Skip to content

pybel/openbiolink-bel

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

11 Commits
 
 

Repository files navigation

BEL Export of OpenBioLink

This repository used to contain exports of OpenBioLink as Biological Expression Language (BEL). Now, the exports are available directly through their Zenodo page zenodo . 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.

Download OpenBioLink as BEL

The network is available in two BEL formats:

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

Format Descriptions

BEL Script

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')

Nodelink JSON

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')