ChemicalSubstance Celecoxib (PUBCHEM.COMPOUND:2662) - Gene COX1 (HGNC:9604)

[MarkDWilliams]

Query: celecoxibNoHop
PK: cf42e088-ef4a-45e1-a839-1562fb202901
PUBCHEM.COMPOUND:2662
HGNC:9604
Control: inhibits, negatively_regulates, decreases_activity_of etc
Results Tracking Sheet

Updated 6/22/2021

[edeutsch]

I think the PK listed above is an older one; it does not match the screen shot.

[MarkDWilliams]

Ah, you are correct. My mistake. I have edited the original.

[MarkDWilliams]

A few tools return results for this, but my understanding is that a query with two identified nodes but an unspecified edge connecting them should return the edges that connect them which does not seem to be the case for any of the results returned.

[vdancik]

Indeed that's the case of MolePro - it ignores ids of the object node.

[cbizon]

It looks like Aragorn had a component fall down this morning. It's back up now and returning results for this query when called directly. If you rerun, you will hopefully get 4 answers back from aragorn corresponding to these predictes:

related_to
affected_by
molecularly_interacts_with
decreases_activity_of

[MarkDWilliams]

I'm not sure I have the permissions to cancel the meeting for tomorrow, but given that Juneteenth was just recognized as a Federal holiday, the NCATS folks won't be able to make it. I plan to go ahead with this query for our standup on Tuesday the 22nd

[bill-baumgartner]

@sstemann & @MarkDWilliams, I am scheduled to be out of the office today so I won't be able to attend today's standup.

Initial thoughts on this query with regard to the Text Mining Provider: our chemicals are normalized to CHEBI currently, and proteins/genes to Protein Ontology identifiers. We are working on a solution to facilitate the protein/gene conflation issue as well as our use of species-non-specific protein identifiers (NCATSTranslator/Text-Mining-Provider-Roadmap#81, NCATSTranslator/Text-Mining-Provider-Roadmap#88). Our chemical normalization will likely remain CHEBI-specific going forward however, so this query will always return zero hits from our KGs as written. I will look into its ability to return results when using the CHEBI id for Celecoxib when I return to the office. One of our pipelines is overly aggressive when it comes to filtering potential false positives for chemicals, and I think that is in play here.

[marcdubybroad]

The Genetics KP doesn't have ChemicalSubstance data, so it returning 0 results is expected.

[CaseyTa]

We're not expecting any results from OpenPredict or COHD. I've removed assignment for myself and @arifx, but please let me know if we should remain assigned.

[andrewsu]

BTE returns a syntactically valid, non-zero response. But it is not executing the query as intended -- the fix is being tracked in biothings/biothings_explorer#112

[dkoslicki]

Not sure why Expander agent is tagged in this one, due to returning results. Removing the tag, but LMK if there remains and issue for Expander agent

[rajshruti18]

CAM-KP does not have data on 'Celecoxib' and COX1 gene; therefore, it returns 0 results.