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Ontology for whole-cell modeling

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Ontology for whole-cell modeling


Installing the ontology for use in Python

  1. Install this Python package with pip

    pip install git+[all]

    This command will install this Python package, including the ontology (in OBO format) and the Python code for using the ontology. Once installed, the ontology will be located at pkg_resources.resource_filename('wc_onto', 'onto.obo').

  2. Obtain a BioPortal API key

  3. Save your BioPortal API key to a configuration file (~/.wc/wc_onto.cfg)

            key = <BioPortal API key>
  4. Import the package. The other ontologies which wc_onto references will automatically be downloaded the first time that the package is imported.

    from wc_onto import onto

Downloading the ontology

Alternatively, the ontology can be downloaded (in OBO format) from GitHub or BioPortal


Please see the API documentation.


The package is released under the MIT license.

Development team

This package was developed by the Karr Lab at the Icahn School of Medicine at Mount Sinai in New York, USA.

Questions and comments

Please contact the Karr Lab with any questions or comments.

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