PyBEL-OLS

A PyBEL [1] extension for building BEL resources with the EBI [2] Ontology Lookup Service.

Installation

Get the Latest

Download the most recent code from GitHub with:

$ pip install git+https://github.com/pybel/pybel-ols.git

For Developers

Clone the repository from GitHub and install in editable mode with:

$ git clone https://github.com/pybel/pybel-ols.git
$ cd pybel-ols
$ pip install -e .

Getting Started

The main goal is to generate a namespace file. For example, to generate a namespace for the Human Phenotype Ontology, abbreviated with the prefix hp, the following command can be used:

$ pybel-ols namespace_from_ols hp --encoding "O" --output ~/Desktop/hp.belns

Where --encoding "O" tells it that all terms in this ontology correspond to the pathology/phenotype BEL type.

Alternatively, the '-b' option can be used to specify an alternate OLS instance

$ pybel-ols namespace_from_ols hp --encoding O --output ~/Desktop/hp.belns -b https://localhost/ols

References

[1]	Hoyt, C. T., et al. (2017). PyBEL: a Computational Framework for Biological Expression Language. Bioinformatics, 34(December), 1–2.

[2]	Cote, R., et al. (2006). The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics, 7, 1–7.