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Quick start

.. currentmodule:: ontobio

This guide assumes you have already installed ontobio. If not, then follow the steps in the :ref:`installation` section.

Command Line

You can use a lot of the functionality without coding a line of python, via the command line wrappers in the bin directory. For example, to search on ontology for matching labels:

ogr.py -r mp %cerebellum%

See the :ref:`commandline` section for more details.

Notebooks

We provide Jupyter Notebooks to illustrate the functionality of the python library. These can also be used interactively.

See the :ref:`notebooks` section for more details.

Python

This code example shows some of the basics of working with remote ontologies and associations

from ontobio.ontol_factory import OntologyFactory
from ontobio.assoc_factory import AssociationSetFactory

## label IDs for convenience
MOUSE = 'NCBITaxon:10090'
NUCLEUS = 'GO:0005634'
TRANSCRIPTION_FACTOR = 'GO:0003700'
PART_OF = 'BFO:0000050'

## Create an ontology object containing all of GO, with relations filtered
ofactory = OntologyFactory()
ont = ofactory.create('go').subontology(relations=['subClassOf', PART_OF])

## Create an AssociationSet object with all mouse GO annotations
afactory = AssociationSetFactory()
aset = afactory.create(ontology=ont,
                       subject_category='gene',
                       object_category='function',
                       taxon=MOUSE)

genes = aset.query([TRANSCRIPTION_FACTOR],[NUCLEUS])
print("Mouse TF genes NOT annotated to nucleus: {}".format(len(genes)))
for g in genes:
    print("  Gene: {} {}".format(g,aset.label(g)))

See the notebooks for more examples. For more documentation on specific components, see the rest of these docs, or skip forward to the :doc:`api` docs.

Web Services

See the :doc:`biolink` section