wc_onto documentation¶

Ontology for whole-cell modeling.

The following example illustrates how to use the ontology in Python:

from wc_onto import onto
species_term = onto['WC:species']

Contents¶

Installation¶

Prerequisites¶

Python
Pip

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 pkg_resources.resource_filename('wc_onto', 'onto.obo').

Obtain a BioPortal API key

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

[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

Download latest revision from GitHub
Download latest snapshot from BioPortal

About¶

License¶

The software is released under the MIT license

The MIT License (MIT)

Copyright (c) 2019 Karr Lab

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

Development team¶

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

Acknowledgements¶

Questions and comments¶

Please contact the Karr Lab with any questions or comments.