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biolink predicates no longer exist in latest Biolink Model #23

Open jdr0887 opened 1 year ago

jdr0887 commented 1 year ago

The following predicates are not found in the latest Biolink Model:

https://github.com/NCATSTranslator/Clinical-Data-Committee-Tracking-Voting/blob/0a85448c4cd4735e4d508036d0b2708b2cc86494/GetCreative()_DrugDiscoveryRepurposing_RarePulmonaryDisease/Path_A/Path_A_no_overlay_chem_%2Breg_gene.json#L38-L46

For reference, the Biolink Model can be found here: https://github.com/biolink/biolink-model/blob/master/biolink-model.yaml

bill-baumgartner commented 1 year ago

Thanks Jason. Sorry for that oversight. I will see if I can convert the queries to use qualified predicates and then will figure out which environment to use for testing. FWIW - when I tested this last week, results were returned.

bill-baumgartner commented 1 year ago

Note: I may have spoken too soon on the comment below. If all of the predicates are now represented as biolink:affects then it might be possible to OR together their constraints to replicate the original predicates shown above.

Interestingly, it does not look like we can fully replicate this query using qualifiers. Mixing qualifiers with different predicates on the same edge is not currently supported in TRAPI. See the TRAPI documentation on qualifier_constraints (which I have copied here for convenience).

 qualifier_constraints:
          type: array
          description: >-
            A list of QualifierConstraints that provide nuance to the QEdge.
            If multiple QualifierConstraints are provided, there is an OR
            relationship between them. If the QEdge has multiple
            predicates or if the QNodes that correspond to the subject or
            object of this QEdge have multiple categories or multiple
            curies, then qualifier_constraints MUST NOT be specified
            because these complex use cases are not supported at this time.
bill-baumgartner commented 1 year ago

@jdr0887 See updated queries in PR #24. These should now comply with Biolink 3.x. Let me know if there are further issues.

nlharris commented 1 year ago

@sierra-moxon commented:

These eliminated predicates are prime use cases for the qualifier methodology. Many examples here: https://biolink.github.io/biolink-model/guidelines/association-examples-with-qualifiers.html and here: https://biolink.github.io/biolink-model/guidelines/reading-a-qualifier-based-statement.html