The Causal Biological Networks (CBN) database is composed of multiple versions of over 120 modular, manually curated, BEL-scripted biological network models supported by over 80,000 unique pieces of evidence from the scientific literature.
They represent causal signaling pathways across a wide range of biological processes including cell fate, cell stress, cell proliferation, inflammation, tissue repair and angiogenesis in the pulmonary and vascular systems.
The networks were built within defined biological boundaries for inclusion of signaling pathways within particular context (species, tissues, cell types, experiment types)
The network models are encoded in the Biological Expression Language (BEL), a highly specific biological language that describes biological relationships in computable form, specifying protein abundance, activity or modifcation information as well as tissue, species or experiment context information.
The network models provide a high degree of granularity capturing biological molecules including protein, DNA variants, coding and non-coding RNA, chemicals, lipids, methylation states or other modifications (e.g., phosphorylation), as well as disease mechanisms.
The nodes in the network models are connected by causally related edges.
Most causal edges in the network models are supported by at least one (often multiple) literature reference and are annotated with a variety of metadata, including species, tissue and cell type.
The networks are evolving and all different versions are made available in CBN. 98 first generation networks describing lung and vascular biology have been published in six peer-reviewed articles. 50 network models have been consolidated from the 92 lung-relevant networks and enriched with COPD-relevant mechanisms and represent the second generation network models. In addition to peer review, those models have undergone a refinement by experts from the scientific community via the network verification challenge (https://bionet.sbvimprover.com). Further refinement is still under way and new versions will be included in future releases of the database.
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Database and Website Features
Search for networks by keyword, gene, protein, or small molecule name, biological process, pubmed identifier of supporting evidence...
Open and view specific network
Browse and filter nodes and edges
Browse scientific evidences behind causal edges in the neworks
View different versions of networks (when there are multiple versions)
Download / export
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Export network view as svg image
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Selected networks from the CBN database are subjected to crowd-verification on the https://bionet.sbvimprover.com website in the frame of the sbv IMPROVER network verification challenge. Updated networks are then deposited back into CBN as new versions.