https://github.com/karrlab/wc_onto

Ontology for whole-cell modeling
https://github.com/karrlab/wc_onto

bioinformatics computational-biology ontology single-cell systems-biology whole-cell-modeling

Last synced: about 1 month ago
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Ontology for whole-cell modeling

• Host: GitHub
• URL: https://github.com/karrlab/wc_onto
• Owner: KarrLab
• License: mit
• Created: 2019-03-26T22:30:22.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2020-12-16T18:18:02.000Z (almost 5 years ago)
• Last Synced: 2025-08-27T06:08:30.530Z (about 1 month ago)
• Topics: bioinformatics, computational-biology, ontology, single-cell, systems-biology, whole-cell-modeling
• Language: Python
• Size: 316 KB
• Stars: 1
• Watchers: 7
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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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 = 

    ```    

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.