Metadata-Version: 2.1
Name: ontquery
Version: 0.0.5
Summary: a framework querying ontology terms
Home-page: https://github.com/tgbugs/ontquery
Author: Tom Gillespie
Author-email: tgbugs@gmail.com
License: MIT
Description: # ontquery
        [![PyPI version](https://badge.fury.io/py/ontquery.svg)](https://pypi.org/project/ontquery/)
        [![Build Status](https://travis-ci.org/tgbugs/ontquery.svg?branch=master)](https://travis-ci.org/tgbugs/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](https://scicrunch.org/register) and then [get an api key](https://scicrunch.org/account/developer).
        
        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
        ```python
        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
        ```
        ```python
        query('mouse')
        ```
        3 potential matches are shown:
        ```python
        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
        
Keywords: ontology terminology scigraph interlex term lookup
Platform: UNKNOWN
Description-Content-Type: text/markdown
Provides-Extra: dev
Provides-Extra: services
