Skip to main content

`uberon_py` is a package for querying the Uberon ontology from python.

Project description

uberon-py: a python package for the Uberon ontology

:construction: :construction: This package is under development (particularly the documentation) :construction: :construction:

Summary

I created this package to be able to easily interrogate relationships between Uberon terms in Python.

Usage

Example usage:

# read an ontology in obo format
obo = uberon-py.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 = uberon-py.Relations(source_terms,target_terms,relations_of_interest[,obo.ont).relations

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

uberon_py-0.0a1.tar.gz (4.5 kB view hashes)

Uploaded source

Built Distribution

uberon_py-0.0a1-py2-none-any.whl (17.3 kB view hashes)

Uploaded py2

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page