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Overview

OpenBEL is an open source language and software platform for capturing and managing biological knowledge. BEL (Biological Expression Language) was designed to be human read and writable, and easy for biologists to learn.

The use of OpenBEL and its standard way of expressing information can accelerate the pace of technology innovation and scientific discovery in areas such as network visualization of neural brain function; understanding of complex inter-related disease biology; comparison of human diseases with various animal models; deep investigation of drug efficacy and toxicity; as well as development of innovative therapeutics and diagnostics for personalized healthcare.

OpenBEL also provides tools to capture, integrate and store BEL knowledge as graphs for analysis and visualization. The BEL framework tool integrates BEL knowledge across different representational vocabularies and ontologies by maintaining a data mapping between them. This allows BEL knowledge from disparate sources to be accurately merged into a single graph.

OpenBEL Community Links of Interest

Projects using BEL

Projects using BEL include: NDex (Network Data Exchange project), the sbv IMPROVER Network Verification Challenge, and BioCreative V.

Example BEL

BEL captures causal and correlative relationships within the context they were observed in. Consider the following snippet of BEL showing correlative and causal relationships:

Example of BEL knowledge
# There exists a positive correlation between the disease process of Werner Syndrome and "Genomic Instability" / "Aging, Premature".
SET Citation = {"PubMed", "J Biol Chem 2004 Apr 2 279(14) 13659-67","14734561"}
SET Evidence = "Werner's syndrome (WS) is an inherited disease characterized by genomic instability and premature aging."
pathology(MESHD:"Werner Syndrome") positiveCorrelation pathology(MESHD:"Genomic Instability")
pathology(MESHD:"Werner Syndrome") positiveCorrelation pathology(MESHD:"Aging, Premature")

# The ku70 (protein encoded by gene XRCC6) and ku80 (protein encoded by gene XRCC5) binds with the WRN protein and directly increases its activity.
SET Evidence = "We have previously reported that WRN interacts with Ku70/80 and this interaction strongly stimulates WRN exonuclease activity."
complex(p(HGNC:XRCC5), p(HGNC:XRCC6), p(HGNC:WRN)) => cat(p(HGNC:WRN))

# Individual bindings of XRCC5, XRCC6, and PARP1 proteins to the WRN protein with the Cell Nucleus.
SET Evidence = "To this end, we identified three proteins that are stably associated with WRN in nuclear extracts. Two of these proteins, Ku70 and Ku80, were identified by immunoblot analysis. The third polypeptide,which was identified by mass spectrometry analysis, is identical to poly(ADP-ribose) polymerase-1(PARP-1), a 113-kDa enzyme that functions as a sensor of DNA damage."
SET CellStructure = "Cell Nucleus"
complex(p(HGNC:XRCC5), p(HGNC:WRN))
complex(p(HGNC:XRCC6), p(HGNC:WRN))
complex(p(HGNC:PARP1), p(HGNC:WRN))

The full source of this BEL document is here.

 

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