Ontology for whole-cell modeling
Installing the ontology for use in Python
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
Obtain a BioPortal API key
Save your BioPortal API key to a configuration file (
[wc_onto] [[bioportal]] key = <BioPortal API key>
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.
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.