BioPAX
Encyclopedia
BioPAX is a RDF
/OWL
-based
standard language to represent biological pathway
s
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
) 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
.
Resource Description Framework
The Resource Description Framework is a family of World Wide Web Consortium specifications originally designed as a metadata data model...
/OWL
Web Ontology Language
The Web Ontology Language is a family of knowledge representation languages for authoring ontologies.The languages are characterised by formal semantics and RDF/XML-based serializations for the Semantic Web...
-based
standard language to represent biological pathway
Biological pathway
A biological pathway is a number of biochemical steps, linked together, with a start and an end. The activity within a pathway should is a flow of molecules. Some typical types of biochemical pathways are metabolic pathways and signaling pathways. The Reactome is a curated information source, with...
s
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
Reactome is a database of biological pathways. There are several Reactomes that concentrate on a specific organism, the largest of these is focused on human biology, but includes pathway steps inferred to exist in humans based on experimental data from model organisms and pathways computationally...
) 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
Open Biomedical Ontologies
Open Biomedical Ontologies is an effort to create controlled vocabularies for shared use across different biological and medical domains. As of 2006, OBO forms part of the resources of the U.S...
.
Databases with BioPAX Export
Online databases offering BioPAX export include:- Signaling Gateway Molecule Pages (SGMP)
- ReactomeReactomeReactome is a database of biological pathways. There are several Reactomes that concentrate on a specific organism, the largest of these is focused on human biology, but includes pathway steps inferred to exist in humans based on experimental data from model organisms and pathways computationally...
- BioCyc
- INOH
- BioModels
- Nature/NCI Pathway Interaction DatabaseNCI-Nature Pathway Interaction DatabaseThe is a free biomedical database of human cellular signaling pathways. The database contains information about the molecular interactions and reactions that take place in cells, with a particular focus on processes that might be relevant to cancer research and treatment. The database was...
- Cancer Cell Map
- Pathway Commons
- NetpathNetpathNetPath is a manually curated resource of human signal transduction pathways. It is a joint effort between Pandey Lab at the Johns Hopkins University and the Institute of Bioinformatics , Bangalore, India, and is also worked on by other parties....
- A curated resource of signal transduction pathways in humans - ConsensusPathDBConsensusPathDBThe ConsensusPathDB is a molecular functional interaction database, integrating information on protein interactions, signaling, metabolism and gene regulation in humans. ConsensusPathDB includes functional interactions from 12 databases...
- A database integrating human functional interaction networks - PANTHER (List of Pathways)
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 SBMLSBMLThe Systems Biology Markup Language 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 users and developers...
, as part of the Virtual Cell. - ChiBE (Chisio BioPAX Editor), an application for visualizing and editing BioPAX.
- BioPAX Validator an application to check rules and best practices (project wiki)