A PyBEL [1] extension for building BEL resources with the EBI [2] Ontology Lookup Service.
Download the most recent code from GitHub with:
$ pip install git+https://github.com/pybel/pybel-ols.git
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 .
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
[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. |