Ontolopy is a package for working with ontology (.obo) files from Python.
Project description
Ontolopy a python package for working with .obo files
:construction: This package is in development :construction:
Please see the docs for the most up-to-date information:
You can access versioned docs at /versions/{version}
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Installation
Ontolopy is available on pip, and can be installed using:
pip install ontolopy
Usage
Example usage:
import ontolopy
# read an ontology in obo format
obo = ontolopy.Obo('path_to_file/uberon_ext.obo')
# find relationships between terms of interest:
# (in this case, are any of the source_terms, is_a or part_of the brain?)
source_terms = ['UBERON:0003290', 'UBERON:0003369', 'UBERON:0003703']
target_terms = ['UBERON:0000955'] # brain term
relations_of_interest = ['is_a', 'part_of']
relations = ontolopy.Relations(
source_terms,
target_terms,
relations_of_interest,
obo.ont
).relations
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