Ontology Queries structure

ga4gh / g2p-team

GitHub Repo for the Genotype to Phenotype Task Team

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Ontology Queries structure #7

Open bwalsh opened 9 years ago

bwalsh commented 9 years ago

Leaving this open for commentary/additions

Ontology Queries

The 'ontologySource' is assumed to be equivalent to an Ontologies 'prefix'. However, no agreement or mechanism exists to align the ontologySource string to a specific URI.

Recommend: collapsing ontologySource and identifier into a single field 'ontologyURI'

Discussion

During the call @mellybelly mentioned there was an yaml file to provide a mapping of commonly used sources.

bwalsh commented 9 years ago

Hi Brian, take a look at: https://github.com/monarch-initiative/dipper/blob/master/dipper/curie_map.yaml

Also see: https://github.com/cmungall/biocontext

cheers, Melissa

antbro commented 9 years ago

Hi Brian I can see the logic, but thinking of longer term and broader utility I would worry about situations in which only the prefix or suffix are needed (e.g., a network usage in which a single or a local ontology is agreed as the one to use). Baking these together compromises flexibility, keeping them separate does no real harm (does it?)

bwalsh commented 9 years ago

Agreed. With Melissa's contribution above, it gives us an internal mapping of 'prefix' to 'ontology url'