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Add get_sssom_mappings_by_curie to BioportalImplementation class #17

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merged 3 commits into from
Apr 14, 2022

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pkalita-lbl
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This method uses the /ontologies/:ontology/classes/:cls/mappings endpoint to get mappings and reformats them in SSSOM format.

Caveats:

  • The BioPortal API has an issue where a lot of duplicate mappings are reported. We are not trying to resolve that duplication here and instead just passing the results through.
  • The BioPortal API reports a source field for each mapping and we are manually translating that to a SKOS term, but this may be up for refinement
  • The method will accept a CURIE as defined by the MappingProviderInterface but since the BioPortal API generally deals with URIs and not CURIEs the SSSOM subject_id and predicate_id fields will be URIs

@pkalita-lbl pkalita-lbl requested a review from cmungall April 14, 2022 20:43
SOURCE_TO_PREDICATE = {
'CUI': 'skos:closeMatch',
'LOOM': 'skos:closeMatch',
'REST': 'skos:relatedMatch', # maybe??
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yeh it's not super clear which skos property to use (other than SAME_URI), I think this is good enough to get started!

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2 participants