Bio2BEL ExCAPE-DB

Convert curated assays from ExCAPE-DB to BEL.

Installation

bio2bel_excape can be installed easily from PyPI with the following code in your favorite terminal:

$ python3 -m pip install bio2bel_excape

or from the latest code on GitHub with:

$ python3 -m pip install git+https://github.com/bio2bel/excape.git

Setup

Python REPL

>>> import bio2bel_excape
>>> excape_manager = bio2bel_excape.Manager()
>>> excape_manager.populate()

Command Line Utility

bio2bel_excape populate

Tests

Bio2BEL ExCAPE uses tox for testing. After cloning the repository, install tox with:

$ python3 -m pip install tox

And run it in the base directory (the one that contains tox.ini) with:

$ tox

References

• Sun, J., et al. (2017). ExCAPE-DB: An integrated large scale dataset facilitating Big Data analysis in chemogenomics. Journal of Cheminformatics, 9(1), 1–9.
• https://zenodo.org/record/173258/files/pubchem.chembl.dataset4publication_inchi_smiles.tsv.xz?download=1