BTE no results on Workflow B.1 query

[vgardner-renci]

https://arax.ncats.io/?source=ARS&id=0445a10f-05b6-4bf3-82a5-586a55655e1c

[vgardner-renci]

@andrewsu request for update

[andrewsu]

This doesn't look like a one-hop query to me. From the dev-info on the arax link, I get the query below. Can someone help me with a reality check please? @vgardner-renci

{
  "message": {
    "query_graph": {
      "edges": {
        "e0": {
          "object": "n1",
          "predicates": [
            "biolink:correlated_with"
          ],
          "subject": "n0"
        },
        "e1": {
          "object": "n2",
          "predicates": [
            "biolink:condition_associated_with_gene"
          ],
          "subject": "n1"
        },
        "e2": {
          "object": "n3",
          "predicates": [
            "biolink:related_to"
          ],
          "subject": "n2"
        }
      },
      "nodes": {
        "n0": {
          "ids": [
            "MONDO:0005359"
          ],
          "name": "drug-induced liver injury"
        },
        "n1": {
          "categories": [
            "biolink:DiseaseOrPhenotypicFeature"
          ],
          "name": "Disease Or Phenotypic Feature"
        },
        "n2": {
          "categories": [
            "biolink:Gene"
          ],
          "name": "Gene"
        },
        "n3": {
          "categories": [
            "biolink:ChemicalSubstance"
          ],
          "name": "Chemical Substance"
        }
      }
    }
  }
}

[vgardner-renci]

@andrewsu The issue was described incorrectly. I have changed the title.

[tursynay]

Could be scalability issue or topology issue

[andrewsu]

This is a three-hop linear query: DILI -- correlated with --> [DiseaseOrPhenotypicFeature] -- condition_associated_with_gene --> [Gene] -- related_to --> [ChemicalSubstance]

[tursynay]

Chunlei says most of the queries can be retried. Chunlei will test offline and comment here

[newgene]

Verified that the above query works now, but BTE currently returns empty results

[vgardner-renci]

Sending query to ARS eventually yields "error" after 10 minutes.

[andrewsu]

I confirmed that the prod instance at https://api.bte.ncats.io/v1/query returns a 504 timeout error, and that this query successfully executes (with zero results) on our dev instance https://dev.api.bte.ncats.io/v1/query/ and locally.

As to why we have zero results, BTE gets zero hits after the first edge because we currently do not have any resource that uses the correlated_with predicate. I suspect that would change when https://github.com/biothings/BioThings_Explorer_TRAPI/issues/223 and/or https://github.com/biothings/BioThings_Explorer_TRAPI/issues/213 is addressed.

Also noting that this is workflow B.1 https://github.com/NCATSTranslator/minihackathons/blob/main/2021-12_demo/workflowB/B.1_DILI-three-hop-from-disease-or-phenotypic-feature_trapi.json

[tursynay]

actively working on, a couple of blockers but progress being made

[vgardner-renci]

@andrewsu request for update

[tursynay]

Also in progress, check in next week

[tursynay]

Dependent on #68