BioPAX

Biological Pathways Exchange language (RDF/XML)

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BioPAX.org

(biopax.github.io)

Biological Pathways 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. BioPAX Paper was published in Nature Biotechnology in 2010.

SAB

The current scientific advisory board (SAB) members are:

  • Gary Bader, University of Toronto
  • Peter D'Eustachio, New York University
  • Henning Hermjakob, European Bioinformatics Institute
  • Nicolas LeNovere, European Bioinformatics Institute
  • Peter Karp, SRI International
  • Chris Sander, cBio, Memorial Sloan-Kettering Cancer Center (MSKCC), Dana-Farber Cancer Center (DFCI), Harvard Medical School (HMS)
  • "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>
    

    Links:

    PS:

    Official BioPAX web site www.biopax.org has been at CBIO MSKCC until 2013; then it moved to Sourceforge (Project-Web hosting, biopax.sf.net) and still resides there. Site configuration and some static content are stored in the Hg repository. And we are thinking of a better design (not using .htaccess, MediaWiki and PHP) and migrating here.

    Sincerely yours,

    BioPAX team.