KarrLab/wc_onto

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# WC-Onto

Ontology for whole-cell modeling

## Installation

### 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')``.

2. Obtain a [BioPortal API key](http://bioportal.bioontology.org/)
3. Save your BioPortal API key to a configuration file (``~/.wc/wc_onto.cfg``)
    ```
    [wc_onto]
        [[bioportal]]
            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

* Download [latest revision](https://raw.githubusercontent.com/KarrLab/wc_onto/master/wc_onto/onto.obo) from GitHub
* Download [latest snapshot](https://bioportal.bioontology.org/ontologies/WC) from BioPortal

## Documentation
Please see the [API documentation](https://docs.karrlab.org/wc_onto).

## License
The package is released under the [MIT license](LICENSE).

## Development team
This package was developed by the [Karr Lab](https://www.karrlab.org) at the Icahn School of Medicine at Mount Sinai in New York, USA.

## Questions and comments
Please contact the [Karr Lab](https://www.karrlab.org) with any questions or comments.