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adding source_record_url support #148

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merged 10 commits into from
Jun 18, 2024
Merged

adding source_record_url support #148

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7638ec9
biothings bindingdb: change ref_url -> source_url for diff handling
colleenXu Mar 27, 2024
b056dab
biothings bindingdb: update testExample comments
colleenXu Mar 28, 2024
8e15162
Merge branch 'master' into source_record_urls
colleenXu Apr 2, 2024
f262855
biothings rare source: change ref_url -> source_url for diff handling
colleenXu Apr 2, 2024
daf82f4
mygene geneToDisease clingen: change ref_url -> source_url
colleenXu Apr 2, 2024
db7672f
Merge branch 'master' into source_record_urls
colleenXu Apr 9, 2024
53a5955
Merge branch 'master' into source_record_urls
colleenXu Apr 10, 2024
cae5165
Merge branch 'master' into source_record_urls
colleenXu Apr 10, 2024
10cd799
Merge branch 'master' into source_record_urls
colleenXu Apr 10, 2024
68fd753
biothings rare-source: revert to using ref_url
colleenXu Apr 17, 2024
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10 changes: 5 additions & 5 deletions bindingdb/smartapi.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -606,7 +606,7 @@ components:
"$ref": "#/components/x-bte-response-mapping/pubchem-object"
testExamples:
- qInput: "UniProtKB:Q08722" ## Leukocyte surface antigen CD47
oneOutput: "INCHIKEY:CLTVCCLZSPKLRB-NRGGWPRRSA-N" ## CHEMBL4474790 / H-D-Lys-N(Me)Arg-Phe-Tyr-Val-Val-Nle-Trp-Lys-D-Lys-OH
oneOutput: "INCHIKEY:CLTVCCLZSPKLRB-NRGGWPRRSA-N" ## PUBCHEM.COMPOUND:155537282 / CHEMBL4474790
ligand-protein:
- supportBatch: true
useTemplating: true
Expand Down Expand Up @@ -637,8 +637,8 @@ components:
response_mapping:
"$ref": "#/components/x-bte-response-mapping/uniprot-subject"
testExamples:
- qInput: "INCHIKEY:NZLXOECMDRNZDN-GUYCJALGSA-N" ## US10736883, Example 387.0
oneOutput: "UniProtKB:P35414" ## Apelin receptor / APLNR
- qInput: "INCHIKEY:NZLXOECMDRNZDN-GUYCJALGSA-N" ## PUBCHEM.COMPOUND:134553288 (US10736883, Example 387.0)
oneOutput: "UniProtKB:P35414" ## NCBIGene:187 (Apelin receptor / APLNR)
x-bte-response-mapping:
## note on references:
## sometimes the doi + pmid will refer to the same publication (so..."duplicate" references)
Expand All @@ -651,7 +651,7 @@ components:
input_name: subject.name ## was called "Target Name Assigned by Curator or DataSource"
ref_pmid: relation.pmid ## no prefix
ref_doi: relation.article_doi
ref_url: relation.bindingdb_link
source_url: relation.bindingdb_link
## commenting out because data-processing / biolink-modeling issues
# in_taxon: subject.organism ## was called "Target Source Organism According to Curator or DataSource"
# bindingdb_curation_datasource: relation.curation_datasource ## Curation/DataSource
Expand All @@ -662,7 +662,7 @@ components:
input_name: object.name
ref_pmid: relation.pmid ## no prefix
ref_doi: relation.article_doi
ref_url: relation.bindingdb_link
source_url: relation.bindingdb_link
## commenting out because data-processing / biolink-modeling issues
# in_taxon: subject.organism
# bindingdb_curation_datasource: relation.curation_datasource
Expand Down
2 changes: 1 addition & 1 deletion mygene.info/openapi_full.yml
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Expand Up @@ -1295,7 +1295,7 @@ components:
# go_qualifier: go.CC.qualifier ## seems to be like a relation
clingen:
MONDO: clingen.clinical_validity.mondo ## HAS PREFIX (MONDO)
ref_url: clingen.clinical_validity.online_report
source_url: clingen.clinical_validity.online_report
## commenting out because data-processing / biolink-modeling issues
# ## possible values for classification: definitive, moderate, limited, disputed, refuted (!!!), no known disease relationship (!!!)
# clingen_clinical_validity_classification: clingen.clinical_validity.classification
Expand Down