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tgbugs / ontquery

a framework querying ontology terms
MIT License
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species/strain lookup #6

Open bendichter opened 6 years ago

bendichter commented 6 years ago

Is there a way currently to reference an ontological term for the rat species or for a specific strain of mouse?

tgbugs commented 6 years ago

If I understand the question correctly, yes. The NIF ontology imports taxslim which covers a subset of NCBITaxon and has pretty much every experimental organism we are likely to need. Mouse is OntTerm('NCBITaxon:10090', label='Mus musculus') and rat is OntTerm('NCBITaxon:10116', label='Rattus norvegicus'). Both of those return as expected from query('rat') and query('mouse').

Strains are not in the NIF ontology yet, but they are coming. See https://github.com/SciCrunch/NIF-Ontology/issues/70 for reference.

bendichter commented 6 years ago

Wrt species, perfect, I'll test all the species we are likely to need. Wrt stains, I see it's a bit more complicated, but it looks like that thread is heading in the right direction.