This repository used to contain exports of OpenBioLink as Biological Expression Language (BEL). Now, the exports are available directly through their Zenodo page . The research article describing OpenBioLink is:

OpenBioLink: A benchmarking framework for large-scale biomedical link prediction Breit, A., Ott, S., Agibetov, A., & Samwald, M. Bioinformatics (2020)

BEL is a domain specific language that enables the expression of biological relationships in a machine-readable format. It is supported by the PyBEL software ecosystem.

The network is available in two BEL formats:

• BEL Script - see description below
• Nodelink JSON - see description below

BEL Script is the de facto standard for BEL, which all BEL-aware applications should be able to consume. It contains information about the nodes, edges, and their biological context in a domain-specific language. It can be parsed with PyBEL or other BEL parsers.

The BEL Script is available from this URL: https://zenodo.org/record/3834052/files/openbiolink.bel.gz. If there's an update on Zenodo, update the record accordingly.

Example opening BEL Script using pybel.from_bel_script_gz():

from pybel import from_bel_script_gz
graph = from_bel_script_gz('openbiolink.bel.gz')

Node-link is the format popularized by Javascript frameworks like D3 for representing network information. Since the main data structire in PyBEL is a network, it often makes sense to use Nodelink JSON as a pre-compiled data structure for BEL (since parsing/compiling BEL takes a lot longer than JSON). The schema is specific to PyBEL, but this is the fastest to load.

The BEL Script is available from this URL: https://zenodo.org/record/3834052/files/openbiolink.bel.nodelink.json.gz?download=1. If there's an update on Zenodo, update the record accordingly.

Example opening Nodelink JSON using pybel.from_nodelink_gz():

from pybel import from_nodelink_gz
graph = from_nodelink_gz('openbiolink.bel.nodelink.json.gz')