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BioThings PFOCR: add source_record_url field #153

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Aug 1, 2024
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BioThings PFOCR: add source_record_url field #153

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35 changes: 19 additions & 16 deletions pfocr/smartapi.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -575,7 +575,7 @@ components:
## - Pathways don't have formal IDs that can be used
gene-chem:
## https://biothings.ncats.io/pfocr/query?q=_exists_:associatedWith.mentions.chemicals%20AND%20_exists_:associatedWith.mentions.genes
## 44081 documents. not clear how many gene-chem pairs there are.
## 34857 documents. not clear how many gene-chem pairs there are.
- supportBatch: true
useTemplating: true ## flag to say templating is being used below
inputs:
Expand All @@ -593,7 +593,7 @@ components:
parameters:
fields: >-
associatedWith.mentions.chemicals.mesh,
associatedWith.figureUrl,associatedWith.pmc
associatedWith.figureUrl,associatedWith.pmc,associatedWith.pfocrUrl
size: 1000
predicate: occurs_together_in_literature_with
source: "infores:pfocr"
Expand All @@ -603,7 +603,7 @@ components:
"$ref": "#/components/x-bte-response-mapping/chem"
testExamples:
- qInput: "NCBIGene:3620" ## IDO1
oneOutput: "MESH:D004958" ## Estradiol
oneOutput: "MESH:D004958" ## Estradiol / CHEBI:16469
## should have 2 figures: https://biothings.ncats.io/pfocr/query?q=associatedWith.mentions.chemicals.mesh:D004958%20AND%20associatedWith.mentions.genes.ncbigene:3620
chem-gene:
- supportBatch: true
Expand All @@ -623,7 +623,7 @@ components:
parameters:
fields: >-
associatedWith.mentions.genes.ncbigene,
associatedWith.figureUrl,associatedWith.pmc
associatedWith.figureUrl,associatedWith.pmc,associatedWith.pfocrUrl
size: 1000
predicate: occurs_together_in_literature_with
source: "infores:pfocr"
Expand All @@ -637,7 +637,7 @@ components:
## should have 9 figures: https://biothings.ncats.io/pfocr/query?q=associatedWith.mentions.chemicals.mesh:C000541%20AND%20associatedWith.mentions.genes.ncbigene:208
disease-chem:
## https://biothings.ncats.io/pfocr/query?q=_exists_:associatedWith.mentions.diseases%20AND%20_exists_:associatedWith.mentions.chemicals
## 9232 documents. not clear how many disease-chem pairs there are.
## 10180 documents. not clear how many disease-chem pairs there are.
- supportBatch: true
useTemplating: true ## flag to say templating is being used below
inputs:
Expand All @@ -655,7 +655,7 @@ components:
parameters:
fields: >-
associatedWith.mentions.chemicals.mesh,
associatedWith.figureUrl,associatedWith.pmc
associatedWith.figureUrl,associatedWith.pmc,associatedWith.pfocrUrl
size: 1000
predicate: occurs_together_in_literature_with
source: "infores:pfocr"
Expand All @@ -665,8 +665,8 @@ components:
"$ref": "#/components/x-bte-response-mapping/chem"
testExamples:
- qInput: "MESH:D006623" ## von Hippel-Lindau Disease
oneOutput: "MESH:C516667" ## pazopanib
## should have 9 figures: https://biothings.ncats.io/pfocr/query?q=associatedWith.mentions.chemicals.mesh:C516667%20AND%20associatedWith.mentions.diseases.mesh:D006623
oneOutput: "MESH:C516667" ## pazopanib / CHEBI:71219
## should have 2 figures: https://biothings.ncats.io/pfocr/query?q=associatedWith.mentions.chemicals.mesh:C516667%20AND%20associatedWith.mentions.diseases.mesh:D006623
chem-disease:
- supportBatch: true
useTemplating: true ## flag to say templating is being used below
Expand All @@ -685,7 +685,7 @@ components:
parameters:
fields: >-
associatedWith.mentions.diseases.mesh,
associatedWith.figureUrl,associatedWith.pmc
associatedWith.figureUrl,associatedWith.pmc,associatedWith.pfocrUrl
size: 1000
predicate: occurs_together_in_literature_with
source: "infores:pfocr"
Expand All @@ -695,11 +695,11 @@ components:
"$ref": "#/components/x-bte-response-mapping/disease"
testExamples:
- qInput: "MESH:D002945" ## Cisplatin
oneOutput: "MESH:D009369" ## Neoplasms
## should have 18 figures: https://biothings.ncats.io/pfocr/query?q=associatedWith.mentions.chemicals.mesh:D002945%20AND%20associatedWith.mentions.diseases.mesh:D009369
oneOutput: "MESH:D009369" ## Neoplasms / MONDO:0005070
## should have 22 figures: https://biothings.ncats.io/pfocr/query?q=associatedWith.mentions.chemicals.mesh:D002945%20AND%20associatedWith.mentions.diseases.mesh:D009369
disease-gene:
## https://biothings.ncats.io/pfocr/query?q=_exists_:associatedWith.mentions.diseases%20AND%20_exists_:associatedWith.mentions.genes
## 13354 documents. not clear how many disease-gene pairs there are.
## 11338 documents. not clear how many disease-gene pairs there are.
- supportBatch: true
useTemplating: true ## flag to say templating is being used below
inputs:
Expand All @@ -717,7 +717,7 @@ components:
parameters:
fields: >-
associatedWith.mentions.genes.ncbigene,
associatedWith.figureUrl,associatedWith.pmc
associatedWith.figureUrl,associatedWith.pmc,associatedWith.pfocrUrl
size: 1000
predicate: occurs_together_in_literature_with
source: "infores:pfocr"
Expand Down Expand Up @@ -747,7 +747,7 @@ components:
parameters:
fields: >-
associatedWith.mentions.diseases.mesh,
associatedWith.figureUrl,associatedWith.pmc
associatedWith.figureUrl,associatedWith.pmc,associatedWith.pfocrUrl
size: 1000
predicate: occurs_together_in_literature_with
source: "infores:pfocr"
Expand All @@ -757,20 +757,23 @@ components:
"$ref": "#/components/x-bte-response-mapping/disease"
testExamples:
- qInput: "NCBIGene:3791" ## KDR
oneOutput: "MESH:D002318" ## Cardiovascular Diseases
## should have 1 figure: https://biothings.ncats.io/pfocr/query?q=associatedWith.mentions.genes.ncbigene:3791%20AND%20associatedWith.mentions.diseases.mesh:D002318
oneOutput: "MESH:D002289" ## non-small cell lung carcinoma / MONDO:0005233
## should have 3 figures: https://biothings.ncats.io/pfocr/query?q=associatedWith.mentions.genes.ncbigene:3791%20AND%20associatedWith.mentions.diseases.mesh:D002289
x-bte-response-mapping:
## not including because because data-processing / biolink-modeling issues
## - associatedWith.title (title of figure)
chem:
MESH: associatedWith.mentions.chemicals.mesh ## no prefix
ref_url: associatedWith.figureUrl
ref_pmcid: associatedWith.pmc ## no prefix (but IDs start with "PMC")
source_url: associatedWith.pfocrUrl
gene:
NCBIGene: associatedWith.mentions.genes.ncbigene ## no prefix
ref_url: associatedWith.figureUrl
ref_pmcid: associatedWith.pmc
source_url: associatedWith.pfocrUrl
disease:
MESH: associatedWith.mentions.diseases.mesh ## no prefix
ref_url: associatedWith.figureUrl
ref_pmcid: associatedWith.pmc
source_url: associatedWith.pfocrUrl