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Add a dynamic ValueSet expander #370

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cmungall opened this issue Dec 1, 2022 · 0 comments
Closed

Add a dynamic ValueSet expander #370

cmungall opened this issue Dec 1, 2022 · 0 comments

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@cmungall
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cmungall commented Dec 1, 2022

For full context, see:

We would like a method that takes a value set like

  GoMembrane:
    pv_formula: CURIE
    reachable_from:
      include_self: true
      source_ontology: obo:go
      source_nodes:
        - GO:0016020 ## membrane

and adds in all permissible values:

    permissible_values:
      GO:0090512:
        text: GO:0090512
        description: eisosome membrane domain/MCC
        meaning: GO:0090512
      GO:0000421:
        text: GO:0000421
        description: autophagosome membrane
        meaning: GO:0000421
      GO:0009279:
        text: GO:0009279
        description: cell outer membrane
        meaning: GO:0009279
      GO:0005778:
...

This could take an optional configuration file like this:

resource_resolvers:
  bioregistry:wikidata:
    shorthand: "wikidata:"
prefix_resolvers:
  obo:
    shorthand_prefix: "sqlite:obo"

That would map different source_ontology values to different adapters/implementations

Currently only backends supported by OAK would be used (sqlite, obo, owl, bioportal, ols, ubergraph, ...) but in future a FHIR backend could be used - see #351

This should work for both fhir value sets and linkml value sets, but we can proceed incrementally starting with the latter

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