ChemicalEntity <ameliorates, treats, prevents, affects> DiseaseOrPhenotypicFeature (MONDO:0014007 - Aicardi Syndrome)

[sstemann]

Query: aircardi.json PK: 729a0522-8861-4564-bc32-24e33d7c16f0

This query was submitted to ars-prod (ITRB). Added the treats predicate specifically based on update from Vlado re: MolPro/tree.

[andrewsu]

It appears that BTE is executing this query as expected, but that none of our queried APIs are returning any info. When I swap Aicardi Syndrome for asthma, the same set of API is queried and successfully returns results (see log snippet below). When I broaden the query to ask for any NamedThing connected to Aicardi Syndrome and no predicate constraint, I get 505 results of type Gene, SequenceVariant, and Disease.

97 API queries executed by BTE (Aicardi Syndrome)

``` "message": "call-apis: Successful POST https://biothings.ncats.io/idisk (1 ID): Disease > treated_by > SmallMolecule (obtained 0 records, took 71ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/text_mining_targeted_association (1 ID): Disease > treated_by > SmallMolecule (obtained 0 records, took 66ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > treated_by > SmallMolecule (obtained 0 records, took 59ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/text_mining_targeted_association (1 ID): Disease > treated_by > SmallMolecule (obtained 0 records, took 72ms)", "message": "call-apis: Successful POST https://mychem.info/v1 (1 ID): Disease > approved_for_treatment_by > SmallMolecule (obtained 0 records, took 71ms)", "message": "call-apis: Successful POST https://mychem.info/v1 (1 ID): Disease > treated_by > SmallMolecule (obtained 0 records, took 68ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > treated_by > SmallMolecule (obtained 0 records, took 64ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > treated_by > SmallMolecule (obtained 0 records, took 63ms)", "message": "call-apis: Successful POST https://mychem.info/v1 (1 ID): Disease > treated_by > SmallMolecule (obtained 0 records, took 80ms)", "message": "call-apis: Successful POST https://automat.renci.org/hetio/1.2 (1 ID): Disease > treated_by > ChemicalEntity (obtained 0 records, took 314ms)", "message": "call-apis: Successful POST https://automat.renci.org/drugcentral/1.2 (1 ID): Disease > treated_by > SmallMolecule (obtained 0 records, took 323ms)", "message": "call-apis: Successful POST https://automat.renci.org/hetio/1.2 (1 ID): Disease > treated_by > SmallMolecule (obtained 0 records, took 319ms)", "message": "call-apis: Successful POST https://automat.renci.org/drugcentral/1.2 (1 ID): Disease > treated_by > MolecularMixture (obtained 0 records, took 325ms)", "message": "call-apis: Successful POST https://automat.renci.org/hetio/1.2 (1 ID): Disease > treated_by > MolecularMixture (obtained 0 records, took 320ms)", "message": "call-apis: Successful POST https://automat.renci.org/drugcentral/1.2 (1 ID): Disease > treated_by > ChemicalEntity (obtained 0 records, took 331ms)", "message": "call-apis: Successful POST https://automat.renci.org/biolink/1.2 (1 ID): Disease > treated_by > SmallMolecule (obtained 0 records, took 322ms)", "message": "call-apis: Successful POST https://automat.renci.org/biolink/1.2 (1 ID): Disease > treated_by > MolecularMixture (obtained 0 records, took 321ms)", "message": "call-apis: Successful POST https://automat.renci.org/biolink/1.2 (1 ID): Disease > treated_by > ChemicalEntity (obtained 0 records, took 324ms)", "message": "call-apis: Successful POST https://automat.renci.org/ctd/1.2 (1 ID): Disease > affected_by > ChemicalEntity (obtained 0 records, took 363ms)", "message": "call-apis: Successful POST https://automat.renci.org/ctd/1.2 (1 ID): Disease > affected_by > SmallMolecule (obtained 0 records, took 383ms)", "message": "call-apis: Successful POST https://automat.renci.org/ctd/1.2 (1 ID): Disease > affected_by > MolecularMixture (obtained 0 records, took 382ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > prevented_by > SmallMolecule (obtained 0 records, took 17ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > affected_by > SmallMolecule (obtained 0 records, took 18ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > treated_by > SmallMolecule (obtained 0 records, took 23ms)", "message": "call-apis: Successful POST https://automat.renci.org/biolink/1.2 (1 ID): Disease > treated_by > ComplexMolecularMixture (obtained 0 records, took 292ms)", "message": "call-apis: Successful POST https://automat.renci.org/ctd/1.2 (1 ID): Disease > affected_by > ComplexMolecularMixture (obtained 0 records, took 332ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > prevented_by > SmallMolecule (obtained 0 records, took 21ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > prevented_by > SmallMolecule (obtained 0 records, took 23ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > prevented_by > ChemicalEntity (obtained 0 records, took 22ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > affected_by > SmallMolecule (obtained 0 records, took 15ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > disrupted_by > SmallMolecule (obtained 0 records, took 16ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > affected_by > SmallMolecule (obtained 0 records, took 18ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > treated_by > Drug (obtained 0 records, took 16ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > treated_by > SmallMolecule (obtained 0 records, took 17ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > affected_by > Food (obtained 0 records, took 18ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > treated_by > SmallMolecule (obtained 0 records, took 15ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > prevented_by > SmallMolecule (obtained 0 records, took 16ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > prevented_by > SmallMolecule (obtained 0 records, took 17ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > affected_by > SmallMolecule (obtained 0 records, took 15ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > affected_by > SmallMolecule (obtained 0 records, took 17ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 21ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > disrupted_by > SmallMolecule (obtained 0 records, took 13ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > affected_by > SmallMolecule (obtained 0 records, took 15ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 22ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > affected_by > SmallMolecule (obtained 0 records, took 18ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > affected_by > ChemicalEntity (obtained 0 records, took 15ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > disrupted_by > SmallMolecule (obtained 0 records, took 25ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 14ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > prevented_by > SmallMolecule (obtained 0 records, took 14ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > treated_by > SmallMolecule (obtained 0 records, took 16ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > affected_by > SmallMolecule (obtained 0 records, took 15ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > affected_by > SmallMolecule (obtained 0 records, took 16ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > affected_by > SmallMolecule (obtained 0 records, took 15ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > treated_by > SmallMolecule (obtained 0 records, took 14ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 16ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > affected_by > SmallMolecule (obtained 0 records, took 15ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > disrupted_by > SmallMolecule (obtained 0 records, took 14ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > affected_by > SmallMolecule (obtained 0 records, took 17ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > treated_by > ChemicalEntity (obtained 0 records, took 16ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > treated_by > SmallMolecule (obtained 0 records, took 14ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 16ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > treated_by > SmallMolecule (obtained 0 records, took 17ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 18ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > disrupted_by > SmallMolecule (obtained 0 records, took 19ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > disrupted_by > SmallMolecule (obtained 0 records, took 21ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > disrupted_by > SmallMolecule (obtained 0 records, took 83ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > disrupted_by > SmallMolecule (obtained 0 records, took 83ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > treated_by > SmallMolecule (obtained 0 records, took 89ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 15ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 16ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > disrupted_by > SmallMolecule (obtained 0 records, took 17ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > affected_by > SmallMolecule (obtained 0 records, took 15ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > disrupted_by > ChemicalEntity (obtained 0 records, took 16ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > disrupted_by > SmallMolecule (obtained 0 records, took 21ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > treated_by > SmallMolecule (obtained 0 records, took 12ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > entity_positively_regulated_by_entity > ChemicalEntity (obtained 0 records, took 14ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > prevented_by > Drug (obtained 0 records, took 18ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > prevented_by > SmallMolecule (obtained 0 records, took 12ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 18ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > affected_by > SmallMolecule (obtained 0 records, took 16ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 14ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > treated_by > SmallMolecule (obtained 0 records, took 14ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 16ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 14ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > affected_by > Drug (obtained 0 records, took 14ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > prevented_by > SmallMolecule (obtained 0 records, took 19ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > disrupted_by > SmallMolecule (obtained 0 records, took 14ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 16ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > disrupted_by > SmallMolecule (obtained 0 records, took 15ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > treated_by > SmallMolecule (obtained 0 records, took 13ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > disrupted_by > SmallMolecule (obtained 0 records, took 19ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > disrupted_by > SmallMolecule (obtained 0 records, took 15ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > prevented_by > SmallMolecule (obtained 0 records, took 14ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > prevented_by > SmallMolecule (obtained 0 records, took 13ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > prevented_by > SmallMolecule (obtained 0 records, took 18ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 13ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (1 ID): Disease > treated_by > SmallMolecule (obtained 0 records, took 12ms)", ```

99 API queries executed by BTE (asthma)

``` "message": "call-apis: Successful POST https://mychem.info/v1 (5 IDs): Disease > approved_for_treatment_by > SmallMolecule (obtained 0 records, took 73ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/idisk (5 IDs): Disease > treated_by > SmallMolecule (obtained 3 records, took 97ms)", "message": "call-apis: Successful POST https://mychem.info/v1 (1 ID): Disease > approved_for_treatment_by > SmallMolecule (obtained 6 records, took 123ms)", "message": "call-apis: Successful POST https://mychem.info/v1 (4 IDs): Disease > treated_by > SmallMolecule (obtained 10 records, took 191ms)", "message": "call-apis: Successful POST https://automat.renci.org/hetio/1.2 (1 ID): Disease > treated_by > MolecularMixture (obtained 2 records, took 316ms)", "message": "call-apis: Successful POST https://automat.renci.org/drugcentral/1.2 (1 ID): Disease > treated_by > MolecularMixture (obtained 0 records, took 329ms)", "message": "call-apis: Successful POST https://automat.renci.org/biolink/1.2 (1 ID): Disease > treated_by > MolecularMixture (obtained 14 records, took 435ms)", "message": "call-apis: Successful POST https://automat.renci.org/ctd/1.2 (1 ID): Disease > affected_by > MolecularMixture (obtained 14 records, took 489ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/text_mining_targeted_association (1 ID): Disease > treated_by > SmallMolecule (obtained 10 records, took 617ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > treated_by > SmallMolecule (obtained 147 records, took 853ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > treated_by > SmallMolecule (obtained 0 records, took 957ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > treated_by > SmallMolecule (obtained 32 records, took 961ms)", "message": "call-apis: Successful POST https://automat.renci.org/hetio/1.2 (1 ID): Disease > treated_by > SmallMolecule (obtained 34 records, took 974ms)", "message": "call-apis: Successful POST https://automat.renci.org/hetio/1.2 (1 ID): Disease > treated_by > ChemicalEntity (obtained 37 records, took 974ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/text_mining_targeted_association (1 ID): Disease > treated_by > SmallMolecule (obtained 732 records, took 1s)", "message": "call-apis: Successful POST https://automat.renci.org/biolink/1.2 (1 ID): Disease > treated_by > SmallMolecule (obtained 97 records, took 1s)", "message": "call-apis: Successful POST https://automat.renci.org/ctd/1.2 (1 ID): Disease > affected_by > SmallMolecule (obtained 103 records, took 2s)", "message": "call-apis: Successful POST https://automat.renci.org/biolink/1.2 (1 ID): Disease > treated_by > ChemicalEntity (obtained 130 records, took 2s)", "message": "call-apis: Successful POST https://automat.renci.org/drugcentral/1.2 (1 ID): Disease > treated_by > ChemicalEntity (obtained 58 records, took 2s)", "message": "call-apis: Successful POST https://automat.renci.org/ctd/1.2 (1 ID): Disease > affected_by > ChemicalEntity (obtained 139 records, took 2s)", "message": "call-apis: Successful POST https://automat.renci.org/drugcentral/1.2 (1 ID): Disease > treated_by > SmallMolecule (obtained 58 records, took 2s)", "message": "call-apis: Successful POST https://mychem.info/v1 (5 IDs): Disease > treated_by > SmallMolecule (obtained 0 records, took 31ms)", "message": "call-apis: Successful POST https://mychem.info/v1 (5 IDs): Disease > treated_by > SmallMolecule (obtained 0 records, took 35ms)", "message": "call-apis: Successful POST https://automat.renci.org/biolink/1.2 (1 ID): Disease > treated_by > ComplexMolecularMixture (obtained 2 records, took 298ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > prevented_by > SmallMolecule (obtained 140 records, took 318ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > treated_by > SmallMolecule (obtained 2 records, took 465ms)", "message": "call-apis: Successful POST https://automat.renci.org/ctd/1.2 (1 ID): Disease > affected_by > ComplexMolecularMixture (obtained 4 records, took 461ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > affected_by > SmallMolecule (obtained 66 records, took 420ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > prevented_by > SmallMolecule (obtained 9 records, took 331ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > prevented_by > ChemicalEntity (obtained 0 records, took 369ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > prevented_by > SmallMolecule (obtained 26 records, took 445ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > affected_by > SmallMolecule (obtained 10 records, took 204ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > disrupted_by > SmallMolecule (obtained 44 records, took 298ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > affected_by > SmallMolecule (obtained 13 records, took 387ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > treated_by > Drug (obtained 1 record, took 335ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > treated_by > SmallMolecule (obtained 0 records, took 368ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > affected_by > Food (obtained 1 record, took 380ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > treated_by > SmallMolecule (obtained 1 record, took 235ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > prevented_by > SmallMolecule (obtained 0 records, took 237ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > prevented_by > SmallMolecule (obtained 4 records, took 245ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > affected_by > SmallMolecule (obtained 0 records, took 186ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 320ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > affected_by > SmallMolecule (obtained 2 records, took 357ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > disrupted_by > SmallMolecule (obtained 4 records, took 265ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 310ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > affected_by > SmallMolecule (obtained 0 records, took 359ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > affected_by > SmallMolecule (obtained 0 records, took 245ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > affected_by > ChemicalEntity (obtained 1 record, took 292ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > disrupted_by > SmallMolecule (obtained 8 records, took 295ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > treated_by > SmallMolecule (obtained 1 record, took 213ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > prevented_by > SmallMolecule (obtained 0 records, took 244ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 319ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > affected_by > SmallMolecule (obtained 0 records, took 257ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > affected_by > SmallMolecule (obtained 1 record, took 266ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > affected_by > SmallMolecule (obtained 2 records, took 260ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 216ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > treated_by > SmallMolecule (obtained 0 records, took 228ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > affected_by > SmallMolecule (obtained 0 records, took 301ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > disrupted_by > SmallMolecule (obtained 0 records, took 225ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > treated_by > ChemicalEntity (obtained 0 records, took 231ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > affected_by > SmallMolecule (obtained 0 records, took 301ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 253ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > treated_by > SmallMolecule (obtained 0 records, took 292ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > treated_by > SmallMolecule (obtained 0 records, took 360ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > disrupted_by > SmallMolecule (obtained 0 records, took 206ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > disrupted_by > SmallMolecule (obtained 0 records, took 218ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 1 record, took 251ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > disrupted_by > SmallMolecule (obtained 0 records, took 186ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > disrupted_by > SmallMolecule (obtained 2 records, took 203ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > treated_by > SmallMolecule (obtained 0 records, took 215ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 223ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 249ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > disrupted_by > SmallMolecule (obtained 0 records, took 353ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > affected_by > SmallMolecule (obtained 1 record, took 216ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > disrupted_by > ChemicalEntity (obtained 0 records, took 216ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > disrupted_by > SmallMolecule (obtained 0 records, took 215ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > prevented_by > Drug (obtained 1 record, took 191ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > treated_by > SmallMolecule (obtained 0 records, took 194ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > entity_positively_regulated_by_entity > ChemicalEntity (obtained 0 records, took 215ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > prevented_by > SmallMolecule (obtained 1 record, took 191ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 230ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > affected_by > SmallMolecule (obtained 0 records, took 347ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 198ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > treated_by > SmallMolecule (obtained 0 records, took 272ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 324ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > prevented_by > SmallMolecule (obtained 0 records, took 263ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > affected_by > Drug (obtained 2 records, took 272ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 306ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > disrupted_by > SmallMolecule (obtained 0 records, took 250ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 258ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > disrupted_by > SmallMolecule (obtained 0 records, took 278ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > treated_by > SmallMolecule (obtained 0 records, took 356ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > disrupted_by > SmallMolecule (obtained 0 records, took 356ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > disrupted_by > SmallMolecule (obtained 2 records, took 386ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > prevented_by > SmallMolecule (obtained 0 records, took 243ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > prevented_by > SmallMolecule (obtained 0 records, took 269ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > prevented_by > SmallMolecule (obtained 0 records, took 343ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > treated_by > SmallMolecule (obtained 0 records, took 197ms)", "message": "call-apis: Successful POST https://biothings.ncats.io/semmeddb (5 IDs): Disease > entity_positively_regulated_by_entity > SmallMolecule (obtained 0 records, took 221ms)", ```

[sstemann]

During today's standup Brett ran the query with the more general DO Identifier, results are here:

(no MolPro results) https://arax.ncats.io/?r=51a79358-4ba4-4c84-a9d4-cc2469a6585f

After the standup, I ran the query with the MONDO synonym of the DO identifier, those results are here:

(with MolPro, but looks like ARAX is hanging) https://arax.ncats.io/?r=65fe6fa9-82d3-449a-99d4-63600a5f7fa7

I posted the Query with the MONDO directly to ARAX and it gets 330 results, not sure if the hanging from ARS submission is an issue with ARS or ARAX @MarkDWilliams @dkoslicki https://arax.ncats.io/?r=49550

[edeutsch]

So I looked into this a little bit and situation is puzzling. It seems like we have this situation quite a lot where Aragorn and ARAX appear to not return results, but then when retried manually, everything seems fine. What is the cause?

Starting here from above: https://arax.ncats.io/?r=65fe6fa9-82d3-449a-99d4-63600a5f7fa7 showing that ARS thinks that ARS and Aragorn are still running.

BTE's first log message: 2022-06-28T16:28:10.210Z INFO: job status available at: http://bte.transltr.io/v1/check_query_status/YJAUqcqutr Explanatories first msg: 2022-06-28T16:27:57 DEBUG: Executing 4 predicate searches.

What came in to ARAX during that time:

ARAX logs: 2022-06-28T16:27:55.830921 INFO: asynchronous Query launching on incoming Query 2022-06-28T16:27:56.603797 INFO: Everything seems in order to begin processing the query asynchronously. Processing will continue and Response will be posted to https://ars-prod.transltr.io/ars/api/messages/cb542053-49c2-4c6e-9c23-690a20284db9 ... 2022-06-28T16:28:38.479569 DEBUG: Writing response JSON to S3 bucket

so ARAX worked on it for 45 seconds and got an answer, this one: https://arax.ncats.io/?r=49540 But when trying to POST the response to https://ars-prod.transltr.io/ars/api/messages/cb542053-49c2-4c6e-9c23-690a20284db9 it received an HTTP 500 in response.

So it seems that in the cases where ARAX appears to be not responding, it appears (at least in this case) that ARAX is doing the work but then receives a 500 when trying to POST the result back to ARS.

Maybe we need to build in some more retries? or maybe something in the response is causing a problem? I wonder if it is too large?

[edeutsch]

I wrote a little script that fetches 49540 and tries to repost it to the callback:

import requests

arax_repsonse_url= 'https://arax.ncats.io/api/arax/v1.2/response/49540'
callback_url = 'https://ars-prod.transltr.io/ars/api/messages/cb542053-49c2-4c6e-9c23-690a20284db9'

response_content = requests.get(arax_repsonse_url, headers={'accept': 'application/json'})

status_code = response_content.status_code
if status_code != 200:
    print("ERROR returned with status "+str(status_code))
    print(response_content)
    exit()

response_dict = response_content.json()
print(f"Retrieved a message with {len(response_dict['message']['results'])} results")

print(f"Submitting to callback {callback_url}")
response_content = requests.post(callback_url, json=response_dict, headers={'accept': 'application/json'})
status_code = response_content.status_code
print(f"Status code is {status_code}")
if status_code != 200:
    print("ERROR returned with status "+str(status_code))
    print(response_content.content)
    exit()

and it yields:

Retrieved a message with 330 results
Submitting to callback https://ars-prod.transltr.io/ars/api/messages/cb542053-49c2-4c6e-9c23-690a20284db9
Status code is 500
ERROR returned with status 500
b'Internal server error'

My wild guess is that it's a size thing. We had trouble with this in the past. could it be that ars-prod doesn't have the fix to let it receive POSTs larger than X MB. I recall that nginx had to be tweaked for ars.transltr.io? Just guessing...

[sstemann]

https://ui.test.transltr.io/main/results?l=Aicardi%20Syndrome&i=MONDO:0010568&t=0&q=d1d73626-7167-40e4-b38b-5f9cfef698eb