BioPAX (Biological Pathway Exchange) is a
RDF/
OWL
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-based
standard language to represent
biological pathways
at the molecular and cellular level. Its major use is to facilitate the exchange of pathway data.
Pathway data captures our understanding of biological processes, but
its rapid growth necessitates development of databases and computational tools to aid
interpretation. However, the current fragmentation of pathway information across many
databases with incompatible formats presents barriers to its effective use. BioPAX solves this
problem by making pathway data substantially easier to collect, index, interpret and share.
BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and
gene regulation networks. BioPAX was created through a community process. Through BioPAX,
millions of interactions organized into thousands of pathways across many organisms, from a
growing number of sources, are available. Thus, large amounts of pathway data are available in a
computable form to support visualization, analysis and biological discovery.
It is supported by a variety of online databases (e.g.
Reactome
Reactome is a free online database of biological pathways. There are several Reactomes that concentrate on specific organisms, the largest of these is focused on human biology, the following description concentrates on the human Reactome. It is aut ...
) and tools. The latest released version is BioPAX Level 3. There is also an effort to create a version of BioPAX as part of
OBO
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.
Governance and development
The next version of BioPAX, Level 4, is being developed by a community of researchers. Development is coordinated by board of editors and facilitated by various BioPAX work groups.
Systems Biology Pathway Exchange (SBPAX) is an extension for Level 3 and proposal for Level 4 to add quantitative data and
systems biology terms (such as
Systems Biology Ontology). SBPAX export has been implemented by the
pathway databases
Signaling Gateway Molecule Pages and the
SABIO-Reaction Kinetics Database
SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics) is a web-accessible database storing information about biochemical Chemical reaction, reactions and their Enzyme kinetics, kinetic properties.
SABIO-RK comprises a reac ...
. SBPAX import has been implemented by the cellular modeling framework
Virtual Cell.
Other proposals for Level 4 include improved support for
Semantic Web, validation and visualization.
Databases with BioPAX Export
Online databases offering BioPAX export include:
Signaling Gateway Molecule Pages (SGMP)*
Reactome
Reactome is a free online database of biological pathways. There are several Reactomes that concentrate on specific organisms, the largest of these is focused on human biology, the following description concentrates on the human Reactome. It is aut ...
*
BioCyc
The BioCyc database collection is an assortment of organism specific Pathway/Genome Databases (PGDBs) that provide reference to genome and metabolic pathway information for thousands of organisms. As of June 2021, there were over 17,800 databases w ...
INOHBioModels*
Nature/NCI Pathway Interaction Database
Cancer Cell MapPathway Commons*
Netpath - A curated resource of signal transduction pathways in humans
*
ConsensusPathDB - A database integrating human functional interaction networks
PANTHERList of Pathways
*
WikiPathways
WikiPathways is a community resource for contributing and maintaining content dedicated to biological pathways. Any registered WikiPathways user can contribute, and anybody can become a registered user. Contributions are monitored by a group of ad ...
*
PharmGKB
The Pharmacogenomics Knowledgebase (PharmGKB) is a publicly available, online knowledge base responsible for the aggregation, curation, integration and dissemination of knowledge regarding the impact of human genetic variation on drug response. It ...
br>
PharmGKB
Software
Software supporting BioPAX include:
Paxtools a Java API for handling BioPAX files
Systems Biology Linker (Sybil) an application for visualizing BioPAX and converting BioPAX to
SBML
The Systems Biology Markup Language (SBML) is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of use ...
, as part of the
Virtual Cell.
ChiBE(Chisio BioPAX Editor),
[Babur, Ozgun, Ugur Dogrusoz, Emek Demir, and Chris Sander. "ChiBE: interactive visualization and manipulation of BioPAX pathway models." Bioinformatics 26, no. 3 (2010): 429-431.] an application for visualizing and editing BioPAX.
BioPAX Validator- syntax and semantic rules and best practices
project wiki
Cytoscapeincludes a BioPAX reader and other extensions, such as PathwayCommons plugin and CyPath2 app.
BiNoM a cytoscape plugin for network analysis, with functions to import and export BioPAX level 3 files.
BioPAX-pattern a Java API for defining and searching graph patterns in BioPAX files.
See also
*
SBML
The Systems Biology Markup Language (SBML) is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of use ...
Linked Open Vocabularies
References
External links
BioPAX homepageBioPAX Sourceforge Wiki
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Systems biology
Bioinformatics
Semantic Web
Domain-specific knowledge representation languages