutput: "SNOMEDCT:386033004" ## Neuropathy (disorder) - PhenoSNOMEDCT_decreased_DiseaseSNOMEDCT-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-SNOMEDCT" - # testExamples: - # - qInput: "SNOMEDCT:386033004" ## Neuropathy (disorder) - # oneOutput: "SNOMEDCT:166816003" ## Serum lipids high (finding) - PhenoHP_decreased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 3804 records - - supportBatch: true - useTemplating: true - inputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "MONDO:0007743" ## attention deficit-hyperactivity disorder + # oneOutput: "HP:0031807" ## Increased basophil count + PhenoHP_increased_DiseaseNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ## 86 records + -supportBatch: true + useTemplating: true + inputs: - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "HP:0001894" ## Thrombocytosis + # oneOutput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission + PhenoHP_increased_DiseaseNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "NCIT:C167118" ## Influenza A Virus Positive + # oneOutput: "HP:0012101" ## Decreased serum creatinine + PhenoHP_increased_DiseaseSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + ## 1055 records + -supportBatch: true + useTemplating: true + inputs: - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "HP:0000093" ## Proteinuria - # oneOutput: "HP:0001649" ## Tachycardia - PhenoHP_decreased_PhenoHP-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "HP:0003259" ## Elevated serum creatinine + # oneOutput: "SNOMEDCT:711150003" ## Long-term current use of anticoagulant (situation) + PhenoHP_increased_DiseaseSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "SNOMEDCT:191519005" ## Dementia associated with another disease (disorder) + # oneOutput: "HP:0031956" ## Elevated serum aspartate aminotransferase + PhenoHP_increased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 10355 records + -supportBatch: true + useTemplating: true + inputs: - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "HP:0002014" ## Diarrhea + # oneOutput: "HP:0001899" ## Increased hematocrit + PhenoHP_increased_PhenoHP_rev: + -supportBatch: true + useTemplating: true + inputs: - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-HP" - # testExamples: - # - qInput: "HP:0001386" ## Joint swelling - # oneOutput: "HP:0000093" ## Proteinuria - PhenoHP_decreased_PhenoNCIT: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "HP:0001882" ## Leukopenia + # oneOutput: "HP:0032372" ## Increased peripheral blast count + PhenoHP_increased_PhenoNCIT: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 170 records - - supportBatch: true - useTemplating: true - inputs: + ## 733 records + -supportBatch: true + useTemplating: true + inputs: - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "HP:0100512" ## Low levels of vitamin D + # oneOutput: "NCIT:C167118" ## Influenza A Virus Positive + PhenoHP_increased_PhenoNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "HP:0012085" ## Pyuria - # oneOutput: "NCIT:C167118" ## Influenza B Virus Positive - PhenoHP_decreased_PhenoNCIT-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: NCIT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-HP" - # testExamples: - # - qInput: "NCIT:C146650" ## Clostridium difficile Positive - # oneOutput: "HP:0012085" ## Pyuria - PhenoHP_decreased_PhenoSNOMEDCT: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "NCIT:C167118" ## Influenza A Virus Positive + # oneOutput: "HP:0002905" ## Hyperphosphatemia + PhenoHP_increased_PhenoSNOMEDCT: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ## 26 records - - supportBatch: true - useTemplating: true - inputs: + ## 78 records + -supportBatch: true + useTemplating: true + inputs: - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "HP:0011423" ## Hyperchloremia - # oneOutput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) - PhenoHP_decreased_PhenoSNOMEDCT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "HP:0001894" ## Thrombocytosis + # oneOutput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) + PhenoHP_increased_PhenoSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "SNOMEDCT:386033004" ## Neuropathy (disorder) + # oneOutput: "HP:0002923" ## Rheumatoid factor positive + PhenoHP_increased_ProcedureNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT + ## 67 records + -supportBatch: true + useTemplating: true + inputs: - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-HP" - # testExamples: - # - qInput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) - # oneOutput: "HP:0002902" ## Hyponatremia + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "HP:0011016" ## Abnormality of urine glucose concentration + # oneOutput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission + PhenoHP_increased_ProcedureNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "NCIT:C146650" ## Clostridium difficile Positive + # oneOutput: "HP:0032473" ## Decreased urine urobilinogen + PhenoNCIT_decreased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 1170 records + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "NCIT:C159516" ## Liver Lesion + # oneOutput: "MONDO:0005100" ## systemic sclerosis + PhenoNCIT_decreased_DiseaseMONDO_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: MONDO + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "MONDO:0017276" ## frontotemporal dementia + # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive + PhenoNCIT_decreased_DiseaseNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ## 7 records + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C15546" ## Breast Cancer Screening + # oneOutput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission + PhenoNCIT_decreased_DiseaseNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C159516" ## Liver Lesion + # oneOutput: "NCIT:C15546" ## Breast Cancer Screening + PhenoNCIT_decreased_DiseaseSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + ## 94 records + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C146650" ## Clostridium difficile Positive + # oneOutput: "SNOMEDCT:54404000" ## Cervical radiculopathy (disorder) + PhenoNCIT_decreased_DiseaseSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) + # oneOutput: "NCIT:C15546" ## Breast Cancer Screening PhenoNCIT_decreased_PhenoHP: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 64 records - - supportBatch: true - useTemplating: true - inputs: + ## 705 records + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - # oneOutput: "HP:0002919" ## Ketonuria - PhenoNCIT_decreased_PhenoHP-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "NCIT:C141278" ## Adenovirus Positive + # oneOutput: "HP:0033077" ## Increased circulating free T4 level + PhenoNCIT_decreased_PhenoHP_rev: + -supportBatch: true + useTemplating: true + inputs: - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-NCIT" - # testExamples: - # - qInput: "HP:0002829" ## Arthralgia - # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "HP:0031507" ## Decreased circulating T4 level + # oneOutput: "NCIT:C51691" ## Arthroplasty PhenoNCIT_decreased_PhenoNCIT: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 1 record - - supportBatch: true - useTemplating: true - inputs: - - id: NCIT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + ## 56 records + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - # oneOutput: "NCIT:C167118" ## Influenza B Virus Positive - PhenoNCIT_decreased_PhenoNCIT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C51691" ## Arthroplasty + # oneOutput: "NCIT:C155871" ## Herpes Simplex Virus Infection + PhenoNCIT_decreased_PhenoNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-NCIT" - # testExamples: - # - qInput: "NCIT:C167118" ## Influenza B Virus Positive - # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - ## no records for PhenoNCIT_decreased_PhenoSNOMEDCT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C141278" ## Adenovirus Positive + # oneOutput: "NCIT:C159516" ## Liver Lesion + PhenoNCIT_decreased_PhenoSNOMEDCT: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - PhenoSNOMEDCT_decreased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 16 records - - supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "SNOMEDCT:166816003" ## Serum lipids high (finding) - # oneOutput: "HP:0031098" ## Decreased thyroid-stimulating hormone level - PhenoSNOMEDCT_decreased_PhenoHP-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + ## 9 records + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + # oneOutput: "SNOMEDCT:239792003" ## Seronegative rheumatoid arthritis (disorder) + PhenoNCIT_decreased_PhenoSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-SNOMEDCT" - # testExamples: - # - qInput: "HP:0001882" ## Leukopenia - # oneOutput: "SNOMEDCT:166816003" ## Serum lipids high (finding) - ## no records for PhenoSNOMEDCT_decreased_PhenoNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## no records for PhenoSNOMEDCT_decreased_PhenoSNOMEDCT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - PhenoHP_decreased_ProcedureNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure - ## 6 records - - supportBatch: true - useTemplating: true - inputs: - - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:237519003" ## Autoimmune hypothyroidism (disorder) + # oneOutput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission + PhenoNCIT_decreased_ProcedureNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT + ## 7 records + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "HP:0003141" ## Increased LDL cholesterol concentration - # oneOutput: "NCIT:C15271" ## Liver Transplantation - PhenoHP_decreased_ProcedureNCIT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C52007" ## Arthrodesis + # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive + PhenoNCIT_decreased_ProcedureNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Procedure - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-HP" - # testExamples: - # - qInput: "NCIT:C15271" ## Liver Transplantation - # oneOutput: "HP:0031965" ## Increased RBC distribution width - ## no records for PhenoNCIT_decreased_ProcedureNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure - ## no records for PhenoSNOMEDCT_decreased_ProcedureNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure - ChemCHEBI_increased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 4590 records - - supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "CHEBI:100241" ## ciprofloxacin - # oneOutput: "MONDO:0005230" ## cellulitis (disease) - ChemCHEBI_increased_DiseaseMONDO-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C3587" ## Chronic Lymphocytic Leukemia in Remission + # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive + PhenoNCIT_increased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 380 records + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + # oneOutput: "MONDO:0007488" ## Lewy body dementia + PhenoNCIT_increased_DiseaseMONDO_rev: + -supportBatch: true + useTemplating: true + inputs: - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.CHEBI, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: CHEBI - semantic: SmallMolecule - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" - # testExamples: - # - qInput: "MONDO:0005101" ## ulcerative colitis (disease) - # oneOutput: "CHEBI:100241" ## ciprofloxacin - ChemCHEBI_increased_DiseaseNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## 2 records - - supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "MONDO:0004979" ## asthma + # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive + PhenoNCIT_increased_DiseaseNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ## 3 records + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "CHEBI:5801" ## hydroxychloroquine - # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - ChemCHEBI_increased_DiseaseNCIT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C3587" ## Chronic Lymphocytic Leukemia in Remission + # oneOutput: "NCIT:C15271" ## Liver Transplantation + PhenoNCIT_increased_DiseaseNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.CHEBI, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: CHEBI - semantic: SmallMolecule - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" - # testExamples: - # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - # oneOutput: "CHEBI:87732" ## warfarin - ChemCHEBI_increased_DiseaseSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 282 records - - supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "CHEBI:15409" ## menthol - # oneOutput: "SNOMEDCT:709073001" ## Neurocognitive disorder (disorder) - ChemCHEBI_increased_DiseaseSNOMEDCT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C15271" ## Liver Transplantation + # oneOutput: "NCIT:C167118" ## Influenza A Virus Positive + PhenoNCIT_increased_DiseaseSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + ## 36 records + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C51691" ## Arthroplasty + # oneOutput: "SNOMEDCT:197352008" ## Toxic hepatitis (disorder) + PhenoNCIT_increased_DiseaseSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.CHEBI, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: CHEBI - semantic: SmallMolecule - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" - # testExamples: - # - qInput: "SNOMEDCT:76571007" ## Septic shock (disorder) - # oneOutput: "CHEBI:15407" ## ephedrine - ChemUNII_increased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 401 records - - supportBatch: true - useTemplating: true - inputs: - - id: UNII - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "UNII:1BJ477IO2L" ## gadobutrol - # oneOutput: "MONDO:0005804" ## hyperprolactinemia (disease) - ChemUNII_increased_DiseaseMONDO-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.UNII, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: UNII - semantic: SmallMolecule - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-UNII" - # testExamples: - # - qInput: "MONDO:0005665" ## Bell's palsy - # oneOutput: "UNII:1BJ477IO2L" ## gadobutrol - ChemUNII_increased_DiseaseNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## 1 record - - supportBatch: true - useTemplating: true - inputs: - - id: UNII - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) + # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + PhenoNCIT_increased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 395 records + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "UNII:E47C0NF7LV" ## enoxaparin - # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - ChemUNII_increased_DiseaseNCIT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "NCIT:C159516" ## Liver Lesion + # oneOutput: "HP:0025066" ## Decreased mean corpuscular volume + PhenoNCIT_increased_PhenoHP_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: HP + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "HP:0001297" ## Stroke + # oneOutput: "NCIT:C167118" ## Influenza A Virus Positive + PhenoNCIT_increased_PhenoNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## 34 records + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.UNII, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: UNII - semantic: SmallMolecule - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-UNII" - # testExamples: - # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - # oneOutput: "UNII:E47C0NF7LV" ## enoxaparin - ChemUNII_increased_DiseaseSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 30 records - - supportBatch: true - useTemplating: true - inputs: - - id: UNII - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "UNII:T2410KM04A" ## heparin - # oneOutput: "SNOMEDCT:127295002" ## Traumatic brain injury (disorder) - ChemUNII_increased_DiseaseSNOMEDCT-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.UNII, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: UNII - semantic: SmallMolecule - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-UNII" - # testExamples: - # - qInput: "SNOMEDCT:239792003" ## Seronegative rheumatoid arthritis (disorder) - # oneOutput: "UNII:FYS6T7F842" ## adalimumab - ProcedureNCIT_increased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 29 records - - supportBatch: true - useTemplating: true - inputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission + # oneOutput: "NCIT:C15271" ## Liver Transplantation + PhenoNCIT_increased_PhenoNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Procedure - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "NCIT:C50815" ## Aortic Valve Replacement - # oneOutput: "MONDO:0005025" ## endocarditis (disease) - ProcedureNCIT_increased_DiseaseMONDO-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission + # oneOutput: "NCIT:C3587" ## Chronic Lymphocytic Leukemia in Remission + PhenoNCIT_increased_PhenoSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + ## 1 records + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-NCIT" - # testExamples: - # - qInput: "MONDO:0024317" ## chronic pain syndrome - # oneOutput: "NCIT:C52007" ## Arthrodesis - ## no records for ProcedureNCIT_increased_DiseaseNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ProcedureNCIT_increased_DiseaseSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C38033" ## Arthroscopy + # oneOutput: "SNOMEDCT:197354009" ## Toxic liver disease (disorder) + PhenoNCIT_increased_PhenoSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:197354009" ## Toxic liver disease (disorder) + # oneOutput: "NCIT:C3587" ## Chronic Lymphocytic Leukemia in Remission + PhenoNCIT_increased_ProcedureNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT ## 3 records - - supportBatch: true - useTemplating: true - inputs: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Procedure - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C52007" ## Arthrodesis + # oneOutput: "NCIT:C159516" ## Liver Lesion + PhenoNCIT_increased_ProcedureNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C155871" ## Herpes Simplex Virus Infection + # oneOutput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission + PhenoSNOMEDCT_decreased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 307 records + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C15546" ## Breast Cancer Screening - # oneOutput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) - ProcedureNCIT_increased_DiseaseSNOMEDCT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "SNOMEDCT:711150003" ## Long-term current use of anticoagulant (situation) + # oneOutput: "MONDO:0011786" ## allergic rhinitis + PhenoSNOMEDCT_decreased_DiseaseMONDO_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: MONDO + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "MONDO:0008383" ## rheumatoid arthritis + # oneOutput: "SNOMEDCT:201839001" ## Primary coxarthrosis, bilateral (disorder) + PhenoSNOMEDCT_decreased_DiseaseNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ## 1 records + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:2415007" ## Lumbosacral radiculopathy (disorder) - # oneOutput: "NCIT:C52007" ## Arthrodesis - ChemCHEBI_increased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 4955 records - - supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "CHEBI:100241" ## ciprofloxacin - # oneOutput: "HP:0012213" ## Decreased glomerular filtration rate - ChemCHEBI_increased_PhenoHP-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.CHEBI, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: CHEBI - semantic: SmallMolecule - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" - # testExamples: - # - qInput: "HP:0011897" ## Neutrophilia - # oneOutput: "CHEBI:100241" ## ciprofloxacin - ChemCHEBI_increased_PhenoNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 222 records - - supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:127295002" ## Traumatic brain injury (disorder) + # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + PhenoSNOMEDCT_decreased_DiseaseNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "CHEBI:167638" ## labetalol - # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive - ChemCHEBI_increased_PhenoNCIT-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: NCIT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.CHEBI, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: CHEBI - semantic: SmallMolecule - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" - # testExamples: - # - qInput: "NCIT:C167118" ## Influenza B Virus Positive - # oneOutput: "CHEBI:16714" ## codeine - ChemCHEBI_increased_PhenoSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ## 15 records - - supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C167118" ## Influenza A Virus Positive + # oneOutput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) + PhenoSNOMEDCT_decreased_DiseaseSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + ## 26 records + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "CHEBI:6888" ## methylprednisolone - # oneOutput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) - ChemCHEBI_increased_PhenoSNOMEDCT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "SNOMEDCT:709073001" ## Neurocognitive disorder (disorder) + # oneOutput: "SNOMEDCT:197354009" ## Toxic liver disease (disorder) + PhenoSNOMEDCT_decreased_DiseaseSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.CHEBI, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: CHEBI - semantic: SmallMolecule - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" - # testExamples: - # - qInput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) - # oneOutput: "CHEBI:7476" ## naproxen - ChemUNII_increased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 390 records - - supportBatch: true - useTemplating: true - inputs: - - id: UNII - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "UNII:1BJ477IO2L" ## gadobutrol - # oneOutput: "HP:0025406" ## Asthenia - ChemUNII_increased_PhenoHP-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.UNII, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: UNII - semantic: SmallMolecule - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-UNII" - # testExamples: - # - qInput: "HP:0011227" ## Elevated C-reactive protein level - # oneOutput: "UNII:1BJ477IO2L" ## gadobutrol - ChemUNII_increased_PhenoNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 26 records - - supportBatch: true - useTemplating: true - inputs: - - id: UNII - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "UNII:T2410KM04A" ## heparin - # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive - ChemUNII_increased_PhenoNCIT-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: NCIT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.UNII, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: UNII - semantic: SmallMolecule - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-UNII" - # testExamples: - # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - # oneOutput: "UNII:E47C0NF7LV" ## enoxaparin - ## no records for ChemUNII_increased_PhenoSNOMEDCT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ProcedureNCIT_increased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 21 records - - supportBatch: true - useTemplating: true - inputs: - - id: NCIT - semantic: Procedure - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "NCIT:C50815" ## Aortic Valve Replacement - # oneOutput: "HP:0002094" ## Dyspnea - ProcedureNCIT_increased_PhenoHP-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "SNOMEDCT:2415007" ## Lumbosacral radiculopathy (disorder) + # oneOutput: "SNOMEDCT:239792003" ## Seronegative rheumatoid arthritis (disorder) + PhenoSNOMEDCT_decreased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 217 records + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "SNOMEDCT:191519005" ## Dementia associated with another disease (disorder) + # oneOutput: "HP:0031506" ## Increased circulating T4 level + PhenoSNOMEDCT_decreased_PhenoHP_rev: + -supportBatch: true + useTemplating: true + inputs: - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-NCIT" - # testExamples: - # - qInput: "HP:0001919" ## Acute kidney injury - # oneOutput: "NCIT:C50815" ## Aortic Valve Replacement - ## no records for ProcedureNCIT_increased_PhenoNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## no records for ProcedureNCIT_increased_PhenoSNOMEDCT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ChemCHEBI_increased_ProcedureNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Procedure - ## 19 records - - supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "CHEBI:3311" ## calcium carbonate - # oneOutput: "NCIT:C15271" ## Liver Transplantation - ChemCHEBI_increased_ProcedureNCIT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "HP:0001397" ## Hepatic steatosis + # oneOutput: "SNOMEDCT:166816003" ## Serum lipids high (finding) + PhenoSNOMEDCT_decreased_PhenoNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## 25 records + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:47049007" ## Ankylosis of spine (disorder) + # oneOutput: "NCIT:C3587" ## Chronic Lymphocytic Leukemia in Remission + PhenoSNOMEDCT_decreased_PhenoNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Procedure - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.CHEBI, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: CHEBI - semantic: SmallMolecule - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" - # testExamples: - # - qInput: "NCIT:C15271" ## Liver Transplantation - # oneOutput: "CHEBI:534" ## docusate - ChemUNII_increased_ProcedureNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Procedure + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C15271" ## Liver Transplantation + # oneOutput: "SNOMEDCT:197354009" ## Toxic liver disease (disorder) + PhenoSNOMEDCT_decreased_PhenoSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT ## 2 records - - supportBatch: true - useTemplating: true - inputs: - - id: UNII - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "UNII:3FYP5M0IJX" ## sennosides - # oneOutput: "NCIT:C15271" ## Liver Transplantation - ChemUNII_increased_ProcedureNCIT-rev: - - supportBatch: true - useTemplating: true - inputs: + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "SNOMEDCT:191519005" ## Dementia associated with another disease (disorder) + # oneOutput: "SNOMEDCT:127295002" ## Traumatic brain injury (disorder) + PhenoSNOMEDCT_decreased_PhenoSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "SNOMEDCT:386033004" ## Neuropathy (disorder) + # oneOutput: "SNOMEDCT:47049007" ## Ankylosis of spine (disorder) + PhenoSNOMEDCT_decreased_ProcedureNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT + ## 2 records + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:197352008" ## Toxic hepatitis (disorder) + # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + PhenoSNOMEDCT_decreased_ProcedureNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Procedure - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.UNII, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: UNII - semantic: SmallMolecule - predicate: associated_with - qualifiers: - subject_direction_qualifier: increased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-UNII" - # testExamples: - # - qInput: "NCIT:C15271" ## Liver Transplantation - # oneOutput: "UNII:T2410KM04A" ## heparin - ## no records for ProcedureNCIT_increased_ProcedureNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Procedure - ChemCHEBI_decreased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 4281 records - - supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "CHEBI:100241" ## ciprofloxacin - # oneOutput: "MONDO:0005298" ## osteoporosis - ChemCHEBI_decreased_DiseaseMONDO-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C155871" ## Herpes Simplex Virus Infection + # oneOutput: "SNOMEDCT:76571007" ## Septic shock (disorder) + PhenoSNOMEDCT_increased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 158 records + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "SNOMEDCT:54404000" ## Cervical radiculopathy (disorder) + # oneOutput: "MONDO:0005420" ## hypothyroidism + PhenoSNOMEDCT_increased_DiseaseMONDO_rev: + -supportBatch: true + useTemplating: true + inputs: - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.CHEBI, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: CHEBI - semantic: SmallMolecule - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" - # testExamples: - # - qInput: "MONDO:0005173" ## actinic keratosis (disease) - # oneOutput: "CHEBI:100241" ## ciprofloxacin - ChemCHEBI_decreased_DiseaseNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## 1 record - - supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "CHEBI:5855" ## ibuprofen - # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - ChemCHEBI_decreased_DiseaseNCIT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "MONDO:0020066" ## Ehlers-Danlos syndrome + # oneOutput: "SNOMEDCT:127295002" ## Traumatic brain injury (disorder) + PhenoSNOMEDCT_increased_DiseaseNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ## 2 records + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:711150003" ## Long-term current use of anticoagulant (situation) + # oneOutput: "NCIT:C167118" ## Influenza A Virus Positive + PhenoSNOMEDCT_increased_DiseaseNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.CHEBI, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: CHEBI - semantic: SmallMolecule - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" - # testExamples: - # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - # oneOutput: "CHEBI:5855" ## ibuprofen - ChemCHEBI_decreased_DiseaseSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 288 records - - supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + # oneOutput: "SNOMEDCT:386033004" ## Neuropathy (disorder) + PhenoSNOMEDCT_increased_DiseaseSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + ## 13 records + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "CHEBI:119915" ## fentanyl - # oneOutput: "SNOMEDCT:54404000" ## Cervical radiculopathy (disorder) - ChemCHEBI_decreased_DiseaseSNOMEDCT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "SNOMEDCT:2415007" ## Lumbosacral radiculopathy (disorder) + # oneOutput: "SNOMEDCT:709073001" ## Neurocognitive disorder (disorder) + PhenoSNOMEDCT_increased_DiseaseSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.CHEBI, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: CHEBI - semantic: SmallMolecule - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" - # testExamples: - # - qInput: "SNOMEDCT:237519003" ## Autoimmune hypothyroidism (disorder) - # oneOutput: "CHEBI:119915" ## fentanyl - ChemUNII_decreased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 41 records - - supportBatch: true - useTemplating: true - inputs: - - id: UNII - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "UNII:3FYP5M0IJX" ## sennosides - # oneOutput: "MONDO:0004946" ## hypoglycemia - ChemUNII_decreased_DiseaseMONDO-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.UNII, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: UNII - semantic: SmallMolecule - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-UNII" - # testExamples: - # - qInput: "MONDO:0004375" ## end stage renal failure - # oneOutput: "UNII:3FYP5M0IJX" ## sennosides - ## no records for ChemUNII_decreased_DiseaseNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ChemUNII_decreased_DiseaseSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 2 records - - supportBatch: true - useTemplating: true - inputs: - - id: UNII - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "SNOMEDCT:386033004" ## Neuropathy (disorder) + # oneOutput: "SNOMEDCT:202805003" ## Sacroiliac disorder (disorder) + PhenoSNOMEDCT_increased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 113 records + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "SNOMEDCT:201839001" ## Primary coxarthrosis, bilateral (disorder) + # oneOutput: "HP:0003259" ## Elevated serum creatinine + PhenoSNOMEDCT_increased_PhenoHP_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: HP + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "HP:0002829" ## Arthralgia + # oneOutput: "SNOMEDCT:66944004" ## Autoimmune thyroiditis (disorder) + PhenoSNOMEDCT_increased_PhenoNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## 5 records + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "UNII:OP401G7OJC" ## etanercept - # oneOutput: "SNOMEDCT:239792003" ## Seronegative rheumatoid arthritis (disorder) - ChemUNII_decreased_DiseaseSNOMEDCT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:166816003" ## Serum lipids high (finding) + # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + PhenoSNOMEDCT_increased_PhenoNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C159516" ## Liver Lesion + # oneOutput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) + PhenoSNOMEDCT_increased_ProcedureNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT + ## 1 records + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.UNII, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: UNII - semantic: SmallMolecule - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-UNII" - # testExamples: - # - qInput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) - # oneOutput: "UNII:OP401G7OJC" ## etanercept + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:201839001" ## Primary coxarthrosis, bilateral (disorder) + # oneOutput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission + PhenoSNOMEDCT_increased_ProcedureNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C167118" ## Influenza A Virus Positive + # oneOutput: "SNOMEDCT:197352008" ## Toxic hepatitis (disorder) ProcedureNCIT_decreased_DiseaseMONDO: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 60 records - - supportBatch: true - useTemplating: true - inputs: + ## 721 records + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Procedure - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.MONDO, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "NCIT:C167118" ## Influenza A Virus Positive + # oneOutput: "MONDO:0012883" ## acute promyelocytic leukemia + ProcedureNCIT_decreased_DiseaseMONDO_rev: + -supportBatch: true + useTemplating: true + inputs: - id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "NCIT:C15546" ## Breast Cancer Screening - # oneOutput: "MONDO:0007743" ## attention deficit-hyperactivity disorder - ProcedureNCIT_decreased_DiseaseMONDO-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: MONDO - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-NCIT" - # testExamples: - # - qInput: "MONDO:0005294" ## peripheral vascular disease - # oneOutput: "NCIT:C15546" ## Breast Cancer Screening - ## no records for ProcedureNCIT_decreased_DiseaseNCIT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "MONDO:0005393" ## gout + # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + ProcedureNCIT_decreased_DiseaseNCIT: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ## 4 records + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C159516" ## Liver Lesion + # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + ProcedureNCIT_decreased_DiseaseNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + # oneOutput: "NCIT:C141278" ## Adenovirus Positive ProcedureNCIT_decreased_DiseaseSNOMEDCT: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 4 records - - supportBatch: true - useTemplating: true - inputs: + ## 58 records + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Procedure - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + # oneOutput: "SNOMEDCT:66944004" ## Autoimmune thyroiditis (disorder) + ProcedureNCIT_decreased_DiseaseSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C15546" ## Breast Cancer Screening - # oneOutput: "SNOMEDCT:54404000" ## Cervical radiculopathy (disorder) - ProcedureNCIT_decreased_DiseaseSNOMEDCT-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - semantic: Disease - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:711150003" ## Long-term current use of anticoagulant (situation) + # oneOutput: "NCIT:C141278" ## Adenovirus Positive + ProcedureNCIT_decreased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 502 records + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:239792003" ## Seronegative rheumatoid arthritis (disorder) - # oneOutput: "NCIT:C15546" ## Breast Cancer Screening - ChemCHEBI_decreased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 5600 records - - supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "NCIT:C141278" ## Adenovirus Positive + # oneOutput: "HP:0001260" ## Dysarthria + ProcedureNCIT_decreased_PhenoHP_rev: + -supportBatch: true + useTemplating: true + inputs: - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "CHEBI:100241" ## ciprofloxacin - # oneOutput: "HP:0002904" ## Hyperbilirubinemia - ChemCHEBI_decreased_PhenoHP-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.CHEBI, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: CHEBI - semantic: SmallMolecule - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" - # testExamples: - # - qInput: "HP:0002829" ## Arthralgia - # oneOutput: "CHEBI:100241" ## ciprofloxacin - ChemCHEBI_decreased_PhenoNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 191 records - - supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "HP:0011900" ## Hypofibrinogenemia + # oneOutput: "NCIT:C167118" ## Influenza A Virus Positive + ProcedureNCIT_decreased_PhenoNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## 56 records + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "CHEBI:135866" ## clindamycin - # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - ChemCHEBI_decreased_PhenoNCIT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C159516" ## Liver Lesion + # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive + ProcedureNCIT_decreased_PhenoNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.CHEBI, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: CHEBI - semantic: SmallMolecule - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" - # testExamples: - # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - # oneOutput: "CHEBI:119915" ## fentanyl - ChemCHEBI_decreased_PhenoSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ## 28 records - - supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.SNOMEDCT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "CHEBI:2955" ## azithromycin - # oneOutput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) - ChemCHEBI_decreased_PhenoSNOMEDCT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission + # oneOutput: "NCIT:C167118" ## Influenza A Virus Positive + ProcedureNCIT_decreased_PhenoSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + ## 4 records + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C52007" ## Arthrodesis + # oneOutput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) + ProcedureNCIT_decreased_PhenoSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.CHEBI, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: CHEBI - semantic: SmallMolecule - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" - # testExamples: - # - qInput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) - # oneOutput: "CHEBI:4636" ## diphenhydramine - ChemUNII_decreased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 113 records - - supportBatch: true - useTemplating: true - inputs: - - id: UNII - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "UNII:1BJ477IO2L" ## gadobutrol - # oneOutput: "HP:0031969" ## Reduced blood urea nitrogen - ChemUNII_decreased_PhenoHP-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.UNII, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: UNII - semantic: SmallMolecule - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-UNII" - # testExamples: - # - qInput: "HP:0031098" ## Decreased thyroid-stimulating hormone level - # oneOutput: "UNII:1BJ477IO2L" ## gadobutrol - ChemUNII_decreased_PhenoNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 1 record - - supportBatch: true - useTemplating: true - inputs: - - id: UNII - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) + # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive + ProcedureNCIT_decreased_ProcedureNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT + ## 3 records + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "UNII:1BJ477IO2L" ## gadobutrol - # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - ChemUNII_decreased_PhenoNCIT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C38033" ## Arthroscopy + # oneOutput: "NCIT:C167118" ## Influenza A Virus Positive + ProcedureNCIT_decreased_ProcedureNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.UNII, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: UNII - semantic: SmallMolecule - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-UNII" - # testExamples: - # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - # oneOutput: "UNII:1BJ477IO2L" ## gadobutrol - ## no records for ChemUNII_decreased_PhenoSNOMEDCT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ProcedureNCIT_decreased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 81 records - - supportBatch: true - useTemplating: true - inputs: + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C146650" ## Clostridium difficile Positive + # oneOutput: "NCIT:C155871" ## Herpes Simplex Virus Infection + ProcedureNCIT_increased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 209 records + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Procedure - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.HP, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "NCIT:C15546" ## Breast Cancer Screening - # oneOutput: "HP:0001882" ## Leukopenia - ProcedureNCIT_decreased_PhenoHP-rev: - - supportBatch: true - useTemplating: true - inputs: - - id: HP - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + # oneOutput: "MONDO:0006694" ## cerebral atherosclerosis + ProcedureNCIT_increased_DiseaseMONDO_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: MONDO + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "MONDO:0005155" ## cirrhosis of liver + # oneOutput: "NCIT:C38033" ## Arthroscopy + ProcedureNCIT_increased_DiseaseNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ## 2 records + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-NCIT" - # testExamples: - # - qInput: "HP:0001681" ## Angina pectoris - # oneOutput: "NCIT:C15546" ## Breast Cancer Screening - ProcedureNCIT_decreased_PhenoNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 5 records - - supportBatch: true - useTemplating: true - inputs: + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C3587" ## Chronic Lymphocytic Leukemia in Remission + # oneOutput: "NCIT:C15271" ## Liver Transplantation + ProcedureNCIT_increased_DiseaseNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission + # oneOutput: "NCIT:C3587" ## Chronic Lymphocytic Leukemia in Remission + ProcedureNCIT_increased_DiseaseSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + ## 20 records + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Procedure - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission + # oneOutput: "SNOMEDCT:197352008" ## Toxic hepatitis (disorder) + ProcedureNCIT_increased_DiseaseSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: Disease + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:2415007" ## Lumbosacral radiculopathy (disorder) + # oneOutput: "NCIT:C52007" ## Arthrodesis + ProcedureNCIT_increased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 158 records + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C15546" ## Breast Cancer Screening - # oneOutput: "NCIT:C167118" ## Influenza B Virus Positive - ProcedureNCIT_decreased_PhenoNCIT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "NCIT:C141278" ## Adenovirus Positive + # oneOutput: "HP:0001369" ## Arthritis + ProcedureNCIT_increased_PhenoHP_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: HP + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "HP:0008151" ## Prolonged prothrombin time + # oneOutput: "NCIT:C155871" ## Herpes Simplex Virus Infection + ProcedureNCIT_increased_PhenoNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## 4 records + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: PhenotypicFeature - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C167118" ## Influenza A Virus Positive + # oneOutput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission + ProcedureNCIT_increased_PhenoNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-NCIT" - # testExamples: - # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - # oneOutput: "NCIT:C15546" ## Breast Cancer Screening - ## no records for ProcedureNCIT_decreased_PhenoSNOMEDCT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C159516" ## Liver Lesion + # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + ProcedureNCIT_increased_PhenoSNOMEDCT: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ChemCHEBI_decreased_ProcedureNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure - ## 8 records - - supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - object.NCIT, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: + ## 2 records + -supportBatch: true + useTemplating: true + inputs: + - id: NCIT + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C155871" ## Herpes Simplex Virus Infection + # oneOutput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) + ProcedureNCIT_increased_PhenoSNOMEDCT_rev: + -supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + - semantic: PhenotypicFeature + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:197354009" ## Toxic liver disease (disorder) + # oneOutput: "NCIT:C51691" ## Arthroplasty + ProcedureNCIT_increased_ProcedureNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT + ## 2 records + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "CHEBI:6637" ## magnesium hydroxide - # oneOutput: "NCIT:C15271" ## Liver Transplantation - ChemCHEBI_decreased_ProcedureNCIT-rev: - - supportBatch: true - useTemplating: true - inputs: + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C15546" ## Breast Cancer Screening + # oneOutput: "NCIT:C167118" ## Influenza A Virus Positive + ProcedureNCIT_increased_ProcedureNCIT_rev: + -supportBatch: true + useTemplating: true + inputs: - id: NCIT - semantic: Procedure - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: >- - subject.CHEBI, - association.edge_attributes, - subject.name,object.name - size: 1000 - outputs: - - id: CHEBI - semantic: SmallMolecule - predicate: associated_with - qualifiers: - subject_direction_qualifier: decreased - subject_aspect_qualifier: likelihood - response_mapping: - "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" - # testExamples: - # - qInput: "NCIT:C15271" ## Liver Transplantation - # oneOutput: "CHEBI:5855" ## ibuprofen - ## no records for ChemUNII_decreased_ProcedureNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure - ## no records for ProcedureNCIT_decreased_ProcedureNCIT - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure + - semantic: Procedure + requestBody: + body: >- + { + "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources + size: 1000 + outputs: + -id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C155871" ## Herpes Simplex Virus Infection + # oneOutput: "NCIT:C51691" ## Arthroplasty + x-bte-response-mapping: object-MONDO: MONDO: object.MONDO input_name: subject.name output_name: object.name edge-attributes: association.edge_attributes + trapi_sources: association.sources object-NCIT: NCIT: object.NCIT input_name: subject.name output_name: object.name edge-attributes: association.edge_attributes + trapi_sources: association.sources object-SNOMEDCT: SNOMEDCT: object.SNOMEDCT input_name: subject.name output_name: object.name edge-attributes: association.edge_attributes + trapi_sources: association.sources object-HP: HP: object.HP input_name: subject.name output_name: object.name edge-attributes: association.edge_attributes + trapi_sources: association.sources object-CHEBI: CHEBI: object.CHEBI input_name: subject.name output_name: object.name edge-attributes: association.edge_attributes + trapi_sources: association.sources object-UNII: UNII: object.UNII input_name: subject.name output_name: object.name edge-attributes: association.edge_attributes + trapi_sources: association.sources subject-MONDO: MONDO: subject.MONDO input_name: object.name output_name: subject.name edge-attributes: association.edge_attributes + trapi_sources: association.sources subject-NCIT: NCIT: subject.NCIT input_name: object.name output_name: subject.name edge-attributes: association.edge_attributes + trapi_sources: association.sources subject-SNOMEDCT: SNOMEDCT: subject.SNOMEDCT input_name: object.name output_name: subject.name edge-attributes: association.edge_attributes + trapi_sources: association.sources subject-HP: HP: subject.HP input_name: object.name output_name: subject.name edge-attributes: association.edge_attributes + trapi_sources: association.sources subject-CHEBI: CHEBI: subject.CHEBI input_name: object.name output_name: subject.name edge-attributes: association.edge_attributes + trapi_sources: association.sources subject-UNII: UNII: subject.UNII input_name: object.name output_name: subject.name edge-attributes: association.edge_attributes + trapi_sources: association.sources From 869daf0fcefe20dc23b6b353af9e0b27de7373b9 Mon Sep 17 00:00:00 2001 From: GitHubbit <10294502+GitHubbit@users.noreply.github.com> Date: Wed, 31 May 2023 19:45:35 -0400 Subject: [PATCH 2/6] Fixed typo in the x-bte-response-mapping section --- ehr_risk_kp.yaml | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/ehr_risk_kp.yaml b/ehr_risk_kp.yaml index 604518a..dd3e362 100644 --- a/ehr_risk_kp.yaml +++ b/ehr_risk_kp.yaml @@ -7747,70 +7747,70 @@ components: input_name: subject.name output_name: object.name edge-attributes: association.edge_attributes - trapi_sources: association.sources + trapi_sources: source.edge_sources object-NCIT: NCIT: object.NCIT input_name: subject.name output_name: object.name edge-attributes: association.edge_attributes - trapi_sources: association.sources + trapi_sources: source.edge_sources object-SNOMEDCT: SNOMEDCT: object.SNOMEDCT input_name: subject.name output_name: object.name edge-attributes: association.edge_attributes - trapi_sources: association.sources + trapi_sources: source.edge_sources object-HP: HP: object.HP input_name: subject.name output_name: object.name edge-attributes: association.edge_attributes - trapi_sources: association.sources + trapi_sources: source.edge_sources object-CHEBI: CHEBI: object.CHEBI input_name: subject.name output_name: object.name edge-attributes: association.edge_attributes - trapi_sources: association.sources + trapi_sources: source.edge_sources object-UNII: UNII: object.UNII input_name: subject.name output_name: object.name edge-attributes: association.edge_attributes - trapi_sources: association.sources + trapi_sources: source.edge_sources subject-MONDO: MONDO: subject.MONDO input_name: object.name output_name: subject.name edge-attributes: association.edge_attributes - trapi_sources: association.sources + trapi_sources: source.edge_sources subject-NCIT: NCIT: subject.NCIT input_name: object.name output_name: subject.name edge-attributes: association.edge_attributes - trapi_sources: association.sources + trapi_sources: source.edge_sources subject-SNOMEDCT: SNOMEDCT: subject.SNOMEDCT input_name: object.name output_name: subject.name edge-attributes: association.edge_attributes - trapi_sources: association.sources + trapi_sources: source.edge_sources subject-HP: HP: subject.HP input_name: object.name output_name: subject.name edge-attributes: association.edge_attributes - trapi_sources: association.sources + trapi_sources: source.edge_sources subject-CHEBI: CHEBI: subject.CHEBI input_name: object.name output_name: subject.name edge-attributes: association.edge_attributes - trapi_sources: association.sources + trapi_sources: source.edge_sources subject-UNII: UNII: subject.UNII input_name: object.name output_name: subject.name edge-attributes: association.edge_attributes - trapi_sources: association.sources + trapi_sources: source.edge_sources From b21194f372b676ff2950e96e2e008654a5e1e8f0 Mon Sep 17 00:00:00 2001 From: GitHubbit <10294502+GitHubbit@users.noreply.github.com> Date: Fri, 2 Jun 2023 12:49:06 -0400 Subject: [PATCH 3/6] Saving unofficial developer notebook here for reference --- legacy_parsers/EHR_Risk_parser.ipynb | 12376 +++++++++++++++++++++++++ 1 file changed, 12376 insertions(+) create mode 100644 legacy_parsers/EHR_Risk_parser.ipynb diff --git a/legacy_parsers/EHR_Risk_parser.ipynb b/legacy_parsers/EHR_Risk_parser.ipynb new file mode 100644 index 0000000..6e1564d --- /dev/null +++ b/legacy_parsers/EHR_Risk_parser.ipynb @@ -0,0 +1,12376 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "4d2996ec", + "metadata": {}, + "outputs": [], + "source": [ + "# qualifiers to include: https://github.com/biolink/biolink-model/issues/1050" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "0dc9bbef", + "metadata": {}, + "outputs": [], + "source": [ + "import pandas as pd\n", + "import json\n", + "import sys, os\n", + "import numpy as np" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "92478b80", + "metadata": { + "scrolled": true + }, + "outputs": [ + { + "data": { + "text/html": [ + "
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idnamecategoryxrefprovided_by
0HP:0025181Abdominal aseptic abscessbiolink:PhenotypicFeatureNaNEHR Risk Provider (Multiomics)
1HP:0002027Abdominal painbiolink:PhenotypicFeatureNaNEHR Risk Provider (Multiomics)
2HP:0003115Abnormal EKGbiolink:PhenotypicFeatureNaNEHR Risk Provider (Multiomics)
3HP:0006919Abnormal aggressive, impulsive or violent beha...biolink:PhenotypicFeatureNaNEHR Risk Provider (Multiomics)
4HP:0003119Abnormal circulating lipid concentrationbiolink:PhenotypicFeatureNaNEHR Risk Provider (Multiomics)
..................
801CHEBI:27300vitamin dbiolink:ChemicalSubstanceNaNEHR Risk Provider (Multiomics)
802CHEBI:33234vitamin ebiolink:ChemicalSubstanceNaNEHR Risk Provider (Multiomics)
803CHEBI:87732warfarinbiolink:ChemicalSubstanceNaNEHR Risk Provider (Multiomics)
804CHEBI:36560zinc oxidebiolink:ChemicalSubstanceNaNEHR Risk Provider (Multiomics)
805CHEBI:10125zolpidembiolink:ChemicalSubstanceNaNEHR Risk Provider (Multiomics)
\n", + "

806 rows × 5 columns

\n", + "
" + ], + "text/plain": [ + " id name \\\n", + "0 HP:0025181 Abdominal aseptic abscess \n", + "1 HP:0002027 Abdominal pain \n", + "2 HP:0003115 Abnormal EKG \n", + "3 HP:0006919 Abnormal aggressive, impulsive or violent beha... \n", + "4 HP:0003119 Abnormal circulating lipid concentration \n", + ".. ... ... \n", + "801 CHEBI:27300 vitamin d \n", + "802 CHEBI:33234 vitamin e \n", + "803 CHEBI:87732 warfarin \n", + "804 CHEBI:36560 zinc oxide \n", + "805 CHEBI:10125 zolpidem \n", + "\n", + " category xref provided_by \n", + "0 biolink:PhenotypicFeature NaN EHR Risk Provider (Multiomics) \n", + "1 biolink:PhenotypicFeature NaN EHR Risk Provider (Multiomics) \n", + "2 biolink:PhenotypicFeature NaN EHR Risk Provider (Multiomics) \n", + "3 biolink:PhenotypicFeature NaN EHR Risk Provider (Multiomics) \n", + "4 biolink:PhenotypicFeature NaN EHR Risk Provider (Multiomics) \n", + ".. ... ... ... \n", + "801 biolink:ChemicalSubstance NaN EHR Risk Provider (Multiomics) \n", + "802 biolink:ChemicalSubstance NaN EHR Risk Provider (Multiomics) \n", + "803 biolink:ChemicalSubstance NaN EHR Risk Provider (Multiomics) \n", + "804 biolink:ChemicalSubstance NaN EHR Risk Provider (Multiomics) \n", + "805 biolink:ChemicalSubstance NaN EHR Risk Provider (Multiomics) \n", + "\n", + "[806 rows x 5 columns]" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# nodes_filepath = os.path.join(\"../../data\", \"ehr_risk_nodes_data_2023_03_09.csv\")\n", + "# edges_filepath = os.path.join(\"../../data\", \"ehr_risk_edges_data_2023_03_09.csv\")\n", + "nodes_filepath = os.path.join(\"../../data\", \"ehr_risk_nodes_data_2022_06_01.csv\")\n", + "edges_filepath = os.path.join(\"../../data\", \"ehr_risk_edges_data_2022_06_01.csv\")\n", + "nodes_data = pd.read_csv(nodes_filepath, sep = ',')\n", + "edges_data = pd.read_csv(edges_filepath, sep = ',')\n", + "\n", + "nodes_data" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "0cb5c158", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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idnamecategoryxrefprovided_by
511MONDO:0009421hypogonadism, malebiolink:DiseaseNaNEHR Risk Provider (Multiomics)
\n", + "
" + ], + "text/plain": [ + " id name category xref \\\n", + "511 MONDO:0009421 hypogonadism, male biolink:Disease NaN \n", + "\n", + " provided_by \n", + "511 EHR Risk Provider (Multiomics) " + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "nodes_data.loc[nodes_data['name'].isin(['hypogonadism, male'])]" + ] + }, + { + "cell_type": "markdown", + "id": "0a92a7a5", + "metadata": {}, + "source": [ + "# There appears to be duplicate CURIEs \n", + "## This should be fixed at the enclave level" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "d9673bb6", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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idnamecategoryxrefprovided_by
0HP:0025181Abdominal aseptic abscessbiolink:PhenotypicFeatureNaNEHR Risk Provider (Multiomics)
1HP:0002027Abdominal painbiolink:PhenotypicFeatureNaNEHR Risk Provider (Multiomics)
2HP:0003115Abnormal EKGbiolink:PhenotypicFeatureNaNEHR Risk Provider (Multiomics)
3HP:0006919Abnormal aggressive, impulsive or violent beha...biolink:PhenotypicFeatureNaNEHR Risk Provider (Multiomics)
4HP:0003119Abnormal circulating lipid concentrationbiolink:PhenotypicFeatureNaNEHR Risk Provider (Multiomics)
..................
801CHEBI:27300vitamin dbiolink:ChemicalSubstanceNaNEHR Risk Provider (Multiomics)
802CHEBI:33234vitamin ebiolink:ChemicalSubstanceNaNEHR Risk Provider (Multiomics)
803CHEBI:87732warfarinbiolink:ChemicalSubstanceNaNEHR Risk Provider (Multiomics)
804CHEBI:36560zinc oxidebiolink:ChemicalSubstanceNaNEHR Risk Provider (Multiomics)
805CHEBI:10125zolpidembiolink:ChemicalSubstanceNaNEHR Risk Provider (Multiomics)
\n", + "

804 rows × 5 columns

\n", + "
" + ], + "text/plain": [ + " id name \\\n", + "0 HP:0025181 Abdominal aseptic abscess \n", + "1 HP:0002027 Abdominal pain \n", + "2 HP:0003115 Abnormal EKG \n", + "3 HP:0006919 Abnormal aggressive, impulsive or violent beha... \n", + "4 HP:0003119 Abnormal circulating lipid concentration \n", + ".. ... ... \n", + "801 CHEBI:27300 vitamin d \n", + "802 CHEBI:33234 vitamin e \n", + "803 CHEBI:87732 warfarin \n", + "804 CHEBI:36560 zinc oxide \n", + "805 CHEBI:10125 zolpidem \n", + "\n", + " category xref provided_by \n", + "0 biolink:PhenotypicFeature NaN EHR Risk Provider (Multiomics) \n", + "1 biolink:PhenotypicFeature NaN EHR Risk Provider (Multiomics) \n", + "2 biolink:PhenotypicFeature NaN EHR Risk Provider (Multiomics) \n", + "3 biolink:PhenotypicFeature NaN EHR Risk Provider (Multiomics) \n", + "4 biolink:PhenotypicFeature NaN EHR Risk Provider (Multiomics) \n", + ".. ... ... ... \n", + "801 biolink:ChemicalSubstance NaN EHR Risk Provider (Multiomics) \n", + "802 biolink:ChemicalSubstance NaN EHR Risk Provider (Multiomics) \n", + "803 biolink:ChemicalSubstance NaN EHR Risk Provider (Multiomics) \n", + "804 biolink:ChemicalSubstance NaN EHR Risk Provider (Multiomics) \n", + "805 biolink:ChemicalSubstance NaN EHR Risk Provider (Multiomics) \n", + "\n", + "[804 rows x 5 columns]" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# there appears to be multiple CURIEs given for a node of the same name. Get just 1 CURIE for each name\n", + "nodes_data = nodes_data.drop_duplicates(subset='id', keep=\"first\")\n", + "nodes_data" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "3eec3454", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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idnamecategoryxrefprovided_by
0HP:0025181Abdominal aseptic abscessbiolink:PhenotypicFeatureNaNEHR Risk Provider (Multiomics)
1HP:0002027Abdominal painbiolink:PhenotypicFeatureNaNEHR Risk Provider (Multiomics)
2HP:0003115Abnormal EKGbiolink:PhenotypicFeatureNaNEHR Risk Provider (Multiomics)
3HP:0006919Abnormal aggressive, impulsive or violent beha...biolink:PhenotypicFeatureNaNEHR Risk Provider (Multiomics)
4HP:0003119Abnormal circulating lipid concentrationbiolink:PhenotypicFeatureNaNEHR Risk Provider (Multiomics)
..................
801CHEBI:27300vitamin dbiolink:ChemicalEntityNaNEHR Risk Provider (Multiomics)
802CHEBI:33234vitamin ebiolink:ChemicalEntityNaNEHR Risk Provider (Multiomics)
803CHEBI:87732warfarinbiolink:ChemicalEntityNaNEHR Risk Provider (Multiomics)
804CHEBI:36560zinc oxidebiolink:ChemicalEntityNaNEHR Risk Provider (Multiomics)
805CHEBI:10125zolpidembiolink:ChemicalEntityNaNEHR Risk Provider (Multiomics)
\n", + "

804 rows × 5 columns

\n", + "
" + ], + "text/plain": [ + " id name \\\n", + "0 HP:0025181 Abdominal aseptic abscess \n", + "1 HP:0002027 Abdominal pain \n", + "2 HP:0003115 Abnormal EKG \n", + "3 HP:0006919 Abnormal aggressive, impulsive or violent beha... \n", + "4 HP:0003119 Abnormal circulating lipid concentration \n", + ".. ... ... \n", + "801 CHEBI:27300 vitamin d \n", + "802 CHEBI:33234 vitamin e \n", + "803 CHEBI:87732 warfarin \n", + "804 CHEBI:36560 zinc oxide \n", + "805 CHEBI:10125 zolpidem \n", + "\n", + " category xref provided_by \n", + "0 biolink:PhenotypicFeature NaN EHR Risk Provider (Multiomics) \n", + "1 biolink:PhenotypicFeature NaN EHR Risk Provider (Multiomics) \n", + "2 biolink:PhenotypicFeature NaN EHR Risk Provider (Multiomics) \n", + "3 biolink:PhenotypicFeature NaN EHR Risk Provider (Multiomics) \n", + "4 biolink:PhenotypicFeature NaN EHR Risk Provider (Multiomics) \n", + ".. ... ... ... \n", + "801 biolink:ChemicalEntity NaN EHR Risk Provider (Multiomics) \n", + "802 biolink:ChemicalEntity NaN EHR Risk Provider (Multiomics) \n", + "803 biolink:ChemicalEntity NaN EHR Risk Provider (Multiomics) \n", + "804 biolink:ChemicalEntity NaN EHR Risk Provider (Multiomics) \n", + "805 biolink:ChemicalEntity NaN EHR Risk Provider (Multiomics) \n", + "\n", + "[804 rows x 5 columns]" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# biolink:ChemicalSubstance has been depecrated. Use biolink:ChemicalEntity instead (change all values ChemicalSubstance--->ChemialEntity)\n", + "nodes_data[\"category\"].mask(nodes_data[\"category\"] == \"biolink:ChemicalSubstance\", \"biolink:ChemicalEntity\" , inplace=True )\n", + "nodes_data\n" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "af3fe28d", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "804" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Check if the xref column is all NaN or empty\n", + "# get count of null values \n", + "nodes_data['xref'].isna().sum()\n", + "\n", + "# since xref is empty, we won't use it" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "id": "d3bdd0e5", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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subjectpredicateobjectrelationprovided_byprovided_datecategoryclassifierauc_rocp_valuefeature_importancefeature_coefficientlog_positive_patient_countlog_negative_patient_count
0HP:0008629biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.000000NaN8.79639957
1MONDO:0010643biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.999872NaN8.58521257
2UNII:25ADE2236Lbiolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.936767NaN4.55817757
3UNII:K16AIQ8CTMbiolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.998563NaN4.35752257
4MONDO:0007972biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.093959NaN3.92606457
.............................................
237099MONDO:0013600biolink:associated_with_decreased_likelihood_ofHP:0033106RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9568600.245984NaN-0.79041857
237100MONDO:0016264biolink:associated_with_decreased_likelihood_ofHP:0033106RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9568600.984249NaN-0.79608557
237101MONDO:0004565biolink:associated_with_decreased_likelihood_ofHP:0033106RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9568600.820564NaN-0.80397357
237102CHEBI:28864biolink:associated_with_decreased_likelihood_ofHP:0033106RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9568600.472603NaN-0.82257557
237103HP:0011947biolink:associated_with_decreased_likelihood_ofHP:0033106RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9568600.000207NaN-0.82573157
\n", + "

237104 rows × 14 columns

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" + ], + "text/plain": [ + " subject predicate \\\n", + "0 HP:0008629 biolink:associated_with_increased_likelihood_of \n", + "1 MONDO:0010643 biolink:associated_with_increased_likelihood_of \n", + "2 UNII:25ADE2236L biolink:associated_with_increased_likelihood_of \n", + "3 UNII:K16AIQ8CTM biolink:associated_with_increased_likelihood_of \n", + "4 MONDO:0007972 biolink:associated_with_increased_likelihood_of \n", + "... ... ... \n", + "237099 MONDO:0013600 biolink:associated_with_decreased_likelihood_of \n", + "237100 MONDO:0016264 biolink:associated_with_decreased_likelihood_of \n", + "237101 MONDO:0004565 biolink:associated_with_decreased_likelihood_of \n", + "237102 CHEBI:28864 biolink:associated_with_decreased_likelihood_of \n", + "237103 HP:0011947 biolink:associated_with_decreased_likelihood_of \n", + "\n", + " object relation provided_by provided_date \\\n", + "0 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "1 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "2 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "3 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "4 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "... ... ... ... ... \n", + "237099 HP:0033106 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237100 HP:0033106 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237101 HP:0033106 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237102 HP:0033106 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237103 HP:0033106 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "\n", + " category classifier auc_roc p_value \\\n", + "0 biolink:Association Logistic Regression 0.840132 0.000000 \n", + "1 biolink:Association Logistic Regression 0.840132 0.999872 \n", + "2 biolink:Association Logistic Regression 0.840132 0.936767 \n", + "3 biolink:Association Logistic Regression 0.840132 0.998563 \n", + "4 biolink:Association Logistic Regression 0.840132 0.093959 \n", + "... ... ... ... ... \n", + "237099 biolink:Association Logistic Regression 0.956860 0.245984 \n", + "237100 biolink:Association Logistic Regression 0.956860 0.984249 \n", + "237101 biolink:Association Logistic Regression 0.956860 0.820564 \n", + "237102 biolink:Association Logistic Regression 0.956860 0.472603 \n", + "237103 biolink:Association Logistic Regression 0.956860 0.000207 \n", + "\n", + " feature_importance feature_coefficient log_positive_patient_count \\\n", + "0 NaN 8.796399 5 \n", + "1 NaN 8.585212 5 \n", + "2 NaN 4.558177 5 \n", + "3 NaN 4.357522 5 \n", + "4 NaN 3.926064 5 \n", + "... ... ... ... \n", + "237099 NaN -0.790418 5 \n", + "237100 NaN -0.796085 5 \n", + "237101 NaN -0.803973 5 \n", + "237102 NaN -0.822575 5 \n", + "237103 NaN -0.825731 5 \n", + "\n", + " log_negative_patient_count \n", + "0 7 \n", + "1 7 \n", + "2 7 \n", + "3 7 \n", + "4 7 \n", + "... ... \n", + "237099 7 \n", + "237100 7 \n", + "237101 7 \n", + "237102 7 \n", + "237103 7 \n", + "\n", + "[237104 rows x 14 columns]" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "edges_data" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "29d182f7", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "array(['biolink:associated_with_increased_likelihood_of',\n", + " 'biolink:associated_with_decreased_likelihood_of'], dtype=object)" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# sanity check on predicates\n", + "edges_data['predicate'].unique()" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "id": "2f5092be", + "metadata": { + "scrolled": true + }, + "outputs": [ + { + "data": { + "text/html": [ + "
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subjectpredicateobjectrelationprovided_byprovided_datecategoryclassifierauc_rocp_valuefeature_importancefeature_coefficientnum_patients_with_conditionnum_patients_without_condition
0HP:0008629biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.000000NaN8.796399996699999902
1MONDO:0010643biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.999872NaN8.5852129993810000835
2UNII:25ADE2236Lbiolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.936767NaN4.5581779977010000939
3UNII:K16AIQ8CTMbiolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.998563NaN4.357522999109998659
4MONDO:0007972biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.093959NaN3.9260641002429998750
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237099MONDO:0013600biolink:associated_with_decreased_likelihood_ofHP:0033106RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9568600.245984NaN-0.790418999229995233
237100MONDO:0016264biolink:associated_with_decreased_likelihood_ofHP:0033106RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9568600.984249NaN-0.7960859982210002245
237101MONDO:0004565biolink:associated_with_decreased_likelihood_ofHP:0033106RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9568600.820564NaN-0.803973999379999068
237102CHEBI:28864biolink:associated_with_decreased_likelihood_ofHP:0033106RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9568600.472603NaN-0.8225759958810000517
237103HP:0011947biolink:associated_with_decreased_likelihood_ofHP:0033106RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9568600.000207NaN-0.8257311000739995547
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237104 rows × 14 columns

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" + ], + "text/plain": [ + " subject predicate \\\n", + "0 HP:0008629 biolink:associated_with_increased_likelihood_of \n", + "1 MONDO:0010643 biolink:associated_with_increased_likelihood_of \n", + "2 UNII:25ADE2236L biolink:associated_with_increased_likelihood_of \n", + "3 UNII:K16AIQ8CTM biolink:associated_with_increased_likelihood_of \n", + "4 MONDO:0007972 biolink:associated_with_increased_likelihood_of \n", + "... ... ... \n", + "237099 MONDO:0013600 biolink:associated_with_decreased_likelihood_of \n", + "237100 MONDO:0016264 biolink:associated_with_decreased_likelihood_of \n", + "237101 MONDO:0004565 biolink:associated_with_decreased_likelihood_of \n", + "237102 CHEBI:28864 biolink:associated_with_decreased_likelihood_of \n", + "237103 HP:0011947 biolink:associated_with_decreased_likelihood_of \n", + "\n", + " object relation provided_by provided_date \\\n", + "0 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "1 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "2 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "3 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "4 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "... ... ... ... ... \n", + "237099 HP:0033106 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237100 HP:0033106 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237101 HP:0033106 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237102 HP:0033106 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237103 HP:0033106 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "\n", + " category classifier auc_roc p_value \\\n", + "0 biolink:Association Logistic Regression 0.840132 0.000000 \n", + "1 biolink:Association Logistic Regression 0.840132 0.999872 \n", + "2 biolink:Association Logistic Regression 0.840132 0.936767 \n", + "3 biolink:Association Logistic Regression 0.840132 0.998563 \n", + "4 biolink:Association Logistic Regression 0.840132 0.093959 \n", + "... ... ... ... ... \n", + "237099 biolink:Association Logistic Regression 0.956860 0.245984 \n", + "237100 biolink:Association Logistic Regression 0.956860 0.984249 \n", + "237101 biolink:Association Logistic Regression 0.956860 0.820564 \n", + "237102 biolink:Association Logistic Regression 0.956860 0.472603 \n", + "237103 biolink:Association Logistic Regression 0.956860 0.000207 \n", + "\n", + " feature_importance feature_coefficient num_patients_with_condition \\\n", + "0 NaN 8.796399 99669 \n", + "1 NaN 8.585212 99938 \n", + "2 NaN 4.558177 99770 \n", + "3 NaN 4.357522 99910 \n", + "4 NaN 3.926064 100242 \n", + "... ... ... ... \n", + "237099 NaN -0.790418 99922 \n", + "237100 NaN -0.796085 99822 \n", + "237101 NaN -0.803973 99937 \n", + "237102 NaN -0.822575 99588 \n", + "237103 NaN -0.825731 100073 \n", + "\n", + " num_patients_without_condition \n", + "0 9999902 \n", + "1 10000835 \n", + "2 10000939 \n", + "3 9998659 \n", + "4 9998750 \n", + "... ... \n", + "237099 9995233 \n", + "237100 10002245 \n", + "237101 9999068 \n", + "237102 10000517 \n", + "237103 9995547 \n", + "\n", + "[237104 rows x 14 columns]" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "edges_data[\"num_patients_with_condition\"] = 10**(edges_data['log_positive_patient_count']) # convert log pos patient count to an actual # \n", + "edges_data[\"num_patients_without_condition\"] = 10**(edges_data['log_negative_patient_count']) # convert log neg patient count to an actual # \n", + "edges_data[\"num_patients_with_condition\"] = np.random.poisson(edges_data['num_patients_with_condition']) # add poisson noise injection\n", + "edges_data[\"num_patients_without_condition\"] = np.random.poisson(edges_data['num_patients_without_condition']) # add poisson noise injection\n", + "edges_data = edges_data.drop(['log_positive_patient_count', 'log_negative_patient_count'], axis=1)\n", + "edges_data" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "id": "ef4fb895", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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subjectpredicateobjectrelationprovided_byprovided_datecategoryclassifierauc_rocp_valuefeature_importancefeature_coefficientnum_patients_with_conditionnum_patients_without_conditionnodes_frozenset
0HP:0008629biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.000000NaN8.796399996699999902(HP:0000360, HP:0008629)
1MONDO:0010643biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.999872NaN8.5852129993810000835(HP:0000360, MONDO:0010643)
2UNII:25ADE2236Lbiolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.936767NaN4.5581779977010000939(UNII:25ADE2236L, HP:0000360)
3UNII:K16AIQ8CTMbiolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.998563NaN4.357522999109998659(HP:0000360, UNII:K16AIQ8CTM)
4MONDO:0007972biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.093959NaN3.9260641002429998750(MONDO:0007972, HP:0000360)
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237099MONDO:0013600biolink:associated_with_decreased_likelihood_ofHP:0033106RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9568600.245984NaN-0.790418999229995233(MONDO:0013600, HP:0033106)
237100MONDO:0016264biolink:associated_with_decreased_likelihood_ofHP:0033106RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9568600.984249NaN-0.7960859982210002245(MONDO:0016264, HP:0033106)
237101MONDO:0004565biolink:associated_with_decreased_likelihood_ofHP:0033106RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9568600.820564NaN-0.803973999379999068(HP:0033106, MONDO:0004565)
237102CHEBI:28864biolink:associated_with_decreased_likelihood_ofHP:0033106RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9568600.472603NaN-0.8225759958810000517(CHEBI:28864, HP:0033106)
237103HP:0011947biolink:associated_with_decreased_likelihood_ofHP:0033106RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9568600.000207NaN-0.8257311000739995547(HP:0011947, HP:0033106)
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237104 rows × 15 columns

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" + ], + "text/plain": [ + " subject predicate \\\n", + "0 HP:0008629 biolink:associated_with_increased_likelihood_of \n", + "1 MONDO:0010643 biolink:associated_with_increased_likelihood_of \n", + "2 UNII:25ADE2236L biolink:associated_with_increased_likelihood_of \n", + "3 UNII:K16AIQ8CTM biolink:associated_with_increased_likelihood_of \n", + "4 MONDO:0007972 biolink:associated_with_increased_likelihood_of \n", + "... ... ... \n", + "237099 MONDO:0013600 biolink:associated_with_decreased_likelihood_of \n", + "237100 MONDO:0016264 biolink:associated_with_decreased_likelihood_of \n", + "237101 MONDO:0004565 biolink:associated_with_decreased_likelihood_of \n", + "237102 CHEBI:28864 biolink:associated_with_decreased_likelihood_of \n", + "237103 HP:0011947 biolink:associated_with_decreased_likelihood_of \n", + "\n", + " object relation provided_by provided_date \\\n", + "0 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "1 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "2 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "3 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "4 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "... ... ... ... ... \n", + "237099 HP:0033106 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237100 HP:0033106 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237101 HP:0033106 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237102 HP:0033106 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237103 HP:0033106 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "\n", + " category classifier auc_roc p_value \\\n", + "0 biolink:Association Logistic Regression 0.840132 0.000000 \n", + "1 biolink:Association Logistic Regression 0.840132 0.999872 \n", + "2 biolink:Association Logistic Regression 0.840132 0.936767 \n", + "3 biolink:Association Logistic Regression 0.840132 0.998563 \n", + "4 biolink:Association Logistic Regression 0.840132 0.093959 \n", + "... ... ... ... ... \n", + "237099 biolink:Association Logistic Regression 0.956860 0.245984 \n", + "237100 biolink:Association Logistic Regression 0.956860 0.984249 \n", + "237101 biolink:Association Logistic Regression 0.956860 0.820564 \n", + "237102 biolink:Association Logistic Regression 0.956860 0.472603 \n", + "237103 biolink:Association Logistic Regression 0.956860 0.000207 \n", + "\n", + " feature_importance feature_coefficient num_patients_with_condition \\\n", + "0 NaN 8.796399 99669 \n", + "1 NaN 8.585212 99938 \n", + "2 NaN 4.558177 99770 \n", + "3 NaN 4.357522 99910 \n", + "4 NaN 3.926064 100242 \n", + "... ... ... ... \n", + "237099 NaN -0.790418 99922 \n", + "237100 NaN -0.796085 99822 \n", + "237101 NaN -0.803973 99937 \n", + "237102 NaN -0.822575 99588 \n", + "237103 NaN -0.825731 100073 \n", + "\n", + " num_patients_without_condition nodes_frozenset \n", + "0 9999902 (HP:0000360, HP:0008629) \n", + "1 10000835 (HP:0000360, MONDO:0010643) \n", + "2 10000939 (UNII:25ADE2236L, HP:0000360) \n", + "3 9998659 (HP:0000360, UNII:K16AIQ8CTM) \n", + "4 9998750 (MONDO:0007972, HP:0000360) \n", + "... ... ... \n", + "237099 9995233 (MONDO:0013600, HP:0033106) \n", + "237100 10002245 (MONDO:0016264, HP:0033106) \n", + "237101 9999068 (HP:0033106, MONDO:0004565) \n", + "237102 10000517 (CHEBI:28864, HP:0033106) \n", + "237103 9995547 (HP:0011947, HP:0033106) \n", + "\n", + "[237104 rows x 15 columns]" + ] + }, + "execution_count": 11, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Convert columns A and B to frozenset\n", + "# df['AB'] = df[['A', 'B']].apply(frozenset, axis=1)\n", + "edges_data['nodes_frozenset'] = edges_data[['subject', 'object']].apply(frozenset, axis=1)\n", + "edges_data" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "id": "610615b0", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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subjectpredicateobjectrelationprovided_byprovided_datecategoryclassifierauc_rocp_valuefeature_importancefeature_coefficientnum_patients_with_conditionnum_patients_without_condition
0HP:0008629biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.000000NaN8.796399996699999902
1MONDO:0010643biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.999872NaN8.5852129993810000835
2UNII:25ADE2236Lbiolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.936767NaN4.5581779977010000939
3UNII:K16AIQ8CTMbiolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.998563NaN4.357522999109998659
4MONDO:0007972biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.093959NaN3.9260641002429998750
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237099MONDO:0013600biolink:associated_with_decreased_likelihood_ofHP:0033106RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9568600.245984NaN-0.790418999229995233
237100MONDO:0016264biolink:associated_with_decreased_likelihood_ofHP:0033106RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9568600.984249NaN-0.7960859982210002245
237101MONDO:0004565biolink:associated_with_decreased_likelihood_ofHP:0033106RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9568600.820564NaN-0.803973999379999068
237102CHEBI:28864biolink:associated_with_decreased_likelihood_ofHP:0033106RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9568600.472603NaN-0.8225759958810000517
237103HP:0011947biolink:associated_with_decreased_likelihood_ofHP:0033106RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9568600.000207NaN-0.8257311000739995547
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237104 rows × 14 columns

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" + ], + "text/plain": [ + " subject predicate \\\n", + "0 HP:0008629 biolink:associated_with_increased_likelihood_of \n", + "1 MONDO:0010643 biolink:associated_with_increased_likelihood_of \n", + "2 UNII:25ADE2236L biolink:associated_with_increased_likelihood_of \n", + "3 UNII:K16AIQ8CTM biolink:associated_with_increased_likelihood_of \n", + "4 MONDO:0007972 biolink:associated_with_increased_likelihood_of \n", + "... ... ... \n", + "237099 MONDO:0013600 biolink:associated_with_decreased_likelihood_of \n", + "237100 MONDO:0016264 biolink:associated_with_decreased_likelihood_of \n", + "237101 MONDO:0004565 biolink:associated_with_decreased_likelihood_of \n", + "237102 CHEBI:28864 biolink:associated_with_decreased_likelihood_of \n", + "237103 HP:0011947 biolink:associated_with_decreased_likelihood_of \n", + "\n", + " object relation provided_by provided_date \\\n", + "0 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "1 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "2 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "3 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "4 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "... ... ... ... ... \n", + "237099 HP:0033106 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237100 HP:0033106 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237101 HP:0033106 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237102 HP:0033106 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237103 HP:0033106 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "\n", + " category classifier auc_roc p_value \\\n", + "0 biolink:Association Logistic Regression 0.840132 0.000000 \n", + "1 biolink:Association Logistic Regression 0.840132 0.999872 \n", + "2 biolink:Association Logistic Regression 0.840132 0.936767 \n", + "3 biolink:Association Logistic Regression 0.840132 0.998563 \n", + "4 biolink:Association Logistic Regression 0.840132 0.093959 \n", + "... ... ... ... ... \n", + "237099 biolink:Association Logistic Regression 0.956860 0.245984 \n", + "237100 biolink:Association Logistic Regression 0.956860 0.984249 \n", + "237101 biolink:Association Logistic Regression 0.956860 0.820564 \n", + "237102 biolink:Association Logistic Regression 0.956860 0.472603 \n", + "237103 biolink:Association Logistic Regression 0.956860 0.000207 \n", + "\n", + " feature_importance feature_coefficient num_patients_with_condition \\\n", + "0 NaN 8.796399 99669 \n", + "1 NaN 8.585212 99938 \n", + "2 NaN 4.558177 99770 \n", + "3 NaN 4.357522 99910 \n", + "4 NaN 3.926064 100242 \n", + "... ... ... ... \n", + "237099 NaN -0.790418 99922 \n", + "237100 NaN -0.796085 99822 \n", + "237101 NaN -0.803973 99937 \n", + "237102 NaN -0.822575 99588 \n", + "237103 NaN -0.825731 100073 \n", + "\n", + " num_patients_without_condition \n", + "0 9999902 \n", + "1 10000835 \n", + "2 10000939 \n", + "3 9998659 \n", + "4 9998750 \n", + "... ... \n", + "237099 9995233 \n", + "237100 10002245 \n", + "237101 9999068 \n", + "237102 10000517 \n", + "237103 9995547 \n", + "\n", + "[237104 rows x 14 columns]" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Find duplicate rows based on frozenset of columns A and B\n", + "duplicate_rows = edges_data.duplicated(['nodes_frozenset', 'auc_roc', 'p_value', 'feature_coefficient'])\n", + "\n", + "# Filter the DataFrame to remove duplicate rows\n", + "test = edges_data[~duplicate_rows]\n", + "\n", + "test = test.drop(columns='nodes_frozenset')\n", + "\n", + "test" + ] + }, + { + "cell_type": "code", + "execution_count": 40, + "id": "dc4252fb", + "metadata": {}, + "outputs": [], + "source": [ + "# # create confidence interval column by concatenating 'lower_confidence_bound'and 'upper_confidence_bound', then dropping those columns\n", + "# edges_data['log_odds_ratio_95_confidence_interval'] = edges_data.apply(lambda row: [row['lower_confidence_bound'], row['upper_confidence_bound']], axis=1)\n", + "# edges_data = edges_data.drop(['lower_confidence_bound', 'upper_confidence_bound'], axis=1)\n", + "# edges_data" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "id": "8531ffa3", + "metadata": { + "scrolled": true + }, + "outputs": [ + { + "data": { + "text/html": [ + "
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subjectpredicateobjectrelationprovided_byprovided_datecategory_xclassifierauc_rocp_valuefeature_importancefeature_coefficientnum_patients_with_conditionnum_patients_without_conditionnodes_frozensetidnamecategory_y
0HP:0008629biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.000000NaN8.796399996699999902(HP:0000360, HP:0008629)HP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
1HP:0008629biolink:associated_with_decreased_likelihood_ofHP:0000739RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8761000.985604NaN-0.530062998419999688(HP:0008629, HP:0000739)HP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
2HP:0008629biolink:associated_with_decreased_likelihood_ofHP:0000787RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8411020.981654NaN-1.18066910035410002196(HP:0008629, HP:0000787)HP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
3HP:0008629biolink:associated_with_decreased_likelihood_ofHP:0000790RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9108380.960982NaN-1.2000199983510001455(HP:0008629, HP:0000790)HP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
4HP:0008629biolink:associated_with_increased_likelihood_ofHP:0000870RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8845800.988524NaN1.4326119689996545(HP:0008629, HP:0000870)HP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
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237099HP:0000360biolink:associated_with_decreased_likelihood_ofHP:0032312RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9214170.927675NaN-0.1716079972110001233(HP:0000360, HP:0032312)HP:0000360Tinnitusbiolink:PhenotypicFeature
237100HP:0000360biolink:associated_with_decreased_likelihood_ofHP:0032372RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9900230.962012NaN-2.81756810419998402(HP:0000360, HP:0032372)HP:0000360Tinnitusbiolink:PhenotypicFeature
237101HP:0000360biolink:associated_with_decreased_likelihood_ofHP:0032473RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9632060.989129NaN-5.438955810000998(HP:0000360, HP:0032473)HP:0000360Tinnitusbiolink:PhenotypicFeature
237102HP:0000360biolink:associated_with_decreased_likelihood_ofHP:0033077RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9872300.541701NaN-1.01730910054810003263(HP:0000360, HP:0033077)HP:0000360Tinnitusbiolink:PhenotypicFeature
237103HP:0000360biolink:associated_with_decreased_likelihood_ofHP:0033078RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9341150.807916NaN-0.92952410034510001251(HP:0000360, HP:0033078)HP:0000360Tinnitusbiolink:PhenotypicFeature
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237104 rows × 18 columns

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subjectpredicateobjectrelationprovided_byprovided_datepredicate_categoryclassifierauc_rocp_valuefeature_importancefeature_coefficientnum_patients_with_conditionnum_patients_without_conditionnodes_frozensetsubject_idsubject_namesubject_category
0HP:0008629biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.000000NaN8.796399996699999902(HP:0000360, HP:0008629)HP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
1HP:0008629biolink:associated_with_decreased_likelihood_ofHP:0000739RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8761000.985604NaN-0.530062998419999688(HP:0008629, HP:0000739)HP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
2HP:0008629biolink:associated_with_decreased_likelihood_ofHP:0000787RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8411020.981654NaN-1.18066910035410002196(HP:0008629, HP:0000787)HP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
3HP:0008629biolink:associated_with_decreased_likelihood_ofHP:0000790RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9108380.960982NaN-1.2000199983510001455(HP:0008629, HP:0000790)HP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
4HP:0008629biolink:associated_with_increased_likelihood_ofHP:0000870RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8845800.988524NaN1.4326119689996545(HP:0008629, HP:0000870)HP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
.........................................................
237099HP:0000360biolink:associated_with_decreased_likelihood_ofHP:0032312RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9214170.927675NaN-0.1716079972110001233(HP:0000360, HP:0032312)HP:0000360Tinnitusbiolink:PhenotypicFeature
237100HP:0000360biolink:associated_with_decreased_likelihood_ofHP:0032372RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9900230.962012NaN-2.81756810419998402(HP:0000360, HP:0032372)HP:0000360Tinnitusbiolink:PhenotypicFeature
237101HP:0000360biolink:associated_with_decreased_likelihood_ofHP:0032473RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9632060.989129NaN-5.438955810000998(HP:0000360, HP:0032473)HP:0000360Tinnitusbiolink:PhenotypicFeature
237102HP:0000360biolink:associated_with_decreased_likelihood_ofHP:0033077RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9872300.541701NaN-1.01730910054810003263(HP:0000360, HP:0033077)HP:0000360Tinnitusbiolink:PhenotypicFeature
237103HP:0000360biolink:associated_with_decreased_likelihood_ofHP:0033078RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9341150.807916NaN-0.92952410034510001251(HP:0000360, HP:0033078)HP:0000360Tinnitusbiolink:PhenotypicFeature
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237104 rows × 18 columns

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subjectpredicateobjectrelationprovided_byprovided_datepredicate_categoryclassifierauc_rocp_value...feature_coefficientnum_patients_with_conditionnum_patients_without_conditionnodes_frozensetsubject_idsubject_namesubject_categoryidnamecategory
0HP:0008629biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.000000...8.796399996699999902(HP:0000360, HP:0008629)HP:0008629Pulsatile tinnitusbiolink:PhenotypicFeatureHP:0000360Tinnitusbiolink:PhenotypicFeature
1MONDO:0010643biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.999872...8.5852129993810000835(HP:0000360, MONDO:0010643)MONDO:0010643acute leukemia (disease)biolink:DiseaseHP:0000360Tinnitusbiolink:PhenotypicFeature
2UNII:25ADE2236Lbiolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.936767...4.5581779977010000939(UNII:25ADE2236L, HP:0000360)UNII:25ADE2236Lthrombinbiolink:ChemicalEntityHP:0000360Tinnitusbiolink:PhenotypicFeature
3UNII:K16AIQ8CTMbiolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.998563...4.357522999109998659(HP:0000360, UNII:K16AIQ8CTM)UNII:K16AIQ8CTMpertuzumabbiolink:ChemicalEntityHP:0000360Tinnitusbiolink:PhenotypicFeature
4MONDO:0007972biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.093959...3.9260641002429998750(MONDO:0007972, HP:0000360)MONDO:0007972Meniere diseasebiolink:DiseaseHP:0000360Tinnitusbiolink:PhenotypicFeature
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237099CHEBI:114785biolink:associated_with_decreased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.998503...-5.087542100710007299(HP:0008629, CHEBI:114785)CHEBI:114785erlotinibbiolink:ChemicalEntityHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
237100UNII:52CMI0WC3Ybiolink:associated_with_decreased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.999719...-5.06644510169996273(UNII:52CMI0WC3Y, HP:0008629)UNII:52CMI0WC3Yatezolizumabbiolink:ChemicalEntityHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
237101CHEBI:135738biolink:associated_with_decreased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.998357...-5.0796409789998030(HP:0008629, CHEBI:135738)CHEBI:135738clevidipinebiolink:ChemicalEntityHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
237102MONDO:0004967biolink:associated_with_decreased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.997631...-4.683547100610001385(HP:0008629, MONDO:0004967)MONDO:0004967acute lymphoblastic leukemia (disease)biolink:DiseaseHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
237103HP:0000360biolink:associated_with_increased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.000000...7.5530039979997731(HP:0000360, HP:0008629)HP:0000360Tinnitusbiolink:PhenotypicFeatureHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
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237104 rows × 21 columns

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" + ], + "text/plain": [ + " subject predicate \\\n", + "0 HP:0008629 biolink:associated_with_increased_likelihood_of \n", + "1 MONDO:0010643 biolink:associated_with_increased_likelihood_of \n", + "2 UNII:25ADE2236L biolink:associated_with_increased_likelihood_of \n", + "3 UNII:K16AIQ8CTM biolink:associated_with_increased_likelihood_of \n", + "4 MONDO:0007972 biolink:associated_with_increased_likelihood_of \n", + "... ... ... \n", + "237099 CHEBI:114785 biolink:associated_with_decreased_likelihood_of \n", + "237100 UNII:52CMI0WC3Y biolink:associated_with_decreased_likelihood_of \n", + "237101 CHEBI:135738 biolink:associated_with_decreased_likelihood_of \n", + "237102 MONDO:0004967 biolink:associated_with_decreased_likelihood_of \n", + "237103 HP:0000360 biolink:associated_with_increased_likelihood_of \n", + "\n", + " object relation provided_by provided_date \\\n", + "0 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "1 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "2 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "3 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "4 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "... ... ... ... ... \n", + "237099 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237100 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237101 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237102 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237103 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "\n", + " predicate_category classifier auc_roc p_value ... \\\n", + "0 biolink:Association Logistic Regression 0.840132 0.000000 ... \n", + "1 biolink:Association Logistic Regression 0.840132 0.999872 ... \n", + "2 biolink:Association Logistic Regression 0.840132 0.936767 ... \n", + "3 biolink:Association Logistic Regression 0.840132 0.998563 ... \n", + "4 biolink:Association Logistic Regression 0.840132 0.093959 ... \n", + "... ... ... ... ... ... \n", + "237099 biolink:Association Logistic Regression 0.959791 0.998503 ... \n", + "237100 biolink:Association Logistic Regression 0.959791 0.999719 ... \n", + "237101 biolink:Association Logistic Regression 0.959791 0.998357 ... \n", + "237102 biolink:Association Logistic Regression 0.959791 0.997631 ... \n", + "237103 biolink:Association Logistic Regression 0.959791 0.000000 ... \n", + "\n", + " feature_coefficient num_patients_with_condition \\\n", + "0 8.796399 99669 \n", + "1 8.585212 99938 \n", + "2 4.558177 99770 \n", + "3 4.357522 99910 \n", + "4 3.926064 100242 \n", + "... ... ... \n", + "237099 -5.087542 1007 \n", + "237100 -5.066445 1016 \n", + "237101 -5.079640 978 \n", + "237102 -4.683547 1006 \n", + "237103 7.553003 997 \n", + "\n", + " num_patients_without_condition nodes_frozenset \\\n", + "0 9999902 (HP:0000360, HP:0008629) \n", + "1 10000835 (HP:0000360, MONDO:0010643) \n", + "2 10000939 (UNII:25ADE2236L, HP:0000360) \n", + "3 9998659 (HP:0000360, UNII:K16AIQ8CTM) \n", + "4 9998750 (MONDO:0007972, HP:0000360) \n", + "... ... ... \n", + "237099 10007299 (HP:0008629, CHEBI:114785) \n", + "237100 9996273 (UNII:52CMI0WC3Y, HP:0008629) \n", + "237101 9998030 (HP:0008629, CHEBI:135738) \n", + "237102 10001385 (HP:0008629, MONDO:0004967) \n", + "237103 9997731 (HP:0000360, HP:0008629) \n", + "\n", + " subject_id subject_name \\\n", + "0 HP:0008629 Pulsatile tinnitus \n", + "1 MONDO:0010643 acute leukemia (disease) \n", + "2 UNII:25ADE2236L thrombin \n", + "3 UNII:K16AIQ8CTM pertuzumab \n", + "4 MONDO:0007972 Meniere disease \n", + "... ... ... \n", + "237099 CHEBI:114785 erlotinib \n", + "237100 UNII:52CMI0WC3Y atezolizumab \n", + "237101 CHEBI:135738 clevidipine \n", + "237102 MONDO:0004967 acute lymphoblastic leukemia (disease) \n", + "237103 HP:0000360 Tinnitus \n", + "\n", + " subject_category id name \\\n", + "0 biolink:PhenotypicFeature HP:0000360 Tinnitus \n", + "1 biolink:Disease HP:0000360 Tinnitus \n", + "2 biolink:ChemicalEntity HP:0000360 Tinnitus \n", + "3 biolink:ChemicalEntity HP:0000360 Tinnitus \n", + "4 biolink:Disease HP:0000360 Tinnitus \n", + "... ... ... ... \n", + "237099 biolink:ChemicalEntity HP:0008629 Pulsatile tinnitus \n", + "237100 biolink:ChemicalEntity HP:0008629 Pulsatile tinnitus \n", + "237101 biolink:ChemicalEntity HP:0008629 Pulsatile tinnitus \n", + "237102 biolink:Disease HP:0008629 Pulsatile tinnitus \n", + "237103 biolink:PhenotypicFeature HP:0008629 Pulsatile tinnitus \n", + "\n", + " category \n", + "0 biolink:PhenotypicFeature \n", + "1 biolink:PhenotypicFeature \n", + "2 biolink:PhenotypicFeature \n", + "3 biolink:PhenotypicFeature \n", + "4 biolink:PhenotypicFeature \n", + "... ... \n", + "237099 biolink:PhenotypicFeature \n", + "237100 biolink:PhenotypicFeature \n", + "237101 biolink:PhenotypicFeature \n", + "237102 biolink:PhenotypicFeature \n", + "237103 biolink:PhenotypicFeature \n", + "\n", + "[237104 rows x 21 columns]" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# merging object info from nodes df\n", + "kg = pd.merge(kg, nodes_data[['id', 'name', 'category']], left_on='object', right_on = 'id', how=\"inner\")\n", + "kg" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "id": "b81d60e9", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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subjectpredicateobjectrelationprovided_byprovided_datepredicate_categoryclassifierauc_rocp_value...feature_coefficientnum_patients_with_conditionnum_patients_without_conditionnodes_frozensetsubject_idsubject_namesubject_categoryobject_idobject_nameobject_category
0HP:0008629biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.000000...8.796399996699999902(HP:0000360, HP:0008629)HP:0008629Pulsatile tinnitusbiolink:PhenotypicFeatureHP:0000360Tinnitusbiolink:PhenotypicFeature
1MONDO:0010643biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.999872...8.5852129993810000835(HP:0000360, MONDO:0010643)MONDO:0010643acute leukemia (disease)biolink:DiseaseHP:0000360Tinnitusbiolink:PhenotypicFeature
2UNII:25ADE2236Lbiolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.936767...4.5581779977010000939(UNII:25ADE2236L, HP:0000360)UNII:25ADE2236Lthrombinbiolink:ChemicalEntityHP:0000360Tinnitusbiolink:PhenotypicFeature
3UNII:K16AIQ8CTMbiolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.998563...4.357522999109998659(HP:0000360, UNII:K16AIQ8CTM)UNII:K16AIQ8CTMpertuzumabbiolink:ChemicalEntityHP:0000360Tinnitusbiolink:PhenotypicFeature
4MONDO:0007972biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.093959...3.9260641002429998750(MONDO:0007972, HP:0000360)MONDO:0007972Meniere diseasebiolink:DiseaseHP:0000360Tinnitusbiolink:PhenotypicFeature
..................................................................
237099CHEBI:114785biolink:associated_with_decreased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.998503...-5.087542100710007299(HP:0008629, CHEBI:114785)CHEBI:114785erlotinibbiolink:ChemicalEntityHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
237100UNII:52CMI0WC3Ybiolink:associated_with_decreased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.999719...-5.06644510169996273(UNII:52CMI0WC3Y, HP:0008629)UNII:52CMI0WC3Yatezolizumabbiolink:ChemicalEntityHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
237101CHEBI:135738biolink:associated_with_decreased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.998357...-5.0796409789998030(HP:0008629, CHEBI:135738)CHEBI:135738clevidipinebiolink:ChemicalEntityHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
237102MONDO:0004967biolink:associated_with_decreased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.997631...-4.683547100610001385(HP:0008629, MONDO:0004967)MONDO:0004967acute lymphoblastic leukemia (disease)biolink:DiseaseHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
237103HP:0000360biolink:associated_with_increased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.000000...7.5530039979997731(HP:0000360, HP:0008629)HP:0000360Tinnitusbiolink:PhenotypicFeatureHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
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237104 rows × 21 columns

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" + ], + "text/plain": [ + " subject predicate \\\n", + "0 HP:0008629 biolink:associated_with_increased_likelihood_of \n", + "1 MONDO:0010643 biolink:associated_with_increased_likelihood_of \n", + "2 UNII:25ADE2236L biolink:associated_with_increased_likelihood_of \n", + "3 UNII:K16AIQ8CTM biolink:associated_with_increased_likelihood_of \n", + "4 MONDO:0007972 biolink:associated_with_increased_likelihood_of \n", + "... ... ... \n", + "237099 CHEBI:114785 biolink:associated_with_decreased_likelihood_of \n", + "237100 UNII:52CMI0WC3Y biolink:associated_with_decreased_likelihood_of \n", + "237101 CHEBI:135738 biolink:associated_with_decreased_likelihood_of \n", + "237102 MONDO:0004967 biolink:associated_with_decreased_likelihood_of \n", + "237103 HP:0000360 biolink:associated_with_increased_likelihood_of \n", + "\n", + " object relation provided_by provided_date \\\n", + "0 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "1 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "2 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "3 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "4 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "... ... ... ... ... \n", + "237099 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237100 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237101 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237102 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237103 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "\n", + " predicate_category classifier auc_roc p_value ... \\\n", + "0 biolink:Association Logistic Regression 0.840132 0.000000 ... \n", + "1 biolink:Association Logistic Regression 0.840132 0.999872 ... \n", + "2 biolink:Association Logistic Regression 0.840132 0.936767 ... \n", + "3 biolink:Association Logistic Regression 0.840132 0.998563 ... \n", + "4 biolink:Association Logistic Regression 0.840132 0.093959 ... \n", + "... ... ... ... ... ... \n", + "237099 biolink:Association Logistic Regression 0.959791 0.998503 ... \n", + "237100 biolink:Association Logistic Regression 0.959791 0.999719 ... \n", + "237101 biolink:Association Logistic Regression 0.959791 0.998357 ... \n", + "237102 biolink:Association Logistic Regression 0.959791 0.997631 ... \n", + "237103 biolink:Association Logistic Regression 0.959791 0.000000 ... \n", + "\n", + " feature_coefficient num_patients_with_condition \\\n", + "0 8.796399 99669 \n", + "1 8.585212 99938 \n", + "2 4.558177 99770 \n", + "3 4.357522 99910 \n", + "4 3.926064 100242 \n", + "... ... ... \n", + "237099 -5.087542 1007 \n", + "237100 -5.066445 1016 \n", + "237101 -5.079640 978 \n", + "237102 -4.683547 1006 \n", + "237103 7.553003 997 \n", + "\n", + " num_patients_without_condition nodes_frozenset \\\n", + "0 9999902 (HP:0000360, HP:0008629) \n", + "1 10000835 (HP:0000360, MONDO:0010643) \n", + "2 10000939 (UNII:25ADE2236L, HP:0000360) \n", + "3 9998659 (HP:0000360, UNII:K16AIQ8CTM) \n", + "4 9998750 (MONDO:0007972, HP:0000360) \n", + "... ... ... \n", + "237099 10007299 (HP:0008629, CHEBI:114785) \n", + "237100 9996273 (UNII:52CMI0WC3Y, HP:0008629) \n", + "237101 9998030 (HP:0008629, CHEBI:135738) \n", + "237102 10001385 (HP:0008629, MONDO:0004967) \n", + "237103 9997731 (HP:0000360, HP:0008629) \n", + "\n", + " subject_id subject_name \\\n", + "0 HP:0008629 Pulsatile tinnitus \n", + "1 MONDO:0010643 acute leukemia (disease) \n", + "2 UNII:25ADE2236L thrombin \n", + "3 UNII:K16AIQ8CTM pertuzumab \n", + "4 MONDO:0007972 Meniere disease \n", + "... ... ... \n", + "237099 CHEBI:114785 erlotinib \n", + "237100 UNII:52CMI0WC3Y atezolizumab \n", + "237101 CHEBI:135738 clevidipine \n", + "237102 MONDO:0004967 acute lymphoblastic leukemia (disease) \n", + "237103 HP:0000360 Tinnitus \n", + "\n", + " subject_category object_id object_name \\\n", + "0 biolink:PhenotypicFeature HP:0000360 Tinnitus \n", + "1 biolink:Disease HP:0000360 Tinnitus \n", + "2 biolink:ChemicalEntity HP:0000360 Tinnitus \n", + "3 biolink:ChemicalEntity HP:0000360 Tinnitus \n", + "4 biolink:Disease HP:0000360 Tinnitus \n", + "... ... ... ... \n", + "237099 biolink:ChemicalEntity HP:0008629 Pulsatile tinnitus \n", + "237100 biolink:ChemicalEntity HP:0008629 Pulsatile tinnitus \n", + "237101 biolink:ChemicalEntity HP:0008629 Pulsatile tinnitus \n", + "237102 biolink:Disease HP:0008629 Pulsatile tinnitus \n", + "237103 biolink:PhenotypicFeature HP:0008629 Pulsatile tinnitus \n", + "\n", + " object_category \n", + "0 biolink:PhenotypicFeature \n", + "1 biolink:PhenotypicFeature \n", + "2 biolink:PhenotypicFeature \n", + "3 biolink:PhenotypicFeature \n", + "4 biolink:PhenotypicFeature \n", + "... ... \n", + "237099 biolink:PhenotypicFeature \n", + "237100 biolink:PhenotypicFeature \n", + "237101 biolink:PhenotypicFeature \n", + "237102 biolink:PhenotypicFeature \n", + "237103 biolink:PhenotypicFeature \n", + "\n", + "[237104 rows x 21 columns]" + ] + }, + "execution_count": 16, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "kg.rename(columns = {'id':'object_id',\n", + " 'category': 'object_category',\n", + " 'name': 'object_name'}, inplace = True)\n", + "kg" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "id": "d54c7830", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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subjectpredicateobjectrelationprovided_byprovided_datepredicate_categoryclassifierauc_rocp_value...feature_coefficientnum_patients_with_conditionnum_patients_without_conditionnodes_frozensetsubject_idsubject_namesubject_categoryobject_idobject_nameobject_category
0HP:0008629biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.000000...8.796399996699999902(HP:0000360, HP:0008629)HP:0008629Pulsatile tinnitusbiolink:PhenotypicFeatureHP:0000360Tinnitusbiolink:PhenotypicFeature
1MONDO:0010643biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.999872...8.5852129993810000835(HP:0000360, MONDO:0010643)MONDO:0010643acute leukemia (disease)biolink:DiseaseHP:0000360Tinnitusbiolink:PhenotypicFeature
2UNII:25ADE2236Lbiolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.936767...4.5581779977010000939(UNII:25ADE2236L, HP:0000360)UNII:25ADE2236Lthrombinbiolink:ChemicalEntityHP:0000360Tinnitusbiolink:PhenotypicFeature
3UNII:K16AIQ8CTMbiolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.998563...4.357522999109998659(HP:0000360, UNII:K16AIQ8CTM)UNII:K16AIQ8CTMpertuzumabbiolink:ChemicalEntityHP:0000360Tinnitusbiolink:PhenotypicFeature
4MONDO:0007972biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.093959...3.9260641002429998750(MONDO:0007972, HP:0000360)MONDO:0007972Meniere diseasebiolink:DiseaseHP:0000360Tinnitusbiolink:PhenotypicFeature
..................................................................
237099CHEBI:114785biolink:associated_with_decreased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.998503...-5.087542100710007299(HP:0008629, CHEBI:114785)CHEBI:114785erlotinibbiolink:ChemicalEntityHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
237100UNII:52CMI0WC3Ybiolink:associated_with_decreased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.999719...-5.06644510169996273(UNII:52CMI0WC3Y, HP:0008629)UNII:52CMI0WC3Yatezolizumabbiolink:ChemicalEntityHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
237101CHEBI:135738biolink:associated_with_decreased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.998357...-5.0796409789998030(HP:0008629, CHEBI:135738)CHEBI:135738clevidipinebiolink:ChemicalEntityHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
237102MONDO:0004967biolink:associated_with_decreased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.997631...-4.683547100610001385(HP:0008629, MONDO:0004967)MONDO:0004967acute lymphoblastic leukemia (disease)biolink:DiseaseHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
237103HP:0000360biolink:associated_with_increased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.000000...7.5530039979997731(HP:0000360, HP:0008629)HP:0000360Tinnitusbiolink:PhenotypicFeatureHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
\n", + "

237104 rows × 21 columns

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" + ], + "text/plain": [ + " subject predicate \\\n", + "0 HP:0008629 biolink:associated_with_increased_likelihood_of \n", + "1 MONDO:0010643 biolink:associated_with_increased_likelihood_of \n", + "2 UNII:25ADE2236L biolink:associated_with_increased_likelihood_of \n", + "3 UNII:K16AIQ8CTM biolink:associated_with_increased_likelihood_of \n", + "4 MONDO:0007972 biolink:associated_with_increased_likelihood_of \n", + "... ... ... \n", + "237099 CHEBI:114785 biolink:associated_with_decreased_likelihood_of \n", + "237100 UNII:52CMI0WC3Y biolink:associated_with_decreased_likelihood_of \n", + "237101 CHEBI:135738 biolink:associated_with_decreased_likelihood_of \n", + "237102 MONDO:0004967 biolink:associated_with_decreased_likelihood_of \n", + "237103 HP:0000360 biolink:associated_with_increased_likelihood_of \n", + "\n", + " object relation provided_by provided_date \\\n", + "0 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "1 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "2 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "3 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "4 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "... ... ... ... ... \n", + "237099 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237100 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237101 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237102 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237103 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "\n", + " predicate_category classifier auc_roc p_value ... \\\n", + "0 biolink:Association Logistic Regression 0.840132 0.000000 ... \n", + "1 biolink:Association Logistic Regression 0.840132 0.999872 ... \n", + "2 biolink:Association Logistic Regression 0.840132 0.936767 ... \n", + "3 biolink:Association Logistic Regression 0.840132 0.998563 ... \n", + "4 biolink:Association Logistic Regression 0.840132 0.093959 ... \n", + "... ... ... ... ... ... \n", + "237099 biolink:Association Logistic Regression 0.959791 0.998503 ... \n", + "237100 biolink:Association Logistic Regression 0.959791 0.999719 ... \n", + "237101 biolink:Association Logistic Regression 0.959791 0.998357 ... \n", + "237102 biolink:Association Logistic Regression 0.959791 0.997631 ... \n", + "237103 biolink:Association Logistic Regression 0.959791 0.000000 ... \n", + "\n", + " feature_coefficient num_patients_with_condition \\\n", + "0 8.796399 99669 \n", + "1 8.585212 99938 \n", + "2 4.558177 99770 \n", + "3 4.357522 99910 \n", + "4 3.926064 100242 \n", + "... ... ... \n", + "237099 -5.087542 1007 \n", + "237100 -5.066445 1016 \n", + "237101 -5.079640 978 \n", + "237102 -4.683547 1006 \n", + "237103 7.553003 997 \n", + "\n", + " num_patients_without_condition nodes_frozenset \\\n", + "0 9999902 (HP:0000360, HP:0008629) \n", + "1 10000835 (HP:0000360, MONDO:0010643) \n", + "2 10000939 (UNII:25ADE2236L, HP:0000360) \n", + "3 9998659 (HP:0000360, UNII:K16AIQ8CTM) \n", + "4 9998750 (MONDO:0007972, HP:0000360) \n", + "... ... ... \n", + "237099 10007299 (HP:0008629, CHEBI:114785) \n", + "237100 9996273 (UNII:52CMI0WC3Y, HP:0008629) \n", + "237101 9998030 (HP:0008629, CHEBI:135738) \n", + "237102 10001385 (HP:0008629, MONDO:0004967) \n", + "237103 9997731 (HP:0000360, HP:0008629) \n", + "\n", + " subject_id subject_name \\\n", + "0 HP:0008629 Pulsatile tinnitus \n", + "1 MONDO:0010643 acute leukemia (disease) \n", + "2 UNII:25ADE2236L thrombin \n", + "3 UNII:K16AIQ8CTM pertuzumab \n", + "4 MONDO:0007972 Meniere disease \n", + "... ... ... \n", + "237099 CHEBI:114785 erlotinib \n", + "237100 UNII:52CMI0WC3Y atezolizumab \n", + "237101 CHEBI:135738 clevidipine \n", + "237102 MONDO:0004967 acute lymphoblastic leukemia (disease) \n", + "237103 HP:0000360 Tinnitus \n", + "\n", + " subject_category object_id object_name \\\n", + "0 biolink:PhenotypicFeature HP:0000360 Tinnitus \n", + "1 biolink:Disease HP:0000360 Tinnitus \n", + "2 biolink:ChemicalEntity HP:0000360 Tinnitus \n", + "3 biolink:ChemicalEntity HP:0000360 Tinnitus \n", + "4 biolink:Disease HP:0000360 Tinnitus \n", + "... ... ... ... \n", + "237099 biolink:ChemicalEntity HP:0008629 Pulsatile tinnitus \n", + "237100 biolink:ChemicalEntity HP:0008629 Pulsatile tinnitus \n", + "237101 biolink:ChemicalEntity HP:0008629 Pulsatile tinnitus \n", + "237102 biolink:Disease HP:0008629 Pulsatile tinnitus \n", + "237103 biolink:PhenotypicFeature HP:0008629 Pulsatile tinnitus \n", + "\n", + " object_category \n", + "0 biolink:PhenotypicFeature \n", + "1 biolink:PhenotypicFeature \n", + "2 biolink:PhenotypicFeature \n", + "3 biolink:PhenotypicFeature \n", + "4 biolink:PhenotypicFeature \n", + "... ... \n", + "237099 biolink:PhenotypicFeature \n", + "237100 biolink:PhenotypicFeature \n", + "237101 biolink:PhenotypicFeature \n", + "237102 biolink:PhenotypicFeature \n", + "237103 biolink:PhenotypicFeature \n", + "\n", + "[237104 rows x 21 columns]" + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# ENSURE THERE ARE UNIQUE RECORDS/ROWS\n", + "kg = kg.drop_duplicates(['subject', 'object', 'auc_roc', 'p_value', 'feature_coefficient'], keep='first')\n", + "kg" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "id": "08820f13", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "292\n", + "0\n" + ] + } + ], + "source": [ + "kg_NONE_subjects = kg[kg[\"subject\"].str.contains(\"NONE\")==True]\n", + "print(len(kg_NONE_subjects))\n", + "kg_NONE_objects = kg[kg[\"object\"].str.contains(\"NONE\")==True]\n", + "print(len(kg_NONE_objects))" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "id": "cc1c65fd", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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subjectpredicateobjectrelationprovided_byprovided_datepredicate_categoryclassifierauc_rocp_value...feature_coefficientnum_patients_with_conditionnum_patients_without_conditionnodes_frozensetsubject_idsubject_namesubject_categoryobject_idobject_nameobject_category
0HP:0008629biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.000000...8.796399996699999902(HP:0000360, HP:0008629)HP:0008629Pulsatile tinnitusbiolink:PhenotypicFeatureHP:0000360Tinnitusbiolink:PhenotypicFeature
1MONDO:0010643biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.999872...8.5852129993810000835(HP:0000360, MONDO:0010643)MONDO:0010643acute leukemia (disease)biolink:DiseaseHP:0000360Tinnitusbiolink:PhenotypicFeature
2UNII:25ADE2236Lbiolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.936767...4.5581779977010000939(UNII:25ADE2236L, HP:0000360)UNII:25ADE2236Lthrombinbiolink:ChemicalEntityHP:0000360Tinnitusbiolink:PhenotypicFeature
3UNII:K16AIQ8CTMbiolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.998563...4.357522999109998659(HP:0000360, UNII:K16AIQ8CTM)UNII:K16AIQ8CTMpertuzumabbiolink:ChemicalEntityHP:0000360Tinnitusbiolink:PhenotypicFeature
4MONDO:0007972biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.093959...3.9260641002429998750(MONDO:0007972, HP:0000360)MONDO:0007972Meniere diseasebiolink:DiseaseHP:0000360Tinnitusbiolink:PhenotypicFeature
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237099CHEBI:114785biolink:associated_with_decreased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.998503...-5.087542100710007299(HP:0008629, CHEBI:114785)CHEBI:114785erlotinibbiolink:ChemicalEntityHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
237100UNII:52CMI0WC3Ybiolink:associated_with_decreased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.999719...-5.06644510169996273(UNII:52CMI0WC3Y, HP:0008629)UNII:52CMI0WC3Yatezolizumabbiolink:ChemicalEntityHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
237101CHEBI:135738biolink:associated_with_decreased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.998357...-5.0796409789998030(HP:0008629, CHEBI:135738)CHEBI:135738clevidipinebiolink:ChemicalEntityHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
237102MONDO:0004967biolink:associated_with_decreased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.997631...-4.683547100610001385(HP:0008629, MONDO:0004967)MONDO:0004967acute lymphoblastic leukemia (disease)biolink:DiseaseHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
237103HP:0000360biolink:associated_with_increased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.000000...7.5530039979997731(HP:0000360, HP:0008629)HP:0000360Tinnitusbiolink:PhenotypicFeatureHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
\n", + "

236812 rows × 21 columns

\n", + "
" + ], + "text/plain": [ + " subject predicate \\\n", + "0 HP:0008629 biolink:associated_with_increased_likelihood_of \n", + "1 MONDO:0010643 biolink:associated_with_increased_likelihood_of \n", + "2 UNII:25ADE2236L biolink:associated_with_increased_likelihood_of \n", + "3 UNII:K16AIQ8CTM biolink:associated_with_increased_likelihood_of \n", + "4 MONDO:0007972 biolink:associated_with_increased_likelihood_of \n", + "... ... ... \n", + "237099 CHEBI:114785 biolink:associated_with_decreased_likelihood_of \n", + "237100 UNII:52CMI0WC3Y biolink:associated_with_decreased_likelihood_of \n", + "237101 CHEBI:135738 biolink:associated_with_decreased_likelihood_of \n", + "237102 MONDO:0004967 biolink:associated_with_decreased_likelihood_of \n", + "237103 HP:0000360 biolink:associated_with_increased_likelihood_of \n", + "\n", + " object relation provided_by provided_date \\\n", + "0 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "1 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "2 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "3 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "4 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "... ... ... ... ... \n", + "237099 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237100 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237101 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237102 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237103 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "\n", + " predicate_category classifier auc_roc p_value ... \\\n", + "0 biolink:Association Logistic Regression 0.840132 0.000000 ... \n", + "1 biolink:Association Logistic Regression 0.840132 0.999872 ... \n", + "2 biolink:Association Logistic Regression 0.840132 0.936767 ... \n", + "3 biolink:Association Logistic Regression 0.840132 0.998563 ... \n", + "4 biolink:Association Logistic Regression 0.840132 0.093959 ... \n", + "... ... ... ... ... ... \n", + "237099 biolink:Association Logistic Regression 0.959791 0.998503 ... \n", + "237100 biolink:Association Logistic Regression 0.959791 0.999719 ... \n", + "237101 biolink:Association Logistic Regression 0.959791 0.998357 ... \n", + "237102 biolink:Association Logistic Regression 0.959791 0.997631 ... \n", + "237103 biolink:Association Logistic Regression 0.959791 0.000000 ... \n", + "\n", + " feature_coefficient num_patients_with_condition \\\n", + "0 8.796399 99669 \n", + "1 8.585212 99938 \n", + "2 4.558177 99770 \n", + "3 4.357522 99910 \n", + "4 3.926064 100242 \n", + "... ... ... \n", + "237099 -5.087542 1007 \n", + "237100 -5.066445 1016 \n", + "237101 -5.079640 978 \n", + "237102 -4.683547 1006 \n", + "237103 7.553003 997 \n", + "\n", + " num_patients_without_condition nodes_frozenset \\\n", + "0 9999902 (HP:0000360, HP:0008629) \n", + "1 10000835 (HP:0000360, MONDO:0010643) \n", + "2 10000939 (UNII:25ADE2236L, HP:0000360) \n", + "3 9998659 (HP:0000360, UNII:K16AIQ8CTM) \n", + "4 9998750 (MONDO:0007972, HP:0000360) \n", + "... ... ... \n", + "237099 10007299 (HP:0008629, CHEBI:114785) \n", + "237100 9996273 (UNII:52CMI0WC3Y, HP:0008629) \n", + "237101 9998030 (HP:0008629, CHEBI:135738) \n", + "237102 10001385 (HP:0008629, MONDO:0004967) \n", + "237103 9997731 (HP:0000360, HP:0008629) \n", + "\n", + " subject_id subject_name \\\n", + "0 HP:0008629 Pulsatile tinnitus \n", + "1 MONDO:0010643 acute leukemia (disease) \n", + "2 UNII:25ADE2236L thrombin \n", + "3 UNII:K16AIQ8CTM pertuzumab \n", + "4 MONDO:0007972 Meniere disease \n", + "... ... ... \n", + "237099 CHEBI:114785 erlotinib \n", + "237100 UNII:52CMI0WC3Y atezolizumab \n", + "237101 CHEBI:135738 clevidipine \n", + "237102 MONDO:0004967 acute lymphoblastic leukemia (disease) \n", + "237103 HP:0000360 Tinnitus \n", + "\n", + " subject_category object_id object_name \\\n", + "0 biolink:PhenotypicFeature HP:0000360 Tinnitus \n", + "1 biolink:Disease HP:0000360 Tinnitus \n", + "2 biolink:ChemicalEntity HP:0000360 Tinnitus \n", + "3 biolink:ChemicalEntity HP:0000360 Tinnitus \n", + "4 biolink:Disease HP:0000360 Tinnitus \n", + "... ... ... ... \n", + "237099 biolink:ChemicalEntity HP:0008629 Pulsatile tinnitus \n", + "237100 biolink:ChemicalEntity HP:0008629 Pulsatile tinnitus \n", + "237101 biolink:ChemicalEntity HP:0008629 Pulsatile tinnitus \n", + "237102 biolink:Disease HP:0008629 Pulsatile tinnitus \n", + "237103 biolink:PhenotypicFeature HP:0008629 Pulsatile tinnitus \n", + "\n", + " object_category \n", + "0 biolink:PhenotypicFeature \n", + "1 biolink:PhenotypicFeature \n", + "2 biolink:PhenotypicFeature \n", + "3 biolink:PhenotypicFeature \n", + "4 biolink:PhenotypicFeature \n", + "... ... \n", + "237099 biolink:PhenotypicFeature \n", + "237100 biolink:PhenotypicFeature \n", + "237101 biolink:PhenotypicFeature \n", + "237102 biolink:PhenotypicFeature \n", + "237103 biolink:PhenotypicFeature \n", + "\n", + "[236812 rows x 21 columns]" + ] + }, + "execution_count": 19, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# for some reason, some subject or object ids are empty (they actually literally contain the string \"NONE\")\n", + "kg = kg.dropna(axis=0, subset=['subject'])\n", + "kg = kg.dropna(axis=0, subset=['object'])\n", + "kg = kg[~kg[\"subject\"].str.contains(\"NONE\")==True]\n", + "kg = kg[~kg[\"object\"].str.contains(\"NONE\")==True]\n", + "kg" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "id": "c14460e0", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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subjectpredicateobjectrelationprovided_byprovided_datepredicate_categoryclassifierauc_rocp_value...feature_coefficientnum_patients_with_conditionnum_patients_without_conditionnodes_frozensetsubject_idsubject_namesubject_categoryobject_idobject_nameobject_category
0HP:0008629biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.000000...8.796399996699999902(HP:0000360, HP:0008629)HP:0008629Pulsatile tinnitusbiolink:PhenotypicFeatureHP:0000360Tinnitusbiolink:PhenotypicFeature
1MONDO:0010643biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.999872...8.5852129993810000835(HP:0000360, MONDO:0010643)MONDO:0010643acute leukemia (disease)biolink:DiseaseHP:0000360Tinnitusbiolink:PhenotypicFeature
2UNII:25ADE2236Lbiolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.936767...4.5581779977010000939(UNII:25ADE2236L, HP:0000360)UNII:25ADE2236Lthrombinbiolink:ChemicalEntityHP:0000360Tinnitusbiolink:PhenotypicFeature
3UNII:K16AIQ8CTMbiolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.998563...4.357522999109998659(HP:0000360, UNII:K16AIQ8CTM)UNII:K16AIQ8CTMpertuzumabbiolink:ChemicalEntityHP:0000360Tinnitusbiolink:PhenotypicFeature
4MONDO:0007972biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.093959...3.9260641002429998750(MONDO:0007972, HP:0000360)MONDO:0007972Meniere diseasebiolink:DiseaseHP:0000360Tinnitusbiolink:PhenotypicFeature
..................................................................
237099CHEBI:114785biolink:associated_with_decreased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.998503...-5.087542100710007299(HP:0008629, CHEBI:114785)CHEBI:114785erlotinibbiolink:ChemicalEntityHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
237100UNII:52CMI0WC3Ybiolink:associated_with_decreased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.999719...-5.06644510169996273(UNII:52CMI0WC3Y, HP:0008629)UNII:52CMI0WC3Yatezolizumabbiolink:ChemicalEntityHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
237101CHEBI:135738biolink:associated_with_decreased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.998357...-5.0796409789998030(HP:0008629, CHEBI:135738)CHEBI:135738clevidipinebiolink:ChemicalEntityHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
237102MONDO:0004967biolink:associated_with_decreased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.997631...-4.683547100610001385(HP:0008629, MONDO:0004967)MONDO:0004967acute lymphoblastic leukemia (disease)biolink:DiseaseHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
237103HP:0000360biolink:associated_with_increased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.000000...7.5530039979997731(HP:0000360, HP:0008629)HP:0000360Tinnitusbiolink:PhenotypicFeatureHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeature
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236812 rows × 21 columns

\n", + "
" + ], + "text/plain": [ + " subject predicate \\\n", + "0 HP:0008629 biolink:associated_with_increased_likelihood_of \n", + "1 MONDO:0010643 biolink:associated_with_increased_likelihood_of \n", + "2 UNII:25ADE2236L biolink:associated_with_increased_likelihood_of \n", + "3 UNII:K16AIQ8CTM biolink:associated_with_increased_likelihood_of \n", + "4 MONDO:0007972 biolink:associated_with_increased_likelihood_of \n", + "... ... ... \n", + "237099 CHEBI:114785 biolink:associated_with_decreased_likelihood_of \n", + "237100 UNII:52CMI0WC3Y biolink:associated_with_decreased_likelihood_of \n", + "237101 CHEBI:135738 biolink:associated_with_decreased_likelihood_of \n", + "237102 MONDO:0004967 biolink:associated_with_decreased_likelihood_of \n", + "237103 HP:0000360 biolink:associated_with_increased_likelihood_of \n", + "\n", + " object relation provided_by provided_date \\\n", + "0 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "1 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "2 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "3 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "4 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "... ... ... ... ... \n", + "237099 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237100 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237101 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237102 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237103 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "\n", + " predicate_category classifier auc_roc p_value ... \\\n", + "0 biolink:Association Logistic Regression 0.840132 0.000000 ... \n", + "1 biolink:Association Logistic Regression 0.840132 0.999872 ... \n", + "2 biolink:Association Logistic Regression 0.840132 0.936767 ... \n", + "3 biolink:Association Logistic Regression 0.840132 0.998563 ... \n", + "4 biolink:Association Logistic Regression 0.840132 0.093959 ... \n", + "... ... ... ... ... ... \n", + "237099 biolink:Association Logistic Regression 0.959791 0.998503 ... \n", + "237100 biolink:Association Logistic Regression 0.959791 0.999719 ... \n", + "237101 biolink:Association Logistic Regression 0.959791 0.998357 ... \n", + "237102 biolink:Association Logistic Regression 0.959791 0.997631 ... \n", + "237103 biolink:Association Logistic Regression 0.959791 0.000000 ... \n", + "\n", + " feature_coefficient num_patients_with_condition \\\n", + "0 8.796399 99669 \n", + "1 8.585212 99938 \n", + "2 4.558177 99770 \n", + "3 4.357522 99910 \n", + "4 3.926064 100242 \n", + "... ... ... \n", + "237099 -5.087542 1007 \n", + "237100 -5.066445 1016 \n", + "237101 -5.079640 978 \n", + "237102 -4.683547 1006 \n", + "237103 7.553003 997 \n", + "\n", + " num_patients_without_condition nodes_frozenset \\\n", + "0 9999902 (HP:0000360, HP:0008629) \n", + "1 10000835 (HP:0000360, MONDO:0010643) \n", + "2 10000939 (UNII:25ADE2236L, HP:0000360) \n", + "3 9998659 (HP:0000360, UNII:K16AIQ8CTM) \n", + "4 9998750 (MONDO:0007972, HP:0000360) \n", + "... ... ... \n", + "237099 10007299 (HP:0008629, CHEBI:114785) \n", + "237100 9996273 (UNII:52CMI0WC3Y, HP:0008629) \n", + "237101 9998030 (HP:0008629, CHEBI:135738) \n", + "237102 10001385 (HP:0008629, MONDO:0004967) \n", + "237103 9997731 (HP:0000360, HP:0008629) \n", + "\n", + " subject_id subject_name \\\n", + "0 HP:0008629 Pulsatile tinnitus \n", + "1 MONDO:0010643 acute leukemia (disease) \n", + "2 UNII:25ADE2236L thrombin \n", + "3 UNII:K16AIQ8CTM pertuzumab \n", + "4 MONDO:0007972 Meniere disease \n", + "... ... ... \n", + "237099 CHEBI:114785 erlotinib \n", + "237100 UNII:52CMI0WC3Y atezolizumab \n", + "237101 CHEBI:135738 clevidipine \n", + "237102 MONDO:0004967 acute lymphoblastic leukemia (disease) \n", + "237103 HP:0000360 Tinnitus \n", + "\n", + " subject_category object_id object_name \\\n", + "0 biolink:PhenotypicFeature HP:0000360 Tinnitus \n", + "1 biolink:Disease HP:0000360 Tinnitus \n", + "2 biolink:ChemicalEntity HP:0000360 Tinnitus \n", + "3 biolink:ChemicalEntity HP:0000360 Tinnitus \n", + "4 biolink:Disease HP:0000360 Tinnitus \n", + "... ... ... ... \n", + "237099 biolink:ChemicalEntity HP:0008629 Pulsatile tinnitus \n", + "237100 biolink:ChemicalEntity HP:0008629 Pulsatile tinnitus \n", + "237101 biolink:ChemicalEntity HP:0008629 Pulsatile tinnitus \n", + "237102 biolink:Disease HP:0008629 Pulsatile tinnitus \n", + "237103 biolink:PhenotypicFeature HP:0008629 Pulsatile tinnitus \n", + "\n", + " object_category \n", + "0 biolink:PhenotypicFeature \n", + "1 biolink:PhenotypicFeature \n", + "2 biolink:PhenotypicFeature \n", + "3 biolink:PhenotypicFeature \n", + "4 biolink:PhenotypicFeature \n", + "... ... \n", + "237099 biolink:PhenotypicFeature \n", + "237100 biolink:PhenotypicFeature \n", + "237101 biolink:PhenotypicFeature \n", + "237102 biolink:PhenotypicFeature \n", + "237103 biolink:PhenotypicFeature \n", + "\n", + "[236812 rows x 21 columns]" + ] + }, + "execution_count": 20, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# for some reason, some subject or object ids are empty (they actually literally contain the string \"NONE\")\n", + "# get rid of these rows\n", + "kg = kg[~kg[\"subject\"].str.contains(\"NONE\")==True] # subject and object are all CURIEs, not names\n", + "kg = kg[~kg[\"object\"].str.contains(\"NONE\")==True]\n", + "kg = kg[~kg[\"subject\"].str.contains(\"none\")==True]\n", + "kg = kg[~kg[\"object\"].str.contains(\"none\")==True]\n", + "kg = kg[~kg[\"subject\"].str.contains(\"None\")==True]\n", + "kg = kg[~kg[\"object\"].str.contains(\"None\")==True]\n", + "kg" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5201401a", + "metadata": {}, + "outputs": [], + "source": [ + "# OPTIONAL THRESHOLD\n", + "# kg_pval_subsetted = kg[kg[\"p_value\"] < 0.2]\n", + "# kg_pval_subsetted" + ] + }, + { + "cell_type": "code", + "execution_count": 334, + "id": "e809e4a0", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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subject_category_postfixsubject_prefixincreased_or_decreasedobject_category_postfixobject_prefixCountobject_category_postfix_abbvsubject_category_postfix_abbvjoined_to_match_xbte
0ChemicalEntityCHEBIdecreasedDiseaseMONDO34917DiseaseChemChemCHEBI_decreased_DiseaseMONDO
1ChemicalEntityCHEBIdecreasedDiseaseNCIT212DiseaseChemChemCHEBI_decreased_DiseaseNCIT
2ChemicalEntityCHEBIdecreasedDiseaseSNOMEDCT2917DiseaseChemChemCHEBI_decreased_DiseaseSNOMEDCT
3ChemicalEntityCHEBIdecreasedPhenotypicFeatureHP24505PhenoChemChemCHEBI_decreased_PhenoHP
4ChemicalEntityCHEBIdecreasedPhenotypicFeatureNCIT2254PhenoChemChemCHEBI_decreased_PhenoNCIT
5ChemicalEntityCHEBIdecreasedPhenotypicFeatureSNOMEDCT244PhenoChemChemCHEBI_decreased_PhenoSNOMEDCT
6ChemicalEntityCHEBIdecreasedProcedureNCIT222ProcedureChemChemCHEBI_decreased_ProcedureNCIT
7ChemicalEntityCHEBIincreasedDiseaseMONDO18248DiseaseChemChemCHEBI_increased_DiseaseMONDO
8ChemicalEntityCHEBIincreasedDiseaseNCIT131DiseaseChemChemCHEBI_increased_DiseaseNCIT
9ChemicalEntityCHEBIincreasedDiseaseSNOMEDCT1542DiseaseChemChemCHEBI_increased_DiseaseSNOMEDCT
10ChemicalEntityCHEBIincreasedPhenotypicFeatureHP13225PhenoChemChemCHEBI_increased_PhenoHP
11ChemicalEntityCHEBIincreasedPhenotypicFeatureNCIT1176PhenoChemChemCHEBI_increased_PhenoNCIT
12ChemicalEntityCHEBIincreasedPhenotypicFeatureSNOMEDCT99PhenoChemChemCHEBI_increased_PhenoSNOMEDCT
13ChemicalEntityCHEBIincreasedProcedureNCIT121ProcedureChemChemCHEBI_increased_ProcedureNCIT
14ChemicalEntityUNIIdecreasedDiseaseMONDO5902DiseaseChemChemUNII_decreased_DiseaseMONDO
15ChemicalEntityUNIIdecreasedDiseaseNCIT44DiseaseChemChemUNII_decreased_DiseaseNCIT
16ChemicalEntityUNIIdecreasedDiseaseSNOMEDCT505DiseaseChemChemUNII_decreased_DiseaseSNOMEDCT
17ChemicalEntityUNIIdecreasedPhenotypicFeatureHP3727PhenoChemChemUNII_decreased_PhenoHP
18ChemicalEntityUNIIdecreasedPhenotypicFeatureNCIT381PhenoChemChemUNII_decreased_PhenoNCIT
19ChemicalEntityUNIIdecreasedPhenotypicFeatureSNOMEDCT39PhenoChemChemUNII_decreased_PhenoSNOMEDCT
20ChemicalEntityUNIIdecreasedProcedureNCIT43ProcedureChemChemUNII_decreased_ProcedureNCIT
21ChemicalEntityUNIIincreasedDiseaseMONDO2158DiseaseChemChemUNII_increased_DiseaseMONDO
22ChemicalEntityUNIIincreasedDiseaseNCIT8DiseaseChemChemUNII_increased_DiseaseNCIT
23ChemicalEntityUNIIincreasedDiseaseSNOMEDCT171DiseaseChemChemUNII_increased_DiseaseSNOMEDCT
24ChemicalEntityUNIIincreasedPhenotypicFeatureHP1993PhenoChemChemUNII_increased_PhenoHP
25ChemicalEntityUNIIincreasedPhenotypicFeatureNCIT139PhenoChemChemUNII_increased_PhenoNCIT
26ChemicalEntityUNIIincreasedPhenotypicFeatureSNOMEDCT13PhenoChemChemUNII_increased_PhenoSNOMEDCT
27ChemicalEntityUNIIincreasedProcedureNCIT9ProcedureChemChemUNII_increased_ProcedureNCIT
28DiseaseMONDOdecreasedDiseaseMONDO13640DiseaseDiseaseDiseaseMONDO_decreased_DiseaseMONDO
29DiseaseMONDOdecreasedDiseaseNCIT86DiseaseDiseaseDiseaseMONDO_decreased_DiseaseNCIT
30DiseaseMONDOdecreasedDiseaseSNOMEDCT1237DiseaseDiseaseDiseaseMONDO_decreased_DiseaseSNOMEDCT
31DiseaseMONDOdecreasedPhenotypicFeatureHP10101PhenoDiseaseDiseaseMONDO_decreased_PhenoHP
32DiseaseMONDOdecreasedPhenotypicFeatureNCIT1293PhenoDiseaseDiseaseMONDO_decreased_PhenoNCIT
33DiseaseMONDOdecreasedPhenotypicFeatureSNOMEDCT88PhenoDiseaseDiseaseMONDO_decreased_PhenoSNOMEDCT
34DiseaseMONDOdecreasedProcedureNCIT113ProcedureDiseaseDiseaseMONDO_decreased_ProcedureNCIT
35DiseaseMONDOincreasedDiseaseMONDO14415DiseaseDiseaseDiseaseMONDO_increased_DiseaseMONDO
36DiseaseMONDOincreasedDiseaseNCIT96DiseaseDiseaseDiseaseMONDO_increased_DiseaseNCIT
37DiseaseMONDOincreasedDiseaseSNOMEDCT1129DiseaseDiseaseDiseaseMONDO_increased_DiseaseSNOMEDCT
38DiseaseMONDOincreasedPhenotypicFeatureHP9919PhenoDiseaseDiseaseMONDO_increased_PhenoHP
39DiseaseMONDOincreasedPhenotypicFeatureNCIT527PhenoDiseaseDiseaseMONDO_increased_PhenoNCIT
40DiseaseMONDOincreasedPhenotypicFeatureSNOMEDCT94PhenoDiseaseDiseaseMONDO_increased_PhenoSNOMEDCT
41DiseaseMONDOincreasedProcedureNCIT69ProcedureDiseaseDiseaseMONDO_increased_ProcedureNCIT
42DiseaseNCITdecreasedDiseaseMONDO73DiseaseDiseaseDiseaseNCIT_decreased_DiseaseMONDO
43DiseaseNCITdecreasedDiseaseSNOMEDCT7DiseaseDiseaseDiseaseNCIT_decreased_DiseaseSNOMEDCT
44DiseaseNCITdecreasedPhenotypicFeatureHP44PhenoDiseaseDiseaseNCIT_decreased_PhenoHP
45DiseaseNCITdecreasedPhenotypicFeatureNCIT9PhenoDiseaseDiseaseNCIT_decreased_PhenoNCIT
46DiseaseNCITdecreasedProcedureNCIT1ProcedureDiseaseDiseaseNCIT_decreased_ProcedureNCIT
47DiseaseNCITincreasedDiseaseMONDO82DiseaseDiseaseDiseaseNCIT_increased_DiseaseMONDO
48DiseaseNCITincreasedDiseaseSNOMEDCT6DiseaseDiseaseDiseaseNCIT_increased_DiseaseSNOMEDCT
49DiseaseNCITincreasedPhenotypicFeatureHP66PhenoDiseaseDiseaseNCIT_increased_PhenoHP
50DiseaseNCITincreasedPhenotypicFeatureNCIT1PhenoDiseaseDiseaseNCIT_increased_PhenoNCIT
51DiseaseNCITincreasedPhenotypicFeatureSNOMEDCT1PhenoDiseaseDiseaseNCIT_increased_PhenoSNOMEDCT
52DiseaseSNOMEDCTdecreasedDiseaseMONDO1318DiseaseDiseaseDiseaseSNOMEDCT_decreased_DiseaseMONDO
53DiseaseSNOMEDCTdecreasedDiseaseNCIT10DiseaseDiseaseDiseaseSNOMEDCT_decreased_DiseaseNCIT
54DiseaseSNOMEDCTdecreasedDiseaseSNOMEDCT101DiseaseDiseaseDiseaseSNOMEDCT_decreased_DiseaseSNOMEDCT
55DiseaseSNOMEDCTdecreasedPhenotypicFeatureHP957PhenoDiseaseDiseaseSNOMEDCT_decreased_PhenoHP
56DiseaseSNOMEDCTdecreasedPhenotypicFeatureNCIT116PhenoDiseaseDiseaseSNOMEDCT_decreased_PhenoNCIT
57DiseaseSNOMEDCTdecreasedPhenotypicFeatureSNOMEDCT8PhenoDiseaseDiseaseSNOMEDCT_decreased_PhenoSNOMEDCT
58DiseaseSNOMEDCTdecreasedProcedureNCIT13ProcedureDiseaseDiseaseSNOMEDCT_decreased_ProcedureNCIT
59DiseaseSNOMEDCTincreasedDiseaseMONDO1007DiseaseDiseaseDiseaseSNOMEDCT_increased_DiseaseMONDO
60DiseaseSNOMEDCTincreasedDiseaseNCIT5DiseaseDiseaseDiseaseSNOMEDCT_increased_DiseaseNCIT
61DiseaseSNOMEDCTincreasedDiseaseSNOMEDCT81DiseaseDiseaseDiseaseSNOMEDCT_increased_DiseaseSNOMEDCT
62DiseaseSNOMEDCTincreasedPhenotypicFeatureHP693PhenoDiseaseDiseaseSNOMEDCT_increased_PhenoHP
63DiseaseSNOMEDCTincreasedPhenotypicFeatureNCIT34PhenoDiseaseDiseaseSNOMEDCT_increased_PhenoNCIT
64DiseaseSNOMEDCTincreasedPhenotypicFeatureSNOMEDCT7PhenoDiseaseDiseaseSNOMEDCT_increased_PhenoSNOMEDCT
65DiseaseSNOMEDCTincreasedProcedureNCIT2ProcedureDiseaseDiseaseSNOMEDCT_increased_ProcedureNCIT
66PhenotypicFeatureHPdecreasedDiseaseMONDO18759DiseasePhenoPhenoHP_decreased_DiseaseMONDO
67PhenotypicFeatureHPdecreasedDiseaseNCIT113DiseasePhenoPhenoHP_decreased_DiseaseNCIT
68PhenotypicFeatureHPdecreasedDiseaseSNOMEDCT1532DiseasePhenoPhenoHP_decreased_DiseaseSNOMEDCT
69PhenotypicFeatureHPdecreasedPhenotypicFeatureHP11425PhenoPhenoPhenoHP_decreased_PhenoHP
70PhenotypicFeatureHPdecreasedPhenotypicFeatureNCIT1257PhenoPhenoPhenoHP_decreased_PhenoNCIT
71PhenotypicFeatureHPdecreasedPhenotypicFeatureSNOMEDCT121PhenoPhenoPhenoHP_decreased_PhenoSNOMEDCT
72PhenotypicFeatureHPdecreasedProcedureNCIT132ProcedurePhenoPhenoHP_decreased_ProcedureNCIT
73PhenotypicFeatureHPincreasedDiseaseMONDO12086DiseasePhenoPhenoHP_increased_DiseaseMONDO
74PhenotypicFeatureHPincreasedDiseaseNCIT86DiseasePhenoPhenoHP_increased_DiseaseNCIT
75PhenotypicFeatureHPincreasedDiseaseSNOMEDCT1055DiseasePhenoPhenoHP_increased_DiseaseSNOMEDCT
76PhenotypicFeatureHPincreasedPhenotypicFeatureHP10355PhenoPhenoPhenoHP_increased_PhenoHP
77PhenotypicFeatureHPincreasedPhenotypicFeatureNCIT733PhenoPhenoPhenoHP_increased_PhenoNCIT
78PhenotypicFeatureHPincreasedPhenotypicFeatureSNOMEDCT78PhenoPhenoPhenoHP_increased_PhenoSNOMEDCT
79PhenotypicFeatureHPincreasedProcedureNCIT67ProcedurePhenoPhenoHP_increased_ProcedureNCIT
80PhenotypicFeatureNCITdecreasedDiseaseMONDO1170DiseasePhenoPhenoNCIT_decreased_DiseaseMONDO
81PhenotypicFeatureNCITdecreasedDiseaseNCIT7DiseasePhenoPhenoNCIT_decreased_DiseaseNCIT
82PhenotypicFeatureNCITdecreasedDiseaseSNOMEDCT94DiseasePhenoPhenoNCIT_decreased_DiseaseSNOMEDCT
83PhenotypicFeatureNCITdecreasedPhenotypicFeatureHP705PhenoPhenoPhenoNCIT_decreased_PhenoHP
84PhenotypicFeatureNCITdecreasedPhenotypicFeatureNCIT56PhenoPhenoPhenoNCIT_decreased_PhenoNCIT
85PhenotypicFeatureNCITdecreasedPhenotypicFeatureSNOMEDCT9PhenoPhenoPhenoNCIT_decreased_PhenoSNOMEDCT
86PhenotypicFeatureNCITdecreasedProcedureNCIT7ProcedurePhenoPhenoNCIT_decreased_ProcedureNCIT
87PhenotypicFeatureNCITincreasedDiseaseMONDO380DiseasePhenoPhenoNCIT_increased_DiseaseMONDO
88PhenotypicFeatureNCITincreasedDiseaseNCIT3DiseasePhenoPhenoNCIT_increased_DiseaseNCIT
89PhenotypicFeatureNCITincreasedDiseaseSNOMEDCT36DiseasePhenoPhenoNCIT_increased_DiseaseSNOMEDCT
90PhenotypicFeatureNCITincreasedPhenotypicFeatureHP395PhenoPhenoPhenoNCIT_increased_PhenoHP
91PhenotypicFeatureNCITincreasedPhenotypicFeatureNCIT34PhenoPhenoPhenoNCIT_increased_PhenoNCIT
92PhenotypicFeatureNCITincreasedPhenotypicFeatureSNOMEDCT1PhenoPhenoPhenoNCIT_increased_PhenoSNOMEDCT
93PhenotypicFeatureNCITincreasedProcedureNCIT3ProcedurePhenoPhenoNCIT_increased_ProcedureNCIT
94PhenotypicFeatureSNOMEDCTdecreasedDiseaseMONDO307DiseasePhenoPhenoSNOMEDCT_decreased_DiseaseMONDO
95PhenotypicFeatureSNOMEDCTdecreasedDiseaseNCIT1DiseasePhenoPhenoSNOMEDCT_decreased_DiseaseNCIT
96PhenotypicFeatureSNOMEDCTdecreasedDiseaseSNOMEDCT26DiseasePhenoPhenoSNOMEDCT_decreased_DiseaseSNOMEDCT
97PhenotypicFeatureSNOMEDCTdecreasedPhenotypicFeatureHP217PhenoPhenoPhenoSNOMEDCT_decreased_PhenoHP
98PhenotypicFeatureSNOMEDCTdecreasedPhenotypicFeatureNCIT25PhenoPhenoPhenoSNOMEDCT_decreased_PhenoNCIT
99PhenotypicFeatureSNOMEDCTdecreasedPhenotypicFeatureSNOMEDCT2PhenoPhenoPhenoSNOMEDCT_decreased_PhenoSNOMEDCT
100PhenotypicFeatureSNOMEDCTdecreasedProcedureNCIT2ProcedurePhenoPhenoSNOMEDCT_decreased_ProcedureNCIT
101PhenotypicFeatureSNOMEDCTincreasedDiseaseMONDO158DiseasePhenoPhenoSNOMEDCT_increased_DiseaseMONDO
102PhenotypicFeatureSNOMEDCTincreasedDiseaseNCIT2DiseasePhenoPhenoSNOMEDCT_increased_DiseaseNCIT
103PhenotypicFeatureSNOMEDCTincreasedDiseaseSNOMEDCT13DiseasePhenoPhenoSNOMEDCT_increased_DiseaseSNOMEDCT
104PhenotypicFeatureSNOMEDCTincreasedPhenotypicFeatureHP113PhenoPhenoPhenoSNOMEDCT_increased_PhenoHP
105PhenotypicFeatureSNOMEDCTincreasedPhenotypicFeatureNCIT5PhenoPhenoPhenoSNOMEDCT_increased_PhenoNCIT
106PhenotypicFeatureSNOMEDCTincreasedProcedureNCIT1ProcedurePhenoPhenoSNOMEDCT_increased_ProcedureNCIT
107ProcedureNCITdecreasedDiseaseMONDO721DiseaseProcedureProcedureNCIT_decreased_DiseaseMONDO
108ProcedureNCITdecreasedDiseaseNCIT4DiseaseProcedureProcedureNCIT_decreased_DiseaseNCIT
109ProcedureNCITdecreasedDiseaseSNOMEDCT58DiseaseProcedureProcedureNCIT_decreased_DiseaseSNOMEDCT
110ProcedureNCITdecreasedPhenotypicFeatureHP502PhenoProcedureProcedureNCIT_decreased_PhenoHP
111ProcedureNCITdecreasedPhenotypicFeatureNCIT56PhenoProcedureProcedureNCIT_decreased_PhenoNCIT
112ProcedureNCITdecreasedPhenotypicFeatureSNOMEDCT4PhenoProcedureProcedureNCIT_decreased_PhenoSNOMEDCT
113ProcedureNCITdecreasedProcedureNCIT3ProcedureProcedureProcedureNCIT_decreased_ProcedureNCIT
114ProcedureNCITincreasedDiseaseMONDO209DiseaseProcedureProcedureNCIT_increased_DiseaseMONDO
115ProcedureNCITincreasedDiseaseNCIT2DiseaseProcedureProcedureNCIT_increased_DiseaseNCIT
116ProcedureNCITincreasedDiseaseSNOMEDCT20DiseaseProcedureProcedureNCIT_increased_DiseaseSNOMEDCT
117ProcedureNCITincreasedPhenotypicFeatureHP158PhenoProcedureProcedureNCIT_increased_PhenoHP
118ProcedureNCITincreasedPhenotypicFeatureNCIT4PhenoProcedureProcedureNCIT_increased_PhenoNCIT
119ProcedureNCITincreasedPhenotypicFeatureSNOMEDCT2PhenoProcedureProcedureNCIT_increased_PhenoSNOMEDCT
120ProcedureNCITincreasedProcedureNCIT2ProcedureProcedureProcedureNCIT_increased_ProcedureNCIT
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\n", + "22 ChemicalEntity UNII increased \n", + "23 ChemicalEntity UNII increased \n", + "24 ChemicalEntity UNII increased \n", + "25 ChemicalEntity UNII increased \n", + "26 ChemicalEntity UNII increased \n", + "27 ChemicalEntity UNII increased \n", + "28 Disease MONDO decreased \n", + "29 Disease MONDO decreased \n", + "30 Disease MONDO decreased \n", + "31 Disease MONDO decreased \n", + "32 Disease MONDO decreased \n", + "33 Disease MONDO decreased \n", + "34 Disease MONDO decreased \n", + "35 Disease MONDO increased \n", + "36 Disease MONDO increased \n", + "37 Disease MONDO increased \n", + "38 Disease MONDO increased \n", + "39 Disease MONDO increased \n", + "40 Disease MONDO increased \n", + "41 Disease MONDO increased \n", + "42 Disease NCIT decreased \n", + "43 Disease NCIT decreased \n", + "44 Disease NCIT decreased \n", + "45 Disease NCIT decreased \n", + "46 Disease NCIT decreased \n", + "47 Disease NCIT increased \n", + "48 Disease NCIT increased \n", + "49 Disease NCIT increased \n", + "50 Disease NCIT increased \n", + "51 Disease NCIT increased \n", + "52 Disease SNOMEDCT decreased \n", + "53 Disease SNOMEDCT decreased \n", + "54 Disease SNOMEDCT decreased \n", + "55 Disease SNOMEDCT decreased \n", + "56 Disease SNOMEDCT decreased \n", + "57 Disease SNOMEDCT decreased \n", + "58 Disease SNOMEDCT decreased \n", + "59 Disease SNOMEDCT increased \n", + "60 Disease SNOMEDCT increased \n", + "61 Disease SNOMEDCT increased \n", + "62 Disease SNOMEDCT increased \n", + "63 Disease SNOMEDCT increased \n", + "64 Disease SNOMEDCT increased \n", + "65 Disease SNOMEDCT increased \n", + "66 PhenotypicFeature HP decreased \n", + "67 PhenotypicFeature HP decreased \n", + "68 PhenotypicFeature HP decreased \n", + "69 PhenotypicFeature HP decreased \n", + "70 PhenotypicFeature HP decreased \n", + "71 PhenotypicFeature HP decreased \n", + "72 PhenotypicFeature HP decreased \n", + "73 PhenotypicFeature HP increased \n", + "74 PhenotypicFeature HP increased \n", + "75 PhenotypicFeature HP increased \n", + "76 PhenotypicFeature HP increased \n", + "77 PhenotypicFeature HP increased \n", + "78 PhenotypicFeature HP increased \n", + "79 PhenotypicFeature HP increased \n", + "80 PhenotypicFeature NCIT decreased \n", + "81 PhenotypicFeature NCIT decreased \n", + "82 PhenotypicFeature NCIT decreased \n", + "83 PhenotypicFeature NCIT decreased \n", + "84 PhenotypicFeature NCIT decreased \n", + "85 PhenotypicFeature NCIT decreased \n", + "86 PhenotypicFeature NCIT decreased \n", + "87 PhenotypicFeature NCIT increased \n", + "88 PhenotypicFeature NCIT increased \n", + "89 PhenotypicFeature NCIT increased \n", + "90 PhenotypicFeature NCIT increased \n", + "91 PhenotypicFeature NCIT increased \n", + "92 PhenotypicFeature NCIT increased \n", + "93 PhenotypicFeature NCIT increased \n", + "94 PhenotypicFeature SNOMEDCT decreased \n", + "95 PhenotypicFeature SNOMEDCT decreased \n", + "96 PhenotypicFeature SNOMEDCT decreased \n", + "97 PhenotypicFeature SNOMEDCT decreased \n", + "98 PhenotypicFeature SNOMEDCT decreased \n", + "99 PhenotypicFeature SNOMEDCT decreased \n", + "100 PhenotypicFeature SNOMEDCT decreased \n", + "101 PhenotypicFeature SNOMEDCT increased \n", + "102 PhenotypicFeature SNOMEDCT increased \n", + "103 PhenotypicFeature SNOMEDCT increased \n", + "104 PhenotypicFeature SNOMEDCT increased \n", + "105 PhenotypicFeature SNOMEDCT increased \n", + "106 PhenotypicFeature SNOMEDCT increased \n", + "107 Procedure NCIT decreased \n", + "108 Procedure NCIT decreased \n", + "109 Procedure NCIT decreased \n", + "110 Procedure NCIT decreased \n", + "111 Procedure NCIT decreased \n", + "112 Procedure NCIT decreased \n", + "113 Procedure NCIT decreased \n", + "114 Procedure NCIT increased \n", + "115 Procedure NCIT increased \n", + "116 Procedure NCIT increased \n", + "117 Procedure NCIT increased \n", + "118 Procedure NCIT increased \n", + "119 Procedure NCIT increased \n", + "120 Procedure NCIT increased \n", + "\n", + " object_category_postfix object_prefix Count object_category_postfix_abbv \\\n", + "0 Disease MONDO 34917 Disease \n", + "1 Disease NCIT 212 Disease \n", + "2 Disease SNOMEDCT 2917 Disease \n", + "3 PhenotypicFeature HP 24505 Pheno \n", + "4 PhenotypicFeature NCIT 2254 Pheno \n", + "5 PhenotypicFeature SNOMEDCT 244 Pheno \n", + "6 Procedure NCIT 222 Procedure \n", + "7 Disease MONDO 18248 Disease \n", + "8 Disease NCIT 131 Disease \n", + "9 Disease SNOMEDCT 1542 Disease \n", + "10 PhenotypicFeature HP 13225 Pheno \n", + "11 PhenotypicFeature NCIT 1176 Pheno \n", + "12 PhenotypicFeature SNOMEDCT 99 Pheno \n", + "13 Procedure NCIT 121 Procedure \n", + "14 Disease MONDO 5902 Disease \n", + "15 Disease NCIT 44 Disease \n", + "16 Disease SNOMEDCT 505 Disease \n", + "17 PhenotypicFeature HP 3727 Pheno \n", + "18 PhenotypicFeature NCIT 381 Pheno \n", + "19 PhenotypicFeature SNOMEDCT 39 Pheno \n", + "20 Procedure NCIT 43 Procedure \n", + "21 Disease MONDO 2158 Disease \n", + "22 Disease NCIT 8 Disease \n", + "23 Disease SNOMEDCT 171 Disease \n", + "24 PhenotypicFeature HP 1993 Pheno \n", + "25 PhenotypicFeature NCIT 139 Pheno \n", + "26 PhenotypicFeature SNOMEDCT 13 Pheno \n", + "27 Procedure NCIT 9 Procedure \n", + "28 Disease MONDO 13640 Disease \n", + "29 Disease NCIT 86 Disease \n", + "30 Disease SNOMEDCT 1237 Disease \n", + "31 PhenotypicFeature HP 10101 Pheno \n", + "32 PhenotypicFeature NCIT 1293 Pheno \n", + "33 PhenotypicFeature SNOMEDCT 88 Pheno \n", + "34 Procedure NCIT 113 Procedure \n", + "35 Disease MONDO 14415 Disease \n", + "36 Disease NCIT 96 Disease \n", + "37 Disease SNOMEDCT 1129 Disease \n", + "38 PhenotypicFeature HP 9919 Pheno \n", + "39 PhenotypicFeature NCIT 527 Pheno \n", + "40 PhenotypicFeature SNOMEDCT 94 Pheno \n", + "41 Procedure NCIT 69 Procedure \n", + "42 Disease MONDO 73 Disease \n", + "43 Disease SNOMEDCT 7 Disease \n", + "44 PhenotypicFeature HP 44 Pheno \n", + "45 PhenotypicFeature NCIT 9 Pheno \n", + "46 Procedure NCIT 1 Procedure \n", + "47 Disease MONDO 82 Disease \n", + "48 Disease SNOMEDCT 6 Disease \n", + "49 PhenotypicFeature HP 66 Pheno \n", + "50 PhenotypicFeature NCIT 1 Pheno \n", + "51 PhenotypicFeature SNOMEDCT 1 Pheno \n", + "52 Disease MONDO 1318 Disease \n", + "53 Disease NCIT 10 Disease \n", + "54 Disease SNOMEDCT 101 Disease \n", + "55 PhenotypicFeature HP 957 Pheno \n", + "56 PhenotypicFeature NCIT 116 Pheno \n", + "57 PhenotypicFeature SNOMEDCT 8 Pheno \n", + "58 Procedure NCIT 13 Procedure \n", + "59 Disease MONDO 1007 Disease \n", + "60 Disease NCIT 5 Disease \n", + "61 Disease SNOMEDCT 81 Disease \n", + "62 PhenotypicFeature HP 693 Pheno \n", + "63 PhenotypicFeature NCIT 34 Pheno \n", + "64 PhenotypicFeature SNOMEDCT 7 Pheno \n", + "65 Procedure NCIT 2 Procedure \n", + "66 Disease MONDO 18759 Disease \n", + "67 Disease NCIT 113 Disease \n", + "68 Disease SNOMEDCT 1532 Disease \n", + "69 PhenotypicFeature HP 11425 Pheno \n", + "70 PhenotypicFeature NCIT 1257 Pheno \n", + "71 PhenotypicFeature SNOMEDCT 121 Pheno \n", + "72 Procedure NCIT 132 Procedure \n", + "73 Disease MONDO 12086 Disease \n", + "74 Disease NCIT 86 Disease \n", + "75 Disease SNOMEDCT 1055 Disease \n", + "76 PhenotypicFeature HP 10355 Pheno \n", + "77 PhenotypicFeature NCIT 733 Pheno \n", + "78 PhenotypicFeature SNOMEDCT 78 Pheno \n", + "79 Procedure NCIT 67 Procedure \n", + "80 Disease MONDO 1170 Disease \n", + "81 Disease NCIT 7 Disease \n", + "82 Disease SNOMEDCT 94 Disease \n", + "83 PhenotypicFeature HP 705 Pheno \n", + "84 PhenotypicFeature NCIT 56 Pheno \n", + "85 PhenotypicFeature SNOMEDCT 9 Pheno \n", + "86 Procedure NCIT 7 Procedure \n", + "87 Disease MONDO 380 Disease \n", + "88 Disease NCIT 3 Disease \n", + "89 Disease SNOMEDCT 36 Disease \n", + "90 PhenotypicFeature HP 395 Pheno \n", + "91 PhenotypicFeature NCIT 34 Pheno \n", + "92 PhenotypicFeature SNOMEDCT 1 Pheno \n", + "93 Procedure NCIT 3 Procedure \n", + "94 Disease MONDO 307 Disease \n", + "95 Disease NCIT 1 Disease \n", + "96 Disease SNOMEDCT 26 Disease \n", + "97 PhenotypicFeature HP 217 Pheno \n", + "98 PhenotypicFeature NCIT 25 Pheno \n", + "99 PhenotypicFeature SNOMEDCT 2 Pheno \n", + "100 Procedure NCIT 2 Procedure \n", + "101 Disease MONDO 158 Disease \n", + "102 Disease NCIT 2 Disease \n", + "103 Disease SNOMEDCT 13 Disease \n", + "104 PhenotypicFeature HP 113 Pheno \n", + "105 PhenotypicFeature NCIT 5 Pheno \n", + "106 Procedure NCIT 1 Procedure \n", + "107 Disease MONDO 721 Disease \n", + "108 Disease NCIT 4 Disease \n", + "109 Disease SNOMEDCT 58 Disease \n", + "110 PhenotypicFeature HP 502 Pheno \n", + "111 PhenotypicFeature NCIT 56 Pheno \n", + "112 PhenotypicFeature SNOMEDCT 4 Pheno \n", + "113 Procedure NCIT 3 Procedure \n", + "114 Disease MONDO 209 Disease \n", + "115 Disease NCIT 2 Disease \n", + "116 Disease SNOMEDCT 20 Disease \n", + "117 PhenotypicFeature HP 158 Pheno \n", + "118 PhenotypicFeature NCIT 4 Pheno \n", + "119 PhenotypicFeature SNOMEDCT 2 Pheno \n", + "120 Procedure NCIT 2 Procedure \n", + "\n", + " subject_category_postfix_abbv joined_to_match_xbte \n", + "0 Chem ChemCHEBI_decreased_DiseaseMONDO \n", + "1 Chem ChemCHEBI_decreased_DiseaseNCIT \n", + "2 Chem ChemCHEBI_decreased_DiseaseSNOMEDCT \n", + "3 Chem ChemCHEBI_decreased_PhenoHP \n", + "4 Chem ChemCHEBI_decreased_PhenoNCIT \n", + "5 Chem ChemCHEBI_decreased_PhenoSNOMEDCT \n", + "6 Chem ChemCHEBI_decreased_ProcedureNCIT \n", + "7 Chem ChemCHEBI_increased_DiseaseMONDO \n", + "8 Chem ChemCHEBI_increased_DiseaseNCIT \n", + "9 Chem ChemCHEBI_increased_DiseaseSNOMEDCT \n", + "10 Chem ChemCHEBI_increased_PhenoHP \n", + "11 Chem ChemCHEBI_increased_PhenoNCIT \n", + "12 Chem ChemCHEBI_increased_PhenoSNOMEDCT \n", + "13 Chem ChemCHEBI_increased_ProcedureNCIT \n", + "14 Chem ChemUNII_decreased_DiseaseMONDO \n", + "15 Chem ChemUNII_decreased_DiseaseNCIT \n", + "16 Chem ChemUNII_decreased_DiseaseSNOMEDCT \n", + "17 Chem ChemUNII_decreased_PhenoHP \n", + "18 Chem ChemUNII_decreased_PhenoNCIT \n", + "19 Chem ChemUNII_decreased_PhenoSNOMEDCT \n", + "20 Chem ChemUNII_decreased_ProcedureNCIT \n", + "21 Chem ChemUNII_increased_DiseaseMONDO \n", + "22 Chem ChemUNII_increased_DiseaseNCIT \n", + "23 Chem ChemUNII_increased_DiseaseSNOMEDCT \n", + "24 Chem ChemUNII_increased_PhenoHP \n", + "25 Chem ChemUNII_increased_PhenoNCIT \n", + "26 Chem ChemUNII_increased_PhenoSNOMEDCT \n", + "27 Chem ChemUNII_increased_ProcedureNCIT \n", + "28 Disease DiseaseMONDO_decreased_DiseaseMONDO \n", + "29 Disease DiseaseMONDO_decreased_DiseaseNCIT \n", + "30 Disease DiseaseMONDO_decreased_DiseaseSNOMEDCT \n", + "31 Disease DiseaseMONDO_decreased_PhenoHP \n", + "32 Disease DiseaseMONDO_decreased_PhenoNCIT \n", + "33 Disease DiseaseMONDO_decreased_PhenoSNOMEDCT \n", + "34 Disease DiseaseMONDO_decreased_ProcedureNCIT \n", + "35 Disease DiseaseMONDO_increased_DiseaseMONDO \n", + "36 Disease DiseaseMONDO_increased_DiseaseNCIT \n", + "37 Disease DiseaseMONDO_increased_DiseaseSNOMEDCT \n", + "38 Disease DiseaseMONDO_increased_PhenoHP \n", + "39 Disease DiseaseMONDO_increased_PhenoNCIT \n", + "40 Disease DiseaseMONDO_increased_PhenoSNOMEDCT \n", + "41 Disease DiseaseMONDO_increased_ProcedureNCIT \n", + "42 Disease DiseaseNCIT_decreased_DiseaseMONDO \n", + "43 Disease DiseaseNCIT_decreased_DiseaseSNOMEDCT \n", + "44 Disease DiseaseNCIT_decreased_PhenoHP \n", + "45 Disease DiseaseNCIT_decreased_PhenoNCIT \n", + "46 Disease DiseaseNCIT_decreased_ProcedureNCIT \n", + "47 Disease DiseaseNCIT_increased_DiseaseMONDO \n", + "48 Disease DiseaseNCIT_increased_DiseaseSNOMEDCT \n", + "49 Disease DiseaseNCIT_increased_PhenoHP \n", + "50 Disease DiseaseNCIT_increased_PhenoNCIT \n", + "51 Disease DiseaseNCIT_increased_PhenoSNOMEDCT \n", + "52 Disease DiseaseSNOMEDCT_decreased_DiseaseMONDO \n", + "53 Disease DiseaseSNOMEDCT_decreased_DiseaseNCIT \n", + "54 Disease DiseaseSNOMEDCT_decreased_DiseaseSNOMEDCT \n", + "55 Disease DiseaseSNOMEDCT_decreased_PhenoHP \n", + "56 Disease DiseaseSNOMEDCT_decreased_PhenoNCIT \n", + "57 Disease DiseaseSNOMEDCT_decreased_PhenoSNOMEDCT \n", + "58 Disease DiseaseSNOMEDCT_decreased_ProcedureNCIT \n", + "59 Disease DiseaseSNOMEDCT_increased_DiseaseMONDO \n", + "60 Disease DiseaseSNOMEDCT_increased_DiseaseNCIT \n", + "61 Disease DiseaseSNOMEDCT_increased_DiseaseSNOMEDCT \n", + "62 Disease DiseaseSNOMEDCT_increased_PhenoHP \n", + "63 Disease DiseaseSNOMEDCT_increased_PhenoNCIT \n", + "64 Disease DiseaseSNOMEDCT_increased_PhenoSNOMEDCT \n", + "65 Disease DiseaseSNOMEDCT_increased_ProcedureNCIT \n", + "66 Pheno PhenoHP_decreased_DiseaseMONDO \n", + "67 Pheno PhenoHP_decreased_DiseaseNCIT \n", + "68 Pheno PhenoHP_decreased_DiseaseSNOMEDCT \n", + "69 Pheno PhenoHP_decreased_PhenoHP \n", + "70 Pheno PhenoHP_decreased_PhenoNCIT \n", + "71 Pheno PhenoHP_decreased_PhenoSNOMEDCT \n", + "72 Pheno PhenoHP_decreased_ProcedureNCIT \n", + "73 Pheno PhenoHP_increased_DiseaseMONDO \n", + "74 Pheno PhenoHP_increased_DiseaseNCIT \n", + "75 Pheno PhenoHP_increased_DiseaseSNOMEDCT \n", + "76 Pheno PhenoHP_increased_PhenoHP \n", + "77 Pheno PhenoHP_increased_PhenoNCIT \n", + "78 Pheno PhenoHP_increased_PhenoSNOMEDCT \n", + "79 Pheno PhenoHP_increased_ProcedureNCIT \n", + "80 Pheno PhenoNCIT_decreased_DiseaseMONDO \n", + "81 Pheno PhenoNCIT_decreased_DiseaseNCIT \n", + "82 Pheno PhenoNCIT_decreased_DiseaseSNOMEDCT \n", + "83 Pheno PhenoNCIT_decreased_PhenoHP \n", + "84 Pheno PhenoNCIT_decreased_PhenoNCIT \n", + "85 Pheno PhenoNCIT_decreased_PhenoSNOMEDCT \n", + "86 Pheno PhenoNCIT_decreased_ProcedureNCIT \n", + "87 Pheno PhenoNCIT_increased_DiseaseMONDO \n", + "88 Pheno PhenoNCIT_increased_DiseaseNCIT \n", + "89 Pheno PhenoNCIT_increased_DiseaseSNOMEDCT \n", + "90 Pheno PhenoNCIT_increased_PhenoHP \n", + "91 Pheno PhenoNCIT_increased_PhenoNCIT \n", + "92 Pheno PhenoNCIT_increased_PhenoSNOMEDCT \n", + "93 Pheno PhenoNCIT_increased_ProcedureNCIT \n", + "94 Pheno PhenoSNOMEDCT_decreased_DiseaseMONDO \n", + "95 Pheno PhenoSNOMEDCT_decreased_DiseaseNCIT \n", + "96 Pheno PhenoSNOMEDCT_decreased_DiseaseSNOMEDCT \n", + "97 Pheno PhenoSNOMEDCT_decreased_PhenoHP \n", + "98 Pheno PhenoSNOMEDCT_decreased_PhenoNCIT \n", + "99 Pheno PhenoSNOMEDCT_decreased_PhenoSNOMEDCT \n", + "100 Pheno PhenoSNOMEDCT_decreased_ProcedureNCIT \n", + "101 Pheno PhenoSNOMEDCT_increased_DiseaseMONDO \n", + "102 Pheno PhenoSNOMEDCT_increased_DiseaseNCIT \n", + "103 Pheno PhenoSNOMEDCT_increased_DiseaseSNOMEDCT \n", + "104 Pheno PhenoSNOMEDCT_increased_PhenoHP \n", + "105 Pheno PhenoSNOMEDCT_increased_PhenoNCIT \n", + "106 Pheno PhenoSNOMEDCT_increased_ProcedureNCIT \n", + "107 Procedure ProcedureNCIT_decreased_DiseaseMONDO \n", + "108 Procedure ProcedureNCIT_decreased_DiseaseNCIT \n", + "109 Procedure ProcedureNCIT_decreased_DiseaseSNOMEDCT \n", + "110 Procedure ProcedureNCIT_decreased_PhenoHP \n", + "111 Procedure ProcedureNCIT_decreased_PhenoNCIT \n", + "112 Procedure ProcedureNCIT_decreased_PhenoSNOMEDCT \n", + "113 Procedure ProcedureNCIT_decreased_ProcedureNCIT \n", + "114 Procedure ProcedureNCIT_increased_DiseaseMONDO \n", + "115 Procedure ProcedureNCIT_increased_DiseaseNCIT \n", + "116 Procedure ProcedureNCIT_increased_DiseaseSNOMEDCT \n", + "117 Procedure ProcedureNCIT_increased_PhenoHP \n", + "118 Procedure ProcedureNCIT_increased_PhenoNCIT \n", + "119 Procedure ProcedureNCIT_increased_PhenoSNOMEDCT \n", + "120 Procedure ProcedureNCIT_increased_ProcedureNCIT " + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "# get a list of meta-triples for this KP: make it look like what BTE wants as closely as possible (see yaml)\n", + "# X_BTE KNOWN OPERATIONS TO ADD\n", + "# unique combos of subject-prefix / subject-category / predicate / object-prefix / object-category \n", + "# (and qualifier-set, if applicable)\n", + "\n", + "# Use the grouped[\"joined_to_match_xbte\"] column made below to create the tags and x-bte-kgs-operations portions in ehr_risk_kg.yaml\n", + " \n", + "meta_triples = kg.copy()\n", + "\n", + "meta_triples[\"subject_prefix\"] = meta_triples[\"subject\"].str.split(\":\").str[0]\n", + "meta_triples[\"object_prefix\"] = meta_triples[\"object\"].str.split(\":\").str[0]\n", + "\n", + "meta_triples[\"subject_category_postfix\"] = meta_triples[\"subject_category\"].str.split(\":\").str[1]\n", + "meta_triples[\"object_category_postfix\"] = meta_triples[\"object_category\"].str.split(\":\").str[1]\n", + "\n", + "meta_triples['increased_or_decreased'] = None\n", + "meta_triples.loc[meta_triples['predicate'].str.contains('increased', case=False, na=False), 'increased_or_decreased'] = 'increased'\n", + "meta_triples.loc[meta_triples['predicate'].str.contains('decreased', case=False, na=False), 'increased_or_decreased'] = 'decreased'\n", + "\n", + "# unique combos of subject-prefix / subject-category / predicate / object-prefix / object-category\n", + "\n", + "# Define the columns you want to combine\n", + "columns_to_combine = ['subject_category_postfix', 'subject_prefix', 'increased_or_decreased', 'object_category_postfix', 'object_prefix']\n", + "\n", + "# Group by the combination of columns and count the occurrences\n", + "grouped = meta_triples.groupby(columns_to_combine).size().reset_index(name='Count')\n", + "grouped['object_category_postfix_abbv'] = grouped['object_category_postfix'].str.replace('PhenotypicFeature', 'Pheno')\n", + "grouped['subject_category_postfix_abbv'] = grouped['subject_category_postfix'].str.replace('PhenotypicFeature', 'Pheno')\n", + "\n", + "grouped['object_category_postfix_abbv'] = grouped['object_category_postfix_abbv'].str.replace('ChemicalEntity', 'Chem')\n", + "grouped['subject_category_postfix_abbv'] = grouped['subject_category_postfix_abbv'].str.replace('ChemicalEntity', 'Chem')\n", + "\n", + "grouped['joined_to_match_xbte'] = grouped['subject_category_postfix_abbv'].astype(str) + grouped['subject_prefix'].astype(str) + '_' + grouped['increased_or_decreased'].astype(str) + '_' + grouped['object_category_postfix_abbv'].astype(str) + grouped['object_prefix'].astype(str)\n", + "\n", + "# grouped.to_csv('yaml_all_metatriples.tsv', sep=\"\\t\")\n", + "# # Print the DataFrame with unique combinations and their counts\n", + "\n", + "with pd.option_context(\"display.max_rows\", 30000):\n", + " display(grouped)\n", + " " + ] + }, + { + "cell_type": "code", + "execution_count": 335, + "id": "ac11f711", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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subjectpredicateobjectrelationprovided_byprovided_datepredicate_categoryclassifierauc_rocp_value...num_patients_without_conditionnodes_frozensetsubject_idsubject_namesubject_categoryobject_idobject_nameobject_categorysubject_prefixobject_prefix
0HP:0008629biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.000000...9999902(HP:0000360, HP:0008629)HP:0008629Pulsatile tinnitusbiolink:PhenotypicFeatureHP:0000360Tinnitusbiolink:PhenotypicFeatureHPHP
1MONDO:0010643biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.999872...10000835(HP:0000360, MONDO:0010643)MONDO:0010643acute leukemia (disease)biolink:DiseaseHP:0000360Tinnitusbiolink:PhenotypicFeatureMONDOHP
2UNII:25ADE2236Lbiolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.936767...10000939(UNII:25ADE2236L, HP:0000360)UNII:25ADE2236Lthrombinbiolink:ChemicalEntityHP:0000360Tinnitusbiolink:PhenotypicFeatureUNIIHP
3UNII:K16AIQ8CTMbiolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.998563...9998659(HP:0000360, UNII:K16AIQ8CTM)UNII:K16AIQ8CTMpertuzumabbiolink:ChemicalEntityHP:0000360Tinnitusbiolink:PhenotypicFeatureUNIIHP
4MONDO:0007972biolink:associated_with_increased_likelihood_ofHP:0000360RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.8401320.093959...9998750(MONDO:0007972, HP:0000360)MONDO:0007972Meniere diseasebiolink:DiseaseHP:0000360Tinnitusbiolink:PhenotypicFeatureMONDOHP
..................................................................
237099CHEBI:114785biolink:associated_with_decreased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.998503...10007299(HP:0008629, CHEBI:114785)CHEBI:114785erlotinibbiolink:ChemicalEntityHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeatureCHEBIHP
237100UNII:52CMI0WC3Ybiolink:associated_with_decreased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.999719...9996273(UNII:52CMI0WC3Y, HP:0008629)UNII:52CMI0WC3Yatezolizumabbiolink:ChemicalEntityHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeatureUNIIHP
237101CHEBI:135738biolink:associated_with_decreased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.998357...9998030(HP:0008629, CHEBI:135738)CHEBI:135738clevidipinebiolink:ChemicalEntityHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeatureCHEBIHP
237102MONDO:0004967biolink:associated_with_decreased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.997631...10001385(HP:0008629, MONDO:0004967)MONDO:0004967acute lymphoblastic leukemia (disease)biolink:DiseaseHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeatureMONDOHP
237103HP:0000360biolink:associated_with_increased_likelihood_ofHP:0008629RO:0003308EHR Risk Provider (Multiomics)2022-05-18biolink:AssociationLogistic Regression0.9597910.000000...9997731(HP:0000360, HP:0008629)HP:0000360Tinnitusbiolink:PhenotypicFeatureHP:0008629Pulsatile tinnitusbiolink:PhenotypicFeatureHPHP
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236812 rows × 23 columns

\n", + "
" + ], + "text/plain": [ + " subject predicate \\\n", + "0 HP:0008629 biolink:associated_with_increased_likelihood_of \n", + "1 MONDO:0010643 biolink:associated_with_increased_likelihood_of \n", + "2 UNII:25ADE2236L biolink:associated_with_increased_likelihood_of \n", + "3 UNII:K16AIQ8CTM biolink:associated_with_increased_likelihood_of \n", + "4 MONDO:0007972 biolink:associated_with_increased_likelihood_of \n", + "... ... ... \n", + "237099 CHEBI:114785 biolink:associated_with_decreased_likelihood_of \n", + "237100 UNII:52CMI0WC3Y biolink:associated_with_decreased_likelihood_of \n", + "237101 CHEBI:135738 biolink:associated_with_decreased_likelihood_of \n", + "237102 MONDO:0004967 biolink:associated_with_decreased_likelihood_of \n", + "237103 HP:0000360 biolink:associated_with_increased_likelihood_of \n", + "\n", + " object relation provided_by provided_date \\\n", + "0 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "1 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "2 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "3 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "4 HP:0000360 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "... ... ... ... ... \n", + "237099 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237100 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237101 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237102 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "237103 HP:0008629 RO:0003308 EHR Risk Provider (Multiomics) 2022-05-18 \n", + "\n", + " predicate_category classifier auc_roc p_value ... \\\n", + "0 biolink:Association Logistic Regression 0.840132 0.000000 ... \n", + "1 biolink:Association Logistic Regression 0.840132 0.999872 ... \n", + "2 biolink:Association Logistic Regression 0.840132 0.936767 ... \n", + "3 biolink:Association Logistic Regression 0.840132 0.998563 ... \n", + "4 biolink:Association Logistic Regression 0.840132 0.093959 ... \n", + "... ... ... ... ... ... \n", + "237099 biolink:Association Logistic Regression 0.959791 0.998503 ... \n", + "237100 biolink:Association Logistic Regression 0.959791 0.999719 ... \n", + "237101 biolink:Association Logistic Regression 0.959791 0.998357 ... \n", + "237102 biolink:Association Logistic Regression 0.959791 0.997631 ... \n", + "237103 biolink:Association Logistic Regression 0.959791 0.000000 ... \n", + "\n", + " num_patients_without_condition nodes_frozenset \\\n", + "0 9999902 (HP:0000360, HP:0008629) \n", + "1 10000835 (HP:0000360, MONDO:0010643) \n", + "2 10000939 (UNII:25ADE2236L, HP:0000360) \n", + "3 9998659 (HP:0000360, UNII:K16AIQ8CTM) \n", + "4 9998750 (MONDO:0007972, HP:0000360) \n", + "... ... ... \n", + "237099 10007299 (HP:0008629, CHEBI:114785) \n", + "237100 9996273 (UNII:52CMI0WC3Y, HP:0008629) \n", + "237101 9998030 (HP:0008629, CHEBI:135738) \n", + "237102 10001385 (HP:0008629, MONDO:0004967) \n", + "237103 9997731 (HP:0000360, HP:0008629) \n", + "\n", + " subject_id subject_name \\\n", + "0 HP:0008629 Pulsatile tinnitus \n", + "1 MONDO:0010643 acute leukemia (disease) \n", + "2 UNII:25ADE2236L thrombin \n", + "3 UNII:K16AIQ8CTM pertuzumab \n", + "4 MONDO:0007972 Meniere disease \n", + "... ... ... \n", + "237099 CHEBI:114785 erlotinib \n", + "237100 UNII:52CMI0WC3Y atezolizumab \n", + "237101 CHEBI:135738 clevidipine \n", + "237102 MONDO:0004967 acute lymphoblastic leukemia (disease) \n", + "237103 HP:0000360 Tinnitus \n", + "\n", + " subject_category object_id object_name \\\n", + "0 biolink:PhenotypicFeature HP:0000360 Tinnitus \n", + "1 biolink:Disease HP:0000360 Tinnitus \n", + "2 biolink:ChemicalEntity HP:0000360 Tinnitus \n", + "3 biolink:ChemicalEntity HP:0000360 Tinnitus \n", + "4 biolink:Disease HP:0000360 Tinnitus \n", + "... ... ... ... \n", + "237099 biolink:ChemicalEntity HP:0008629 Pulsatile tinnitus \n", + "237100 biolink:ChemicalEntity HP:0008629 Pulsatile tinnitus \n", + "237101 biolink:ChemicalEntity HP:0008629 Pulsatile tinnitus \n", + "237102 biolink:Disease HP:0008629 Pulsatile tinnitus \n", + "237103 biolink:PhenotypicFeature HP:0008629 Pulsatile tinnitus \n", + "\n", + " object_category subject_prefix object_prefix \n", + "0 biolink:PhenotypicFeature HP HP \n", + "1 biolink:PhenotypicFeature MONDO HP \n", + "2 biolink:PhenotypicFeature UNII HP \n", + "3 biolink:PhenotypicFeature UNII HP \n", + "4 biolink:PhenotypicFeature MONDO HP \n", + "... ... ... ... \n", + "237099 biolink:PhenotypicFeature CHEBI HP \n", + "237100 biolink:PhenotypicFeature UNII HP \n", + "237101 biolink:PhenotypicFeature CHEBI HP \n", + "237102 biolink:PhenotypicFeature MONDO HP \n", + "237103 biolink:PhenotypicFeature HP HP \n", + "\n", + "[236812 rows x 23 columns]" + ] + }, + "execution_count": 335, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# need this (dataframe called kg_yaml) to lookup examples for testExamples (qInput and oneOutput) portion of yaml\n", + "# additionally need this generate portion of x-bte-response-mapping\n", + "\n", + "kg_yaml = kg.copy()\n", + "\n", + "kg_yaml[\"subject_prefix\"] = kg_yaml[\"subject\"].str.split(\":\").str[0]\n", + "kg_yaml[\"object_prefix\"] = kg_yaml[\"object\"].str.split(\":\").str[0]\n", + "\n", + "kg_yaml" + ] + }, + { + "cell_type": "code", + "execution_count": 339, + "id": "f5c776cc", + "metadata": {}, + "outputs": [], + "source": [ + "# the following code writes the tags and x-bte-kgs-operations of ehr_risk_kg.yaml to an output file titled 'x-bte-kgs-operations-response-mapping.txt'\n", + "# copy paste the output to the relevant section in the yaml\n", + "with open('x-bte-kgs-operations-response-mapping.txt', 'w+') as file:\n", + " file.write(\" tags:\" + \"\\n\")\n", + " file.write(\" - query:\" + \"\\n\")\n", + " file.write(f\" ## {len(grouped)} operations based on TSV of KG\" + \"\\n\")\n", + " for index, row in grouped.iterrows():\n", + " file.write(f\" ## - {row['joined_to_match_xbte']}\" + \"\\n\")\n", + " file.write(\" x-bte-kgs-operations\" + \"\\n\")\n", + " for index, row in grouped.iterrows(): \n", + " file.write(f\" - $ref: '#/components/x-bte-kgs-operations/{row['joined_to_match_xbte']}'\" + \"\\n\")\n", + " file.write(f\" - $ref: '#/components/x-bte-kgs-operations/{row['joined_to_match_xbte']}-rev'\" + \"\\n\")\n", + " " + ] + }, + { + "cell_type": "code", + "execution_count": 340, + "id": "232ad5c1", + "metadata": {}, + "outputs": [], + "source": [ + "# the following code writes the x-bte-kgs-operations of ehr_risk_kg.yaml to an output file titled 'x-bte-kgs-operations-response-mapping.txt'\n", + "# copy paste the output to the relevant section in the yaml\n", + "\n", + "with open('x-bte-kgs-operations-response-mapping.txt', 'a') as file:\n", + " file.write(\" \" + \"x-bte-kgs-operations:\" + \"\\n\")\n", + " for index, row in grouped.iterrows():\n", + " xbte_header = f'{row[\"joined_to_match_xbte\"]}:'\n", + " file.write(\" \" + xbte_header + \"\\n\")\n", + " \n", + " base_url = \"https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=\"\n", + " url = base_url + f'''subject.type:\"biolink:{row['subject_category_postfix']}\"%20AND%20_exists_:subject.\"biolink:{row['subject_prefix']}\"%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:\"biolink:{row['object_category_postfix']}\"%20AND%20_exists_:object.{row['object_prefix']}'''\n", + " commented_url = \"## \" + url\n", + " file.write(\" \" + commented_url + \"\\n\")\n", + " \n", + " file.write(\" ## \" + str(row[\"Count\"]) + \" records\" + \"\\n\")\n", + " \n", + " file.write(\" -supportBatch: true\" + \"\\n\")\n", + " file.write(\" useTemplating: true\" + \"\\n\")\n", + " file.write(\" inputs:\" + \"\\n\")\n", + " \n", + " file.write(f\" - id: {row['subject_prefix']}\" + \"\\n\")\n", + " file.write(f\" - semantic: {row['subject_category_postfix']}\" + \"\\n\")\n", + " \n", + " file.write(\" requestBody:\" + \"\\n\")\n", + " file.write(\" body: >-\" + \"\\n\")\n", + " \n", + " file.write(\" {\" + \"\\n\")\n", + " q_string = f\"\"\" \"q\": [ {{ queryInputs | rmPrefix() | wrap ( '[\"' , '\",\"biolink:{row['subject_category_postfix']}\", \"associated_with_{row['increased_or_decreased']}_likelihood_of\", \"biolink:{row['object_category_postfix']}\"]') }} ]\"\"\"\n", + " file.write(' ' + q_string + \"\\n\") \n", + " scopes_string = f\"\"\" \"scopes\": [\"subject.{row['subject_prefix']}\", \"subject.type\", \"association.predicate\", \"object.type\"]\"\"\"\n", + " file.write(' ' + scopes_string + \"\\n\") \n", + " file.write(\" }\" + \"\\n\")\n", + " \n", + " file.write(\" parameters:\" + \"\\n\")\n", + " file.write(f\" fields: object.{row['object_prefix']}, association.edge_attributes, subject.name, object.name, source.edge_sources\" + \"\\n\")\n", + " file.write(f\" size: 1000\" + \"\\n\")\n", + " \n", + " file.write(\" outputs:\" + \"\\n\")\n", + " file.write(f\" -id: {row['object_prefix']}\" + \"\\n\")\n", + " file.write(f\" semantic: {row['object_category_postfix']}\" + \"\\n\")\n", + " \n", + " file.write(\" predicate: associated_with\" + \"\\n\")\n", + " file.write(\" qualifiers:\" + \"\\n\")\n", + " file.write(f\" object_direction_qualifier: {row['increased_or_decreased']}\" + \"\\n\")\n", + " file.write(f\" object_aspect_qualifier: likelihood\" + \"\\n\")\n", + " \n", + " file.write(\" response_mapping:\" + \"\\n\")\n", + " file.write(f' \"ref\": \"#/components/x-bte-response-mapping/object-{row[\"object_prefix\"]}\"' + \"\\n\")\n", + " \n", + " file.write(\" # testExamples:\" + \"\\n\")\n", + " sub_prefix = row[\"subject_prefix\"]\n", + " obj_prefix = row[\"object_prefix\"]\n", + " matched_rows = kg_yaml.loc[(kg_yaml['subject_prefix'] == sub_prefix) & (kg_yaml['object_prefix'] == obj_prefix)]\n", + " select_row = matched_rows.sample()\n", + " qInput = select_row['subject'].values[0]\n", + " qName = select_row['subject_name'].values[0]\n", + " oneOutput = select_row['object'].values[0]\n", + " oneOutputName = select_row['object_name'].values[0]\n", + " file.write(f' # - qInput: \"{qInput}\" ## {qName} ' + \"\\n\")\n", + " file.write(f' # oneOutput: \"{oneOutput}\" ## {oneOutputName} ' + \"\\n\")\n", + " \n", + " #### DO REVERSE #### \n", + " \n", + " xbte_header_rev = f'{row[\"joined_to_match_xbte\"]}_rev:'\n", + " file.write(\" \" + xbte_header_rev + \"\\n\")\n", + "\n", + " file.write(\" -supportBatch: true\" + \"\\n\")\n", + " file.write(\" useTemplating: true\" + \"\\n\")\n", + " file.write(\" inputs:\" + \"\\n\")\n", + " \n", + " file.write(f\" - id: {row['object_prefix']}\" + \"\\n\")\n", + " file.write(f\" - semantic: {row['object_category_postfix']}\" + \"\\n\")\n", + " \n", + " file.write(\" requestBody:\" + \"\\n\")\n", + " file.write(\" body: >-\" + \"\\n\")\n", + " \n", + " file.write(\" {\" + \"\\n\")\n", + " q_string = f\"\"\" \"q\": [ {{ queryInputs | rmPrefix() | wrap ( '[\"' , '\",\"biolink:{row['subject_category_postfix']}\", \"associated_with_{row['increased_or_decreased']}_likelihood_of\", \"biolink:{row['object_category_postfix']}\"]') }} ]\"\"\"\n", + " file.write(' ' + q_string + \"\\n\") \n", + " scopes_string = f\"\"\" \"scopes\": [\"object.{row['object_prefix']}\", \"subject.type\", \"association.predicate\", \"object.type\"]\"\"\"\n", + " file.write(' ' + scopes_string + \"\\n\") \n", + " file.write(\" }\" + \"\\n\")\n", + " \n", + " file.write(\" parameters:\" + \"\\n\")\n", + " file.write(f\" fields: subject.{row['subject_prefix']}, association.edge_attributes, subject.name, object.name, source.edge_sources\" + \"\\n\")\n", + " file.write(f\" size: 1000\" + \"\\n\")\n", + " \n", + " file.write(\" outputs:\" + \"\\n\")\n", + " file.write(f\" -id: {row['subject_prefix']}\" + \"\\n\")\n", + " file.write(f\" semantic: {row['subject_category_postfix']}\" + \"\\n\")\n", + " \n", + " file.write(\" predicate: associated_with\" + \"\\n\")\n", + " file.write(\" qualifiers:\" + \"\\n\")\n", + " file.write(f\" object_direction_qualifier: {row['increased_or_decreased']}\" + \"\\n\")\n", + " file.write(f\" object_aspect_qualifier: likelihood\" + \"\\n\")\n", + " \n", + " file.write(\" response_mapping:\" + \"\\n\")\n", + " file.write(f' \"ref\": \"#/components/x-bte-response-mapping/object-{row[\"subject_prefix\"]}\"' + \"\\n\")\n", + " \n", + " file.write(\" # testExamples:\" + \"\\n\")\n", + " sub_prefix = row[\"subject_prefix\"]\n", + " obj_prefix = row[\"object_prefix\"]\n", + " matched_rows = kg_yaml.loc[(kg_yaml['subject_prefix'] == sub_prefix) & (kg_yaml['object_prefix'] == obj_prefix)]\n", + " select_row = matched_rows.sample()\n", + " qInput = select_row['object'].values[0]\n", + " qName = select_row['object_name'].values[0]\n", + " oneOutput = select_row['subject'].values[0]\n", + " oneOutputName = select_row['subject_name'].values[0]\n", + " file.write(f' # - qInput: \"{qInput}\" ## {qName} ' + \"\\n\")\n", + " file.write(f' # oneOutput: \"{oneOutput}\" ## {oneOutputName} ' + \"\\n\")\n", + " \n", + " \n", + "\n", + " " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "9bbc605f", + "metadata": {}, + "outputs": [], + "source": [ + "Output example for x-bte-kgs-operations\n", + "\n", + " ChemCHEBI_decreased_PhenoNCIT:\n", + " ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT\n", + " ## 191 records\n", + " - supportBatch: true\n", + " useTemplating: true \n", + " inputs:\n", + " - id: CHEBI\n", + " semantic: SmallMolecule\n", + " requestBodyType: object\n", + " requestBody:\n", + " body: >-\n", + " {\n", + " \"q\": [ {{ queryInputs | rmPrefix() | wrap ( '[\"' , '\",\"biolink:ChemicalEntity\", \"associated_with_decreased_likelihood_of\", \"biolink:PhenotypicFeature\"]') }} ],\n", + " \"scopes\": [\"subject.CHEBI\", \"subject.type\", \"association.predicate\", \"object.type\"]\n", + " }\n", + " parameters:\n", + " fields: >-\n", + " object.NCIT,\n", + " association.edge_attributes,\n", + " subject.name,object.name\n", + " size: 1000\n", + " outputs:\n", + " - id: NCIT\n", + " semantic: PhenotypicFeature\n", + " predicate: associated_with\n", + " qualifiers:\n", + " object_direction_qualifier: decreased\n", + " object_aspect_qualifier: likelihood\n", + " response_mapping:\n", + " \"$ref\": \"#/components/x-bte-response-mapping/object-NCIT\"\n", + " # testExamples:\n", + " # - qInput: \"CHEBI:135866\" ## clindamycin\n", + " # oneOutput: \"NCIT:C171647\" ## SARS Coronavirus 2 Positive\n", + " ChemCHEBI_decreased_PhenoNCIT-rev:\n", + " - supportBatch: true\n", + " useTemplating: true \n", + " inputs:\n", + " - id: NCIT\n", + " semantic: PhenotypicFeature\n", + " requestBodyType: object\n", + " requestBody:\n", + " body: >-\n", + " {\n", + " \"q\": [ {{ queryInputs | rmPrefix() | wrap( '[\"' , '\",\"biolink:ChemicalEntity\", \"associated_with_decreased_likelihood_of\", \"biolink:PhenotypicFeature\"]') }} ],\n", + " \"scopes\": [\"object.NCIT\", \"subject.type\", \"association.predicate\", \"object.type\"]\n", + " }\n", + " parameters:\n", + " fields: >-\n", + " subject.CHEBI,\n", + " association.edge_attributes,\n", + " subject.name,object.name\n", + " size: 1000\n", + " outputs:\n", + " - id: CHEBI\n", + " semantic: SmallMolecule\n", + " predicate: associated_with\n", + " qualifiers:\n", + " subject_direction_qualifier: decreased\n", + " subject_aspect_qualifier: likelihood\n", + " response_mapping:\n", + " \"$ref\": \"#/components/x-bte-response-mapping/subject-CHEBI\"\n", + " # testExamples:\n", + " # - qInput: \"NCIT:C171647\" ## SARS Coronavirus 2 Positive\n", + " # oneOutput: \"CHEBI:119915\" ## fentanyl" + ] + }, + { + "cell_type": "code", + "execution_count": 341, + "id": "d834fe3e", + "metadata": {}, + "outputs": [], + "source": [ + "# the following code writes the x-bte-response-maping of ehr_risk_kg.yaml to an output file titled 'x-bte-kgs-operations-response-mapping.txt'\n", + "# copy paste the output to the relevant section in the yaml\n", + "with open('x-bte-kgs-operations-response-mapping.txt', 'a') as file:\n", + " file.write(\" \" + \"x-bte-response-mapping:\" + \"\\n\")\n", + " for sprefix in list(kg_yaml['subject_prefix'].unique()):\n", + " file.write(f\" subject-{sprefix}:\" + \"\\n\")\n", + " file.write(f\" {sprefix}: subject.{sprefix}\" + \"\\n\")\n", + " file.write(f\" input_name: subject.name\" + \"\\n\")\n", + " file.write(f\" output_name: object.name\" + \"\\n\")\n", + " file.write(f\" edge-attributes: sources.edge_attributes\" + \"\\n\")\n", + " file.write(f\" trapi_sources: source.edge_sources\" + \"\\n\")\n", + " for oprefix in list(kg_yaml['object_prefix'].unique()):\n", + " file.write(f\" object-{oprefix}:\" + \"\\n\")\n", + " file.write(f\" {oprefix}: object.{oprefix}\" + \"\\n\")\n", + " file.write(f\" input_name: object.name\" + \"\\n\")\n", + " file.write(f\" output_name: subject.name\" + \"\\n\")\n", + " file.write(f\" edge-attributes: sources.edge_attributes\" + \"\\n\")\n", + " file.write(f\" trapi_sources: source.edge_sources\" + \"\\n\")\n" + ] + }, + { + "cell_type": "code", + "execution_count": 325, + "id": "30781582", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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subjectobjectpredicatecount
111072HP:0001974NCIT:C167118biolink:associated_with_decreased_likelihood_of4
211014NCIT:C167118HP:0001974biolink:associated_with_decreased_likelihood_of4
117058HP:0002900NCIT:C167118biolink:associated_with_increased_likelihood_of4
122579HP:0003124NCIT:C167118biolink:associated_with_decreased_likelihood_of4
117810HP:0002902NCIT:C167118biolink:associated_with_increased_likelihood_of3
...............
78133CHEBI:77431MONDO:0004721biolink:associated_with_decreased_likelihood_of1
78134CHEBI:77431MONDO:0004866biolink:associated_with_decreased_likelihood_of1
78135CHEBI:77431MONDO:0004868biolink:associated_with_increased_likelihood_of1
78136CHEBI:77431MONDO:0004946biolink:associated_with_increased_likelihood_of1
234248UNII:X85G7936GVSNOMEDCT:76571007biolink:associated_with_decreased_likelihood_of1
\n", + "

234249 rows × 4 columns

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" + ], + "text/plain": [ + " subject object \\\n", + "111072 HP:0001974 NCIT:C167118 \n", + "211014 NCIT:C167118 HP:0001974 \n", + "117058 HP:0002900 NCIT:C167118 \n", + "122579 HP:0003124 NCIT:C167118 \n", + "117810 HP:0002902 NCIT:C167118 \n", + "... ... ... \n", + "78133 CHEBI:77431 MONDO:0004721 \n", + "78134 CHEBI:77431 MONDO:0004866 \n", + "78135 CHEBI:77431 MONDO:0004868 \n", + "78136 CHEBI:77431 MONDO:0004946 \n", + "234248 UNII:X85G7936GV SNOMEDCT:76571007 \n", + "\n", + " predicate count \n", + "111072 biolink:associated_with_decreased_likelihood_of 4 \n", + "211014 biolink:associated_with_decreased_likelihood_of 4 \n", + "117058 biolink:associated_with_increased_likelihood_of 4 \n", + "122579 biolink:associated_with_decreased_likelihood_of 4 \n", + "117810 biolink:associated_with_increased_likelihood_of 3 \n", + "... ... ... \n", + "78133 biolink:associated_with_decreased_likelihood_of 1 \n", + "78134 biolink:associated_with_decreased_likelihood_of 1 \n", + "78135 biolink:associated_with_increased_likelihood_of 1 \n", + "78136 biolink:associated_with_increased_likelihood_of 1 \n", + "234248 biolink:associated_with_decreased_likelihood_of 1 \n", + "\n", + "[234249 rows x 4 columns]" + ] + }, + "execution_count": 325, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# # check to see how many identical triples there are in KG (requested by BTE)\n", + "# identical_triples_check = kg.groupby(['subject','object', 'predicate']).size().reset_index().rename(columns={0:'count'}).sort_values(by=['count'], ascending=False)\n", + "# identical_triples_check" + ] + }, + { + "cell_type": "markdown", + "id": "647beb4b", + "metadata": {}, + "source": [ + "# Make a cleaned version of the parser below" + ] + }, + { + "cell_type": "code", + "execution_count": 32, + "id": "9a68e6a8", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{\n", + " \"_id\": \"HP:0008629_HP:0000360_0.8401321539277617_00_8796399245685702_10102731\",\n", + " \"subject\": {\n", + " \"HP\": \"0008629\",\n", + " \"id\": \"HP:0008629\",\n", + " \"name\": \"Pulsatile tinnitus\",\n", + " \"type\": \"biolink:PhenotypicFeature\"\n", + " },\n", + " \"association\": {\n", + " \"predicate\": \"associated_with_increased_likelihood_of\",\n", + " \"edge_attributes\": [\n", + " {\n", + " \"attribute_type_id\": \"biolink:has_supporting_study_result\",\n", + " \"value\": \"We train a large collection of multivariable, binary logistic regression models on EHR data for each specific condition/disease/outcome. Features include labs, medications, and phenotypes. Directed edges point from risk factors to specific outcomes (diseases, phenotype, or medication exposure).\",\n", + " \"attributes\": [\n", + " {\n", + " \"attribute_type_id\": \"biolink:supporting_study_method_type\",\n", + " \"value\": \"STATO:0000149\",\n", + " \"description\": \"Binomial logistic regression for analysis of dichotomous dependent variable (in this case, for having this particular condition/disease/outcome or not)\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:update_date\",\n", + " \"value\": \"2022-05-18\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:p_value\",\n", + " \"value\": 0.0,\n", + " \"description\": \"The p-value represents the probability of observing the estimated coefficient (or more extreme value) under the assumption of the null hypothesis (which assumes that there is no relationship between the independent variable and outcome variable). The p-value associated with each coefficient helps determine whether the relationship between the independent variable and the outcome is statistically significant. A low p-value suggests that the observed relationship between the independent variable and the outcome is unlikely to occur by chance alone, providing evidence against the null hypothesis.\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"STATO:0000209\",\n", + " \"value\": 0.8401321539277617,\n", + " \"description\": \"The AUROC provides a way to evaluate the model's ability to discriminate between the two classes (the presenece of absence of condition/disease/outcome). Values range between 0-1; the higher the AUROC, the better the model's ability to discriminate between clasess.\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:log_odds_ratio\",\n", + " \"value\": 8.796399245685702,\n", + " \"description\": \"The logarithm of the odds ratio (log odds ratio), or the ratio of the odds of event Y occurring in an exposed group versus the odds of event Y occurring in a non-exposed group.\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:supporting_study_cohort\",\n", + " \"value\": \"age < 18 excluded\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:supporting_study_date_range\",\n", + " \"value\": \"2020-2022 (prediction)\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:supporting_study_size\",\n", + " \"value\": 10102731,\n", + " \"description\": \"The total number of patients or participants within a sample population.\"\n", + " }\n", + " ]\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:primary_knowledge_source\",\n", + " \"value\": \"infores:biothings-multiomics-ehr-risk\",\n", + " \"value_type_id\": \"biolink:InformationResource\",\n", + " \"value_url\": \"http://smart-api.info/registry?q=d86a24f6027ffe778f84ba10a7a1861a\",\n", + " \"description\": \"The EHR Risk KP is created and maintained by the Multiomics Provider team from the Institute for Systems Biology in Seattle, WA. Through a partnership with Providence/Swedish Health Services and Institute for Systems Biology, we analyze over 26 million EHRs. We use these records to train a large collection of interpretable machine learning models which are integrated into a single large Knowledge Graph, with directed edges pointing from risk factors to specific outcomes (diseases, phenotype, or medication exposure).\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:supporting_data_source\",\n", + " \"value\": \"infores:providence-st-joseph-ehr\",\n", + " \"value_type_id\": \"biolink:InformationResource\",\n", + " \"value_url\": \"https://github.com/NCATSTranslator/Translator-All/wiki/EHR-Risk-KP\",\n", + " \"description\": \"A partnership with Providence/Swedish Health Services and Institute for Systems Biology allows analysis of 26 million EHRs from patients in seven states in the US, including Alaska, California, Montana, Oregon, Washington, Texas, and New Mexico. 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Features include labs, medications, and phenotypes. Directed edges point from risk factors to specific outcomes (diseases, phenotype, or medication exposure).\",\n", + " \"attributes\": [\n", + " {\n", + " \"attribute_type_id\": \"biolink:supporting_study_method_type\",\n", + " \"value\": \"STATO:0000149\",\n", + " \"description\": \"Binomial logistic regression for analysis of dichotomous dependent variable (in this case, for having this particular condition/disease/outcome or not)\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:update_date\",\n", + " \"value\": \"2022-05-18\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:p_value\",\n", + " \"value\": 0.8886902851131677,\n", + " \"description\": \"The p-value represents the probability of observing the estimated coefficient (or more extreme value) under the assumption of the null hypothesis (which assumes that there is no relationship between the independent variable and outcome variable). The p-value associated with each coefficient helps determine whether the relationship between the independent variable and the outcome is statistically significant. A low p-value suggests that the observed relationship between the independent variable and the outcome is unlikely to occur by chance alone, providing evidence against the null hypothesis.\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"STATO:0000209\",\n", + " \"value\": 0.8401321539277617,\n", + " \"description\": \"The AUROC provides a way to evaluate the model's ability to discriminate between the two classes (the presenece of absence of condition/disease/outcome). Values range between 0-1; the higher the AUROC, the better the model's ability to discriminate between clasess.\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:log_odds_ratio\",\n", + " \"value\": 1.0571543050145833,\n", + " \"description\": \"The logarithm of the odds ratio (log odds ratio), or the ratio of the odds of event Y occurring in an exposed group versus the odds of event Y occurring in a non-exposed group.\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:supporting_study_cohort\",\n", + " \"value\": \"age < 18 excluded\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:supporting_study_date_range\",\n", + " \"value\": \"2020-2022 (prediction)\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:supporting_study_size\",\n", + " \"value\": 10098612,\n", + " \"description\": \"The total number of patients or participants within a sample population.\"\n", + " }\n", + " ]\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:primary_knowledge_source\",\n", + " \"value\": \"infores:biothings-multiomics-ehr-risk\",\n", + " \"value_type_id\": \"biolink:InformationResource\",\n", + " \"value_url\": \"http://smart-api.info/registry?q=d86a24f6027ffe778f84ba10a7a1861a\",\n", + " \"description\": \"The EHR Risk KP is created and maintained by the Multiomics Provider team from the Institute for Systems Biology in Seattle, WA. Through a partnership with Providence/Swedish Health Services and Institute for Systems Biology, we analyze over 26 million EHRs. We use these records to train a large collection of interpretable machine learning models which are integrated into a single large Knowledge Graph, with directed edges pointing from risk factors to specific outcomes (diseases, phenotype, or medication exposure).\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:supporting_data_source\",\n", + " \"value\": \"infores:providence-st-joseph-ehr\",\n", + " \"value_type_id\": \"biolink:InformationResource\",\n", + " \"value_url\": \"https://github.com/NCATSTranslator/Translator-All/wiki/EHR-Risk-KP\",\n", + " \"description\": \"A partnership with Providence/Swedish Health Services and Institute for Systems Biology allows analysis of 26 million EHRs from patients in seven states in the US, including Alaska, California, Montana, Oregon, Washington, Texas, and New Mexico. Please email data-access@isbscience.org for more information.\"\n", + " }\n", + " ]\n", + " },\n", + " \"object\": {\n", + " \"HP\": \"0000360\",\n", + " \"id\": \"HP:0000360\",\n", + " \"name\": \"Tinnitus\",\n", + " \"type\": \"biolink:PhenotypicFeature\"\n", + " },\n", + " \"source\": {\n", + " \"edge_sources\": [\n", + " {\n", + " \"resource_id\": \"infores:biothings-multiomics-ehr-risk\",\n", + " \"resource_role\": \"primary_knowledge_source\",\n", + " \"upstream_resource_ids\": \"infores:providence-st-joseph-ehr\"\n", + " },\n", + " {\n", + " \"resource_id\": \"infores:providence-st-joseph-ehr\",\n", + " \"resource_role\": \"supporting_data_source\"\n", + " }\n", + " ]\n", + " }\n", + "}\n", + "{\n", + " \"_id\": \"MONDO:0001119_HP:0000360_0.8401321539277617_09257571836006121_1042593529879973_10100198\",\n", + " \"subject\": {\n", + " \"MONDO\": \"0001119\",\n", + " \"id\": \"MONDO:0001119\",\n", + " \"name\": \"premature menopause\",\n", + " \"type\": \"biolink:Disease\"\n", + " },\n", + " \"association\": {\n", + " \"predicate\": \"associated_with_increased_likelihood_of\",\n", + " \"edge_attributes\": [\n", + " {\n", + " \"attribute_type_id\": \"biolink:has_supporting_study_result\",\n", + " \"value\": \"We train a large collection of multivariable, binary logistic regression models on EHR data for each specific condition/disease/outcome. 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Please email data-access@isbscience.org for more information.\"\n", + " }\n", + " ]\n", + " },\n", + " \"object\": {\n", + " \"HP\": \"0000360\",\n", + " \"id\": \"HP:0000360\",\n", + " \"name\": \"Tinnitus\",\n", + " \"type\": \"biolink:PhenotypicFeature\"\n", + " },\n", + " \"source\": {\n", + " \"edge_sources\": [\n", + " {\n", + " \"resource_id\": \"infores:biothings-multiomics-ehr-risk\",\n", + " \"resource_role\": \"primary_knowledge_source\",\n", + " \"upstream_resource_ids\": \"infores:providence-st-joseph-ehr\"\n", + " },\n", + " {\n", + " \"resource_id\": \"infores:providence-st-joseph-ehr\",\n", + " \"resource_role\": \"supporting_data_source\"\n", + " }\n", + " ]\n", + " }\n", + "}\n", + "{\n", + " \"_id\": \"CHEBI:15407_HP:0000360_0.8401321539277617_0002238827241549002_10328062673251501_10092760\",\n", + " \"subject\": {\n", + " \"CHEBI\": \"15407\",\n", + " \"id\": \"CHEBI:15407\",\n", + " \"name\": \"ephedrine\",\n", + " \"type\": \"biolink:ChemicalEntity\"\n", + " },\n", + " \"association\": {\n", + " \"predicate\": \"associated_with_increased_likelihood_of\",\n", + " \"edge_attributes\": [\n", + " {\n", + " \"attribute_type_id\": \"biolink:has_supporting_study_result\",\n", + " \"value\": \"We train a large collection of multivariable, binary logistic regression models on EHR data for each specific condition/disease/outcome. Features include labs, medications, and phenotypes. Directed edges point from risk factors to specific outcomes (diseases, phenotype, or medication exposure).\",\n", + " \"attributes\": [\n", + " {\n", + " \"attribute_type_id\": \"biolink:supporting_study_method_type\",\n", + " \"value\": \"STATO:0000149\",\n", + " \"description\": \"Binomial logistic regression for analysis of dichotomous dependent variable (in this case, for having this particular condition/disease/outcome or not)\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:update_date\",\n", + " \"value\": \"2022-05-18\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:p_value\",\n", + " \"value\": 0.002238827241549002,\n", + " \"description\": \"The p-value represents the probability of observing the estimated coefficient (or more extreme value) under the assumption of the null hypothesis (which assumes that there is no relationship between the independent variable and outcome variable). The p-value associated with each coefficient helps determine whether the relationship between the independent variable and the outcome is statistically significant. A low p-value suggests that the observed relationship between the independent variable and the outcome is unlikely to occur by chance alone, providing evidence against the null hypothesis.\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"STATO:0000209\",\n", + " \"value\": 0.8401321539277617,\n", + " \"description\": \"The AUROC provides a way to evaluate the model's ability to discriminate between the two classes (the presenece of absence of condition/disease/outcome). Values range between 0-1; the higher the AUROC, the better the model's ability to discriminate between clasess.\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:log_odds_ratio\",\n", + " \"value\": 1.0328062673251501,\n", + " \"description\": \"The logarithm of the odds ratio (log odds ratio), or the ratio of the odds of event Y occurring in an exposed group versus the odds of event Y occurring in a non-exposed group.\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:supporting_study_cohort\",\n", + " \"value\": \"age < 18 excluded\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:supporting_study_date_range\",\n", + " \"value\": \"2020-2022 (prediction)\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:supporting_study_size\",\n", + " \"value\": 10092760,\n", + " \"description\": \"The total number of patients or participants within a sample population.\"\n", + " }\n", + " ]\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:primary_knowledge_source\",\n", + " \"value\": \"infores:biothings-multiomics-ehr-risk\",\n", + " \"value_type_id\": \"biolink:InformationResource\",\n", + " \"value_url\": \"http://smart-api.info/registry?q=d86a24f6027ffe778f84ba10a7a1861a\",\n", + " \"description\": \"The EHR Risk KP is created and maintained by the Multiomics Provider team from the Institute for Systems Biology in Seattle, WA. Through a partnership with Providence/Swedish Health Services and Institute for Systems Biology, we analyze over 26 million EHRs. We use these records to train a large collection of interpretable machine learning models which are integrated into a single large Knowledge Graph, with directed edges pointing from risk factors to specific outcomes (diseases, phenotype, or medication exposure).\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:supporting_data_source\",\n", + " \"value\": \"infores:providence-st-joseph-ehr\",\n", + " \"value_type_id\": \"biolink:InformationResource\",\n", + " \"value_url\": \"https://github.com/NCATSTranslator/Translator-All/wiki/EHR-Risk-KP\",\n", + " \"description\": \"A partnership with Providence/Swedish Health Services and Institute for Systems Biology allows analysis of 26 million EHRs from patients in seven states in the US, including Alaska, California, Montana, Oregon, Washington, Texas, and New Mexico. Please email data-access@isbscience.org for more information.\"\n", + " }\n", + " ]\n", + " },\n", + " \"object\": {\n", + " \"HP\": \"0000360\",\n", + " \"id\": \"HP:0000360\",\n", + " \"name\": \"Tinnitus\",\n", + " \"type\": \"biolink:PhenotypicFeature\"\n", + " },\n", + " \"source\": {\n", + " \"edge_sources\": [\n", + " {\n", + " \"resource_id\": \"infores:biothings-multiomics-ehr-risk\",\n", + " \"resource_role\": \"primary_knowledge_source\",\n", + " \"upstream_resource_ids\": \"infores:providence-st-joseph-ehr\"\n", + " },\n", + " {\n", + " \"resource_id\": \"infores:providence-st-joseph-ehr\",\n", + " \"resource_role\": \"supporting_data_source\"\n", + " }\n", + " ]\n", + " }\n", + "}\n", + "Document IDs appear to be unique\n", + "\n", + "\n", + "\n" + ] + } + ], + "source": [ + "import pandas as pd\n", + "import json\n", + "import sys, os\n", + "import numpy as np\n", + "\n", + "def parse_ehr_risk(data_folder):\n", + "\n", + " edges_filename = \"ehr_risk_edges_data_2022_06_01.csv\"\n", + " nodes_filename = \"ehr_risk_nodes_data_2022_06_01.csv\"\n", + "\n", + " nodes_filepath = os.path.join(data_folder, nodes_filename)\n", + " edges_filepath = os.path.join(data_folder, edges_filename)\n", + " nodes_data = pd.read_csv(nodes_filepath, sep = ',')\n", + " edges_data = pd.read_csv(edges_filepath, sep = ',')\n", + " \n", + " # the nodes file has duplicate ids; fix in enclave in future\n", + " nodes_data = nodes_data.drop_duplicates(subset='id', keep=\"first\")\n", + " \n", + " # biolink category biolink:ChemicalSubstance has been deprecated. Use biolink:ChemicalEntity instead\n", + " nodes_data[\"category\"].mask(nodes_data[\"category\"] == \"biolink:ChemicalSubstance\", \"biolink:ChemicalEntity\" , inplace=True )\n", + "\n", + " # we originally provided the # of patients with condition --> log + patient count, and # of patients without condition --> log - patient count\n", + " # get the approximate total number of patients in the study and call it \"total_sample_size\"\n", + " edges_data[\"num_patients_with_condition\"] = 10**(edges_data['log_positive_patient_count']) # convert log pos patient count to an actual # \n", + " edges_data[\"num_patients_without_condition\"] = 10**(edges_data['log_negative_patient_count']) # convert log neg patient count to an actual #\n", + " edges_data = edges_data.drop(['log_positive_patient_count', 'log_negative_patient_count'], axis=1)\n", + " edges_data[\"total_sample_size\"] = edges_data[\"num_patients_with_condition\"] + edges_data[\"num_patients_without_condition\"]\n", + " edges_data = edges_data.drop(['num_patients_with_condition', 'num_patients_without_condition'], axis=1)\n", + " edges_data[\"total_sample_size\"] = np.random.poisson(edges_data[\"total_sample_size\"]) # add poisson noise injection \n", + "\n", + "# # create confidence interval column by concatenating 'lower_confidence_bound'and 'upper_confidence_bound', then dropping those columns\n", + "# edges_data['log_odds_ratio_95_confidence_interval'] = edges_data.apply(lambda row: [row['lower_confidence_bound'], row['upper_confidence_bound']], axis=1)\n", + "# edges_data = edges_data.drop(['lower_confidence_bound', 'upper_confidence_bound'], axis=1)\n", + " \n", + " # ----- RE-CONSTRUCT KG FROM NODES AND EDGES FILES ------ #\n", + " # merge the subject names, categories and ids from the nodes csv/table to the edges table\n", + " kg = pd.merge(edges_data, nodes_data[['id', 'name', 'category']], left_on='subject', right_on = 'id', how=\"inner\")\n", + " kg.rename(columns = {'category_x':'predicate_category',\n", + " 'category_y': 'subject_category',\n", + " 'id': 'subject_id',\n", + " 'name': 'subject_name'}, inplace = True)\n", + " # merge the object names, categories and ids from the nodes csv/table to the edges table\n", + " kg = pd.merge(kg, nodes_data[['id', 'name', 'category']], left_on='object', right_on = 'id', how=\"inner\")\n", + " kg.rename(columns = {'id':'object_id',\n", + " 'category': 'object_category',\n", + " 'name': 'object_name'}, inplace = True)\n", + " # ----- ------------------------------------------ ------ #\n", + " \n", + " # ensure there are no duplicates\n", + " kg = kg.drop_duplicates(['subject', 'object', 'auc_roc', 'p_value', 'feature_coefficient'], keep='first')\n", + " \n", + " # some of the subjects/objects contain the string literal \"NONE\" (specific culprit is COVID Negative or something) Should look into this in future \n", + " kg = kg[~kg[\"subject\"].str.contains(\"NONE\")==True] # subject and object are all CURIEs, not names\n", + " kg = kg[~kg[\"object\"].str.contains(\"NONE\")==True]\n", + " kg = kg[~kg[\"subject\"].str.contains(\"none\")==True]\n", + " kg = kg[~kg[\"object\"].str.contains(\"none\")==True]\n", + " kg = kg[~kg[\"subject\"].str.contains(\"None\")==True]\n", + " kg = kg[~kg[\"object\"].str.contains(\"None\")==True]\n", + " \n", + " id_list = [] # use this to check if your document IDs are unique. Collect them and see if they're all unique\n", + " \n", + " # iterate through each row in KG to yield json formatted triple\n", + " for index, row in kg[:40].iterrows(): # comment for testing \n", + " id_dict = {} # this is the outter dict that holds inner dicts: subject_dict, association_dict, object_dict, and source_dict\n", + " subject_dict = {} # inner dict\n", + " association_dict = {} # inner dict\n", + " object_dict = {} # inner dict\n", + " source_dict = {} # inner dict (provides provenance as per TRAPI 1.4 standards)\n", + "\n", + " # id generated by concatenating the following: subject_id CURIE, object_id CURIE, AUCROC (removing decimal point) and p-value (removing decimal point), feature coeffcient (removing decimal point), and total sample size\n", + " doc_id = \"{}_{}_{}_{}_{}_{}\".format(row[\"subject\"],\n", + " row[\"object\"],\n", + " str(row['auc_roc']),\n", + " str(row['p_value']).replace('.', ''),\n", + " str(row['feature_coefficient']).replace('.', ''),\n", + " str(row[\"total_sample_size\"]))\n", + "\n", + " id_list.append(doc_id)\n", + " id_dict[\"_id\"] = doc_id\n", + " subject_dict[\"{}\".format(row[\"subject\"].split(':')[0])] = \"{}\".format(row[\"subject\"].split(':')[1]) # create the subject dict from the rows of the df \n", + " subject_dict[\"id\"] = row[\"subject\"]\n", + " subject_dict[\"name\"] = row[\"subject_name\"]\n", + " subject_dict[\"type\"] = row[\"subject_category\"]\n", + "\n", + " association_dict[\"predicate\"] = \"{}\".format(row[\"predicate\"].split(':')[1]) # create the association dict from the rows of the df. Edge attributes need extra work. The predicate is separated out into qualified predicate by X-BTE annotation, so we don't have to worry about qualifiers here\n", + " association_dict[\"edge_attributes\"] = []\n", + "\n", + " source_dict[\"edge_sources\"] = []\n", + "\n", + " association_dict[\"edge_attributes\"].append(\n", + " {\n", + " \"attribute_type_id\":\"biolink:has_supporting_study_result\",\n", + " \"value\":\"We train a large collection of multivariable, binary logistic regression models on EHR data for each specific condition/disease/outcome. Features include labs, medications, and phenotypes. Directed edges point from risk factors to specific outcomes (diseases, phenotype, or medication exposure).\",\n", + " \"attributes\": [\n", + " {\n", + " \"attribute_type_id\": \"biolink:supporting_study_method_type\",\n", + " \"value\": \"STATO:0000149\",\n", + " \"description\": \"Binomial logistic regression for analysis of dichotomous dependent variable (in this case, for having this particular condition/disease/outcome or not)\"\n", + " },\n", + " {\n", + " \"attribute_type_id\":\"biolink:update_date\",\n", + " \"value\":row[\"provided_date\"]\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:p_value\",\n", + " \"value\": row[\"p_value\"],\n", + " \"description\": \"The p-value represents the probability of observing the estimated coefficient (or more extreme value) under the assumption of the null hypothesis (which assumes that there is no relationship between the independent variable and outcome variable). The p-value associated with each coefficient helps determine whether the relationship between the independent variable and the outcome is statistically significant. A low p-value suggests that the observed relationship between the independent variable and the outcome is unlikely to occur by chance alone, providing evidence against the null hypothesis.\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"STATO:0000209\",\n", + " \"value\": row[\"auc_roc\"],\n", + " \"description\": \"The AUROC provides a way to evaluate the model's ability to discriminate between the two classes (the presenece of absence of condition/disease/outcome). Values range between 0-1; the higher the AUROC, the better the model's ability to discriminate between clasess.\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:log_odds_ratio\",\n", + " \"value\": row['feature_coefficient'],\n", + " \"description\": \"The logarithm of the odds ratio (log odds ratio), or the ratio of the odds of event Y occurring in an exposed group versus the odds of event Y occurring in a non-exposed group.\"\n", + " },\n", + "# {\n", + "# \"attribute_type_id\": \"biolink:log_odds_ratio_95_confidence_interval\",\n", + "# \"value\": row['log_odds_ratio_95_confidence_interval'],\n", + "# \"description\": \"log_odds_ratio_95_confidence_interval\"\n", + "# },\n", + " {\n", + " \"attribute_type_id\": \"biolink:supporting_study_cohort\",\n", + " \"value\": \"age < 18 excluded\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:supporting_study_date_range\",\n", + " \"value\": \"2020-2022 (prediction)\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:total_sample_size\",\n", + " \"value\": row[\"total_sample_size\"],\n", + " \"description\": \"The total number of patients or participants within a sample population.\"\n", + " }\n", + " ]\n", + " }\n", + " )\n", + " association_dict[\"edge_attributes\"].append(\n", + " {\n", + " \"attribute_type_id\":\"biolink:primary_knowledge_source\",\n", + " \"value\":\"infores:biothings-multiomics-ehr-risk\",\n", + " \"value_type_id\": \"biolink:InformationResource\",\n", + " \"value_url\": \"http://smart-api.info/registry?q=d86a24f6027ffe778f84ba10a7a1861a\",\n", + " \"description\": \"The EHR Risk KP is created and maintained by the Multiomics Provider team from the Institute for Systems Biology in Seattle, WA. Through a partnership with Providence/Swedish Health Services and Institute for Systems Biology, we analyze over 26 million EHRs. We use these records to train a large collection of interpretable machine learning models which are integrated into a single large Knowledge Graph, with directed edges pointing from risk factors to specific outcomes (diseases, phenotype, or medication exposure).\",\n", + " }\n", + " )\n", + " association_dict[\"edge_attributes\"].append(\n", + " {\n", + " \"attribute_type_id\":\"biolink:supporting_data_source\",\n", + " \"value\":\"infores:providence-st-joseph-ehr\",\n", + " \"value_type_id\": \"biolink:InformationResource\",\n", + " \"value_url\": \"https://github.com/NCATSTranslator/Translator-All/wiki/EHR-Risk-KP\",\n", + " \"description\": \"A partnership with Providence/Swedish Health Services and Institute for Systems Biology allows analysis of 26 million EHRs from patients in seven states in the US, including Alaska, California, Montana, Oregon, Washington, Texas, and New Mexico. Please email data-access@isbscience.org for more information.\",\n", + " }\n", + " )\n", + "\n", + " object_dict[\"{}\".format(row[\"object\"].split(':')[0])] = \"{}\".format(row[\"object\"].split(':')[1]) # create the object dict from the rows of the df \n", + " object_dict[\"id\"] = row[\"object\"]\n", + " object_dict[\"name\"] = row[\"object_name\"]\n", + " object_dict[\"type\"] = row[\"object_category\"]\n", + "\n", + " source_dict[\"edge_sources\"].append(\n", + " {\n", + " \"resource_id\": \"infores:biothings-multiomics-ehr-risk\",\n", + " \"resource_role\": \"primary_knowledge_source\",\n", + " \"upstream_resource_ids\": \"infores:providence-st-joseph-ehr\"\n", + " }\n", + " )\n", + "\n", + " source_dict[\"edge_sources\"].append(\n", + " {\n", + " \"resource_id\": \"infores:providence-st-joseph-ehr\",\n", + " \"resource_role\": \"supporting_data_source\"\n", + " }\n", + " )\n", + "\n", + " id_dict[\"subject\"] = subject_dict # put the subject, association, object, and source dicts into the outer dict called id_dict\n", + " id_dict[\"association\"] = association_dict\n", + " id_dict[\"object\"] = object_dict\n", + " id_dict[\"source\"] = source_dict\n", + " \n", + " # throw error for any rows that are missing any relevant values, such as subject name, subject id/CURIE, subject category, p-value, etc...\n", + " try:\n", + " assert not {x for x in {row[\"total_sample_size\"],\n", + " row[\"subject\"],\n", + " row[\"subject_name\"],\n", + " row[\"subject_category\"],\n", + " row[\"object\"],\n", + " row[\"object_name\"],\n", + " row[\"object_category\"],\n", + " row[\"p_value\"],\n", + " row[\"auc_roc\"],\n", + " row['feature_coefficient']} if x in {None,\n", + " \"NONE\",\n", + " \"None\",\n", + " \"none\",\n", + " \"NA\"}}, \"Error: All values including subject and object IDs, categories, names, p-value, AUC-ROC, and feature coefficient must be non-null and not contain string literal None or NONE\"\n", + " print(json.dumps(id_dict, indent=2)) # uncomment for testing\n", + "# print(index) # uncomment for testing\n", + "# yield id_dict # comment for testing\n", + " except AssertionError as msg:\n", + " print(msg)\n", + "\n", + " if len(id_list) != len(set(id_list)):\n", + " print(\"You do not have unique document IDs for each edge in your KG. Either you have duplicate rows/edges, or you simply didn't make a unique identifer (Document ID) for each one.\\n\\n\\n\")\n", + " else:\n", + " print(\"Document IDs appear to be unique\\n\\n\\n\")\n", + " \n", + " \n", + " " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "f3a074a8", + "metadata": {}, + "outputs": [], + "source": [ + "import pandas as pd\n", + "import json\n", + "import sys, os\n", + "import numpy as np\n", + "\n", + "def parse_ehr_risk(data_folder):\n", + "\n", + " edges_filename = \"ehr_risk_edges_data_2022_06_01.csv\"\n", + " nodes_filename = \"ehr_risk_nodes_data_2022_06_01.csv\"\n", + "\n", + " nodes_filepath = os.path.join(data_folder, nodes_filename)\n", + " edges_filepath = os.path.join(data_folder, edges_filename)\n", + " nodes_data = pd.read_csv(nodes_filepath, sep = ',')\n", + " edges_data = pd.read_csv(edges_filepath, sep = ',')\n", + " \n", + " # the nodes file has duplicate ids; fix in enclave in future\n", + " nodes_data = nodes_data.drop_duplicates(subset='id', keep=\"first\")\n", + " \n", + " # biolink category biolink:ChemicalSubstance has been deprecated. Use biolink:ChemicalEntity instead\n", + " nodes_data[\"category\"].mask(nodes_data[\"category\"] == \"biolink:ChemicalSubstance\", \"biolink:ChemicalEntity\" , inplace=True )\n", + "\n", + " # we originally provided the # of patients with condition --> log + patient count, and # of patients without condition --> log - patient count\n", + " # get the approximate total number of patients in the study and call it \"total_sample_size\"\n", + " edges_data[\"num_patients_with_condition\"] = 10**(edges_data['log_positive_patient_count']) # convert log pos patient count to an actual # \n", + " edges_data[\"num_patients_without_condition\"] = 10**(edges_data['log_negative_patient_count']) # convert log neg patient count to an actual #\n", + " edges_data = edges_data.drop(['log_positive_patient_count', 'log_negative_patient_count'], axis=1)\n", + " edges_data[\"total_sample_size\"] = edges_data[\"num_patients_with_condition\"] + edges_data[\"num_patients_without_condition\"]\n", + " edges_data = edges_data.drop(['num_patients_with_condition', 'num_patients_without_condition'], axis=1)\n", + " edges_data[\"total_sample_size\"] = np.random.poisson(edges_data[\"total_sample_size\"]) # add poisson noise injection \n", + "\n", + "# # create confidence interval column by concatenating 'lower_confidence_bound'and 'upper_confidence_bound', then dropping those columns\n", + "# edges_data['log_odds_ratio_95_confidence_interval'] = edges_data.apply(lambda row: [row['lower_confidence_bound'], row['upper_confidence_bound']], axis=1)\n", + "# edges_data = edges_data.drop(['lower_confidence_bound', 'upper_confidence_bound'], axis=1)\n", + " \n", + " # ----- RE-CONSTRUCT KG FROM NODES AND EDGES FILES ------ #\n", + " # merge the subject names, categories and ids from the nodes csv/table to the edges table\n", + " kg = pd.merge(edges_data, nodes_data[['id', 'name', 'category']], left_on='subject', right_on = 'id', how=\"inner\")\n", + " kg.rename(columns = {'category_x':'predicate_category',\n", + " 'category_y': 'subject_category',\n", + " 'id': 'subject_id',\n", + " 'name': 'subject_name'}, inplace = True)\n", + " # merge the object names, categories and ids from the nodes csv/table to the edges table\n", + " kg = pd.merge(kg, nodes_data[['id', 'name', 'category']], left_on='object', right_on = 'id', how=\"inner\")\n", + " kg.rename(columns = {'id':'object_id',\n", + " 'category': 'object_category',\n", + " 'name': 'object_name'}, inplace = True)\n", + " # ----- ------------------------------------------ ------ #\n", + " \n", + " # ensure there are no duplicates\n", + " kg = kg.drop_duplicates(['subject', 'object', 'auc_roc', 'p_value', 'feature_coefficient'], keep='first')\n", + " \n", + " # some of the subjects/objects contain the string literal \"NONE\" (specific culprit is COVID Negative or something) Should look into this in future \n", + " kg = kg[~kg[\"subject\"].str.contains(\"NONE\")==True] # subject and object are all CURIEs, not names\n", + " kg = kg[~kg[\"object\"].str.contains(\"NONE\")==True]\n", + " kg = kg[~kg[\"subject\"].str.contains(\"none\")==True]\n", + " kg = kg[~kg[\"object\"].str.contains(\"none\")==True]\n", + " kg = kg[~kg[\"subject\"].str.contains(\"None\")==True]\n", + " kg = kg[~kg[\"object\"].str.contains(\"None\")==True]\n", + " \n", + " id_list = [] # use this to check if your document IDs are unique. Collect them and see if they're all unique\n", + " \n", + " # iterate through each row in KG to yield json formatted triple\n", + " for index, row in kg[:40].iterrows(): # comment for testing \n", + " id_dict = {} # this is the outter dict that holds inner dicts: subject_dict, association_dict, object_dict, and source_dict\n", + " subject_dict = {} # inner dict\n", + " association_dict = {} # inner dict\n", + " object_dict = {} # inner dict\n", + " source_dict = {} # inner dict (provides provenance as per TRAPI 1.4 standards)\n", + "\n", + " # id generated by concatenating the following: subject_id CURIE, object_id CURIE, AUCROC (removing decimal point) and p-value (removing decimal point), feature coeffcient (removing decimal point), and total sample size\n", + " doc_id = \"{}_{}_{}_{}_{}_{}\".format(row[\"subject\"],\n", + " row[\"object\"],\n", + " str(row['auc_roc']),\n", + " str(row['p_value']).replace('.', ''),\n", + " str(row['feature_coefficient']).replace('.', ''),\n", + " str(row[\"total_sample_size\"]))\n", + "\n", + " id_list.append(doc_id)\n", + " id_dict[\"_id\"] = doc_id\n", + " subject_dict[\"{}\".format(row[\"subject\"].split(':')[0])] = \"{}\".format(row[\"subject\"].split(':')[1]) # create the subject dict from the rows of the df \n", + " subject_dict[\"id\"] = row[\"subject\"]\n", + " subject_dict[\"name\"] = row[\"subject_name\"]\n", + " subject_dict[\"type\"] = row[\"subject_category\"]\n", + "\n", + " association_dict[\"predicate\"] = \"{}\".format(row[\"predicate\"].split(':')[1]) # create the association dict from the rows of the df. Edge attributes need extra work. The predicate is separated out into qualified predicate by X-BTE annotation, so we don't have to worry about qualifiers here\n", + " association_dict[\"edge_attributes\"] = []\n", + "\n", + " source_dict[\"edge_sources\"] = []\n", + "\n", + " association_dict[\"edge_attributes\"].append(\n", + " {\n", + " \"attribute_type_id\":\"biolink:has_supporting_study_result\",\n", + " \"value\":\"We train a large collection of multivariable, binary logistic regression models on EHR data for each specific condition/disease/outcome. Features include labs, medications, and phenotypes. Directed edges point from risk factors to specific outcomes (diseases, phenotype, or medication exposure).\",\n", + " \"attributes\": [\n", + " {\n", + " \"attribute_type_id\": \"biolink:supporting_study_method_type\",\n", + " \"value\": \"STATO:0000149\",\n", + " \"description\": \"Binomial logistic regression for analysis of dichotomous dependent variable (in this case, for having this particular condition/disease/outcome or not)\"\n", + " },\n", + " {\n", + " \"attribute_type_id\":\"biolink:update_date\",\n", + " \"value\":row[\"provided_date\"]\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:p_value\",\n", + " \"value\": row[\"p_value\"],\n", + " \"description\": \"The p-value represents the probability of observing the estimated coefficient (or more extreme value) under the assumption of the null hypothesis (which assumes that there is no relationship between the independent variable and outcome variable). The p-value associated with each coefficient helps determine whether the relationship between the independent variable and the outcome is statistically significant. A low p-value suggests that the observed relationship between the independent variable and the outcome is unlikely to occur by chance alone, providing evidence against the null hypothesis.\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"STATO:0000209\",\n", + " \"value\": row[\"auc_roc\"],\n", + " \"description\": \"The AUROC provides a way to evaluate the model's ability to discriminate between the two classes (the presenece of absence of condition/disease/outcome). Values range between 0-1; the higher the AUROC, the better the model's ability to discriminate between clasess.\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:log_odds_ratio\",\n", + " \"value\": row['feature_coefficient'],\n", + " \"description\": \"The logarithm of the odds ratio (log odds ratio), or the ratio of the odds of event Y occurring in an exposed group versus the odds of event Y occurring in a non-exposed group.\"\n", + " },\n", + "# {\n", + "# \"attribute_type_id\": \"biolink:log_odds_ratio_95_confidence_interval\",\n", + "# \"value\": row['log_odds_ratio_95_confidence_interval'],\n", + "# \"description\": \"log_odds_ratio_95_confidence_interval\"\n", + "# },\n", + " {\n", + " \"attribute_type_id\": \"biolink:supporting_study_cohort\",\n", + " \"value\": \"age < 18 excluded\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:supporting_study_date_range\",\n", + " \"value\": \"2020-2022 (prediction)\"\n", + " },\n", + " {\n", + " \"attribute_type_id\": \"biolink:total_sample_size\",\n", + " \"value\": row[\"total_sample_size\"],\n", + " \"description\": \"The total number of patients or participants within a sample population.\"\n", + " }\n", + " ]\n", + " }\n", + " )\n", + " association_dict[\"edge_attributes\"].append(\n", + " {\n", + " \"attribute_type_id\":\"biolink:primary_knowledge_source\",\n", + " \"value\":\"infores:biothings-multiomics-ehr-risk\",\n", + " \"value_type_id\": \"biolink:InformationResource\",\n", + " \"value_url\": \"http://smart-api.info/registry?q=d86a24f6027ffe778f84ba10a7a1861a\",\n", + " \"description\": \"The EHR Risk KP is created and maintained by the Multiomics Provider team from the Institute for Systems Biology in Seattle, WA. Through a partnership with Providence/Swedish Health Services and Institute for Systems Biology, we analyze over 26 million EHRs. We use these records to train a large collection of interpretable machine learning models which are integrated into a single large Knowledge Graph, with directed edges pointing from risk factors to specific outcomes (diseases, phenotype, or medication exposure).\",\n", + " }\n", + " )\n", + " association_dict[\"edge_attributes\"].append(\n", + " {\n", + " \"attribute_type_id\":\"biolink:supporting_data_source\",\n", + " \"value\":\"infores:providence-st-joseph-ehr\",\n", + " \"value_type_id\": \"biolink:InformationResource\",\n", + " \"value_url\": \"https://github.com/NCATSTranslator/Translator-All/wiki/EHR-Risk-KP\",\n", + " \"description\": \"A partnership with Providence/Swedish Health Services and Institute for Systems Biology allows analysis of 26 million EHRs from patients in seven states in the US, including Alaska, California, Montana, Oregon, Washington, Texas, and New Mexico. Please email data-access@isbscience.org for more information.\",\n", + " }\n", + " )\n", + "\n", + " object_dict[\"{}\".format(row[\"object\"].split(':')[0])] = \"{}\".format(row[\"object\"].split(':')[1]) # create the object dict from the rows of the df \n", + " object_dict[\"id\"] = row[\"object\"]\n", + " object_dict[\"name\"] = row[\"object_name\"]\n", + " object_dict[\"type\"] = row[\"object_category\"]\n", + "\n", + " source_dict[\"edge_sources\"].append(\n", + " {\n", + " \"resource_id\": \"infores:biothings-multiomics-ehr-risk\",\n", + " \"resource_role\": \"primary_knowledge_source\",\n", + " \"upstream_resource_ids\": \"infores:providence-st-joseph-ehr\"\n", + " }\n", + " )\n", + "\n", + " source_dict[\"edge_sources\"].append(\n", + " {\n", + " \"resource_id\": \"infores:providence-st-joseph-ehr\",\n", + " \"resource_role\": \"supporting_data_source\"\n", + " }\n", + " )\n", + "\n", + " id_dict[\"subject\"] = subject_dict # put the subject, association, object, and source dicts into the outer dict called id_dict\n", + " id_dict[\"association\"] = association_dict\n", + " id_dict[\"object\"] = object_dict\n", + " id_dict[\"source\"] = source_dict\n", + " \n", + " # throw error for any rows that are missing any relevant values, such as subject name, subject id/CURIE, subject category, p-value, etc...\n", + "\n", + " try:\n", + " assert not {x for x in {row[\"total_sample_size\"],\n", + " row[\"subject\"],\n", + " row[\"subject_name\"],\n", + " row[\"subject_category\"],\n", + " row[\"object\"],\n", + " row[\"object_name\"],\n", + " row[\"object_category\"],\n", + " row[\"p_value\"],\n", + " row[\"auc_roc\"],\n", + " row['feature_coefficient']} if x in {None,\n", + " \"NONE\",\n", + " \"None\",\n", + " \"none\",\n", + " \"NA\"}}, \"Error: All values including subject and object IDs, categories, names, p-value, AUC-ROC, and feature coefficient must be non-null and not contain string literal None or NONE\"\n", + " print(json.dumps(id_dict, indent=2)) # uncomment for testing\n", + "# print(index) # uncomment for testing\n", + "# yield id_dict # comment for testing\n", + " except AssertionError as msg:\n", + " print(msg)\n", + "\n", + " if len(id_list) != len(set(id_list)):\n", + " print(\"You do not have unique document IDs for each edge in your KG. Either you have duplicate rows/edges, or you simply didn't make a unique identifer (Document ID) for each one.\\n\\n\\n\")\n", + " else:\n", + " print(\"Document IDs appear to be unique\\n\\n\\n\")\n", + "\n", + "\n", + "\n", + "\n", + " " + ] + }, + { + "cell_type": "code", + "execution_count": 151, + "id": "03180ac7", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Document IDs appear to be unique\n", + "\n", + "[{'_id': 'HP:0008629_HP:0000360_0.8401321539277617_00_8796399245685702_10096539', 'subject': {'HP': '0008629', 'id': 'HP:0008629', 'name': 'Pulsatile tinnitus', 'type': 'biolink:PhenotypicFeature'}, 'association': {'predicate': 'associated_with_increased_likelihood_of', 'edge_attributes': [{'attribute_type_id': 'biolink:has_supporting_study_result', 'value': 'We train a large collection of multivariable, binary logistic regression models on EHR data for each specific condition/disease/outcome. Features include labs, medications, and phenotypes. Directed edges point from risk factors to specific outcomes (diseases, phenotype, or medication exposure).', 'attributes': [{'attribute_type_id': 'biolink:supporting_study_method_type', 'value': 'STATO:0000149', 'description': 'Binomial logistic regression for analysis of dichotomous dependent variable (in this case, for having this particular condition/disease/outcome or not)'}, {'attribute_type_id': 'biolink:update_date', 'value': '2022-05-18'}, {'attribute_type_id': 'biolink:p_value', 'value': 0.0, 'description': 'The p-value represents the probability of observing the estimated coefficient (or more extreme value) under the assumption of the null hypothesis (which assumes that there is no relationship between the independent variable and outcome variable). The p-value associated with each coefficient helps determine whether the relationship between the independent variable and the outcome is statistically significant. A low p-value suggests that the observed relationship between the independent variable and the outcome is unlikely to occur by chance alone, providing evidence against the null hypothesis.'}, {'attribute_type_id': 'STATO:0000209', 'value': 0.8401321539277617, 'description': \"The AUROC provides a way to evaluate the model's ability to discriminate between the two classes (the presenece of absence of condition/disease/outcome). Values range between 0-1; the higher the AUROC, the better the model's ability to discriminate between clasess.\"}, {'attribute_type_id': 'biolink:log_odds_ratio', 'value': 8.796399245685702, 'description': 'The logarithm of the odds ratio (log odds ratio), or the ratio of the odds of event Y occurring in an exposed group versus the odds of event Y occurring in a non-exposed group.'}, {'attribute_type_id': 'biolink:supporting_study_cohort', 'value': 'age < 18 excluded'}, {'attribute_type_id': 'biolink:supporting_study_date_range', 'value': '2020-2022 (prediction)'}, {'attribute_type_id': 'biolink:supporting_study_size', 'value': 10096539, 'description': 'The total number of patients or participants within a sample population.'}]}, {'attribute_type_id': 'biolink:primary_knowledge_source', 'value': 'infores:biothings-multiomics-ehr-risk', 'value_type_id': 'biolink:InformationResource', 'value_url': 'http://smart-api.info/registry?q=d86a24f6027ffe778f84ba10a7a1861a', 'description': 'The EHR Risk KP is created and maintained by the Multiomics Provider team from the Institute for Systems Biology in Seattle, WA. Through a partnership with Providence/Swedish Health Services and Institute for Systems Biology, we analyze over 26 million EHRs. We use these records to train a large collection of interpretable machine learning models which are integrated into a single large Knowledge Graph, with directed edges pointing from risk factors to specific outcomes (diseases, phenotype, or medication exposure).'}, {'attribute_type_id': 'biolink:supporting_data_source', 'value': 'infores:providence-st-joseph-ehr', 'value_type_id': 'biolink:InformationResource', 'value_url': 'https://github.com/NCATSTranslator/Translator-All/wiki/EHR-Risk-KP', 'description': 'A partnership with Providence/Swedish Health Services and Institute for Systems Biology allows analysis of 26 million EHRs from patients in seven states in the US, including Alaska, California, Montana, Oregon, Washington, Texas, and New Mexico. 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Features include labs, medications, and phenotypes. Directed edges point from risk factors to specific outcomes (diseases, phenotype, or medication exposure).', 'attributes': [{'attribute_type_id': 'biolink:supporting_study_method_type', 'value': 'STATO:0000149', 'description': 'Binomial logistic regression for analysis of dichotomous dependent variable (in this case, for having this particular condition/disease/outcome or not)'}, {'attribute_type_id': 'biolink:update_date', 'value': '2022-05-18'}, {'attribute_type_id': 'biolink:p_value', 'value': 0.9998721067797812, 'description': 'The p-value represents the probability of observing the estimated coefficient (or more extreme value) under the assumption of the null hypothesis (which assumes that there is no relationship between the independent variable and outcome variable). The p-value associated with each coefficient helps determine whether the relationship between the independent variable and the outcome is statistically significant. A low p-value suggests that the observed relationship between the independent variable and the outcome is unlikely to occur by chance alone, providing evidence against the null hypothesis.'}, {'attribute_type_id': 'STATO:0000209', 'value': 0.8401321539277617, 'description': \"The AUROC provides a way to evaluate the model's ability to discriminate between the two classes (the presenece of absence of condition/disease/outcome). Values range between 0-1; the higher the AUROC, the better the model's ability to discriminate between clasess.\"}, {'attribute_type_id': 'biolink:log_odds_ratio', 'value': 8.585212287149526, 'description': 'The logarithm of the odds ratio (log odds ratio), or the ratio of the odds of event Y occurring in an exposed group versus the odds of event Y occurring in a non-exposed group.'}, {'attribute_type_id': 'biolink:supporting_study_cohort', 'value': 'age < 18 excluded'}, {'attribute_type_id': 'biolink:supporting_study_date_range', 'value': '2020-2022 (prediction)'}, {'attribute_type_id': 'biolink:supporting_study_size', 'value': 10100701, 'description': 'The total number of patients or participants within a sample population.'}]}, {'attribute_type_id': 'biolink:primary_knowledge_source', 'value': 'infores:biothings-multiomics-ehr-risk', 'value_type_id': 'biolink:InformationResource', 'value_url': 'http://smart-api.info/registry?q=d86a24f6027ffe778f84ba10a7a1861a', 'description': 'The EHR Risk KP is created and maintained by the Multiomics Provider team from the Institute for Systems Biology in Seattle, WA. Through a partnership with Providence/Swedish Health Services and Institute for Systems Biology, we analyze over 26 million EHRs. We use these records to train a large collection of interpretable machine learning models which are integrated into a single large Knowledge Graph, with directed edges pointing from risk factors to specific outcomes (diseases, phenotype, or medication exposure).'}, {'attribute_type_id': 'biolink:supporting_data_source', 'value': 'infores:providence-st-joseph-ehr', 'value_type_id': 'biolink:InformationResource', 'value_url': 'https://github.com/NCATSTranslator/Translator-All/wiki/EHR-Risk-KP', 'description': 'A partnership with Providence/Swedish Health Services and Institute for Systems Biology allows analysis of 26 million EHRs from patients in seven states in the US, including Alaska, California, Montana, Oregon, Washington, Texas, and New Mexico. Please email data-access@isbscience.org for more information.'}]}, 'object': {'HP': '0000360', 'id': 'HP:0000360', 'name': 'Tinnitus', 'type': 'biolink:PhenotypicFeature'}, 'source': {'edge_sources': [{'resource_id': 'infores:biothings-multiomics-ehr-risk', 'resource_role': 'primary_knowledge_source', 'upstream_resource_ids': 'infores:providence-st-joseph-ehr'}, {'resource_id': 'infores:providence-st-joseph-ehr', 'resource_role': 'supporting_data_source'}]}}, {'_id': 'UNII:25ADE2236L_HP:0000360_0.8401321539277617_09367666401584368_4558176672832635_10098743', 'subject': {'UNII': '25ADE2236L', 'id': 'UNII:25ADE2236L', 'name': 'thrombin', 'type': 'biolink:ChemicalSubstance'}, 'association': {'predicate': 'associated_with_increased_likelihood_of', 'edge_attributes': [{'attribute_type_id': 'biolink:has_supporting_study_result', 'value': 'We train a large collection of multivariable, binary logistic regression models on EHR data for each specific condition/disease/outcome. 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The p-value associated with each coefficient helps determine whether the relationship between the independent variable and the outcome is statistically significant. A low p-value suggests that the observed relationship between the independent variable and the outcome is unlikely to occur by chance alone, providing evidence against the null hypothesis.'}, {'attribute_type_id': 'STATO:0000209', 'value': 0.8401321539277617, 'description': \"The AUROC provides a way to evaluate the model's ability to discriminate between the two classes (the presenece of absence of condition/disease/outcome). 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The p-value associated with each coefficient helps determine whether the relationship between the independent variable and the outcome is statistically significant. A low p-value suggests that the observed relationship between the independent variable and the outcome is unlikely to occur by chance alone, providing evidence against the null hypothesis.'}, {'attribute_type_id': 'STATO:0000209', 'value': 0.8401321539277617, 'description': \"The AUROC provides a way to evaluate the model's ability to discriminate between the two classes (the presenece of absence of condition/disease/outcome). 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Through a partnership with Providence/Swedish Health Services and Institute for Systems Biology, we analyze over 26 million EHRs. We use these records to train a large collection of interpretable machine learning models which are integrated into a single large Knowledge Graph, with directed edges pointing from risk factors to specific outcomes (diseases, phenotype, or medication exposure).'}, {'attribute_type_id': 'biolink:supporting_data_source', 'value': 'infores:providence-st-joseph-ehr', 'value_type_id': 'biolink:InformationResource', 'value_url': 'https://github.com/NCATSTranslator/Translator-All/wiki/EHR-Risk-KP', 'description': 'A partnership with Providence/Swedish Health Services and Institute for Systems Biology allows analysis of 26 million EHRs from patients in seven states in the US, including Alaska, California, Montana, Oregon, Washington, Texas, and New Mexico. Please email data-access@isbscience.org for more information.'}]}, 'object': {'HP': '0000360', 'id': 'HP:0000360', 'name': 'Tinnitus', 'type': 'biolink:PhenotypicFeature'}, 'source': {'edge_sources': [{'resource_id': 'infores:biothings-multiomics-ehr-risk', 'resource_role': 'primary_knowledge_source', 'upstream_resource_ids': 'infores:providence-st-joseph-ehr'}, {'resource_id': 'infores:providence-st-joseph-ehr', 'resource_role': 'supporting_data_source'}]}}]\n" + ] + } + ], + "source": [ + "def main():\n", + " data_folder = \"../../data\" # uncomment for testing\n", + " parse_ehr_risk(data_folder) \n", + "\n", + " \n", + "if __name__ == \"__main__\":\n", + " main()\n", + "\n", + "# def f(): return list(parse_ehr_risk(data_folder))\n", + "\n", + "# print(f())" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "4f8e6295", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b391313d", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "a9131832", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "7d579a7c", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "3deaf666", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "38af4ce6", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "975b39b8", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "ee8cb830", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "e8da035e", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "36dbb201", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "ea4aaa3b", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1993c430", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5c1a5344", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "d2b7d630", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "87af529d", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "4d0a883a", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "855f14b3", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b9dd7dd4", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "dffef3dd", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "a1f1b174", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "14117bf5", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5b4f2f35", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "f620ac0c", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "f9f8ddcb", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "2c12970b", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "6075e928", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b885d179", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "0ad7fd3a", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "31661afb", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "33b5bdf8", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5f2de47d", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "fc5ba61b", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "dfbc4354", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "6ed22495", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "0005db9e", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "04e71223", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "76b3e63f", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "6399bef2", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "508fcd23", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "80e6c8da", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "81f51f0b", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "ddcf59bd", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "d2f7626b", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "43f24102", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "6b054438", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b600cab2", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "a26f5991", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "d19cabbf", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "ed293615", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "fcff8936", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "67cea542", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "4683b850", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "53da2865", + "metadata": {}, + "outputs": [], + "source": [ + "### from UI, we found duplicate predicate in June 6 2020 edges files" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "658cef8a", + "metadata": {}, + "outputs": [], + "source": [ + "edges_data.loc[(edges_data['subject'] == 'MONDO:0011849') & (edges_data['object'] == 'MONDO:0005083')]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "61b5337d", + "metadata": {}, + "outputs": [], + "source": [ + "edges_data.loc[(edges_data['subject'] == 'MONDO:0005083') & (edges_data['object'] == 'MONDO:0011849')]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "c149a94c", + "metadata": {}, + "outputs": [], + "source": [ + "https://github.com/uhbrar/ReasonerAPI/blob/update_guide/MigrationAndImplementationGuide1-4.md" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "ed91434c", + "metadata": {}, + "outputs": [], + "source": [ + "variable names to use for Clinical Data Committee:\n", + "log_odds_ratio, total_sample_size, log_odds_ratio_95_confidence_interval" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "cecd7f59", + "metadata": {}, + "outputs": [], + "source": [ + "# example 1.4 output from molepro\n", + "{\n", + " \t\"attribute_type_id\": \"biolink:aggregator_knowledge_source\",\t\n", + " \t\"value\": \"infores:molepro\", \n", + " \t\"value_type_id\": \"biolink:InformationResource\", \n", + " \t\"value_url\": \"https://translator.broadinstitute.org/molepro/trapi/v1.0\",\n", + " \t\"description\": \"The Molecular Data Provider KP from NCATS Translator\",\n", + " \t\"attribute_source\": \"infores:molepro\"\n", + " },\n", + "\t{\n", + " \t\"attribute_type_id\": \"biolink:aggregator_knowledge_source\",\n", + " \t\"value\": \"infores:chembl\",\n", + " \t\"value_type_id\": \"biolink:InformationResource\", \n", + " \t\"value_url\": \"https://www.ebi.ac.uk/chembl\",\n", + " \t\"description\": \"ChEMBL is a manually curated database of bioactive molecules...\",\n", + " \t\"attribute_source\": \"infores:molepro\"\n", + "\t},\n", + "\t{\n", + " \t\"attribute_type_id\": \"biolink:primary_knowledge_source\",\n", + " \t\"value\": \"infores:clinical-trials-gov\", \n", + " \t\"value_type_id\": \"biolink:InformationResource\", \n", + " \t\"value_url\": \"https://www.clinicaltrials.gov\",\n", + " \t\"description\": \"ClinicalTrials.gov is...\",\n", + " \t\"attribute_source\": \"infores:chembl\"\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "c3a5ca8d", + "metadata": {}, + "outputs": [], + "source": [ + "\"edges\": [\n", + " {\n", + " \"id\": \"Association002\", \n", + " \"category\": \"biolink:FeatureVariableAssociation\",\n", + " \"subject\": \"ncit:C29886\" # Airborne Particulate Matter (PM2.5), \t \n", + " \"predicate\": \"biolink:correlates_with\",\n", + " \"object\": \"tvfo:xxxxx\" # t.b.d. term for 'ED Visits for Asthma',\n", + " \"subject_modifier\": \"biolink:Exposure\",\n", + " \"attributes\": [\n", + "\t{\n", + " \t\"attribute_type_id\": \"biolink:primary_knowledge_source\", \n", + " \t\"value\": \"infores:icees-asthma\", \n", + " \t\"value_type_id\": \"biolink:InformationResource\",\t \n", + " \t\"value_url\": \"https://icees.renci.org:16339\",\n", + " \t\"description\": \"The ICEES Provider ...\",\n", + " \t\"attribute_source\": \"infores:icees-asthma\"\n", + "\t},\n", + "\t{\n", + " \t\"attribute_type_id\": \"biolink:supporting_data_source\", \n", + " \t\"value\": \"infores:us-epa-airborne-pollutant-exposures-data\",\n", + " \t\"value_type_id\": \"biolink:InformationResource\",\t \n", + " \t\"description\": \"US Environmental Protection Agency Airborne Pollutant Exposure Data\",\n", + " \t\"attribute_source\": \"infores:icees-asthma\"\n", + "\t},\n", + "\t{\n", + " \t\"attribute_type_id\": \"biolink:supporting_data_source\", \n", + " \t\"value\": \"infores:unc-cdw-health\",\n", + " \t\"value_type_id\": \"biolink:InformationResource\",\t \n", + " \t\"description\": \"UNC Carolina Data Warehouse for Health Patient EHR Data\",\n", + " \t\"attribute_source\": \"infores:icees-asthma\"\n", + "\t}\n", + " ]\n", + " }\n", + "]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "df78b8ff", + "metadata": {}, + "outputs": [], + "source": [ + "edges_sig[\"num_patients_with_condition\"] = 10**(edges_sig['log_positive_patient_count'])\n", + "edges_sig[\"num_patients_without_condition\"] = 10**(edges_sig['log_negative_patient_count'])\n", + "edges_sig" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.7.6" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} From 2430d242cf27e927a40e26d6cab3d68539da1ced Mon Sep 17 00:00:00 2001 From: GitHubbit <10294502+GitHubbit@users.noreply.github.com> Date: Fri, 2 Jun 2023 12:50:58 -0400 Subject: [PATCH 4/6] Now matching functional TRAPI 1.3 version EXACTLY --- ehr_risk_kp.yaml | 11780 +++++++++++++++++++-------------------------- 1 file changed, 4831 insertions(+), 6949 deletions(-) diff --git a/ehr_risk_kp.yaml b/ehr_risk_kp.yaml index dd3e362..c379d72 100644 --- a/ehr_risk_kp.yaml +++ b/ehr_risk_kp.yaml @@ -3,7 +3,6 @@ info: contact: email: knarsinh@systemsbiology.org name: Kamileh Narsinh - x-id: https://github.com/GitHubbit x-role: responsible developer description: >- Documentation of the BioThings API for Translator Multiomics Team's @@ -26,19 +25,14 @@ servers: url: http://biothings.ncats.io/multiomics_ehr_risk_kp x-maturity: production tags: -- name: multiomics -- name: clinical -- name: ehr -- name: risk - name: disease - name: chemical - name: phenotype - name: procedure - name: association -- name: regression +- name: query - name: translator - name: biothings -- name: bte paths: "/association/{id}": get: @@ -310,372 +304,209 @@ paths: # summary: Make batch gene queries and return matching gene hits tags: - query - ## (122 operations based on TSV) + ## 74 sets (148 operations) ## not included: - ## - ChemCHEBI_decreased_DiseaseMONDO - ## - ChemCHEBI_decreased_DiseaseNCIT - ## - ChemCHEBI_decreased_DiseaseSNOMEDCT - ## - ChemCHEBI_decreased_PhenoHP - ## - ChemCHEBI_decreased_PhenoNCIT - ## - ChemCHEBI_decreased_PhenoSNOMEDCT - ## - ChemCHEBI_decreased_ProcedureNCIT - ## - ChemCHEBI_increased_DiseaseMONDO - ## - ChemCHEBI_increased_DiseaseNCIT - ## - ChemCHEBI_increased_DiseaseSNOMEDCT - ## - ChemCHEBI_increased_PhenoHP - ## - ChemCHEBI_increased_PhenoNCIT - ## - ChemCHEBI_increased_PhenoSNOMEDCT - ## - ChemCHEBI_increased_ProcedureNCIT - ## - ChemUNII_decreased_DiseaseMONDO - ## - ChemUNII_decreased_DiseaseNCIT - ## - ChemUNII_decreased_DiseaseSNOMEDCT - ## - ChemUNII_decreased_PhenoHP - ## - ChemUNII_decreased_PhenoNCIT - ## - ChemUNII_decreased_PhenoSNOMEDCT - ## - ChemUNII_decreased_ProcedureNCIT - ## - ChemUNII_increased_DiseaseMONDO - ## - ChemUNII_increased_DiseaseNCIT - ## - ChemUNII_increased_DiseaseSNOMEDCT - ## - ChemUNII_increased_PhenoHP - ## - ChemUNII_increased_PhenoNCIT - ## - ChemUNII_increased_PhenoSNOMEDCT - ## - ChemUNII_increased_ProcedureNCIT - ## - DiseaseMONDO_decreased_DiseaseMONDO - ## - DiseaseMONDO_decreased_DiseaseNCIT - ## - DiseaseMONDO_decreased_DiseaseSNOMEDCT - ## - DiseaseMONDO_decreased_PhenoHP - ## - DiseaseMONDO_decreased_PhenoNCIT - ## - DiseaseMONDO_decreased_PhenoSNOMEDCT - ## - DiseaseMONDO_decreased_ProcedureNCIT - ## - DiseaseMONDO_increased_DiseaseMONDO - ## - DiseaseMONDO_increased_DiseaseNCIT - ## - DiseaseMONDO_increased_DiseaseSNOMEDCT - ## - DiseaseMONDO_increased_PhenoHP - ## - DiseaseMONDO_increased_PhenoNCIT - ## - DiseaseMONDO_increased_PhenoSNOMEDCT - ## - DiseaseMONDO_increased_ProcedureNCIT - ## - DiseaseNCIT_decreased_DiseaseMONDO - ## - DiseaseNCIT_decreased_DiseaseSNOMEDCT - ## - DiseaseNCIT_decreased_PhenoHP - ## - DiseaseNCIT_decreased_PhenoNCIT - ## - DiseaseNCIT_decreased_ProcedureNCIT - ## - DiseaseNCIT_increased_DiseaseMONDO + ## - DiseaseNCIT_increased_DiseaseNCIT ## - DiseaseNCIT_increased_DiseaseSNOMEDCT + ## - DiseaseSNOMEDCT_increased_DiseaseMONDO + ## - DiseaseSNOMEDCT_increased_DiseaseNCIT + ## - DiseaseSNOMEDCT_increased_DiseaseSNOMEDCT ## - DiseaseNCIT_increased_PhenoHP ## - DiseaseNCIT_increased_PhenoNCIT ## - DiseaseNCIT_increased_PhenoSNOMEDCT - ## - DiseaseSNOMEDCT_decreased_DiseaseMONDO + ## - DiseaseSNOMEDCT_increased_PhenoNCIT + ## - DiseaseSNOMEDCT_increased_PhenoSNOMEDCT + ## - DiseaseNCIT_increased_ProcedureNCIT + ## - DiseaseSNOMEDCT_increased_ProcedureNCIT + ## - DiseaseNCIT_decreased_DiseaseMONDO + ## - DiseaseNCIT_decreased_DiseaseNCIT + ## - DiseaseNCIT_decreased_DiseaseSNOMEDCT ## - DiseaseSNOMEDCT_decreased_DiseaseNCIT ## - DiseaseSNOMEDCT_decreased_DiseaseSNOMEDCT - ## - DiseaseSNOMEDCT_decreased_PhenoHP + ## - DiseaseMONDO_decreased_PhenoSNOMEDCT + ## - DiseaseNCIT_decreased_PhenoHP + ## - DiseaseNCIT_decreased_PhenoNCIT + ## - DiseaseNCIT_decreased_PhenoSNOMEDCT ## - DiseaseSNOMEDCT_decreased_PhenoNCIT ## - DiseaseSNOMEDCT_decreased_PhenoSNOMEDCT + ## - DiseaseNCIT_decreased_ProcedureNCIT ## - DiseaseSNOMEDCT_decreased_ProcedureNCIT - ## - DiseaseSNOMEDCT_increased_DiseaseMONDO - ## - DiseaseSNOMEDCT_increased_DiseaseNCIT - ## - DiseaseSNOMEDCT_increased_DiseaseSNOMEDCT - ## - DiseaseSNOMEDCT_increased_PhenoHP - ## - DiseaseSNOMEDCT_increased_PhenoNCIT - ## - DiseaseSNOMEDCT_increased_PhenoSNOMEDCT - ## - DiseaseSNOMEDCT_increased_ProcedureNCIT - ## - PhenoHP_decreased_DiseaseMONDO - ## - PhenoHP_decreased_DiseaseNCIT - ## - PhenoHP_decreased_DiseaseSNOMEDCT - ## - PhenoHP_decreased_PhenoHP - ## - PhenoHP_decreased_PhenoNCIT - ## - PhenoHP_decreased_PhenoSNOMEDCT - ## - PhenoHP_decreased_ProcedureNCIT - ## - PhenoHP_increased_DiseaseMONDO - ## - PhenoHP_increased_DiseaseNCIT - ## - PhenoHP_increased_DiseaseSNOMEDCT - ## - PhenoHP_increased_PhenoHP - ## - PhenoHP_increased_PhenoNCIT - ## - PhenoHP_increased_PhenoSNOMEDCT - ## - PhenoHP_increased_ProcedureNCIT - ## - PhenoNCIT_decreased_DiseaseMONDO - ## - PhenoNCIT_decreased_DiseaseNCIT - ## - PhenoNCIT_decreased_DiseaseSNOMEDCT - ## - PhenoNCIT_decreased_PhenoHP - ## - PhenoNCIT_decreased_PhenoNCIT - ## - PhenoNCIT_decreased_PhenoSNOMEDCT - ## - PhenoNCIT_decreased_ProcedureNCIT - ## - PhenoNCIT_increased_DiseaseMONDO ## - PhenoNCIT_increased_DiseaseNCIT ## - PhenoNCIT_increased_DiseaseSNOMEDCT - ## - PhenoNCIT_increased_PhenoHP + ## - PhenoSNOMEDCT_increased_DiseaseNCIT ## - PhenoNCIT_increased_PhenoNCIT ## - PhenoNCIT_increased_PhenoSNOMEDCT + ## - PhenoSNOMEDCT_increased_PhenoNCIT + ## - PhenoSNOMEDCT_increased_PhenoSNOMEDCT ## - PhenoNCIT_increased_ProcedureNCIT - ## - PhenoSNOMEDCT_decreased_DiseaseMONDO + ## - PhenoSNOMEDCT_increased_ProcedureNCIT + ## - PhenoNCIT_decreased_DiseaseNCIT ## - PhenoSNOMEDCT_decreased_DiseaseNCIT - ## - PhenoSNOMEDCT_decreased_DiseaseSNOMEDCT - ## - PhenoSNOMEDCT_decreased_PhenoHP + ## - PhenoNCIT_decreased_PhenoSNOMEDCT ## - PhenoSNOMEDCT_decreased_PhenoNCIT ## - PhenoSNOMEDCT_decreased_PhenoSNOMEDCT + ## - PhenoNCIT_decreased_ProcedureNCIT ## - PhenoSNOMEDCT_decreased_ProcedureNCIT - ## - PhenoSNOMEDCT_increased_DiseaseMONDO - ## - PhenoSNOMEDCT_increased_DiseaseNCIT - ## - PhenoSNOMEDCT_increased_DiseaseSNOMEDCT - ## - PhenoSNOMEDCT_increased_PhenoHP - ## - PhenoSNOMEDCT_increased_PhenoNCIT - ## - PhenoSNOMEDCT_increased_ProcedureNCIT - ## - ProcedureNCIT_decreased_DiseaseMONDO - ## - ProcedureNCIT_decreased_DiseaseNCIT - ## - ProcedureNCIT_decreased_DiseaseSNOMEDCT - ## - ProcedureNCIT_decreased_PhenoHP - ## - ProcedureNCIT_decreased_PhenoNCIT - ## - ProcedureNCIT_decreased_PhenoSNOMEDCT - ## - ProcedureNCIT_decreased_ProcedureNCIT - ## - ProcedureNCIT_increased_DiseaseMONDO ## - ProcedureNCIT_increased_DiseaseNCIT - ## - ProcedureNCIT_increased_DiseaseSNOMEDCT - ## - ProcedureNCIT_increased_PhenoHP + ## - ChemUNII_increased_PhenoSNOMEDCT ## - ProcedureNCIT_increased_PhenoNCIT ## - ProcedureNCIT_increased_PhenoSNOMEDCT ## - ProcedureNCIT_increased_ProcedureNCIT + ## - ChemUNII_decreased_DiseaseNCIT + ## - ProcedureNCIT_decreased_DiseaseNCIT + ## - ChemUNII_decreased_PhenoSNOMEDCT + ## - ProcedureNCIT_decreased_PhenoSNOMEDCT + ## - ChemUNII_decreased_ProcedureNCIT + ## - ProcedureNCIT_decreased_ProcedureNCIT x-bte-kgs-operations: - - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_DiseaseMONDO' - - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_DiseaseNCIT' - - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_DiseaseSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_PhenoHP' - - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_PhenoNCIT' - - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_PhenoSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_ProcedureNCIT' - - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_increased_DiseaseMONDO' - - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_increased_DiseaseNCIT' - - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_increased_DiseaseSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_increased_PhenoHP' - - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_increased_PhenoNCIT' - - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_increased_PhenoSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_increased_ProcedureNCIT' - - $ref: '#/components/x-bte-kgs-operations/ChemUNII_decreased_DiseaseMONDO' - - $ref: '#/components/x-bte-kgs-operations/ChemUNII_decreased_DiseaseNCIT' - - $ref: '#/components/x-bte-kgs-operations/ChemUNII_decreased_DiseaseSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/ChemUNII_decreased_PhenoHP' - - $ref: '#/components/x-bte-kgs-operations/ChemUNII_decreased_PhenoNCIT' - - $ref: '#/components/x-bte-kgs-operations/ChemUNII_decreased_PhenoSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/ChemUNII_decreased_ProcedureNCIT' - - $ref: '#/components/x-bte-kgs-operations/ChemUNII_increased_DiseaseMONDO' - - $ref: '#/components/x-bte-kgs-operations/ChemUNII_increased_DiseaseNCIT' - - $ref: '#/components/x-bte-kgs-operations/ChemUNII_increased_DiseaseSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/ChemUNII_increased_PhenoHP' - - $ref: '#/components/x-bte-kgs-operations/ChemUNII_increased_PhenoNCIT' - - $ref: '#/components/x-bte-kgs-operations/ChemUNII_increased_PhenoSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/ChemUNII_increased_ProcedureNCIT' - - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_DiseaseMONDO' - - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_DiseaseNCIT' - - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_DiseaseSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_PhenoHP' - - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_PhenoNCIT' - - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_PhenoSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_ProcedureNCIT' - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_increased_DiseaseMONDO' + - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_increased_DiseaseMONDO-rev' - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_increased_DiseaseNCIT' + - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_increased_DiseaseNCIT-rev' - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_increased_DiseaseSNOMEDCT' + - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_increased_DiseaseSNOMEDCT-rev' + - $ref: '#/components/x-bte-kgs-operations/DiseaseNCIT_increased_DiseaseMONDO' + - $ref: '#/components/x-bte-kgs-operations/DiseaseNCIT_increased_DiseaseMONDO-rev' - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_increased_PhenoHP' + - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_increased_PhenoHP-rev' - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_increased_PhenoNCIT' + - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_increased_PhenoNCIT-rev' - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_increased_PhenoSNOMEDCT' + - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_increased_PhenoSNOMEDCT-rev' + - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_increased_PhenoHP' + - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_increased_PhenoHP-rev' - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_increased_ProcedureNCIT' - - $ref: '#/components/x-bte-kgs-operations/DiseaseNCIT_decreased_DiseaseMONDO' - - $ref: '#/components/x-bte-kgs-operations/DiseaseNCIT_decreased_DiseaseSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/DiseaseNCIT_decreased_PhenoHP' - - $ref: '#/components/x-bte-kgs-operations/DiseaseNCIT_decreased_PhenoNCIT' - - $ref: '#/components/x-bte-kgs-operations/DiseaseNCIT_decreased_ProcedureNCIT' - - $ref: '#/components/x-bte-kgs-operations/DiseaseNCIT_increased_DiseaseMONDO' - - $ref: '#/components/x-bte-kgs-operations/DiseaseNCIT_increased_DiseaseSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/DiseaseNCIT_increased_PhenoHP' - - $ref: '#/components/x-bte-kgs-operations/DiseaseNCIT_increased_PhenoNCIT' - - $ref: '#/components/x-bte-kgs-operations/DiseaseNCIT_increased_PhenoSNOMEDCT' + - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_increased_ProcedureNCIT-rev' + - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_DiseaseMONDO' + - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_DiseaseMONDO-rev' + - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_DiseaseNCIT' + - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_DiseaseNCIT-rev' + - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_DiseaseSNOMEDCT' + - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_DiseaseSNOMEDCT-rev' - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_decreased_DiseaseMONDO' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_decreased_DiseaseNCIT' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_decreased_DiseaseSNOMEDCT' + - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_decreased_DiseaseMONDO-rev' + - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_PhenoHP' + - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_PhenoHP-rev' + - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_PhenoNCIT' + - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_PhenoNCIT-rev' - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_decreased_PhenoHP' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_decreased_PhenoNCIT' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_decreased_PhenoSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_decreased_ProcedureNCIT' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_increased_DiseaseMONDO' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_increased_DiseaseNCIT' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_increased_DiseaseSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_increased_PhenoHP' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_increased_PhenoNCIT' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_increased_PhenoSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_increased_ProcedureNCIT' - - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_DiseaseMONDO' - - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_DiseaseNCIT' - - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_DiseaseSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_PhenoHP' - - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_PhenoNCIT' - - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_PhenoSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_ProcedureNCIT' + - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_decreased_PhenoHP-rev' + - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_ProcedureNCIT' + - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_ProcedureNCIT-rev' - $ref: '#/components/x-bte-kgs-operations/PhenoHP_increased_DiseaseMONDO' + - $ref: '#/components/x-bte-kgs-operations/PhenoHP_increased_DiseaseMONDO-rev' - $ref: '#/components/x-bte-kgs-operations/PhenoHP_increased_DiseaseNCIT' + - $ref: '#/components/x-bte-kgs-operations/PhenoHP_increased_DiseaseNCIT-rev' - $ref: '#/components/x-bte-kgs-operations/PhenoHP_increased_DiseaseSNOMEDCT' + - $ref: '#/components/x-bte-kgs-operations/PhenoHP_increased_DiseaseSNOMEDCT-rev' + - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_increased_DiseaseMONDO' + - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_increased_DiseaseMONDO-rev' + - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_increased_DiseaseMONDO' + - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_increased_DiseaseMONDO-rev' + - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_increased_DiseaseSNOMEDCT' + - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_increased_DiseaseSNOMEDCT-rev' - $ref: '#/components/x-bte-kgs-operations/PhenoHP_increased_PhenoHP' + - $ref: '#/components/x-bte-kgs-operations/PhenoHP_increased_PhenoHP-rev' - $ref: '#/components/x-bte-kgs-operations/PhenoHP_increased_PhenoNCIT' + - $ref: '#/components/x-bte-kgs-operations/PhenoHP_increased_PhenoNCIT-rev' - $ref: '#/components/x-bte-kgs-operations/PhenoHP_increased_PhenoSNOMEDCT' + - $ref: '#/components/x-bte-kgs-operations/PhenoHP_increased_PhenoSNOMEDCT-rev' + - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_increased_PhenoHP' + - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_increased_PhenoHP-rev' + - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_increased_PhenoHP' + - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_increased_PhenoHP-rev' - $ref: '#/components/x-bte-kgs-operations/PhenoHP_increased_ProcedureNCIT' + - $ref: '#/components/x-bte-kgs-operations/PhenoHP_increased_ProcedureNCIT-rev' + - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_DiseaseMONDO' + - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_DiseaseMONDO-rev' + - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_DiseaseNCIT' + - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_DiseaseNCIT-rev' + - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_DiseaseSNOMEDCT' + - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_DiseaseSNOMEDCT-rev' - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_decreased_DiseaseMONDO' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_decreased_DiseaseNCIT' + - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_decreased_DiseaseMONDO-rev' - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_decreased_DiseaseSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_decreased_PhenoHP' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_decreased_PhenoNCIT' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_decreased_PhenoSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_decreased_ProcedureNCIT' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_increased_DiseaseMONDO' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_increased_DiseaseNCIT' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_increased_DiseaseSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_increased_PhenoHP' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_increased_PhenoNCIT' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_increased_PhenoSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_increased_ProcedureNCIT' + - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_decreased_DiseaseSNOMEDCT-rev' - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_decreased_DiseaseMONDO' - - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_decreased_DiseaseNCIT' + - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_decreased_DiseaseMONDO-rev' - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_decreased_DiseaseSNOMEDCT' + - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_decreased_DiseaseSNOMEDCT-rev' + - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_PhenoHP' + - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_PhenoHP-rev' + - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_PhenoNCIT' + - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_PhenoNCIT-rev' + - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_PhenoSNOMEDCT' + - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_PhenoSNOMEDCT-rev' + - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_decreased_PhenoHP' + - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_decreased_PhenoHP-rev' + - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_decreased_PhenoNCIT' + - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_decreased_PhenoNCIT-rev' - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_decreased_PhenoHP' - - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_decreased_PhenoNCIT' - - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_decreased_PhenoSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_decreased_ProcedureNCIT' - - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_increased_DiseaseMONDO' - - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_increased_DiseaseNCIT' - - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_increased_DiseaseSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_increased_PhenoHP' - - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_increased_PhenoNCIT' - - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_increased_ProcedureNCIT' - - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_decreased_DiseaseMONDO' - - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_decreased_DiseaseNCIT' - - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_decreased_DiseaseSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_decreased_PhenoHP' - - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_decreased_PhenoNCIT' - - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_decreased_PhenoSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_decreased_ProcedureNCIT' - - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_increased_DiseaseMONDO' - - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_increased_DiseaseNCIT' - - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_increased_DiseaseSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_increased_PhenoHP' - - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_increased_PhenoNCIT' - - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_increased_PhenoSNOMEDCT' - - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_increased_ProcedureNCIT' - - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_DiseaseMONDO-rev' - - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_DiseaseNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_DiseaseSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_PhenoHP-rev' - - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_PhenoNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_PhenoSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_ProcedureNCIT-rev' + - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_decreased_PhenoHP-rev' + - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_ProcedureNCIT' + - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_ProcedureNCIT-rev' + - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_increased_DiseaseMONDO' - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_increased_DiseaseMONDO-rev' + - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_increased_DiseaseNCIT' - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_increased_DiseaseNCIT-rev' + - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_increased_DiseaseSNOMEDCT' - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_increased_DiseaseSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_increased_PhenoHP-rev' - - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_increased_PhenoNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_increased_PhenoSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_increased_ProcedureNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/ChemUNII_decreased_DiseaseMONDO-rev' - - $ref: '#/components/x-bte-kgs-operations/ChemUNII_decreased_DiseaseNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/ChemUNII_decreased_DiseaseSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/ChemUNII_decreased_PhenoHP-rev' - - $ref: '#/components/x-bte-kgs-operations/ChemUNII_decreased_PhenoNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/ChemUNII_decreased_PhenoSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/ChemUNII_decreased_ProcedureNCIT-rev' + - $ref: '#/components/x-bte-kgs-operations/ChemUNII_increased_DiseaseMONDO' - $ref: '#/components/x-bte-kgs-operations/ChemUNII_increased_DiseaseMONDO-rev' + - $ref: '#/components/x-bte-kgs-operations/ChemUNII_increased_DiseaseNCIT' - $ref: '#/components/x-bte-kgs-operations/ChemUNII_increased_DiseaseNCIT-rev' + - $ref: '#/components/x-bte-kgs-operations/ChemUNII_increased_DiseaseSNOMEDCT' - $ref: '#/components/x-bte-kgs-operations/ChemUNII_increased_DiseaseSNOMEDCT-rev' + - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_increased_DiseaseMONDO' + - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_increased_DiseaseMONDO-rev' + - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_increased_DiseaseSNOMEDCT' + - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_increased_DiseaseSNOMEDCT-rev' + - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_increased_PhenoHP' + - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_increased_PhenoHP-rev' + - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_increased_PhenoNCIT' + - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_increased_PhenoNCIT-rev' + - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_increased_PhenoSNOMEDCT' + - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_increased_PhenoSNOMEDCT-rev' + - $ref: '#/components/x-bte-kgs-operations/ChemUNII_increased_PhenoHP' - $ref: '#/components/x-bte-kgs-operations/ChemUNII_increased_PhenoHP-rev' + - $ref: '#/components/x-bte-kgs-operations/ChemUNII_increased_PhenoNCIT' - $ref: '#/components/x-bte-kgs-operations/ChemUNII_increased_PhenoNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/ChemUNII_increased_PhenoSNOMEDCT-rev' + - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_increased_PhenoHP' + - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_increased_PhenoHP-rev' + - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_increased_ProcedureNCIT' + - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_increased_ProcedureNCIT-rev' + - $ref: '#/components/x-bte-kgs-operations/ChemUNII_increased_ProcedureNCIT' - $ref: '#/components/x-bte-kgs-operations/ChemUNII_increased_ProcedureNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_DiseaseMONDO-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_DiseaseNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_DiseaseSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_PhenoHP-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_PhenoNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_PhenoSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_decreased_ProcedureNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_increased_DiseaseMONDO-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_increased_DiseaseNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_increased_DiseaseSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_increased_PhenoHP-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_increased_PhenoNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_increased_PhenoSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseMONDO_increased_ProcedureNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseNCIT_decreased_DiseaseMONDO-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseNCIT_decreased_DiseaseSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseNCIT_decreased_PhenoHP-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseNCIT_decreased_PhenoNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseNCIT_decreased_ProcedureNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseNCIT_increased_DiseaseMONDO-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseNCIT_increased_DiseaseSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseNCIT_increased_PhenoHP-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseNCIT_increased_PhenoNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseNCIT_increased_PhenoSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_decreased_DiseaseMONDO-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_decreased_DiseaseNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_decreased_DiseaseSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_decreased_PhenoHP-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_decreased_PhenoNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_decreased_PhenoSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_decreased_ProcedureNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_increased_DiseaseMONDO-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_increased_DiseaseNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_increased_DiseaseSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_increased_PhenoHP-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_increased_PhenoNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_increased_PhenoSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/DiseaseSNOMEDCT_increased_ProcedureNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_DiseaseMONDO-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_DiseaseNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_DiseaseSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_PhenoHP-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_PhenoNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_PhenoSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoHP_decreased_ProcedureNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoHP_increased_DiseaseMONDO-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoHP_increased_DiseaseNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoHP_increased_DiseaseSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoHP_increased_PhenoHP-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoHP_increased_PhenoNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoHP_increased_PhenoSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoHP_increased_ProcedureNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_decreased_DiseaseMONDO-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_decreased_DiseaseNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_decreased_DiseaseSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_decreased_PhenoHP-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_decreased_PhenoNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_decreased_PhenoSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_decreased_ProcedureNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_increased_DiseaseMONDO-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_increased_DiseaseNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_increased_DiseaseSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_increased_PhenoHP-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_increased_PhenoNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_increased_PhenoSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoNCIT_increased_ProcedureNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_decreased_DiseaseMONDO-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_decreased_DiseaseNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_decreased_DiseaseSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_decreased_PhenoHP-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_decreased_PhenoNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_decreased_PhenoSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_decreased_ProcedureNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_increased_DiseaseMONDO-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_increased_DiseaseNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_increased_DiseaseSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_increased_PhenoHP-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_increased_PhenoNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/PhenoSNOMEDCT_increased_ProcedureNCIT-rev' + - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_DiseaseMONDO' + - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_DiseaseMONDO-rev' + - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_DiseaseNCIT' + - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_DiseaseNCIT-rev' + - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_DiseaseSNOMEDCT' + - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_DiseaseSNOMEDCT-rev' + - $ref: '#/components/x-bte-kgs-operations/ChemUNII_decreased_DiseaseMONDO' + - $ref: '#/components/x-bte-kgs-operations/ChemUNII_decreased_DiseaseMONDO-rev' + - $ref: '#/components/x-bte-kgs-operations/ChemUNII_decreased_DiseaseSNOMEDCT' + - $ref: '#/components/x-bte-kgs-operations/ChemUNII_decreased_DiseaseSNOMEDCT-rev' + - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_decreased_DiseaseMONDO' - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_decreased_DiseaseMONDO-rev' - - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_decreased_DiseaseNCIT-rev' + - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_decreased_DiseaseSNOMEDCT' - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_decreased_DiseaseSNOMEDCT-rev' + - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_PhenoHP' + - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_PhenoHP-rev' + - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_PhenoNCIT' + - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_PhenoNCIT-rev' + - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_PhenoSNOMEDCT' + - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_PhenoSNOMEDCT-rev' + - $ref: '#/components/x-bte-kgs-operations/ChemUNII_decreased_PhenoHP' + - $ref: '#/components/x-bte-kgs-operations/ChemUNII_decreased_PhenoHP-rev' + - $ref: '#/components/x-bte-kgs-operations/ChemUNII_decreased_PhenoNCIT' + - $ref: '#/components/x-bte-kgs-operations/ChemUNII_decreased_PhenoNCIT-rev' + - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_decreased_PhenoHP' - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_decreased_PhenoHP-rev' + - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_decreased_PhenoNCIT' - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_decreased_PhenoNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_decreased_PhenoSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_decreased_ProcedureNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_increased_DiseaseMONDO-rev' - - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_increased_DiseaseNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_increased_DiseaseSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_increased_PhenoHP-rev' - - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_increased_PhenoNCIT-rev' - - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_increased_PhenoSNOMEDCT-rev' - - $ref: '#/components/x-bte-kgs-operations/ProcedureNCIT_increased_ProcedureNCIT-rev' + - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_ProcedureNCIT' + - $ref: '#/components/x-bte-kgs-operations/ChemCHEBI_decreased_ProcedureNCIT-rev' components: parameters: callback: @@ -689,7 +520,7 @@ components: dotfield: name: dotfield description: >- - Optional, can be used to control the format of the returned chemical object. + Optional, can be used to control the format of the returned object. If "dotfield" is true, the returned data object is returned flattened (no nested objects) using dotfield notation for key names. Default: false. in: query @@ -746,7 +577,7 @@ components: fields: name: fields description: >- - Optional, can be a comma-separated list to limit the fields returned from the chemical object. + Optional, can be a comma-separated list to limit the fields returned from the object. If "fields=all", all available fields will be returned. @@ -761,7 +592,7 @@ components: from: name: from description: >- - Optional, the number of matching chemical hits to skip, starting from 0. Default: 0. + Optional, the number of matching hits to skip, starting from 0. Default: 0. in: query required: false schema: @@ -784,7 +615,7 @@ components: size: name: size description: >- - Optional, the maximum number of matching chemical hits to return (with a cap of 1000 at the moment). Default: 10. + Optional, the maximum number of matching hits to return (with a cap of 1000 at the moment). Default: 10. The combination of "size" and "from" parameters can be used to get paging for a large query. in: query required: false @@ -964,6853 +795,4904 @@ components: ## - association.classifier ## - association.original_predicate ## - association.provided_date - ChemCHEBI_decreased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 34917 records - -supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "CHEBI:3732" ## clarithromycin - # oneOutput: "MONDO:0004721" ## liver neoplasm - ChemCHEBI_decreased_DiseaseMONDO_rev: - -supportBatch: true - useTemplating: true - inputs: + DiseaseMONDO_increased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 2963 records + - supportBatch: true + useTemplating: true ## flag to say templating is being used below + inputs: - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: CHEBI - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-CHEBI" - # testExamples: - # - qInput: "MONDO:0005090" ## schizophrenia (disease) - # oneOutput: "CHEBI:107736" ## metoclopramide - ChemCHEBI_decreased_DiseaseNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## 212 records - -supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "CHEBI:7936" ## paroxetine - # oneOutput: "NCIT:C167118" ## Influenza A Virus Positive - ChemCHEBI_decreased_DiseaseNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: CHEBI - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-CHEBI" - # testExamples: - # - qInput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission - # oneOutput: "CHEBI:3139" ## bleomycin - ChemCHEBI_decreased_DiseaseSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 2917 records - -supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "CHEBI:9332" ## sulfamethoxazole - # oneOutput: "SNOMEDCT:386033004" ## Neuropathy (disorder) - ChemCHEBI_decreased_DiseaseSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: CHEBI - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-CHEBI" - # testExamples: - # - qInput: "SNOMEDCT:2415007" ## Lumbosacral radiculopathy (disorder) - # oneOutput: "CHEBI:4786" ## enalaprilat - ChemCHEBI_decreased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 24505 records - -supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "CHEBI:9123" ## sertraline - # oneOutput: "HP:0031890" ## Increased urine urobilinogen - ChemCHEBI_decreased_PhenoHP_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: CHEBI - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-CHEBI" - # testExamples: - # - qInput: "HP:0000964" ## Eczema - # oneOutput: "CHEBI:41423" ## celecoxib - ChemCHEBI_decreased_PhenoNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 2254 records - -supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "CHEBI:3614" ## chlorhexidine - # oneOutput: "NCIT:C155871" ## Herpes Simplex Virus Infection - ChemCHEBI_decreased_PhenoNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "MONDO:0005068" ## myocardial infarction (disease) + # oneOutput: "MONDO:0005904" ## pericarditis (disease) + DiseaseMONDO_increased_DiseaseMONDO-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: MONDO + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-MONDO" + # testExamples: + # - qInput: "MONDO:0005009" ## congestive heart failure + # oneOutput: "MONDO:0005071" ## nervous system disorder + DiseaseMONDO_increased_DiseaseNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ## 9 records + - supportBatch: true + useTemplating: true + inputs: + - id: MONDO + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: CHEBI - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-CHEBI" - # testExamples: - # - qInput: "NCIT:C141278" ## Adenovirus Positive - # oneOutput: "CHEBI:8435" ## prochlorperazine - ChemCHEBI_decreased_PhenoSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ## 244 records - -supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "CHEBI:85264" ## clavulanate - # oneOutput: "SNOMEDCT:191519005" ## Dementia associated with another disease (disorder) - ChemCHEBI_decreased_PhenoSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: CHEBI - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-CHEBI" - # testExamples: - # - qInput: "SNOMEDCT:127295002" ## Traumatic brain injury (disorder) - # oneOutput: "CHEBI:31440" ## copper sulfate - ChemCHEBI_decreased_ProcedureNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT - ## 222 records - -supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "CHEBI:8884" ## rocuronium - # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - ChemCHEBI_decreased_ProcedureNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "MONDO:0005300" ## chronic kidney disease + # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + DiseaseMONDO_increased_DiseaseNCIT-rev: + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: CHEBI - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-CHEBI" - # testExamples: - # - qInput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission - # oneOutput: "CHEBI:9449" ## terbutaline - ChemCHEBI_increased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 18248 records - -supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "CHEBI:31441" ## fluticasone - # oneOutput: "MONDO:0009410" ## Addison disease - ChemCHEBI_increased_DiseaseMONDO_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: CHEBI - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-CHEBI" - # testExamples: - # - qInput: "MONDO:0008315" ## prostate cancer - # oneOutput: "CHEBI:47426" ## furosemide - ChemCHEBI_increased_DiseaseNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## 131 records - -supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "CHEBI:9449" ## terbutaline - # oneOutput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission - ChemCHEBI_increased_DiseaseNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: CHEBI - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-CHEBI" - # testExamples: - # - qInput: "NCIT:C159516" ## Liver Lesion - # oneOutput: "CHEBI:9943" ## venlafaxine - ChemCHEBI_increased_DiseaseSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 1542 records - -supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "CHEBI:46632" ## clonidine - # oneOutput: "SNOMEDCT:197352008" ## Toxic hepatitis (disorder) - ChemCHEBI_increased_DiseaseSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-MONDO" + # testExamples: + # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + # oneOutput: "MONDO:0005148" ## type 2 diabetes mellitus + DiseaseMONDO_increased_DiseaseSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + ## 200 records + - supportBatch: true + useTemplating: true + inputs: + - id: MONDO + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: CHEBI - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-CHEBI" - # testExamples: - # - qInput: "SNOMEDCT:191519005" ## Dementia associated with another disease (disorder) - # oneOutput: "CHEBI:44185" ## methotrexate - ChemCHEBI_increased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 13225 records - -supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "CHEBI:135738" ## clevidipine - # oneOutput: "HP:0003077" ## Hyperlipidemia - ChemCHEBI_increased_PhenoHP_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: CHEBI - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-CHEBI" - # testExamples: - # - qInput: "HP:0001397" ## Hepatic steatosis - # oneOutput: "CHEBI:6456" ## lidocaine - ChemCHEBI_increased_PhenoNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 1176 records - -supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "CHEBI:8499" ## propranolol - # oneOutput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission - ChemCHEBI_increased_PhenoNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: CHEBI - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-CHEBI" - # testExamples: - # - qInput: "NCIT:C146650" ## Clostridium difficile Positive - # oneOutput: "CHEBI:3207" ## budesonide - ChemCHEBI_increased_PhenoSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ## 99 records - -supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "CHEBI:9600" ## timolol - # oneOutput: "SNOMEDCT:76571007" ## Septic shock (disorder) - ChemCHEBI_increased_PhenoSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "MONDO:0005090" ## schizophrenia (disease) + # oneOutput: "SNOMEDCT:709073001" ## Neurocognitive disorder (disorder) + DiseaseMONDO_increased_DiseaseSNOMEDCT-rev: + - supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: CHEBI - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-CHEBI" - # testExamples: - # - qInput: "SNOMEDCT:709073001" ## Neurocognitive disorder (disorder) - # oneOutput: "CHEBI:601027" ## aliskiren - ChemCHEBI_increased_ProcedureNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT - ## 121 records - -supportBatch: true - useTemplating: true - inputs: - - id: CHEBI - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "CHEBI:3515" ## cefuroxime - # oneOutput: "NCIT:C141278" ## Adenovirus Positive - ChemCHEBI_increased_ProcedureNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.CHEBI, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: CHEBI - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-CHEBI" - # testExamples: - # - qInput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission - # oneOutput: "CHEBI:33283" ## thiamine - ChemUNII_decreased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 5902 records - -supportBatch: true - useTemplating: true - inputs: - - id: UNII - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "UNII:X85G7936GV" ## abciximab - # oneOutput: "MONDO:0005495" ## adrenal gland disease - ChemUNII_decreased_DiseaseMONDO_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-MONDO" + # testExamples: + # - qInput: "SNOMEDCT:386033004" ## Neuropathy (disorder) + # oneOutput: "MONDO:0005301" ## multiple sclerosis + DiseaseNCIT_increased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 1 record + - supportBatch: true + useTemplating: true + inputs: + - id: NCIT + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: UNII - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-UNII" - # testExamples: - # - qInput: "MONDO:0005090" ## schizophrenia (disease) - # oneOutput: "UNII:2S9ZZM9Q9V" ## bevacizumab - ChemUNII_decreased_DiseaseNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## 44 records - -supportBatch: true - useTemplating: true - inputs: - - id: UNII - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "UNII:7EV65EAW6H" ## lanolin - # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive - ChemUNII_decreased_DiseaseNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + # oneOutput: "MONDO:0007140" ## antiphospholipid syndrome + DiseaseNCIT_increased_DiseaseMONDO-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: MONDO + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: UNII - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-UNII" - # testExamples: - # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - # oneOutput: "UNII:91X1KLU43E" ## golimumab - ChemUNII_decreased_DiseaseSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 505 records - -supportBatch: true - useTemplating: true - inputs: - - id: UNII - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "UNII:7D0YB67S97" ## abatacept - # oneOutput: "SNOMEDCT:54404000" ## Cervical radiculopathy (disorder) - ChemUNII_decreased_DiseaseSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: UNII - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-UNII" - # testExamples: - # - qInput: "SNOMEDCT:709073001" ## Neurocognitive disorder (disorder) - # oneOutput: "UNII:7EV65EAW6H" ## lanolin - ChemUNII_decreased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 3727 records - -supportBatch: true - useTemplating: true - inputs: - - id: UNII - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "UNII:I031V2H011" ## tocilizumab - # oneOutput: "HP:0000739" ## Anxiety - ChemUNII_decreased_PhenoHP_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-NCIT" + # testExamples: + # - qInput: "MONDO:0007140" ## antiphospholipid syndrome + # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + ## no records for DiseaseNCIT_increased_DiseaseNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ## no records for DiseaseNCIT_increased_DiseaseSNOMEDCT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + ## no records for DiseaseSNOMEDCT_increased_DiseaseMONDO + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## no records for DiseaseSNOMEDCT_increased_DiseaseNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ## no records for DiseaseSNOMEDCT_increased_DiseaseSNOMEDCT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + DiseaseMONDO_increased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 2107 records + - supportBatch: true + useTemplating: true + inputs: + - id: MONDO + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: UNII - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-UNII" - # testExamples: - # - qInput: "HP:0011897" ## Neutrophilia - # oneOutput: "UNII:9RV78Q2002" ## vedolizumab - ChemUNII_decreased_PhenoNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 381 records - -supportBatch: true - useTemplating: true - inputs: - - id: UNII - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "UNII:25ADE2236L" ## thrombin - # oneOutput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission - ChemUNII_decreased_PhenoNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "MONDO:0005002" ## chronic obstructive pulmonary disease + # oneOutput: "HP:0000739" ## Anxiety + DiseaseMONDO_increased_PhenoHP-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: HP + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-MONDO" + # testExamples: + # - qInput: "HP:0000790" ## Hematuria + # oneOutput: "MONDO:0005002" ## chronic obstructive pulmonary disease + DiseaseMONDO_increased_PhenoNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## 42 records + - supportBatch: true + useTemplating: true + inputs: + - id: MONDO + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: UNII - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-UNII" - # testExamples: - # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - # oneOutput: "UNII:P188ANX8CK" ## trastuzumab - ChemUNII_decreased_PhenoSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ## 39 records - -supportBatch: true - useTemplating: true - inputs: - - id: UNII - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "UNII:I031V2H011" ## tocilizumab - # oneOutput: "SNOMEDCT:191519005" ## Dementia associated with another disease (disorder) - ChemUNII_decreased_PhenoSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: UNII - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-UNII" - # testExamples: - # - qInput: "SNOMEDCT:239792003" ## Seronegative rheumatoid arthritis (disorder) - # oneOutput: "UNII:I5I8VB78VT" ## erenumab - ChemUNII_decreased_ProcedureNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT - ## 43 records - -supportBatch: true - useTemplating: true - inputs: - - id: UNII - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "UNII:OP401G7OJC" ## etanercept - # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive - ChemUNII_decreased_ProcedureNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "MONDO:0005249" ## pneumonia + # oneOutput: "NCIT:C167118" ## Influenza B Virus Positive (Influenza A Virus Positive?) + DiseaseMONDO_increased_PhenoNCIT-rev: + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: UNII - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-UNII" - # testExamples: - # - qInput: "NCIT:C155871" ## Herpes Simplex Virus Infection - # oneOutput: "UNII:A10SJL62JY" ## ocrelizumab - ChemUNII_increased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 2158 records - -supportBatch: true - useTemplating: true - inputs: - - id: UNII - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "UNII:A10SJL62JY" ## ocrelizumab - # oneOutput: "MONDO:0005090" ## schizophrenia (disease) - ChemUNII_increased_DiseaseMONDO_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: UNII - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-UNII" - # testExamples: - # - qInput: "MONDO:0002447" ## endometrial carcinoma (disease) - # oneOutput: "UNII:O43472U9X8" ## obinutuzumab - ChemUNII_increased_DiseaseNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## 8 records - -supportBatch: true - useTemplating: true - inputs: - - id: UNII - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "UNII:E47C0NF7LV" ## enoxaparin - # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - ChemUNII_increased_DiseaseNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: UNII - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-UNII" - # testExamples: - # - qInput: "NCIT:C159516" ## Liver Lesion - # oneOutput: "UNII:73B0K5S26A" ## belimumab - ChemUNII_increased_DiseaseSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 171 records - -supportBatch: true - useTemplating: true - inputs: - - id: UNII - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "UNII:DQ448MW7KS" ## palivizumab - # oneOutput: "SNOMEDCT:197352008" ## Toxic hepatitis (disorder) - ChemUNII_increased_DiseaseSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-MONDO" + # testExamples: + # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + # oneOutput: "MONDO:0005249" ## pneumonia + DiseaseMONDO_increased_PhenoSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + ## 18 records + - supportBatch: true + useTemplating: true + inputs: + - id: MONDO + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: UNII - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-UNII" - # testExamples: - # - qInput: "SNOMEDCT:237519003" ## Autoimmune hypothyroidism (disorder) - # oneOutput: "UNII:4T6H12BN9U" ## petrolatum - ChemUNII_increased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 1993 records - -supportBatch: true - useTemplating: true - inputs: - - id: UNII - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "UNII:K16AIQ8CTM" ## pertuzumab - # oneOutput: "HP:0005518" ## Increased mean corpuscular volume - ChemUNII_increased_PhenoHP_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "MONDO:0004981" ## atrial fibrillation (disease) + # oneOutput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) + DiseaseMONDO_increased_PhenoSNOMEDCT-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-MONDO" + # testExamples: + # - qInput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) + # oneOutput: "MONDO:0005044" ## hypertensive disorder + ## no records for DiseaseNCIT_increased_PhenoHP + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## no records for DiseaseNCIT_increased_PhenoNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## no records for DiseaseNCIT_increased_PhenoSNOMEDCT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + DiseaseSNOMEDCT_increased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 52 records + - supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: UNII - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-UNII" - # testExamples: - # - qInput: "HP:0003124" ## Hypercholesterolemia - # oneOutput: "UNII:FU77B4U5Z0" ## ustekinumab - ChemUNII_increased_PhenoNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 139 records - -supportBatch: true - useTemplating: true - inputs: - - id: UNII - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "UNII:4F4X42SYQ6" ## rituximab - # oneOutput: "NCIT:C155871" ## Herpes Simplex Virus Infection - ChemUNII_increased_PhenoNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: UNII - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-UNII" - # testExamples: - # - qInput: "NCIT:C15271" ## Liver Transplantation - # oneOutput: "UNII:4Z63YK6E0E" ## daratumumab - ChemUNII_increased_PhenoSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ## 13 records - -supportBatch: true - useTemplating: true - inputs: - - id: UNII - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "UNII:73B0K5S26A" ## belimumab - # oneOutput: "SNOMEDCT:237519003" ## Autoimmune hypothyroidism (disorder) - ChemUNII_increased_PhenoSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "SNOMEDCT:2415007" ## Lumbosacral radiculopathy (disorder) + # oneOutput: "HP:0001369" ## Arthritis + DiseaseSNOMEDCT_increased_PhenoHP-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: HP + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: UNII - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-UNII" - # testExamples: - # - qInput: "SNOMEDCT:386033004" ## Neuropathy (disorder) - # oneOutput: "UNII:DPT0O3T46P" ## pembrolizumab - ChemUNII_increased_ProcedureNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT - ## 9 records - -supportBatch: true - useTemplating: true - inputs: - - id: UNII - - semantic: ChemicalEntity - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "UNII:DPT0O3T46P" ## pembrolizumab - # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive - ChemUNII_increased_ProcedureNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-SNOMEDCT" + # testExamples: + # - qInput: "HP:0002385" ## Paraparesis + # oneOutput: "SNOMEDCT:2415007" ## Lumbosacral radiculopathy (disorder) + ## no records for DiseaseSNOMEDCT_increased_PhenoNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## no records for DiseaseSNOMEDCT_increased_PhenoSNOMEDCT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + DiseaseMONDO_increased_ProcedureNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Procedure + ## 69 records + - supportBatch: true + useTemplating: true + inputs: + - id: MONDO + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Procedure"]') }} ], + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "MONDO:0005300" ## chronic kidney disease + # oneOutput: "NCIT:C15271" ## Liver Transplantation + DiseaseMONDO_increased_ProcedureNCIT-rev: + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.UNII, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: UNII - semantic: ChemicalEntity - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-UNII" - # testExamples: - # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - # oneOutput: "UNII:I16QD7X297" ## neomycin + semantic: Procedure + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Procedure"]') }} ], + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-MONDO" + # testExamples: + # - qInput: "NCIT:C15271" ## Liver Transplantation + # oneOutput: "MONDO:0005155" ## cirrhosis of liver + ## no records for DiseaseNCIT_increased_ProcedureNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Procedure + ## no records for DiseaseSNOMEDCT_increased_ProcedureNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Procedure DiseaseMONDO_decreased_DiseaseMONDO: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 13640 records - -supportBatch: true - useTemplating: true - inputs: + ## 190 records + - supportBatch: true + useTemplating: true + inputs: + - id: MONDO + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "MONDO:0005010" ## coronary artery disease - # oneOutput: "MONDO:0005626" ## epithelial neoplasm - DiseaseMONDO_decreased_DiseaseMONDO_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "MONDO:0005148" ## type 2 diabetes mellitus + # oneOutput: "MONDO:0005301" ## multiple sclerosis + DiseaseMONDO_decreased_DiseaseMONDO-rev: + - supportBatch: true + useTemplating: true + inputs: - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "MONDO:0005154" ## liver disease - # oneOutput: "MONDO:0005009" ## congestive heart failure + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-MONDO" + # testExamples: + # - qInput: "MONDO:0002039" ## cognitive disorder + # oneOutput: "MONDO:0005178" ## osteoarthritis DiseaseMONDO_decreased_DiseaseNCIT: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## 86 records - -supportBatch: true - useTemplating: true - inputs: + ## 1 record + - supportBatch: true + useTemplating: true + inputs: - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "MONDO:0004979" ## asthma - # oneOutput: "NCIT:C167118" ## Influenza A Virus Positive - DiseaseMONDO_decreased_DiseaseNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: NCIT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "MONDO:0004981" ## atrial fibrillation (disease) + # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + DiseaseMONDO_decreased_DiseaseNCIT-rev: + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "NCIT:C15271" ## Liver Transplantation - # oneOutput: "MONDO:0001150" ## hydrocephalus + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-MONDO" + # testExamples: + # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + # oneOutput: "MONDO:0004981" ## atrial fibrillation (disease) DiseaseMONDO_decreased_DiseaseSNOMEDCT: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 1237 records - -supportBatch: true - useTemplating: true - inputs: + ## 21 records + - supportBatch: true + useTemplating: true + inputs: + - id: MONDO + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "MONDO:0005311" ## atherosclerosis + # oneOutput: "SNOMEDCT:386033004" ## Neuropathy (disorder) + DiseaseMONDO_decreased_DiseaseSNOMEDCT-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-MONDO" + # testExamples: + # - qInput: "SNOMEDCT:2415007" ## Lumbosacral radiculopathy (disorder) + # oneOutput: "MONDO:0005108" ## viral infectious disease + ## no records for DiseaseNCIT_decreased_DiseaseMONDO + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## no records for DiseaseNCIT_decreased_DiseaseNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ## no records for DiseaseNCIT_decreased_DiseaseSNOMEDCT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + DiseaseSNOMEDCT_decreased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 6 records + - supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) + # oneOutput: "MONDO:0004670" ## lupus erythematosus + DiseaseSNOMEDCT_decreased_DiseaseMONDO-rev: + - supportBatch: true + useTemplating: true + inputs: - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "MONDO:0002959" ## radiculopathy - # oneOutput: "SNOMEDCT:127295002" ## Traumatic brain injury (disorder) - DiseaseMONDO_decreased_DiseaseSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "SNOMEDCT:76571007" ## Septic shock (disorder) - # oneOutput: "MONDO:0005028" ## esophageal adenocarcinoma + semantic: Disease + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-SNOMEDCT" + # testExamples: + # - qInput: "MONDO:0005546" ## fibromyalgia + # oneOutput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) + ## no records for DiseaseSNOMEDCT_decreased_DiseaseNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ## no records for DiseaseSNOMEDCT_decreased_DiseaseSNOMEDCT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT DiseaseMONDO_decreased_PhenoHP: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 10101 records - -supportBatch: true - useTemplating: true - inputs: + ## 426 records + - supportBatch: true + useTemplating: true + inputs: - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "MONDO:0005340" ## alopecia areata - # oneOutput: "HP:0003119" ## Abnormal circulating lipid concentration - DiseaseMONDO_decreased_PhenoHP_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "HP:0001945" ## Fever - # oneOutput: "MONDO:0005155" ## cirrhosis of liver + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "MONDO:0005002" ## chronic obstructive pulmonary disease + # oneOutput: "HP:0033077" ## Increased circulating free T4 level + DiseaseMONDO_decreased_PhenoHP-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: HP + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-MONDO" + # testExamples: + # - qInput: "HP:0025066" ## Decreased mean corpuscular volume + # oneOutput: "MONDO:0005071" ## nervous system disorder DiseaseMONDO_decreased_PhenoNCIT: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 1293 records - -supportBatch: true - useTemplating: true - inputs: + ## 17 records + - supportBatch: true + useTemplating: true + inputs: - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "MONDO:0005090" ## schizophrenia (disease) - # oneOutput: "NCIT:C3587" ## Chronic Lymphocytic Leukemia in Remission - DiseaseMONDO_decreased_PhenoNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "NCIT:C146650" ## Clostridium difficile Positive - # oneOutput: "MONDO:0005180" ## Parkinson disease - DiseaseMONDO_decreased_PhenoSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ## 88 records - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "MONDO:0005148" ## type 2 diabetes mellitus + # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + DiseaseMONDO_decreased_PhenoNCIT-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: NCIT + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "MONDO:0011849" ## psoriatic arthritis - # oneOutput: "SNOMEDCT:2415007" ## Lumbosacral radiculopathy (disorder) - DiseaseMONDO_decreased_PhenoSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-MONDO" + # testExamples: + # - qInput: "NCIT:C146650" ## Clostridium difficile Positive + # oneOutput: "MONDO:0005249" ## pneumonia + ## no records for DiseaseMONDO_decreased_PhenoSNOMEDCT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + ## no records for DiseaseNCIT_decreased_PhenoHP + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## no records for DiseaseNCIT_decreased_PhenoNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## no records for DiseaseNCIT_decreased_PhenoSNOMEDCT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + DiseaseSNOMEDCT_decreased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 22 records + - supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) - # oneOutput: "MONDO:0005485" ## psychotic disorder + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "SNOMEDCT:76571007" ## Septic shock (disorder) + # oneOutput: "HP:0031963" ## Decreased serum anion gap + DiseaseSNOMEDCT_decreased_PhenoHP-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: HP + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-SNOMEDCT" + # testExamples: + # - qInput: "HP:0031969" ## Reduced blood urea nitrogen + # oneOutput: "SNOMEDCT:76571007" ## Septic shock (disorder) + ## no records for DiseaseSNOMEDCT_decreased_PhenoNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## no records for DiseaseSNOMEDCT_decreased_PhenoSNOMEDCT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT DiseaseMONDO_decreased_ProcedureNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT - ## 113 records - -supportBatch: true - useTemplating: true - inputs: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure + ## 1 record + - supportBatch: true + useTemplating: true + inputs: - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "MONDO:0007028" ## rotator cuff syndrome - # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - DiseaseMONDO_decreased_ProcedureNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') }} ], + "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "NCIT:C167118" ## Influenza A Virus Positive - # oneOutput: "MONDO:0001942" ## generalized anxiety disorder - DiseaseMONDO_increased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 14415 records - -supportBatch: true - useTemplating: true - inputs: - - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "MONDO:0004988" ## breast adenocarcinoma - # oneOutput: "MONDO:0004868" ## biliary tract disease - DiseaseMONDO_increased_DiseaseMONDO_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "MONDO:0005011" ## Crohn disease - # oneOutput: "MONDO:0042981" ## aortic valve stenosis - DiseaseMONDO_increased_DiseaseNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## 96 records - -supportBatch: true - useTemplating: true - inputs: - - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "MONDO:0006763" ## frozen shoulder - # oneOutput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission - DiseaseMONDO_increased_DiseaseNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "MONDO:0006011" ## viral hepatitis + # oneOutput: "NCIT:C15271" ## Liver Transplantation + DiseaseMONDO_decreased_ProcedureNCIT-rev: + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "NCIT:C146650" ## Clostridium difficile Positive - # oneOutput: "MONDO:0024317" ## chronic pain syndrome - DiseaseMONDO_increased_DiseaseSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 1129 records - -supportBatch: true - useTemplating: true - inputs: - - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "MONDO:0005344" ## hepatitis B virus infection - # oneOutput: "SNOMEDCT:191519005" ## Dementia associated with another disease (disorder) - DiseaseMONDO_increased_DiseaseSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "SNOMEDCT:54404000" ## Cervical radiculopathy (disorder) - # oneOutput: "MONDO:0005010" ## coronary artery disease - DiseaseMONDO_increased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 9919 records - -supportBatch: true - useTemplating: true - inputs: + semantic: Procedure + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') }} ], + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "MONDO:0005068" ## myocardial infarction (disease) - # oneOutput: "HP:0002829" ## Arthralgia - DiseaseMONDO_increased_PhenoHP_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-MONDO" + # testExamples: + # - qInput: "NCIT:C15271" ## Liver Transplantation + # oneOutput: "MONDO:0006011" ## viral hepatitis + ## no records for DiseaseNCIT_decreased_ProcedureNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure + ## no records for DiseaseSNOMEDCT_decreased_ProcedureNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure + PhenoHP_increased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 3536 records + - supportBatch: true + useTemplating: true + inputs: - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "HP:0001945" ## Fever - # oneOutput: "MONDO:0005230" ## cellulitis (disease) - DiseaseMONDO_increased_PhenoNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 527 records - -supportBatch: true - useTemplating: true - inputs: - - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "MONDO:0005146" ## post-traumatic stress disorder - # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive - DiseaseMONDO_increased_PhenoNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "NCIT:C146650" ## Clostridium difficile Positive - # oneOutput: "MONDO:0005011" ## Crohn disease - DiseaseMONDO_increased_PhenoSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ## 94 records - -supportBatch: true - useTemplating: true - inputs: - - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "MONDO:0013600" ## insomnia (disease) - # oneOutput: "SNOMEDCT:76571007" ## Septic shock (disorder) - DiseaseMONDO_increased_PhenoSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "SNOMEDCT:127295002" ## Traumatic brain injury (disorder) - # oneOutput: "MONDO:0005300" ## chronic kidney disease - DiseaseMONDO_increased_ProcedureNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.MONDO%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT - ## 69 records - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["subject.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "MONDO:0002959" ## radiculopathy - # oneOutput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission - DiseaseMONDO_increased_ProcedureNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "NCIT:C167118" ## Influenza A Virus Positive - # oneOutput: "MONDO:0007488" ## Lewy body dementia - DiseaseNCIT_decreased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 73 records - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "NCIT:C159516" ## Liver Lesion - # oneOutput: "MONDO:0004375" ## end stage renal failure - DiseaseNCIT_decreased_DiseaseMONDO_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "HP:0000093" ## Proteinuria + # oneOutput: "MONDO:0001627" ## dementia (disease) + PhenoHP_increased_DiseaseMONDO-rev: + - supportBatch: true + useTemplating: true + inputs: - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "MONDO:0013662" ## Barrett esophagus - # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - DiseaseNCIT_decreased_DiseaseSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 7 records - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C52007" ## Arthrodesis - # oneOutput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) - DiseaseNCIT_decreased_DiseaseSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:197352008" ## Toxic hepatitis (disorder) - # oneOutput: "NCIT:C155871" ## Herpes Simplex Virus Infection - DiseaseNCIT_decreased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 44 records - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission - # oneOutput: "HP:0002076" ## Migraine - DiseaseNCIT_decreased_PhenoHP_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "HP:0003138" ## Increased blood urea nitrogen - # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive - DiseaseNCIT_decreased_PhenoNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 9 records - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C167118" ## Influenza A Virus Positive - # oneOutput: "NCIT:C159516" ## Liver Lesion - DiseaseNCIT_decreased_PhenoNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C155871" ## Herpes Simplex Virus Infection - # oneOutput: "NCIT:C51691" ## Arthroplasty - DiseaseNCIT_decreased_ProcedureNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT - ## 1 records - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C50815" ## Aortic Valve Replacement - # oneOutput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission - DiseaseNCIT_decreased_ProcedureNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - # oneOutput: "NCIT:C50815" ## Aortic Valve Replacement - DiseaseNCIT_increased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 82 records - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-HP" + # testExamples: + # - qInput: "MONDO:0001650" ## acute cystitis (disease) + # oneOutput: "HP:0000093" ## Proteinuria + PhenoHP_increased_DiseaseNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ## 4 records + - supportBatch: true + useTemplating: true + inputs: + - id: HP + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "NCIT:C52007" ## Arthrodesis - # oneOutput: "MONDO:0001824" ## polyneuropathy - DiseaseNCIT_increased_DiseaseMONDO_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "MONDO:0007256" ## hepatocellular carcinoma - # oneOutput: "NCIT:C50815" ## Aortic Valve Replacement - DiseaseNCIT_increased_DiseaseSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 6 records - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "HP:0003645" ## Prolonged partial thromboplastin time + # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + PhenoHP_increased_DiseaseNCIT-rev: + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C155871" ## Herpes Simplex Virus Infection - # oneOutput: "SNOMEDCT:127295002" ## Traumatic brain injury (disorder) - DiseaseNCIT_increased_DiseaseSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-HP" + # testExamples: + # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + # oneOutput: "HP:0100724" ## Hypercoagulability + PhenoHP_increased_DiseaseSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + ## 253 records + - supportBatch: true + useTemplating: true + inputs: + - id: HP + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) - # oneOutput: "NCIT:C15271" ## Liver Transplantation - DiseaseNCIT_increased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 66 records - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "NCIT:C50815" ## Aortic Valve Replacement - # oneOutput: "HP:0100806" ## Sepsis - DiseaseNCIT_increased_PhenoHP_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "HP:0000870" ## Increased circulating prolactin concentration + # oneOutput: "SNOMEDCT:127295002" ## Traumatic brain injury (disorder) + PhenoHP_increased_DiseaseSNOMEDCT-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "HP:0001974" ## Leukocytosis - # oneOutput: "NCIT:C15271" ## Liver Transplantation - DiseaseNCIT_increased_PhenoNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 1 records - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - DiseaseNCIT_increased_PhenoNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-HP" + # testExamples: + # - qInput: "SNOMEDCT:709073001" ## Neurocognitive disorder (disorder) + # oneOutput: "HP:0000870" ## Increased circulating prolactin concentration + PhenoNCIT_increased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 11 records + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C141278" ## Adenovirus Positive - # oneOutput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission - DiseaseNCIT_increased_PhenoSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ## 1 records - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "NCIT:C159516" ## Liver Lesion + # oneOutput: "MONDO:0005154" ## liver disease + PhenoNCIT_increased_DiseaseMONDO-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: MONDO + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C38033" ## Arthroscopy - # oneOutput: "SNOMEDCT:237519003" ## Autoimmune hypothyroidism (disorder) - DiseaseNCIT_increased_PhenoSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:709073001" ## Neurocognitive disorder (disorder) - # oneOutput: "NCIT:C3587" ## Chronic Lymphocytic Leukemia in Remission - DiseaseSNOMEDCT_decreased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 1318 records - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-NCIT" + # testExamples: + # - qInput: "MONDO:0004948" ## B-cell chronic lymphocytic leukemia + # oneOutput: "NCIT:C3587" ## Chronic Lymphocytic Leukemia in Remission + ## no records for PhenoNCIT_increased_DiseaseNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ## no records for PhenoNCIT_increased_DiseaseSNOMEDCT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + PhenoSNOMEDCT_increased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 27 records + - supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "SNOMEDCT:76571007" ## Septic shock (disorder) - # oneOutput: "MONDO:0020696" ## vitamin B12 deficiency - DiseaseSNOMEDCT_decreased_DiseaseMONDO_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "MONDO:0020108" ## autoimmune hemolytic anemia - # oneOutput: "SNOMEDCT:711150003" ## Long-term current use of anticoagulant (situation) - DiseaseSNOMEDCT_decreased_DiseaseNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## 10 records - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "SNOMEDCT:166816003" ## Serum lipids high (finding) + # oneOutput: "MONDO:0001356" ## iron deficiency anemia + PhenoSNOMEDCT_increased_DiseaseMONDO-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: MONDO + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) - # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - DiseaseSNOMEDCT_decreased_DiseaseNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C167118" ## Influenza A Virus Positive - # oneOutput: "SNOMEDCT:386033004" ## Neuropathy (disorder) - DiseaseSNOMEDCT_decreased_DiseaseSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 101 records - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-SNOMEDCT" + # testExamples: + # - qInput: "MONDO:0006920" ## prediabetes syndrome + # oneOutput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) + ## no records for PhenoSNOMEDCT_increased_DiseaseNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + PhenoSNOMEDCT_increased_DiseaseSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + ## 1 record + - supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "SNOMEDCT:191519005" ## Dementia associated with another disease (disorder) - # oneOutput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) - DiseaseSNOMEDCT_decreased_DiseaseSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "SNOMEDCT:237519003" ## Autoimmune hypothyroidism (disorder) - # oneOutput: "SNOMEDCT:201839001" ## Primary coxarthrosis, bilateral (disorder) - DiseaseSNOMEDCT_decreased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 957 records - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "SNOMEDCT:166816003" ## Serum lipids high (finding) + # oneOutput: "SNOMEDCT:191519005" ## Dementia associated with another disease (disorder) + PhenoSNOMEDCT_increased_DiseaseSNOMEDCT-rev: + - supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "SNOMEDCT:711150003" ## Long-term current use of anticoagulant (situation) - # oneOutput: "HP:0000870" ## Increased circulating prolactin concentration - DiseaseSNOMEDCT_decreased_PhenoHP_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "HP:0003282" ## Low alkaline phosphatase - # oneOutput: "SNOMEDCT:47049007" ## Ankylosis of spine (disorder) - DiseaseSNOMEDCT_decreased_PhenoNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 116 records - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:2415007" ## Lumbosacral radiculopathy (disorder) - # oneOutput: "NCIT:C141278" ## Adenovirus Positive - DiseaseSNOMEDCT_decreased_PhenoNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-SNOMEDCT" + # testExamples: + # - qInput: "SNOMEDCT:191519005" ## Dementia associated with another disease (disorder) + # oneOutput: "SNOMEDCT:166816003" ## Serum lipids high (finding) + PhenoHP_increased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 5487 records + - supportBatch: true + useTemplating: true + inputs: + - id: HP + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "HP:0000093" ## Proteinuria + # oneOutput: "HP:0003155" ## Elevated alkaline phosphatase + PhenoHP_increased_PhenoHP-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: HP + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-HP" + # testExamples: + # - qInput: "HP:0003138" ## Increased blood urea nitrogen + # oneOutput: "HP:0000093" ## Proteinuria + PhenoHP_increased_PhenoNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## 244 records + - supportBatch: true + useTemplating: true + inputs: + - id: HP + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C15271" ## Liver Transplantation - # oneOutput: "SNOMEDCT:386033004" ## Neuropathy (disorder) - DiseaseSNOMEDCT_decreased_PhenoSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ## 8 records - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) - # oneOutput: "SNOMEDCT:197352008" ## Toxic hepatitis (disorder) - DiseaseSNOMEDCT_decreased_PhenoSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "SNOMEDCT:711150003" ## Long-term current use of anticoagulant (situation) - # oneOutput: "SNOMEDCT:201839001" ## Primary coxarthrosis, bilateral (disorder) - DiseaseSNOMEDCT_decreased_ProcedureNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT - ## 13 records - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:76571007" ## Septic shock (disorder) - # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - DiseaseSNOMEDCT_decreased_ProcedureNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "HP:0000988" ## Skin rash + # oneOutput: "NCIT:C155871" ## Herpes Simplex Virus Infection + PhenoHP_increased_PhenoNCIT-rev: + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C155871" ## Herpes Simplex Virus Infection - # oneOutput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) - DiseaseSNOMEDCT_increased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 1007 records - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-HP" + # testExamples: + # - qInput: "NCIT:C159516" ## Liver Lesion + # oneOutput: "HP:0000870" ## Increased circulating prolactin concentration + PhenoHP_increased_PhenoSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + ## 19 records + - supportBatch: true + useTemplating: true + inputs: + - id: HP + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "SNOMEDCT:191519005" ## Dementia associated with another disease (disorder) - # oneOutput: "MONDO:0007147" ## obstructive sleep apnea syndrome - DiseaseSNOMEDCT_increased_DiseaseMONDO_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "MONDO:0005298" ## osteoporosis - # oneOutput: "SNOMEDCT:202805003" ## Sacroiliac disorder (disorder) - DiseaseSNOMEDCT_increased_DiseaseNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## 5 records - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "HP:0001369" ## Arthritis + # oneOutput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) + PhenoHP_increased_PhenoSNOMEDCT-rev: + - supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:709073001" ## Neurocognitive disorder (disorder) - # oneOutput: "NCIT:C159516" ## Liver Lesion - DiseaseSNOMEDCT_increased_DiseaseNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-HP" + # testExamples: + # - qInput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) + # oneOutput: "HP:0011227" ## Elevated C-reactive protein level + PhenoNCIT_increased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 15 records + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission - # oneOutput: "SNOMEDCT:386033004" ## Neuropathy (disorder) - DiseaseSNOMEDCT_increased_DiseaseSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 81 records - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "SNOMEDCT:127295002" ## Traumatic brain injury (disorder) - # oneOutput: "SNOMEDCT:711150003" ## Long-term current use of anticoagulant (situation) - DiseaseSNOMEDCT_increased_DiseaseSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "SNOMEDCT:54404000" ## Cervical radiculopathy (disorder) - # oneOutput: "SNOMEDCT:239792003" ## Seronegative rheumatoid arthritis (disorder) - DiseaseSNOMEDCT_increased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 693 records - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "SNOMEDCT:201839001" ## Primary coxarthrosis, bilateral (disorder) - # oneOutput: "HP:0006775" ## Multiple myeloma - DiseaseSNOMEDCT_increased_PhenoHP_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "HP:0000787" ## Nephrolithiasis - # oneOutput: "SNOMEDCT:76571007" ## Septic shock (disorder) - DiseaseSNOMEDCT_increased_PhenoNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 34 records - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:66944004" ## Autoimmune thyroiditis (disorder) - # oneOutput: "NCIT:C141278" ## Adenovirus Positive - DiseaseSNOMEDCT_increased_PhenoNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + # oneOutput: "HP:0003326" ## Myalgia + PhenoNCIT_increased_PhenoHP-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: HP + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C167118" ## Influenza A Virus Positive - # oneOutput: "SNOMEDCT:201839001" ## Primary coxarthrosis, bilateral (disorder) - DiseaseSNOMEDCT_increased_PhenoSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ## 7 records - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "SNOMEDCT:197352008" ## Toxic hepatitis (disorder) - # oneOutput: "SNOMEDCT:54404000" ## Cervical radiculopathy (disorder) - DiseaseSNOMEDCT_increased_PhenoSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-NCIT" + # testExamples: + # - qInput: "HP:0001397" ## Hepatic steatosis + # oneOutput: "NCIT:C159516" ## Liver Lesion + ## no records for PhenoNCIT_increased_PhenoNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## no records for PhenoNCIT_increased_PhenoSNOMEDCT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + PhenoSNOMEDCT_increased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 15 records + - supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "SNOMEDCT:127295002" ## Traumatic brain injury (disorder) - # oneOutput: "SNOMEDCT:197352008" ## Toxic hepatitis (disorder) - DiseaseSNOMEDCT_increased_ProcedureNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Disease%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT - ## 2 records - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "SNOMEDCT:166816003" ## Serum lipids high (finding) + # oneOutput: "HP:0000964" ## Eczema + PhenoSNOMEDCT_increased_PhenoHP-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: HP + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:201839001" ## Primary coxarthrosis, bilateral (disorder) - # oneOutput: "NCIT:C3587" ## Chronic Lymphocytic Leukemia in Remission - DiseaseSNOMEDCT_increased_ProcedureNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-SNOMEDCT" + # testExamples: + # - qInput: "HP:0002617" ## Vascular dilatation + # oneOutput: "SNOMEDCT:166816003" ## Serum lipids high (finding) + ## no records for PhenoSNOMEDCT_increased_PhenoNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## no records for PhenoSNOMEDCT_increased_PhenoSNOMEDCT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + PhenoHP_increased_ProcedureNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Procedure + ## 15 records + - supportBatch: true + useTemplating: true + inputs: + - id: HP + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Procedure"]') }} ], + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "HP:0001882" ## Leukopenia + # oneOutput: "NCIT:C15271" ## Liver Transplantation + PhenoHP_increased_ProcedureNCIT-rev: + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Disease", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission - # oneOutput: "SNOMEDCT:197354009" ## Toxic liver disease (disorder) + semantic: Procedure + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Procedure"]') }} ], + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-HP" + # testExamples: + # - qInput: "NCIT:C15271" ## Liver Transplantation + # oneOutput: "HP:0012213" ## Decreased glomerular filtration rate + ## no records for PhenoNCIT_increased_ProcedureNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Procedure + ## no records for PhenoSNOMEDCT_increased_ProcedureNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Procedure PhenoHP_decreased_DiseaseMONDO: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 18759 records - -supportBatch: true - useTemplating: true - inputs: + ## 4025 records + - supportBatch: true + useTemplating: true + inputs: - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "HP:0000870" ## Increased circulating prolactin concentration - # oneOutput: "MONDO:0007275" ## carpal tunnel syndrome - PhenoHP_decreased_DiseaseMONDO_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "HP:0000093" ## Proteinuria + # oneOutput: "MONDO:0002253" ## spondylosis + PhenoHP_decreased_DiseaseMONDO-rev: + - supportBatch: true + useTemplating: true + inputs: - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "MONDO:0005130" ## celiac disease - # oneOutput: "HP:0002900" ## Hypokalemia + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-HP" + # testExamples: + # - qInput: "MONDO:0002050" ## depressive disorder + # oneOutput: "HP:0000093" ## Proteinuria PhenoHP_decreased_DiseaseNCIT: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## 113 records - -supportBatch: true - useTemplating: true - inputs: + ## 1 record + - supportBatch: true + useTemplating: true + inputs: - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "HP:0025435" ## Increased lactate dehydrogenase level - # oneOutput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission - PhenoHP_decreased_DiseaseNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "NCIT:C159516" ## Liver Lesion - # oneOutput: "HP:0032237" ## Increased circulating myelocyte count + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "HP:0011991" ## Abnormal neutrophil count + # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + PhenoHP_decreased_DiseaseNCIT-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: NCIT + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-HP" + # testExamples: + # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + # oneOutput: "HP:0011991" ## Abnormal neutrophil count PhenoHP_decreased_DiseaseSNOMEDCT: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 1532 records - -supportBatch: true - useTemplating: true - inputs: + ## 291 records + - supportBatch: true + useTemplating: true + inputs: - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "HP:0012531" ## Pain - # oneOutput: "SNOMEDCT:54404000" ## Cervical radiculopathy (disorder) - PhenoHP_decreased_DiseaseSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) - # oneOutput: "HP:0011877" ## Increased mean platelet volume - PhenoHP_decreased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 11425 records - -supportBatch: true - useTemplating: true - inputs: - - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "HP:0012418" ## Hypoxemia - # oneOutput: "HP:0002919" ## Ketonuria - PhenoHP_decreased_PhenoHP_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "HP:0012343" ## Decreased circulating ferritin concentration - # oneOutput: "HP:0003077" ## Hyperlipidemia - PhenoHP_decreased_PhenoNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 1257 records - -supportBatch: true - useTemplating: true - inputs: - - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "HP:0011227" ## Elevated C-reactive protein level - # oneOutput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission - PhenoHP_decreased_PhenoNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "NCIT:C3587" ## Chronic Lymphocytic Leukemia in Remission - # oneOutput: "HP:0031851" ## Reduced hematocrit - PhenoHP_decreased_PhenoSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ## 121 records - -supportBatch: true - useTemplating: true - inputs: - - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "HP:0012378" ## Fatigue - # oneOutput: "SNOMEDCT:54404000" ## Cervical radiculopathy (disorder) - PhenoHP_decreased_PhenoSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "HP:0000870" ## Increased circulating prolactin concentration + # oneOutput: "SNOMEDCT:54404000" ## Cervical radiculopathy (disorder) + PhenoHP_decreased_DiseaseSNOMEDCT-rev: + - supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) - # oneOutput: "HP:0000023" ## Inguinal hernia - PhenoHP_decreased_ProcedureNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT - ## 132 records - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "HP:0001899" ## Increased hematocrit - # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - PhenoHP_decreased_ProcedureNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-HP" + # testExamples: + # - qInput: "SNOMEDCT:76571007" ## Septic shock (disorder) + # oneOutput: "HP:0000790" ## Hematuria + PhenoNCIT_decreased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 43 records + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "NCIT:C167118" ## Influenza A Virus Positive - # oneOutput: "HP:0001297" ## Stroke - PhenoHP_increased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 12086 records - -supportBatch: true - useTemplating: true - inputs: - - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "HP:0002318" ## Cervical myelopathy - # oneOutput: "MONDO:0002471" ## bursitis - PhenoHP_increased_DiseaseMONDO_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "MONDO:0007743" ## attention deficit-hyperactivity disorder - # oneOutput: "HP:0031807" ## Increased basophil count - PhenoHP_increased_DiseaseNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## 86 records - -supportBatch: true - useTemplating: true - inputs: - - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "HP:0001894" ## Thrombocytosis - # oneOutput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission - PhenoHP_increased_DiseaseNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + # oneOutput: "MONDO:0001711" ## hepatic encephalopathy + PhenoNCIT_decreased_DiseaseMONDO-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: MONDO + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "NCIT:C167118" ## Influenza A Virus Positive - # oneOutput: "HP:0012101" ## Decreased serum creatinine - PhenoHP_increased_DiseaseSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 1055 records - -supportBatch: true - useTemplating: true - inputs: - - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "HP:0003259" ## Elevated serum creatinine - # oneOutput: "SNOMEDCT:711150003" ## Long-term current use of anticoagulant (situation) - PhenoHP_increased_DiseaseSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-NCIT" + # testExamples: + # - qInput: "MONDO:0005247" ## urinary tract infection (disease) + # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + ## no records for PhenoNCIT_decreased_DiseaseNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + PhenoNCIT_decreased_DiseaseSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + ## 3 records + - supportBatch: true + useTemplating: true + inputs: + - id: NCIT + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + # oneOutput: "SNOMEDCT:2415007" ## Lumbosacral radiculopathy (disorder) + PhenoNCIT_decreased_DiseaseSNOMEDCT-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:76571007" ## Septic shock (disorder) + # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + PhenoSNOMEDCT_decreased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 17 records + - supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "SNOMEDCT:166816003" ## Serum lipids high (finding) + # oneOutput: "MONDO:0006920" ## prediabetes syndrome + PhenoSNOMEDCT_decreased_DiseaseMONDO-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: MONDO + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-SNOMEDCT" + # testExamples: + # - qInput: "MONDO:0005391" ## restless legs syndrome + # oneOutput: "SNOMEDCT:166816003" ## Serum lipids high (finding) + ## no records for PhenoSNOMEDCT_decreased_DiseaseNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + PhenoSNOMEDCT_decreased_DiseaseSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + ## 1 record + - supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "SNOMEDCT:166816003" ## Serum lipids high (finding) + # oneOutput: "SNOMEDCT:386033004" ## Neuropathy (disorder) + PhenoSNOMEDCT_decreased_DiseaseSNOMEDCT-rev: + - supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "SNOMEDCT:191519005" ## Dementia associated with another disease (disorder) - # oneOutput: "HP:0031956" ## Elevated serum aspartate aminotransferase - PhenoHP_increased_PhenoHP: + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-SNOMEDCT" + # testExamples: + # - qInput: "SNOMEDCT:386033004" ## Neuropathy (disorder) + # oneOutput: "SNOMEDCT:166816003" ## Serum lipids high (finding) + PhenoHP_decreased_PhenoHP: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 10355 records - -supportBatch: true - useTemplating: true - inputs: + ## 3804 records + - supportBatch: true + useTemplating: true + inputs: - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "HP:0002014" ## Diarrhea - # oneOutput: "HP:0001899" ## Increased hematocrit - PhenoHP_increased_PhenoHP_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "HP:0001882" ## Leukopenia - # oneOutput: "HP:0032372" ## Increased peripheral blast count - PhenoHP_increased_PhenoNCIT: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "HP:0000093" ## Proteinuria + # oneOutput: "HP:0001649" ## Tachycardia + PhenoHP_decreased_PhenoHP-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: HP + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-HP" + # testExamples: + # - qInput: "HP:0001386" ## Joint swelling + # oneOutput: "HP:0000093" ## Proteinuria + PhenoHP_decreased_PhenoNCIT: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 733 records - -supportBatch: true - useTemplating: true - inputs: + ## 170 records + - supportBatch: true + useTemplating: true + inputs: - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "HP:0100512" ## Low levels of vitamin D - # oneOutput: "NCIT:C167118" ## Influenza A Virus Positive - PhenoHP_increased_PhenoNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "NCIT:C167118" ## Influenza A Virus Positive - # oneOutput: "HP:0002905" ## Hyperphosphatemia - PhenoHP_increased_PhenoSNOMEDCT: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "HP:0012085" ## Pyuria + # oneOutput: "NCIT:C167118" ## Influenza B Virus Positive + PhenoHP_decreased_PhenoNCIT-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: NCIT + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-HP" + # testExamples: + # - qInput: "NCIT:C146650" ## Clostridium difficile Positive + # oneOutput: "HP:0012085" ## Pyuria + PhenoHP_decreased_PhenoSNOMEDCT: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ## 78 records - -supportBatch: true - useTemplating: true - inputs: + ## 26 records + - supportBatch: true + useTemplating: true + inputs: - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "HP:0001894" ## Thrombocytosis - # oneOutput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) - PhenoHP_increased_PhenoSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "SNOMEDCT:386033004" ## Neuropathy (disorder) - # oneOutput: "HP:0002923" ## Rheumatoid factor positive - PhenoHP_increased_ProcedureNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT - ## 67 records - -supportBatch: true - useTemplating: true - inputs: - - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "HP:0011016" ## Abnormality of urine glucose concentration - # oneOutput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission - PhenoHP_increased_ProcedureNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "NCIT:C146650" ## Clostridium difficile Positive - # oneOutput: "HP:0032473" ## Decreased urine urobilinogen - PhenoNCIT_decreased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 1170 records - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "NCIT:C159516" ## Liver Lesion - # oneOutput: "MONDO:0005100" ## systemic sclerosis - PhenoNCIT_decreased_DiseaseMONDO_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "MONDO:0017276" ## frontotemporal dementia - # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive - PhenoNCIT_decreased_DiseaseNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## 7 records - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C15546" ## Breast Cancer Screening - # oneOutput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission - PhenoNCIT_decreased_DiseaseNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C159516" ## Liver Lesion - # oneOutput: "NCIT:C15546" ## Breast Cancer Screening - PhenoNCIT_decreased_DiseaseSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 94 records - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C146650" ## Clostridium difficile Positive - # oneOutput: "SNOMEDCT:54404000" ## Cervical radiculopathy (disorder) - PhenoNCIT_decreased_DiseaseSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "HP:0011423" ## Hyperchloremia + # oneOutput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) + PhenoHP_decreased_PhenoSNOMEDCT-rev: + - supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) - # oneOutput: "NCIT:C15546" ## Breast Cancer Screening + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-HP" + # testExamples: + # - qInput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) + # oneOutput: "HP:0002902" ## Hyponatremia PhenoNCIT_decreased_PhenoHP: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 705 records - -supportBatch: true - useTemplating: true - inputs: + ## 64 records + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "NCIT:C141278" ## Adenovirus Positive - # oneOutput: "HP:0033077" ## Increased circulating free T4 level - PhenoNCIT_decreased_PhenoHP_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "HP:0031507" ## Decreased circulating T4 level - # oneOutput: "NCIT:C51691" ## Arthroplasty + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + # oneOutput: "HP:0002919" ## Ketonuria + PhenoNCIT_decreased_PhenoHP-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: HP + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-NCIT" + # testExamples: + # - qInput: "HP:0002829" ## Arthralgia + # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive PhenoNCIT_decreased_PhenoNCIT: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 56 records - -supportBatch: true - useTemplating: true - inputs: + ## 1 record + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C51691" ## Arthroplasty - # oneOutput: "NCIT:C155871" ## Herpes Simplex Virus Infection - PhenoNCIT_decreased_PhenoNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C141278" ## Adenovirus Positive - # oneOutput: "NCIT:C159516" ## Liver Lesion - PhenoNCIT_decreased_PhenoSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ## 9 records - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + # oneOutput: "NCIT:C167118" ## Influenza B Virus Positive + PhenoNCIT_decreased_PhenoNCIT-rev: + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - # oneOutput: "SNOMEDCT:239792003" ## Seronegative rheumatoid arthritis (disorder) - PhenoNCIT_decreased_PhenoSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:237519003" ## Autoimmune hypothyroidism (disorder) - # oneOutput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission - PhenoNCIT_decreased_ProcedureNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT - ## 7 records - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C52007" ## Arthrodesis - # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive - PhenoNCIT_decreased_ProcedureNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-NCIT" + # testExamples: + # - qInput: "NCIT:C167118" ## Influenza B Virus Positive + # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + ## no records for PhenoNCIT_decreased_PhenoSNOMEDCT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + PhenoSNOMEDCT_decreased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 16 records + - supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "SNOMEDCT:166816003" ## Serum lipids high (finding) + # oneOutput: "HP:0031098" ## Decreased thyroid-stimulating hormone level + PhenoSNOMEDCT_decreased_PhenoHP-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: HP + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: SNOMEDCT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-SNOMEDCT" + # testExamples: + # - qInput: "HP:0001882" ## Leukopenia + # oneOutput: "SNOMEDCT:166816003" ## Serum lipids high (finding) + ## no records for PhenoSNOMEDCT_decreased_PhenoNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## no records for PhenoSNOMEDCT_decreased_PhenoSNOMEDCT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + PhenoHP_decreased_ProcedureNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.HP%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure + ## 6 records + - supportBatch: true + useTemplating: true + inputs: + - id: HP + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') }} ], + "scopes": ["subject.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C3587" ## Chronic Lymphocytic Leukemia in Remission - # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive - PhenoNCIT_increased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 380 records - -supportBatch: true - useTemplating: true - inputs: + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "HP:0003141" ## Increased LDL cholesterol concentration + # oneOutput: "NCIT:C15271" ## Liver Transplantation + PhenoHP_decreased_ProcedureNCIT-rev: + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - # oneOutput: "MONDO:0007488" ## Lewy body dementia - PhenoNCIT_increased_DiseaseMONDO_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Procedure + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') }} ], + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-HP" + # testExamples: + # - qInput: "NCIT:C15271" ## Liver Transplantation + # oneOutput: "HP:0031965" ## Increased RBC distribution width + ## no records for PhenoNCIT_decreased_ProcedureNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure + ## no records for PhenoSNOMEDCT_decreased_ProcedureNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure + ChemCHEBI_increased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 4590 records + - supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + semantic: SmallMolecule + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "MONDO:0004979" ## asthma - # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive - PhenoNCIT_increased_DiseaseNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## 3 records - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C3587" ## Chronic Lymphocytic Leukemia in Remission - # oneOutput: "NCIT:C15271" ## Liver Transplantation - PhenoNCIT_increased_DiseaseNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "CHEBI:100241" ## ciprofloxacin + # oneOutput: "MONDO:0005230" ## cellulitis (disease) + ChemCHEBI_increased_DiseaseMONDO-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: MONDO + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.CHEBI, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: CHEBI + semantic: SmallMolecule + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" + # testExamples: + # - qInput: "MONDO:0005101" ## ulcerative colitis (disease) + # oneOutput: "CHEBI:100241" ## ciprofloxacin + ChemCHEBI_increased_DiseaseNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ## 2 records + - supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + semantic: SmallMolecule + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C15271" ## Liver Transplantation - # oneOutput: "NCIT:C167118" ## Influenza A Virus Positive - PhenoNCIT_increased_DiseaseSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 36 records - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "CHEBI:5801" ## hydroxychloroquine + # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + ChemCHEBI_increased_DiseaseNCIT-rev: + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C51691" ## Arthroplasty - # oneOutput: "SNOMEDCT:197352008" ## Toxic hepatitis (disorder) - PhenoNCIT_increased_DiseaseSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.CHEBI, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: CHEBI + semantic: SmallMolecule + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" + # testExamples: + # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + # oneOutput: "CHEBI:87732" ## warfarin + ChemCHEBI_increased_DiseaseSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + ## 282 records + - supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + semantic: SmallMolecule + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) - # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - PhenoNCIT_increased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 395 records - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "CHEBI:15409" ## menthol + # oneOutput: "SNOMEDCT:709073001" ## Neurocognitive disorder (disorder) + ChemCHEBI_increased_DiseaseSNOMEDCT-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.CHEBI, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: CHEBI + semantic: SmallMolecule + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" + # testExamples: + # - qInput: "SNOMEDCT:76571007" ## Septic shock (disorder) + # oneOutput: "CHEBI:15407" ## ephedrine + ChemUNII_increased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 401 records + - supportBatch: true + useTemplating: true + inputs: + - id: UNII + semantic: SmallMolecule + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "UNII:1BJ477IO2L" ## gadobutrol + # oneOutput: "MONDO:0005804" ## hyperprolactinemia (disease) + ChemUNII_increased_DiseaseMONDO-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: MONDO + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.UNII, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: UNII + semantic: SmallMolecule + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-UNII" + # testExamples: + # - qInput: "MONDO:0005665" ## Bell's palsy + # oneOutput: "UNII:1BJ477IO2L" ## gadobutrol + ChemUNII_increased_DiseaseNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ## 1 record + - supportBatch: true + useTemplating: true + inputs: + - id: UNII + semantic: SmallMolecule + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "NCIT:C159516" ## Liver Lesion - # oneOutput: "HP:0025066" ## Decreased mean corpuscular volume - PhenoNCIT_increased_PhenoHP_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "HP:0001297" ## Stroke - # oneOutput: "NCIT:C167118" ## Influenza A Virus Positive - PhenoNCIT_increased_PhenoNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 34 records - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "UNII:E47C0NF7LV" ## enoxaparin + # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + ChemUNII_increased_DiseaseNCIT-rev: + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission - # oneOutput: "NCIT:C15271" ## Liver Transplantation - PhenoNCIT_increased_PhenoNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.UNII, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: UNII + semantic: SmallMolecule + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-UNII" + # testExamples: + # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + # oneOutput: "UNII:E47C0NF7LV" ## enoxaparin + ChemUNII_increased_DiseaseSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + ## 30 records + - supportBatch: true + useTemplating: true + inputs: + - id: UNII + semantic: SmallMolecule + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: SNOMEDCT + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "UNII:T2410KM04A" ## heparin + # oneOutput: "SNOMEDCT:127295002" ## Traumatic brain injury (disorder) + ChemUNII_increased_DiseaseSNOMEDCT-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.UNII, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: UNII + semantic: SmallMolecule + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-UNII" + # testExamples: + # - qInput: "SNOMEDCT:239792003" ## Seronegative rheumatoid arthritis (disorder) + # oneOutput: "UNII:FYS6T7F842" ## adalimumab + ProcedureNCIT_increased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 29 records + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission - # oneOutput: "NCIT:C3587" ## Chronic Lymphocytic Leukemia in Remission - PhenoNCIT_increased_PhenoSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ## 1 records - -supportBatch: true - useTemplating: true - inputs: + semantic: Procedure + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "NCIT:C50815" ## Aortic Valve Replacement + # oneOutput: "MONDO:0005025" ## endocarditis (disease) + ProcedureNCIT_increased_DiseaseMONDO-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: MONDO + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C38033" ## Arthroscopy - # oneOutput: "SNOMEDCT:197354009" ## Toxic liver disease (disorder) - PhenoNCIT_increased_PhenoSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:197354009" ## Toxic liver disease (disorder) - # oneOutput: "NCIT:C3587" ## Chronic Lymphocytic Leukemia in Remission - PhenoNCIT_increased_ProcedureNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-NCIT" + # testExamples: + # - qInput: "MONDO:0024317" ## chronic pain syndrome + # oneOutput: "NCIT:C52007" ## Arthrodesis + ## no records for ProcedureNCIT_increased_DiseaseNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ProcedureNCIT_increased_DiseaseSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT ## 3 records - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C52007" ## Arthrodesis - # oneOutput: "NCIT:C159516" ## Liver Lesion - PhenoNCIT_increased_ProcedureNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C155871" ## Herpes Simplex Virus Infection - # oneOutput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission - PhenoSNOMEDCT_decreased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 307 records - -supportBatch: true - useTemplating: true - inputs: + semantic: Procedure + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "SNOMEDCT:711150003" ## Long-term current use of anticoagulant (situation) - # oneOutput: "MONDO:0011786" ## allergic rhinitis - PhenoSNOMEDCT_decreased_DiseaseMONDO_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "MONDO:0008383" ## rheumatoid arthritis - # oneOutput: "SNOMEDCT:201839001" ## Primary coxarthrosis, bilateral (disorder) - PhenoSNOMEDCT_decreased_DiseaseNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## 1 records - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C15546" ## Breast Cancer Screening + # oneOutput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) + ProcedureNCIT_increased_DiseaseSNOMEDCT-rev: + - supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:127295002" ## Traumatic brain injury (disorder) - # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - PhenoSNOMEDCT_decreased_DiseaseNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C167118" ## Influenza A Virus Positive - # oneOutput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) - PhenoSNOMEDCT_decreased_DiseaseSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 26 records - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "SNOMEDCT:709073001" ## Neurocognitive disorder (disorder) - # oneOutput: "SNOMEDCT:197354009" ## Toxic liver disease (disorder) - PhenoSNOMEDCT_decreased_DiseaseSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "SNOMEDCT:2415007" ## Lumbosacral radiculopathy (disorder) - # oneOutput: "SNOMEDCT:239792003" ## Seronegative rheumatoid arthritis (disorder) - PhenoSNOMEDCT_decreased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 217 records - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "SNOMEDCT:191519005" ## Dementia associated with another disease (disorder) - # oneOutput: "HP:0031506" ## Increased circulating T4 level - PhenoSNOMEDCT_decreased_PhenoHP_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Procedure + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:2415007" ## Lumbosacral radiculopathy (disorder) + # oneOutput: "NCIT:C52007" ## Arthrodesis + ChemCHEBI_increased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 4955 records + - supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + semantic: SmallMolecule + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "HP:0001397" ## Hepatic steatosis - # oneOutput: "SNOMEDCT:166816003" ## Serum lipids high (finding) - PhenoSNOMEDCT_decreased_PhenoNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 25 records - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:47049007" ## Ankylosis of spine (disorder) - # oneOutput: "NCIT:C3587" ## Chronic Lymphocytic Leukemia in Remission - PhenoSNOMEDCT_decreased_PhenoNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "CHEBI:100241" ## ciprofloxacin + # oneOutput: "HP:0012213" ## Decreased glomerular filtration rate + ChemCHEBI_increased_PhenoHP-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: HP + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.CHEBI, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: CHEBI + semantic: SmallMolecule + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" + # testExamples: + # - qInput: "HP:0011897" ## Neutrophilia + # oneOutput: "CHEBI:100241" ## ciprofloxacin + ChemCHEBI_increased_PhenoNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## 222 records + - supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + semantic: SmallMolecule + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C15271" ## Liver Transplantation - # oneOutput: "SNOMEDCT:197354009" ## Toxic liver disease (disorder) - PhenoSNOMEDCT_decreased_PhenoSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ## 2 records - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "CHEBI:167638" ## labetalol + # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive + ChemCHEBI_increased_PhenoNCIT-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: NCIT + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.CHEBI, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: CHEBI + semantic: SmallMolecule + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" + # testExamples: + # - qInput: "NCIT:C167118" ## Influenza B Virus Positive + # oneOutput: "CHEBI:16714" ## codeine + ChemCHEBI_increased_PhenoSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + ## 15 records + - supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + semantic: SmallMolecule + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "SNOMEDCT:191519005" ## Dementia associated with another disease (disorder) - # oneOutput: "SNOMEDCT:127295002" ## Traumatic brain injury (disorder) - PhenoSNOMEDCT_decreased_PhenoSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "CHEBI:6888" ## methylprednisolone + # oneOutput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) + ChemCHEBI_increased_PhenoSNOMEDCT-rev: + - supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "SNOMEDCT:386033004" ## Neuropathy (disorder) - # oneOutput: "SNOMEDCT:47049007" ## Ankylosis of spine (disorder) - PhenoSNOMEDCT_decreased_ProcedureNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.CHEBI, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: CHEBI + semantic: SmallMolecule + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" + # testExamples: + # - qInput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) + # oneOutput: "CHEBI:7476" ## naproxen + ChemUNII_increased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 390 records + - supportBatch: true + useTemplating: true + inputs: + - id: UNII + semantic: SmallMolecule + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "UNII:1BJ477IO2L" ## gadobutrol + # oneOutput: "HP:0025406" ## Asthenia + ChemUNII_increased_PhenoHP-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: HP + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.UNII, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: UNII + semantic: SmallMolecule + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-UNII" + # testExamples: + # - qInput: "HP:0011227" ## Elevated C-reactive protein level + # oneOutput: "UNII:1BJ477IO2L" ## gadobutrol + ChemUNII_increased_PhenoNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## 26 records + - supportBatch: true + useTemplating: true + inputs: + - id: UNII + semantic: SmallMolecule + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: NCIT + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "UNII:T2410KM04A" ## heparin + # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive + ChemUNII_increased_PhenoNCIT-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: NCIT + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.UNII, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: UNII + semantic: SmallMolecule + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-UNII" + # testExamples: + # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + # oneOutput: "UNII:E47C0NF7LV" ## enoxaparin + ## no records for ChemUNII_increased_PhenoSNOMEDCT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + ProcedureNCIT_increased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 21 records + - supportBatch: true + useTemplating: true + inputs: + - id: NCIT + semantic: Procedure + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "NCIT:C50815" ## Aortic Valve Replacement + # oneOutput: "HP:0002094" ## Dyspnea + ProcedureNCIT_increased_PhenoHP-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: HP + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-NCIT" + # testExamples: + # - qInput: "HP:0001919" ## Acute kidney injury + # oneOutput: "NCIT:C50815" ## Aortic Valve Replacement + ## no records for ProcedureNCIT_increased_PhenoNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## no records for ProcedureNCIT_increased_PhenoSNOMEDCT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + ChemCHEBI_increased_ProcedureNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Procedure + ## 19 records + - supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + semantic: SmallMolecule + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Procedure"]') }} ], + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "CHEBI:3311" ## calcium carbonate + # oneOutput: "NCIT:C15271" ## Liver Transplantation + ChemCHEBI_increased_ProcedureNCIT-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: NCIT + semantic: Procedure + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Procedure"]') }} ], + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.CHEBI, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: CHEBI + semantic: SmallMolecule + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" + # testExamples: + # - qInput: "NCIT:C15271" ## Liver Transplantation + # oneOutput: "CHEBI:534" ## docusate + ChemUNII_increased_ProcedureNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Procedure ## 2 records - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:197352008" ## Toxic hepatitis (disorder) - # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - PhenoSNOMEDCT_decreased_ProcedureNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + - supportBatch: true + useTemplating: true + inputs: + - id: UNII + semantic: SmallMolecule + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Procedure"]') }} ], + "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C155871" ## Herpes Simplex Virus Infection - # oneOutput: "SNOMEDCT:76571007" ## Septic shock (disorder) - PhenoSNOMEDCT_increased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 158 records - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "SNOMEDCT:54404000" ## Cervical radiculopathy (disorder) - # oneOutput: "MONDO:0005420" ## hypothyroidism - PhenoSNOMEDCT_increased_DiseaseMONDO_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: increased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "UNII:3FYP5M0IJX" ## sennosides + # oneOutput: "NCIT:C15271" ## Liver Transplantation + ChemUNII_increased_ProcedureNCIT-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: NCIT + semantic: Procedure + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_increased_likelihood_of", "biolink:Procedure"]') }} ], + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.UNII, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: UNII + semantic: SmallMolecule + predicate: associated_with + qualifiers: + subject_direction_qualifier: increased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-UNII" + # testExamples: + # - qInput: "NCIT:C15271" ## Liver Transplantation + # oneOutput: "UNII:T2410KM04A" ## heparin + ## no records for ProcedureNCIT_increased_ProcedureNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_increased_likelihood_of%20AND%20object.type:Procedure + ChemCHEBI_decreased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 4281 records + - supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + semantic: SmallMolecule + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "MONDO:0020066" ## Ehlers-Danlos syndrome - # oneOutput: "SNOMEDCT:127295002" ## Traumatic brain injury (disorder) - PhenoSNOMEDCT_increased_DiseaseNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## 2 records - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:711150003" ## Long-term current use of anticoagulant (situation) - # oneOutput: "NCIT:C167118" ## Influenza A Virus Positive - PhenoSNOMEDCT_increased_DiseaseNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "CHEBI:100241" ## ciprofloxacin + # oneOutput: "MONDO:0005298" ## osteoporosis + ChemCHEBI_decreased_DiseaseMONDO-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: MONDO + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.CHEBI, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: CHEBI + semantic: SmallMolecule + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" + # testExamples: + # - qInput: "MONDO:0005173" ## actinic keratosis (disease) + # oneOutput: "CHEBI:100241" ## ciprofloxacin + ChemCHEBI_decreased_DiseaseNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ## 1 record + - supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + semantic: SmallMolecule + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - # oneOutput: "SNOMEDCT:386033004" ## Neuropathy (disorder) - PhenoSNOMEDCT_increased_DiseaseSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 13 records - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "SNOMEDCT:2415007" ## Lumbosacral radiculopathy (disorder) - # oneOutput: "SNOMEDCT:709073001" ## Neurocognitive disorder (disorder) - PhenoSNOMEDCT_increased_DiseaseSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "CHEBI:5855" ## ibuprofen + # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + ChemCHEBI_decreased_DiseaseNCIT-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: NCIT + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.CHEBI, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: CHEBI + semantic: SmallMolecule + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" + # testExamples: + # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder + # oneOutput: "CHEBI:5855" ## ibuprofen + ChemCHEBI_decreased_DiseaseSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + ## 288 records + - supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + semantic: SmallMolecule + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "SNOMEDCT:386033004" ## Neuropathy (disorder) - # oneOutput: "SNOMEDCT:202805003" ## Sacroiliac disorder (disorder) - PhenoSNOMEDCT_increased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 113 records - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "CHEBI:119915" ## fentanyl + # oneOutput: "SNOMEDCT:54404000" ## Cervical radiculopathy (disorder) + ChemCHEBI_decreased_DiseaseSNOMEDCT-rev: + - supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "SNOMEDCT:201839001" ## Primary coxarthrosis, bilateral (disorder) - # oneOutput: "HP:0003259" ## Elevated serum creatinine - PhenoSNOMEDCT_increased_PhenoHP_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "HP:0002829" ## Arthralgia - # oneOutput: "SNOMEDCT:66944004" ## Autoimmune thyroiditis (disorder) - PhenoSNOMEDCT_increased_PhenoNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 5 records - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.CHEBI, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: CHEBI + semantic: SmallMolecule + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" + # testExamples: + # - qInput: "SNOMEDCT:237519003" ## Autoimmune hypothyroidism (disorder) + # oneOutput: "CHEBI:119915" ## fentanyl + ChemUNII_decreased_DiseaseMONDO: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO + ## 41 records + - supportBatch: true + useTemplating: true + inputs: + - id: UNII + semantic: SmallMolecule + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: MONDO + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "UNII:3FYP5M0IJX" ## sennosides + # oneOutput: "MONDO:0004946" ## hypoglycemia + ChemUNII_decreased_DiseaseMONDO-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: MONDO + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.UNII, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: UNII + semantic: SmallMolecule + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-UNII" + # testExamples: + # - qInput: "MONDO:0004375" ## end stage renal failure + # oneOutput: "UNII:3FYP5M0IJX" ## sennosides + ## no records for ChemUNII_decreased_DiseaseNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT + ChemUNII_decreased_DiseaseSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT + ## 2 records + - supportBatch: true + useTemplating: true + inputs: + - id: UNII + semantic: SmallMolecule + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:166816003" ## Serum lipids high (finding) - # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - PhenoSNOMEDCT_increased_PhenoNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C159516" ## Liver Lesion - # oneOutput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) - PhenoSNOMEDCT_increased_ProcedureNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:PhenotypicFeature%20AND%20_exists_:subject.SNOMEDCT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT - ## 1 records - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "UNII:OP401G7OJC" ## etanercept + # oneOutput: "SNOMEDCT:239792003" ## Seronegative rheumatoid arthritis (disorder) + ChemUNII_decreased_DiseaseSNOMEDCT-rev: + - supportBatch: true + useTemplating: true + inputs: - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["subject.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:201839001" ## Primary coxarthrosis, bilateral (disorder) - # oneOutput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission - PhenoSNOMEDCT_increased_ProcedureNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:PhenotypicFeature", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C167118" ## Influenza A Virus Positive - # oneOutput: "SNOMEDCT:197352008" ## Toxic hepatitis (disorder) + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.UNII, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: UNII + semantic: SmallMolecule + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-UNII" + # testExamples: + # - qInput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) + # oneOutput: "UNII:OP401G7OJC" ## etanercept ProcedureNCIT_decreased_DiseaseMONDO: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 721 records - -supportBatch: true - useTemplating: true - inputs: + ## 60 records + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "NCIT:C167118" ## Influenza A Virus Positive - # oneOutput: "MONDO:0012883" ## acute promyelocytic leukemia - ProcedureNCIT_decreased_DiseaseMONDO_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Procedure + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.MONDO, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "MONDO:0005393" ## gout - # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - ProcedureNCIT_decreased_DiseaseNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## 4 records - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C159516" ## Liver Lesion - # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - ProcedureNCIT_decreased_DiseaseNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-MONDO" + # testExamples: + # - qInput: "NCIT:C15546" ## Breast Cancer Screening + # oneOutput: "MONDO:0007743" ## attention deficit-hyperactivity disorder + ProcedureNCIT_decreased_DiseaseMONDO-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: MONDO + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - # oneOutput: "NCIT:C141278" ## Adenovirus Positive + semantic: Procedure + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-NCIT" + # testExamples: + # - qInput: "MONDO:0005294" ## peripheral vascular disease + # oneOutput: "NCIT:C15546" ## Breast Cancer Screening + ## no records for ProcedureNCIT_decreased_DiseaseNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT ProcedureNCIT_decreased_DiseaseSNOMEDCT: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 58 records - -supportBatch: true - useTemplating: true - inputs: + ## 4 records + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive - # oneOutput: "SNOMEDCT:66944004" ## Autoimmune thyroiditis (disorder) - ProcedureNCIT_decreased_DiseaseSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Procedure + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:711150003" ## Long-term current use of anticoagulant (situation) - # oneOutput: "NCIT:C141278" ## Adenovirus Positive - ProcedureNCIT_decreased_PhenoHP: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 502 records - -supportBatch: true - useTemplating: true - inputs: + semantic: Disease + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "NCIT:C15546" ## Breast Cancer Screening + # oneOutput: "SNOMEDCT:54404000" ## Cervical radiculopathy (disorder) + ProcedureNCIT_decreased_DiseaseSNOMEDCT-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + semantic: Disease + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:Disease"]') }} ], + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "NCIT:C141278" ## Adenovirus Positive - # oneOutput: "HP:0001260" ## Dysarthria - ProcedureNCIT_decreased_PhenoHP_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Procedure + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-NCIT" + # testExamples: + # - qInput: "SNOMEDCT:239792003" ## Seronegative rheumatoid arthritis (disorder) + # oneOutput: "NCIT:C15546" ## Breast Cancer Screening + ChemCHEBI_decreased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 5600 records + - supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + semantic: SmallMolecule + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "HP:0011900" ## Hypofibrinogenemia - # oneOutput: "NCIT:C167118" ## Influenza A Virus Positive - ProcedureNCIT_decreased_PhenoNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 56 records - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C159516" ## Liver Lesion - # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive - ProcedureNCIT_decreased_PhenoNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "CHEBI:100241" ## ciprofloxacin + # oneOutput: "HP:0002904" ## Hyperbilirubinemia + ChemCHEBI_decreased_PhenoHP-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: HP + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.CHEBI, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: CHEBI + semantic: SmallMolecule + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" + # testExamples: + # - qInput: "HP:0002829" ## Arthralgia + # oneOutput: "CHEBI:100241" ## ciprofloxacin + ChemCHEBI_decreased_PhenoNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## 191 records + - supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + semantic: SmallMolecule + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission - # oneOutput: "NCIT:C167118" ## Influenza A Virus Positive - ProcedureNCIT_decreased_PhenoSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ## 4 records - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "CHEBI:135866" ## clindamycin + # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + ChemCHEBI_decreased_PhenoNCIT-rev: + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C52007" ## Arthrodesis - # oneOutput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) - ProcedureNCIT_decreased_PhenoSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.CHEBI, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: CHEBI + semantic: SmallMolecule + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" + # testExamples: + # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + # oneOutput: "CHEBI:119915" ## fentanyl + ChemCHEBI_decreased_PhenoSNOMEDCT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + ## 28 records + - supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + semantic: SmallMolecule + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.SNOMEDCT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) - # oneOutput: "NCIT:C146650" ## Clostridium difficile Positive - ProcedureNCIT_decreased_ProcedureNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT - ## 3 records - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C38033" ## Arthroscopy - # oneOutput: "NCIT:C167118" ## Influenza A Virus Positive - ProcedureNCIT_decreased_ProcedureNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C146650" ## Clostridium difficile Positive - # oneOutput: "NCIT:C155871" ## Herpes Simplex Virus Infection - ProcedureNCIT_increased_DiseaseMONDO: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.MONDO - ## 209 records - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.MONDO, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: MONDO - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-MONDO" - # testExamples: - # - qInput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - # oneOutput: "MONDO:0006694" ## cerebral atherosclerosis - ProcedureNCIT_increased_DiseaseMONDO_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: MONDO - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.MONDO", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "MONDO:0005155" ## cirrhosis of liver - # oneOutput: "NCIT:C38033" ## Arthroscopy - ProcedureNCIT_increased_DiseaseNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.NCIT - ## 2 records - -supportBatch: true - useTemplating: true - inputs: - - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C3587" ## Chronic Lymphocytic Leukemia in Remission - # oneOutput: "NCIT:C15271" ## Liver Transplantation - ProcedureNCIT_increased_DiseaseNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" + # testExamples: + # - qInput: "CHEBI:2955" ## azithromycin + # oneOutput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) + ChemCHEBI_decreased_PhenoSNOMEDCT-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: SNOMEDCT + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.CHEBI, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: CHEBI + semantic: SmallMolecule + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" + # testExamples: + # - qInput: "SNOMEDCT:48440001" ## Arthritis due to gout (disorder) + # oneOutput: "CHEBI:4636" ## diphenhydramine + ChemUNII_decreased_PhenoHP: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP + ## 113 records + - supportBatch: true + useTemplating: true + inputs: + - id: UNII + semantic: SmallMolecule + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "UNII:1BJ477IO2L" ## gadobutrol + # oneOutput: "HP:0031969" ## Reduced blood urea nitrogen + ChemUNII_decreased_PhenoHP-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: HP + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.UNII, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: UNII + semantic: SmallMolecule + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-UNII" + # testExamples: + # - qInput: "HP:0031098" ## Decreased thyroid-stimulating hormone level + # oneOutput: "UNII:1BJ477IO2L" ## gadobutrol + ChemUNII_decreased_PhenoNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT + ## 1 record + - supportBatch: true + useTemplating: true + inputs: + - id: UNII + semantic: SmallMolecule + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.UNII", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C3586" ## Acute Lymphoblastic Leukemia in Remission - # oneOutput: "NCIT:C3587" ## Chronic Lymphocytic Leukemia in Remission - ProcedureNCIT_increased_DiseaseSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Disease%20AND%20_exists_:object.SNOMEDCT - ## 20 records - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "UNII:1BJ477IO2L" ## gadobutrol + # oneOutput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + ChemUNII_decreased_PhenoNCIT-rev: + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: Disease - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission - # oneOutput: "SNOMEDCT:197352008" ## Toxic hepatitis (disorder) - ProcedureNCIT_increased_DiseaseSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: Disease - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:Disease"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:2415007" ## Lumbosacral radiculopathy (disorder) - # oneOutput: "NCIT:C52007" ## Arthrodesis - ProcedureNCIT_increased_PhenoHP: + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.UNII, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: UNII + semantic: SmallMolecule + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-UNII" + # testExamples: + # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + # oneOutput: "UNII:1BJ477IO2L" ## gadobutrol + ## no records for ChemUNII_decreased_PhenoSNOMEDCT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + ProcedureNCIT_decreased_PhenoHP: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.HP - ## 158 records - -supportBatch: true - useTemplating: true - inputs: + ## 81 records + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.HP, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: HP - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-HP" - # testExamples: - # - qInput: "NCIT:C141278" ## Adenovirus Positive - # oneOutput: "HP:0001369" ## Arthritis - ProcedureNCIT_increased_PhenoHP_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Procedure + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.HP, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: HP + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-HP" + # testExamples: + # - qInput: "NCIT:C15546" ## Breast Cancer Screening + # oneOutput: "HP:0001882" ## Leukopenia + ProcedureNCIT_decreased_PhenoHP-rev: + - supportBatch: true + useTemplating: true + inputs: - id: HP - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "HP:0008151" ## Prolonged prothrombin time - # oneOutput: "NCIT:C155871" ## Herpes Simplex Virus Infection - ProcedureNCIT_increased_PhenoNCIT: + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.HP", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: NCIT + semantic: Procedure + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-NCIT" + # testExamples: + # - qInput: "HP:0001681" ## Angina pectoris + # oneOutput: "NCIT:C15546" ## Breast Cancer Screening + ProcedureNCIT_decreased_PhenoNCIT: ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.NCIT - ## 4 records - -supportBatch: true - useTemplating: true - inputs: + ## 5 records + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C167118" ## Influenza A Virus Positive - # oneOutput: "NCIT:C3588" ## Acute Myeloid Leukemia in Remission - ProcedureNCIT_increased_PhenoNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Procedure + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C159516" ## Liver Lesion - # oneOutput: "NCIT:C116994" ## Lupus Anticoagulant Disorder - ProcedureNCIT_increased_PhenoSNOMEDCT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT - ## 2 records - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "NCIT:C15546" ## Breast Cancer Screening + # oneOutput: "NCIT:C167118" ## Influenza B Virus Positive + ProcedureNCIT_decreased_PhenoNCIT-rev: + - supportBatch: true + useTemplating: true + inputs: - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.SNOMEDCT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: SNOMEDCT - semantic: PhenotypicFeature - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-SNOMEDCT" - # testExamples: - # - qInput: "NCIT:C155871" ## Herpes Simplex Virus Infection - # oneOutput: "SNOMEDCT:239791005" ## Seropositive rheumatoid arthritis (disorder) - ProcedureNCIT_increased_PhenoSNOMEDCT_rev: - -supportBatch: true - useTemplating: true - inputs: - - id: SNOMEDCT - - semantic: PhenotypicFeature - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:PhenotypicFeature"]') } ] - "scopes": ["object.SNOMEDCT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "SNOMEDCT:197354009" ## Toxic liver disease (disorder) - # oneOutput: "NCIT:C51691" ## Arthroplasty - ProcedureNCIT_increased_ProcedureNCIT: - ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure%20AND%20_exists_:object.NCIT - ## 2 records - -supportBatch: true - useTemplating: true - inputs: + semantic: PhenotypicFeature + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:Procedure", "associated_with_decreased_likelihood_of", "biolink:PhenotypicFeature"]') }} ], + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["subject.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: object.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C15546" ## Breast Cancer Screening - # oneOutput: "NCIT:C167118" ## Influenza A Virus Positive - ProcedureNCIT_increased_ProcedureNCIT_rev: - -supportBatch: true - useTemplating: true - inputs: + semantic: Procedure + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-NCIT" + # testExamples: + # - qInput: "NCIT:C171647" ## SARS Coronavirus 2 Positive + # oneOutput: "NCIT:C15546" ## Breast Cancer Screening + ## no records for ProcedureNCIT_decreased_PhenoSNOMEDCT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20_exists_:subject.NCIT%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:PhenotypicFeature%20AND%20_exists_:object.SNOMEDCT + ChemCHEBI_decreased_ProcedureNCIT: + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.CHEBI%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure + ## 8 records + - supportBatch: true + useTemplating: true + inputs: + - id: CHEBI + semantic: SmallMolecule + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') }} ], + "scopes": ["subject.CHEBI", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + object.NCIT, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: - id: NCIT - - semantic: Procedure - requestBody: - body: >- - { - "q": [ { queryInputs | rmPrefix() | wrap ( '["' , '","biolink:Procedure", "associated_with_increased_likelihood_of", "biolink:Procedure"]') } ] - "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] - } - parameters: - fields: subject.NCIT, association.edge_attributes, subject.name, object.name, source.edge_sources - size: 1000 - outputs: - -id: NCIT - semantic: Procedure - predicate: associated_with - qualifiers: - object_direction_qualifier: increased - object_aspect_qualifier: likelihood - response_mapping: - "ref": "#/components/x-bte-response-mapping/object-NCIT" - # testExamples: - # - qInput: "NCIT:C155871" ## Herpes Simplex Virus Infection - # oneOutput: "NCIT:C51691" ## Arthroplasty - + semantic: Procedure + predicate: associated_with + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-NCIT" + # testExamples: + # - qInput: "CHEBI:6637" ## magnesium hydroxide + # oneOutput: "NCIT:C15271" ## Liver Transplantation + ChemCHEBI_decreased_ProcedureNCIT-rev: + - supportBatch: true + useTemplating: true + inputs: + - id: NCIT + semantic: Procedure + requestBodyType: object + requestBody: + body: >- + { + "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:ChemicalEntity", "associated_with_decreased_likelihood_of", "biolink:Procedure"]') }} ], + "scopes": ["object.NCIT", "subject.type", "association.predicate", "object.type"] + } + parameters: + fields: >- + subject.CHEBI, + association.edge_attributes, + subject.name,object.name + size: 1000 + outputs: + - id: CHEBI + semantic: SmallMolecule + predicate: associated_with + qualifiers: + subject_direction_qualifier: decreased + subject_aspect_qualifier: likelihood + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-CHEBI" + # testExamples: + # - qInput: "NCIT:C15271" ## Liver Transplantation + # oneOutput: "CHEBI:5855" ## ibuprofen + ## no records for ChemUNII_decreased_ProcedureNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:ChemicalEntity%20AND%20_exists_:subject.UNII%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure + ## no records for ProcedureNCIT_decreased_ProcedureNCIT + ## https://pending.biothings.io/multiomics_ehr_risk_kp/query?q=subject.type:Procedure%20AND%20association.predicate:associated_with_decreased_likelihood_of%20AND%20object.type:Procedure x-bte-response-mapping: object-MONDO: MONDO: object.MONDO input_name: subject.name output_name: object.name edge-attributes: association.edge_attributes - trapi_sources: source.edge_sources object-NCIT: NCIT: object.NCIT input_name: subject.name output_name: object.name edge-attributes: association.edge_attributes - trapi_sources: source.edge_sources object-SNOMEDCT: SNOMEDCT: object.SNOMEDCT input_name: subject.name output_name: object.name edge-attributes: association.edge_attributes - trapi_sources: source.edge_sources object-HP: HP: object.HP input_name: subject.name output_name: object.name edge-attributes: association.edge_attributes - trapi_sources: source.edge_sources object-CHEBI: CHEBI: object.CHEBI input_name: subject.name output_name: object.name edge-attributes: association.edge_attributes - trapi_sources: source.edge_sources object-UNII: UNII: object.UNII input_name: subject.name output_name: object.name edge-attributes: association.edge_attributes - trapi_sources: source.edge_sources subject-MONDO: MONDO: subject.MONDO input_name: object.name output_name: subject.name edge-attributes: association.edge_attributes - trapi_sources: source.edge_sources subject-NCIT: NCIT: subject.NCIT input_name: object.name output_name: subject.name edge-attributes: association.edge_attributes - trapi_sources: source.edge_sources subject-SNOMEDCT: SNOMEDCT: subject.SNOMEDCT input_name: object.name output_name: subject.name edge-attributes: association.edge_attributes - trapi_sources: source.edge_sources subject-HP: HP: subject.HP input_name: object.name output_name: subject.name edge-attributes: association.edge_attributes - trapi_sources: source.edge_sources subject-CHEBI: CHEBI: subject.CHEBI input_name: object.name output_name: subject.name edge-attributes: association.edge_attributes - trapi_sources: source.edge_sources subject-UNII: UNII: subject.UNII input_name: object.name output_name: subject.name - edge-attributes: association.edge_attributes - trapi_sources: source.edge_sources + edge-attributes: association.edge_attributes \ No newline at end of file From fd5c58b642e575f2fd1b2524738bc710f908f557 Mon Sep 17 00:00:00 2001 From: GitHubbit <10294502+GitHubbit@users.noreply.github.com> Date: Fri, 2 Jun 2023 13:37:57 -0400 Subject: [PATCH 5/6] Added support for TRAPI 1.4 provenance (aka the sources section on Edges). --- ehr_risk_kp.yaml | 310 ++++++++++++++++++++++++----------------------- 1 file changed, 161 insertions(+), 149 deletions(-) diff --git a/ehr_risk_kp.yaml b/ehr_risk_kp.yaml index c379d72..a4a9425 100644 --- a/ehr_risk_kp.yaml +++ b/ehr_risk_kp.yaml @@ -813,7 +813,7 @@ components: parameters: fields: >- object.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -844,7 +844,7 @@ components: parameters: fields: >- subject.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -877,7 +877,7 @@ components: parameters: fields: >- object.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -908,7 +908,7 @@ components: parameters: fields: >- subject.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -941,7 +941,7 @@ components: parameters: fields: >- object.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -972,7 +972,7 @@ components: parameters: fields: >- subject.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1005,7 +1005,7 @@ components: parameters: fields: >- object.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1036,7 +1036,7 @@ components: parameters: fields: >- subject.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1079,7 +1079,7 @@ components: parameters: fields: >- object.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1110,7 +1110,7 @@ components: parameters: fields: >- subject.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1143,7 +1143,7 @@ components: parameters: fields: >- object.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1174,7 +1174,7 @@ components: parameters: fields: >- subject.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1207,7 +1207,7 @@ components: parameters: fields: >- object.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1238,7 +1238,7 @@ components: parameters: fields: >- subject.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1277,7 +1277,7 @@ components: parameters: fields: >- object.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1308,7 +1308,7 @@ components: parameters: fields: >- subject.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1345,7 +1345,7 @@ components: parameters: fields: >- object.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1376,7 +1376,7 @@ components: parameters: fields: >- subject.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1413,7 +1413,7 @@ components: parameters: fields: >- object.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1444,7 +1444,7 @@ components: parameters: fields: >- subject.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1477,7 +1477,7 @@ components: parameters: fields: >- object.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1508,7 +1508,7 @@ components: parameters: fields: >- subject.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1541,7 +1541,7 @@ components: parameters: fields: >- object.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1572,7 +1572,7 @@ components: parameters: fields: >- subject.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1611,7 +1611,7 @@ components: parameters: fields: >- object.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1642,7 +1642,7 @@ components: parameters: fields: >- subject.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1679,7 +1679,7 @@ components: parameters: fields: >- object.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1710,7 +1710,7 @@ components: parameters: fields: >- subject.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1743,7 +1743,7 @@ components: parameters: fields: >- object.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1774,7 +1774,7 @@ components: parameters: fields: >- subject.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1815,7 +1815,7 @@ components: parameters: fields: >- object.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1846,7 +1846,7 @@ components: parameters: fields: >- subject.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1883,7 +1883,7 @@ components: parameters: fields: >- object.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1914,7 +1914,7 @@ components: parameters: fields: >- subject.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1951,7 +1951,7 @@ components: parameters: fields: >- object.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -1982,7 +1982,7 @@ components: parameters: fields: >- subject.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2015,7 +2015,7 @@ components: parameters: fields: >- object.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2046,7 +2046,7 @@ components: parameters: fields: >- subject.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2079,7 +2079,7 @@ components: parameters: fields: >- object.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2110,7 +2110,7 @@ components: parameters: fields: >- subject.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2143,7 +2143,7 @@ components: parameters: fields: >- object.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2174,7 +2174,7 @@ components: parameters: fields: >- subject.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2211,7 +2211,7 @@ components: parameters: fields: >- object.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2242,7 +2242,7 @@ components: parameters: fields: >- subject.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2277,7 +2277,7 @@ components: parameters: fields: >- object.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2308,7 +2308,7 @@ components: parameters: fields: >- subject.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2341,7 +2341,7 @@ components: parameters: fields: >- object.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2372,7 +2372,7 @@ components: parameters: fields: >- subject.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2405,7 +2405,7 @@ components: parameters: fields: >- object.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2436,7 +2436,7 @@ components: parameters: fields: >- subject.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2469,7 +2469,7 @@ components: parameters: fields: >- object.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2500,7 +2500,7 @@ components: parameters: fields: >- subject.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2533,7 +2533,7 @@ components: parameters: fields: >- object.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2564,7 +2564,7 @@ components: parameters: fields: >- subject.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2601,7 +2601,7 @@ components: parameters: fields: >- object.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2632,7 +2632,7 @@ components: parameters: fields: >- subject.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2669,7 +2669,7 @@ components: parameters: fields: >- object.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2700,7 +2700,7 @@ components: parameters: fields: >- subject.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2737,7 +2737,7 @@ components: parameters: fields: >- object.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2768,7 +2768,7 @@ components: parameters: fields: >- subject.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2801,7 +2801,7 @@ components: parameters: fields: >- object.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2832,7 +2832,7 @@ components: parameters: fields: >- subject.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2865,7 +2865,7 @@ components: parameters: fields: >- object.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2896,7 +2896,7 @@ components: parameters: fields: >- subject.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2929,7 +2929,7 @@ components: parameters: fields: >- object.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2960,7 +2960,7 @@ components: parameters: fields: >- subject.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -2995,7 +2995,7 @@ components: parameters: fields: >- object.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3026,7 +3026,7 @@ components: parameters: fields: >- subject.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3059,7 +3059,7 @@ components: parameters: fields: >- object.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3090,7 +3090,7 @@ components: parameters: fields: >- subject.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3125,7 +3125,7 @@ components: parameters: fields: >- object.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3156,7 +3156,7 @@ components: parameters: fields: >- subject.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3189,7 +3189,7 @@ components: parameters: fields: >- object.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3220,7 +3220,7 @@ components: parameters: fields: >- subject.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3253,7 +3253,7 @@ components: parameters: fields: >- object.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3284,7 +3284,7 @@ components: parameters: fields: >- subject.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3317,7 +3317,7 @@ components: parameters: fields: >- object.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3348,7 +3348,7 @@ components: parameters: fields: >- subject.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3381,7 +3381,7 @@ components: parameters: fields: >- object.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3412,7 +3412,7 @@ components: parameters: fields: >- subject.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3445,7 +3445,7 @@ components: parameters: fields: >- object.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3476,7 +3476,7 @@ components: parameters: fields: >- subject.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3511,7 +3511,7 @@ components: parameters: fields: >- object.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3542,7 +3542,7 @@ components: parameters: fields: >- subject.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3579,7 +3579,7 @@ components: parameters: fields: >- object.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3610,7 +3610,7 @@ components: parameters: fields: >- subject.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3647,7 +3647,7 @@ components: parameters: fields: >- object.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3678,7 +3678,7 @@ components: parameters: fields: >- subject.CHEBI, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3711,7 +3711,7 @@ components: parameters: fields: >- object.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3742,7 +3742,7 @@ components: parameters: fields: >- subject.CHEBI, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3775,7 +3775,7 @@ components: parameters: fields: >- object.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3806,7 +3806,7 @@ components: parameters: fields: >- subject.CHEBI, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3839,7 +3839,7 @@ components: parameters: fields: >- object.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3870,7 +3870,7 @@ components: parameters: fields: >- subject.UNII, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3903,7 +3903,7 @@ components: parameters: fields: >- object.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3934,7 +3934,7 @@ components: parameters: fields: >- subject.UNII, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3967,7 +3967,7 @@ components: parameters: fields: >- object.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -3998,7 +3998,7 @@ components: parameters: fields: >- subject.UNII, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4031,7 +4031,7 @@ components: parameters: fields: >- object.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4062,7 +4062,7 @@ components: parameters: fields: >- subject.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4097,7 +4097,7 @@ components: parameters: fields: >- object.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4128,7 +4128,7 @@ components: parameters: fields: >- subject.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4161,7 +4161,7 @@ components: parameters: fields: >- object.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4192,7 +4192,7 @@ components: parameters: fields: >- subject.CHEBI, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4225,7 +4225,7 @@ components: parameters: fields: >- object.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4256,7 +4256,7 @@ components: parameters: fields: >- subject.CHEBI, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4289,7 +4289,7 @@ components: parameters: fields: >- object.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4320,7 +4320,7 @@ components: parameters: fields: >- subject.CHEBI, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4353,7 +4353,7 @@ components: parameters: fields: >- object.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4384,7 +4384,7 @@ components: parameters: fields: >- subject.UNII, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4417,7 +4417,7 @@ components: parameters: fields: >- object.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4448,7 +4448,7 @@ components: parameters: fields: >- subject.UNII, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4483,7 +4483,7 @@ components: parameters: fields: >- object.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4514,7 +4514,7 @@ components: parameters: fields: >- subject.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4551,7 +4551,7 @@ components: parameters: fields: >- object.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4582,7 +4582,7 @@ components: parameters: fields: >- subject.CHEBI, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4615,7 +4615,7 @@ components: parameters: fields: >- object.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4646,7 +4646,7 @@ components: parameters: fields: >- subject.UNII, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4681,7 +4681,7 @@ components: parameters: fields: >- object.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4712,7 +4712,7 @@ components: parameters: fields: >- subject.CHEBI, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4745,7 +4745,7 @@ components: parameters: fields: >- object.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4776,7 +4776,7 @@ components: parameters: fields: >- subject.CHEBI, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4809,7 +4809,7 @@ components: parameters: fields: >- object.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4840,7 +4840,7 @@ components: parameters: fields: >- subject.CHEBI, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4873,7 +4873,7 @@ components: parameters: fields: >- object.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4904,7 +4904,7 @@ components: parameters: fields: >- subject.UNII, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4939,7 +4939,7 @@ components: parameters: fields: >- object.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -4970,7 +4970,7 @@ components: parameters: fields: >- subject.UNII, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -5003,7 +5003,7 @@ components: parameters: fields: >- object.MONDO, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -5034,7 +5034,7 @@ components: parameters: fields: >- subject.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -5069,7 +5069,7 @@ components: parameters: fields: >- object.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -5100,7 +5100,7 @@ components: parameters: fields: >- subject.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -5133,7 +5133,7 @@ components: parameters: fields: >- object.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -5164,7 +5164,7 @@ components: parameters: fields: >- subject.CHEBI, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -5197,7 +5197,7 @@ components: parameters: fields: >- object.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -5228,7 +5228,7 @@ components: parameters: fields: >- subject.CHEBI, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -5261,7 +5261,7 @@ components: parameters: fields: >- object.SNOMEDCT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -5292,7 +5292,7 @@ components: parameters: fields: >- subject.CHEBI, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -5325,7 +5325,7 @@ components: parameters: fields: >- object.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -5356,7 +5356,7 @@ components: parameters: fields: >- subject.UNII, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -5389,7 +5389,7 @@ components: parameters: fields: >- object.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -5420,7 +5420,7 @@ components: parameters: fields: >- subject.UNII, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -5455,7 +5455,7 @@ components: parameters: fields: >- object.HP, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -5486,7 +5486,7 @@ components: parameters: fields: >- subject.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -5519,7 +5519,7 @@ components: parameters: fields: >- object.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -5550,7 +5550,7 @@ components: parameters: fields: >- subject.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -5585,7 +5585,7 @@ components: parameters: fields: >- object.NCIT, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -5616,7 +5616,7 @@ components: parameters: fields: >- subject.CHEBI, - association.edge_attributes, + association.edge_attributes,source.edge_sources, subject.name,object.name size: 1000 outputs: @@ -5641,58 +5641,70 @@ components: input_name: subject.name output_name: object.name edge-attributes: association.edge_attributes + trapi_sources: source.edge_sources object-NCIT: NCIT: object.NCIT input_name: subject.name output_name: object.name edge-attributes: association.edge_attributes + trapi_sources: source.edge_sources object-SNOMEDCT: SNOMEDCT: object.SNOMEDCT input_name: subject.name output_name: object.name edge-attributes: association.edge_attributes + trapi_sources: source.edge_sources object-HP: HP: object.HP input_name: subject.name output_name: object.name edge-attributes: association.edge_attributes + trapi_sources: source.edge_sources object-CHEBI: CHEBI: object.CHEBI input_name: subject.name output_name: object.name edge-attributes: association.edge_attributes + trapi_sources: source.edge_sources object-UNII: UNII: object.UNII input_name: subject.name output_name: object.name edge-attributes: association.edge_attributes + trapi_sources: source.edge_sources subject-MONDO: MONDO: subject.MONDO input_name: object.name output_name: subject.name edge-attributes: association.edge_attributes + trapi_sources: source.edge_sources subject-NCIT: NCIT: subject.NCIT input_name: object.name output_name: subject.name edge-attributes: association.edge_attributes + trapi_sources: source.edge_sources subject-SNOMEDCT: SNOMEDCT: subject.SNOMEDCT input_name: object.name output_name: subject.name edge-attributes: association.edge_attributes + trapi_sources: source.edge_sources subject-HP: HP: subject.HP input_name: object.name output_name: subject.name edge-attributes: association.edge_attributes + trapi_sources: source.edge_sources subject-CHEBI: CHEBI: subject.CHEBI input_name: object.name output_name: subject.name edge-attributes: association.edge_attributes + trapi_sources: source.edge_sources subject-UNII: UNII: subject.UNII input_name: object.name output_name: subject.name - edge-attributes: association.edge_attributes \ No newline at end of file + edge-attributes: association.edge_attributes + trapi_sources: source.edge_sources \ No newline at end of file From 3a852c55f4d348c41af1b23d4693c4ec29fb39eb Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Wed, 28 Jun 2023 14:00:38 -0700 Subject: [PATCH 6/6] fix typo from fixing merge conflicts --- ehr_risk_kp.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/ehr_risk_kp.yaml b/ehr_risk_kp.yaml index c08b588..ac3ed3d 100644 --- a/ehr_risk_kp.yaml +++ b/ehr_risk_kp.yaml @@ -5708,4 +5708,3 @@ components: output_name: subject.name edge-attributes: association.edge_attributes trapi_sources: source.edge_sources - edge-attributes: association.edge_attributes