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NCATSTranslator / Feedback

A repo for tracking gaps in Translator data and finding ways to fill them.
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Recent queries in CI returning validation errors Service Provided SemMedDB attribute_type_ids #639

Closed edeutsch closed 1 month ago

edeutsch commented 9 months ago

This recent result: https://arax.ci.transltr.io/?r=663047cb-3be8-4d5b-accf-9e269b16528b

Shows validation errors for multiple actors. At least some of them seem to be traceable to Service Provider:

Errors:
* Knowledge Graph Edge Attribute Type Id Not:
=> Edge has a value that is not a CURIE for attribute_type_id
    $ infores:semmeddb -> infores:biothings-semmeddb -> infores:service-provider-trapi -> infores:arax
        # original_object_name:
        - edge_id: 
            PUBCHEM.COMPOUND:72941511[biolink:ChemicalEntity]--biolink:treats->MONDO:0007147[biolink:Disease]
            CHEBI:50847[biolink:ChemicalEntity]--biolink:treats->MONDO:0007147[biolink:Disease]
            PUBCHEM.COMPOUND:9852188[biolink:Drug|biolink:ChemicalEntity|biolink:MolecularMixture]--biolink:treats->MONDO:0007147[biolink:Disease]
            MESH:D007166[biolink:ChemicalEntity]--biolink:treats->MONDO:0007147[biolink:Disease]
            UBERON:0008826[biolink:ChemicalEntity]--biolink:treats->MONDO:0007147[biolink:Disease]
            CHEBI:26537[biolink:ChemicalEntity]--biolink:treats->MONDO:0007147[biolink:Disease]
            MESH:D012739[biolink:ChemicalEntity]--biolink:treats->MONDO:0007147[biolink:Disease]

i.e. "original_object_name" is not a CURIE.

colleenXu commented 8 months ago

This should be addressed in BTE dev/CI since 12/15 https://github.com/biothings/biothings_explorer/issues/761#issuecomment-1858707087

andrewsu commented 1 month ago

Haven't been seeing recent validation errors, so closing...