Disease (MONDO:0018874) - related_to - NamedThing - related_to - SmallMolecule (PUBCHEM.COMPOUND:90448953)

[sstemann]

Query: D.1_PLX51107-acute-myeloid-leukemia.json PK: ec8a6be7-393e-4de6-979e-820b29ac42a7 Control: PLX 51107, a small molecule inhibitor of the BET family bromodomains BRD2, BRD3, BRD4, and BRDT (https://clinicaltrials.gov/ct2/show/NCT04022785) Results Tracking Sheet

[andrewsu]

TLDR: BTE appears to be working as designed, and is returning zero results because no data source reports any entities linked to PUBCHEM.COMPOUND:90448953.

BTE returns no results for e01 (isolated in the query in Box 1) despite making 386 API calls on 17 API endpoints (Box 2). Replacing PUBCHEM.COMPOUND:90448953 with PUBCHEM.COMPOUND:5291 (imatinib) yields many results, so structurally everything appears to be working correctly.

Box 1:

{
  "message": {
    "query_graph": {
      "edges": {
        "e01": {
          "subject": "n01",
            "object": "n02",
        "predicates":["biolink:related_to"]
        }
      },
      "nodes": {
        "n01": {
          "categories": ["biolink:NamedThing"]
        },
        "n02": {
          "ids": ["PUBCHEM.COMPOUND:90448953"],
          "categories": ["biolink:SmallMolecule"]
        }
      }
    }
  }
}

Box 2:

     86 automat.renci.org/ctd/1.2/query
     70 automat.renci.org/uberongraph/1.2/query
     32 biothings.ncats.io/multiomics_wellness_kp/query
     26 automat.renci.org/cord19/1.2/query
     21 automat.renci.org/drugcentral/1.2/query
     20 automat.renci.org/biolink/1.2/query
     20 icees.renci.org:16339/query
     20 icees.renci.org:16341/query
     18 automat.renci.org/hetio/1.2/query
     15 automat.renci.org/hmdb/1.2/query
     15 automat.renci.org/pharos/1.2/query
     14 automat.renci.org/gtopdb/1.2/query
     11 automat.renci.org/ontological-hierarchy/1.2/query
     10 cohd.io/api/query
      5 mychem.info/v1/query
      2 mydisease.info/v1/query
      1 biothings.ncats.io/dgidb/query

[vdancik]

We currently have no connections for PLX 51107; we are working on upgrading to that latest ChEMBL version that should add connections to BRD4