1. Installation

1.1. Prerequisites

  • Python

  • Pip

1.2. Installing the ontology for use in Python

  1. Install this Python package with pip:

    pip install git+https://github.com/KarrLab/wc_onto.git#egg=wc_onto[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').

  1. Obtain a BioPortal API key

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

    [wc_onto]
    [[bioportal]]
        key = <BioPortal API key>

  3. 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

1.3. Downloading the ontology

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