Biological Pathway Exchange (BioPAX) is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data. It is an open and collaborative effort by the community of researchers, software developers, and institutions. BioPAX is defined in OWL DL and is represented in the RDF/XML format. For more details, see Demir E et al. 2010. The BioPAX community standard for pathway data sharing, Nature Biotechnology. 28(9).
Links:
- BioPAX ontology and documentation releases
- Specification development
- Archive and downloads
- Google group
- Wiki(archive; mediawiki got spammed, and we put it down in 2014)
- BioPAX validator
- BioPAX @ COMBINE
- View BioPAX via
- WebProtege(requires an account)
- OWLdoc
- WebVOWL
"Hello World" example:
<?xml version="1.0" encoding="UTF-8"?>
<rdf:RDF
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" xml:base="">
<owl:Ontology rdf:about="">
<owl:imports rdf:resource="http://www.biopax.org/release/biopax-level3.owl#" />
</owl:Ontology>
<bp:Protein rdf:about="http://my.example.com/biopax#HelloWorld">
<bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hello World!</bp:displayName>
</bp:Protein>
</rdf:RDF>
More examples examples
Scientific Advisory Board