BEL Export of Causal Biological Networks Database ====================== This repository contains exports of the Causal Biologial Networks Database (CBN) as Biological Expression Language (BEL). The research article describing the CBN is:
Causal biological network database: A comprehensive platform of causal biological network models focused on the pulmonary and vascular systems. Talikka, M., Boue, S., & Schlage, W. K. Computational Systems Toxicology (2015) 65–93. DOI: 10.1007/978-1-4939-2778-4_3
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 in the /bel directory:
In the human_2.0, you can also find the networks in both the raw and grounded formats. These are ultimately combine to make the full exports in the bel/ directory. All edges maintain tags as to their provenance from which network they came.
This repository and its maintainers are not affiliated with the content creators at sbv IMPROVER project nor Philip Morris International, but they have graciously allowed us to redistribute their content with the following message:
The sbv IMPROVER project, the website and the Symposia are part of a collaborative project designed to enable scientists to learn about and contribute to the development of a new crowd sourcing method for verification of scientific data and results. The current challenges, website and biological network models were developed and are maintained as part of a collaboration among Selventa, OrangeBus and ADS. The project is led and funded by Philip Morris International. For more information on the focus of Philip Morris International’s research, please visit www.pmi.com.
Please cite:
as well as any relevant publications.
BEL Script is the de facto standard for BEL, which all BEL-aware applications should be able to consume. It contains informations about the nodes, edges, and their biological context in a domain-specific language. It can be parsed with PyBEL or other BEL parsers.
Example opening BEL Script using pybel.from_bel_script_gz():
from pybel import from_bel_script_gz
graph = from_bel_script_gz('human_2.0.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.
Example opening Nodelink JSON using pybel.from_nodelink_gz():
from pybel import from_nodelink_gz
graph = from_nodelink_gz('human_2.0.bel.nodelink.json.gz')