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update ORPHANET -> orphanet #136

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merged 5 commits into from
Feb 21, 2024
Merged

update ORPHANET -> orphanet #136

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9fdd058
mydisease, biothings rare source: update ORPHANET -> orphanet
colleenXu Dec 5, 2023
227087c
Merge branch 'master' into orphanet-change
colleenXu Dec 13, 2023
727b9c2
complex portal: ORPHANET->orphanet change
colleenXu Dec 13, 2023
6128bb4
Merge branch 'master' into orphanet-change
colleenXu Dec 14, 2023
126dfc0
Merge branch 'master' into orphanet-change
colleenXu Feb 21, 2024
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14 changes: 7 additions & 7 deletions complexportal/smartapi.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -112,7 +112,7 @@ components:
- supportBatch: false
useTemplating: true
inputs:
- id: ORPHANET
- id: orphanet
semantic: Disease
outputs:
- id: ComplexPortal
Expand All @@ -125,7 +125,7 @@ components:
response_mapping:
"$ref": "#/components/x-bte-response-mapping/complex-output"
testExamples:
- qInput: "ORPHANET:848" ## Beta-thalassemia
- qInput: "orphanet:848" ## Beta-thalassemia
oneOutput: "ComplexPortal:CPX-2158" ## Hemoglobin HbA complex
bp2complex:
- supportBatch: false
Expand Down Expand Up @@ -215,7 +215,7 @@ components:
# - id: ComplexPortal
# semantic: MacromolecularComplex
# outputs:
# - id: ORPHANET
# - id: orphanet
# semantic: Disease
# parameters:
# id: "{{ queryInputs }}" ## no prefix
Expand All @@ -228,9 +228,9 @@ components:
# .disease_ids = (.diseases | map([ . | match("\\[(\\S*)\\]"; "g") | .captures | .[0] | .string | split(":") | last ]) | flatten)
# response_mapping:
# "$ref": "#/components/x-bte-response-mapping/complex2disease"
# testExamples:
# - qInput: "ComplexPortal:CPX-2158" ## Hemoglobin HbA complex
# oneOutput: "ORPHANET:848" ## Beta-thalassemia
# # testExamples:
# # - qInput: "ComplexPortal:CPX-2158" ## Hemoglobin HbA complex
# # oneOutput: "orphanet:848" ## Beta-thalassemia
x-bte-response-mapping:
complex-output:
ComplexPortal: elements.complexAC
Expand All @@ -246,5 +246,5 @@ components:
CHEBI: participants.identifier
complex2disease:
## this is a field made with JQ-post-processing
ORPHANET: disease_ids
orphanet: disease_ids

10 changes: 5 additions & 5 deletions mydisease.info/smartapi.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -658,7 +658,7 @@ components:
omim:
OMIM: hpo.omim ## no prefix
orphanet:
ORPHANET: hpo.orphanet ## no prefix
orphanet: hpo.orphanet ## no prefix
mondo: ## added for a bunch of operations
MONDO: mondo.mondo ## HAS PREFIX (MONDO)
ctd-mesh-disease: ## added for chemical-disease operation
Expand Down Expand Up @@ -824,7 +824,7 @@ components:
- supportBatch: true
useTemplating: true
inputs:
- id: ORPHANET
- id: orphanet
semantic: Disease
requestBody:
body:
Expand Down Expand Up @@ -867,7 +867,7 @@ components:
response_mapping:
"$ref": "#/components/x-bte-response-mapping/disease-phenotype"
testExamples:
- qInput: "ORPHANET:881" ## Turner Syndrome
- qInput: "orphanet:881" ## Turner Syndrome
oneOutput: "HP:0000137" ## Abnormality of the ovary
## for ctd-based operations:
## - when the mydisease parser maps the resources' IDs to MONDO, are there situations where a MESH and a OMIM ID map to the same MONDO?
Expand Down Expand Up @@ -1035,7 +1035,7 @@ components:
q: "{{ queryInputs }}"
scopes: hpo.phenotype_related_to_disease.hpo_id
outputs:
- id: ORPHANET
- id: orphanet
semantic: Disease
parameters:
fields: hpo.orphanet
Expand All @@ -1046,7 +1046,7 @@ components:
"$ref": "#/components/x-bte-response-mapping/orphanet"
testExamples:
- qInput: "HP:0000224" ## Hypogeusia
oneOutput: "ORPHANET:99857" ## Secondary Syringomyelia
oneOutput: "orphanet:99857" ## Secondary Syringomyelia
chemical-disease:
- supportBatch: true
useTemplating: true
Expand Down
10 changes: 5 additions & 5 deletions ncats_rare_source/smartapi.yaml
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Expand Up @@ -596,7 +596,7 @@ components:
q: "{{ queryInputs }}" ## no prefix
scopes: entrezgene
outputs:
- id: ORPHANET
- id: orphanet
semantic: Disease
parameters:
## orphanet ID has no prefix
Expand All @@ -608,12 +608,12 @@ components:
"$ref": "#/components/x-bte-response-mapping/diseaseOrphanet-object"
testExamples:
- qInput: "NCBIGene:100" ## ADA
oneOutput: "ORPHANET:39041" ## Omenn syndrome
oneOutput: "orphanet:39041" ## Omenn syndrome
diseaseOrphanet-gene:
- supportBatch: true
useTemplating: true
inputs:
- id: ORPHANET
- id: orphanet
semantic: Disease
requestBody:
body:
Expand All @@ -632,7 +632,7 @@ components:
response_mapping:
"$ref": "#/components/x-bte-response-mapping/gene-object"
testExamples:
- qInput: "ORPHANET:110" ## Bardet-Biedl syndrome
- qInput: "orphanet:110" ## Bardet-Biedl syndrome
oneOutput: "NCBIGene:10806" ## SDCCAG8
gene-diseaseUMLS:
- supportBatch: true
Expand Down Expand Up @@ -689,7 +689,7 @@ components:
## didn't add names for gene -> disease. when I tried, the co-occurrence urls would appear on every Edge,
## when they're supposed to show up only on the edge they correspond to
diseaseOrphanet-object:
ORPHANET: raresource.disease.orphanet ## no prefix
orphanet: raresource.disease.orphanet ## no prefix
ref_url: raresource.disease.cooccurrence_url
## this url leads to a webpage with literature supporting the gene-disease relationship
diseaseUMLS-object:
Expand Down