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NCATSTranslator / testing

Materials and tools for testing Translator components
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Gene (WDR45 HGNC:28912) - similar to - NamedThing #90

Open sstemann opened 3 years ago

sstemann commented 3 years ago

Query: similar_to.json PK: 2d5422be-ee30-4133-bbe3-6ae4c2d530a9 HGNC:28912

Results Tracking Sheet

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brettasmi commented 3 years ago

We only support this predicate for biolink:disease--similar_to--biolink:disease

Is there something specific that this query is trying to surface?

colleenXu commented 3 years ago

BTE returns a response without any TRAPI validation errors and with the correct node categories (Gene) when rerunning the query (PK: 5938b379-5d31-474b-8759-3f0aad404bb7).

I'm not sure what happened with BTE in the earlier run (where the category of the nodes was "undefined" instead of Gene). @newgene @andrewsu

bill-baumgartner commented 3 years ago

Text Mining Provider does not support biolink:similar_to so zero results are expected. Running the query now directly against the Text Mining Provider endpoint returns an empty knowledge graph as expected.

The single reported result WDR45 biolink:homologous_to MGI:1859606 is the same single result reported by BTE, as is the reported TRAPI validation error. Text Mining Provider does not contain biolink:homologous_to assertions. I will follow up with the Service Provider to investigate further.

sstemann commented 3 years ago

We only support this predicate for biolink:disease--similar_to--biolink:disease

Is there something specific that this query is trying to surface?

we're looking for the gene in different model organisms

rajshruti18 commented 3 years ago

CAM-KP does not have the predicate 'similar_to', so 0 result is expected.

pg427 commented 3 years ago

Explanatory agent does not support "biolink:similar_to" predicates in our current implementation. We are currenly in midst of a major design update, expected completion by September Relay, post which we can expect to see some results.

marcdubybroad commented 3 years ago

The Genetics KP does not support biolink:similar_to so zero results are expected.

sierra-moxon commented 3 years ago

'homologous_to', 'paralogous_to' and 'orthologous_to' are in the 'similar_to' predicate hierarchy (the are children of 'similar_to'). Just confirming that none of these 'child' predicates are supported either?

vdancik commented 3 years ago

MolePro does not support similar_to predicate for genes.

sstemann commented 3 years ago

'homologous_to', 'paralogous_to' and 'orthologous_to' are in the 'similar_to' predicate hierarchy (the are children of 'similar_to'). Just confirming that none of these 'child' predicates are supported either?

@sierra-moxon we started 'homologous_to' and then generalized to 'similar_to' - same results from ARAX and BTE for both.

GregHydeDartmouth commented 3 years ago

The issue with CHP's response message not showing as trapi-compliant has been solved. See https://arax.ncats.io/?source=ARS&id=7cc6155f-63b7-40ca-9cfd-4ddb2c3a176f for reference. Similar to issue 91 we believe the "error" status to be correct as we return a 400 error according to the curie prefix not being digestible by our system. To the larger issue CHP doesn't contain any edges under biolink:similar_to in the predicate ontology so 0 results is expected.