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tgbugs / ontquery

a framework querying ontology terms
MIT License
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`query(label='hippocampus', prefix='UBERON')` #2

Closed bendichter closed 6 years ago

bendichter commented 6 years ago

'brain' and 'hypothalamus' work, but 'hippocampus' doesn't get any results. Do you know why that might be?

tgbugs commented 6 years ago

If you search OntTerm(label='hippocampus') you will got find results because label only returns exact matches does not search synonyms, OntTerm(term='hippocampus') will find 3 results. If you searched with term= and did not that is quite strange and I would want to know more.

One query pattern that I use frequently is to progressively broaden your search like this:

OntTerm(label='brain') 
OntTerm(term='brain')
OntTerm(search='brain')

Another pattern is to start broad and become more narrow:

OntTerm(term='brain')
OntTerm(label='brain')

(brain is not actually a case where either of these patterns are useful).

As a side note hippocampus without any qualifiers is one of the go to examples where the meaning of a term can vary significantly between fields.

bendichter commented 6 years ago

Thanks for clearing that up. Huh, interesting, I didn't know "hippocampus" was so contentious! That's why I like that the Allen Brain Atlas shows you an image of the region when you select terms.