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Predicate Validation / Deprecated Predicates #220

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EvanDietzMorris opened this issue Jul 2, 2024 · 0 comments
Open

Predicate Validation / Deprecated Predicates #220

EvanDietzMorris opened this issue Jul 2, 2024 · 0 comments
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@EvanDietzMorris
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#219 brought to my attention a couple tangential issues:

I see that bl-lookup does not indicate when a predicate is deprecated, so currently we send DGIdb:binder to bl-lookup and it returns biolink:binds which is deprecated but it looks valid:
https://bl-lookup-sri.renci.org/resolve_predicate?predicate=DGIdb%3Abinder&version=latest

ORION does not validate predicates with the biolink model because it assumes bl-lookup handled that.

We want to replace bl-lookup service calls with the biolink model toolkit in ORION anyway, so we could tell during normalization when we use a deprecated predicate, but the ORION KG validation/qc stage should also flag them.

We would still need to change the predicates in parsers or add new mappings to biolink when a predicate gets deprecated that we map to, but at least we would know when that happens.

@hina-shah hina-shah added enhancement New feature or request ORION labels Oct 1, 2024
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