Ontolopy a python package for working with .obo files

🚧 This package is in development 🚧

Please see the docs for the most up-to-date information: You can access versioned docs at /versions/{version} like this

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