Quick start¶
This guide assumes you have already installed ontobio. If not, then follow the steps in the 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 Command Line 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 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 API docs.