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NCATSTranslator / testing

Materials and tools for testing Translator components
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Chemical Substance (PUBCHEM.COMPOUND:5291 Imatinab) - Correlated With - DiseaseOrPhenotypicFeature #88

Open sstemann opened 3 years ago

sstemann commented 3 years ago

Query: imatinabCorrelatedWith.json PK: 4972ff48-816d-4725-8b08-a4d775e919bd PUBCHEM.COMPOUND:5291

Results Tracking Sheet

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marcdubybroad commented 3 years ago

The genetics KP doesn't have chemical substance data, so no results are expected.

vdancik commented 3 years ago

MolePro does not contain data supporting correlated with disease or phenotypic feature relationships.

GregHydeDartmouth commented 3 years ago

In this case we do not handle PUBCHEM.COMPOUND curie prefixes. The output message reflects this: {"message": {"query_graph": {"nodes": {"n0": {"ids": ["PUBCHEM.COMPOUND:5291"], "categories": ["biolink:ChemicalSubstance"]}, "n1": {"categories": ["biolink:DiseaseOrPhenotypicFeature"]}}, "edges": {"e0": {"subject": "n0", "object": "n1", "predicates": ["biolink:correlated_with"]}}}}, "callback": "http://0.0.0.0:8000/ars/api/messages/fb5b3356-bd05-49e7-957e-8c13ed78a87c", "status": "Bad request.Unsupported Prefix: PUBCHEM.COMPOUND"}

HOWEVER, this is not a trapi compliant message, we need to include and empty knowledge graph and results graph. That is what is tripping the error back from the ARS.

Please see our issue for more details. Should be fixed soon!

Sharma05 commented 3 years ago

Aragorn returns results for this query. Please see the brief summary on the results here

rajshruti18 commented 3 years ago

CAM-KP does not have data on disease or phenotypic feature, so 0 result is expected.

GregHydeDartmouth commented 3 years ago

We've corrected the issue of not returning the empty knowledge graph and results graph on an exception. We now return a trapi compliant message indicating we do not handle PUBCHEM.COMPOUND curies, see here. If changed to a CHEMBL.COMPOUND we would also not account for biolink:chemical substance so no results is expected here.