ontquery 0.0.5

a framework querying ontology terms

ontquery

a framework querying ontology terms

SciCrunch api key

If you don't have your own SciGraph instance you will need a SciCunch API key in order to run the demos (e.g. python __init__.py).

To do this go to SciCrunch and register for an account and then get an api key.

You can then set the SCICRUNCH_API_KEY environment variable. For example in bash export SCICRUNCH_API_KEY=my-api-key.

See https://github.com/tgbugs/ontquery/blob/db8cad7463704bce9010651c3744452aa5370114/ontquery/__init__.py#L557-L558 for how to pass the key in.

Usage

from ontquery import OntQuery, SciGraphRemote, OntTerm, OntCuries

import os
from pyontutils.core import PREFIXES as uPREFIXES
curies = OntCuries(uPREFIXES)
api_key = os.environ['SCICRUNCH_API_KEY']
query = OntQuery(SciGraphRemote(api_key=api_key))
OntTerm.query = query

query('mouse')

3 potential matches are shown:

Query {'term': 'mouse', 'limit': 10} returned more than one result. Please review.

OntTerm('NCBITaxon:10090', label='Mus musculus', synonyms=['mouse', 'house mouse', 'mice C57BL/6xCBA/CaJ hybrid', 'Mus muscaris'])

OntTerm('NCBITaxon:10088', label='Mus <mouse, genus>', synonyms=['mouse', 'Mus', 'mice'])

OntTerm('BIRNLEX:167', label='Mouse', synonyms=['mouse', 'Mus musculus', 'house mouse'])

The one we are looking for is Mus musculus, and we can select that with OntTerm(label='Mus musculus') or with OntTerm(curie='NCBITaxon:10090').

This workflow works for a variety of categories:

• species (e.g. 'mouse', 'rat', 'rhesus macaque')
• brain area (e.g. 'hippocampus', 'CA1', 'S1')
• cell type (e.g. 'mossy cell', 'pyramidal cell')
• institution (e.g. 'UC San Francisco', 'Brown University')
• disease (e.g. "Parkinson's Disease", 'ALS')

Building for release

python setup.py sdist --release && python setup.py bdist_wheel --universal --release Building a release requires a working install of pyontutils in order to build the scigraph client library. The --release tells setup to build the scigraph client.

Related issues

https://github.com/NeurodataWithoutBorders/nwb-schema/issues/1#issuecomment-368741867

https://github.com/NeurodataWithoutBorders/nwb-schema/issues/1#issuecomment-369215854