File format links

Pathway data

• BioPax
  • The Biological Pathways Exchange format is from the BioPax group containing representatives from NIST, SRI, Aventis, Genoscope, Argonne National Labs, the Memorial Sloan-Kettering Cancer Center, Harvard, Stanford, Columbia University, and the University of Tornoto.
  • The format describes chemical reaction networks for biological pathways. The format uses domain knowledge and ontologies to characterize molecules and interactions. BioPax closely follows the data model introduced in the PSI-MI file format.
  • See also XML, which defines the basic structural syntax of a BioPax file. See RDF, built atop XML and used to embed metadata describing structures and relationships. And see OWL, built atop RDF, to describe ontologies and the vocabulary of BioPax itself.
• CellML
  • The Cell Markup Language format is from the University of Auckland. The format describes ??.
  • See also XML, which defines the basic structural syntax of a CellML file. Also see MathML used for ??, and RDF, used to embed metadata within a CellML document.
• PSI-MI
  • The Molecular Interaction format is from the Proteomics Standards Initiative, a consortium of database providers including BIND, DIP, IntAct, MINT, MIPS, GlaxoSmithKline, CellZome, Hybrigenics, and the Universities of Bielefeld, Bordeaux, Cambridge, etc.
• SBML
  • The Systems Biology Markup Language format is from a consortia including members from the Systems Biology Institute, Molecular Sciences Institute, California Institute of Technology, the University of Hertfordshire, California State University, Northridge, and others.
  • The format describes arbitrary chemical reaction networks, compartments, and simulation parameters.
  • See also XML, which defines the basic structural syntax of an SBML file. Also see MathML, used for defining SBML's kinetic rate law equations.

Ontologies

• Gene Ontology GO flat file format
  • The Gene Ontology flat file format is from the Gene Ontology Project.
  • The format describes the graph structure of the project's ontologies. The format is now deprecated in favor of the OBO format.
• Open Biomedical Ontologies OBO flat file format
  • The OBO flat file format is from Open Biomedical Ontologies group, and most notibly the Gene Ontology Project.
  • The format describes the graph structure of the project's ontologies and replaces the Gene Ontology project's earlier GO format.

Other data

• GML
  • The Graph Markup Language, developed for the Graphlet tool.
  • The format describes simple node-and-edge graph structures. Component locations, labels, colors, and icons may be controlled. The format is primarily a graph drawing format, but it can be used by Cytoscape for network interchange.
• SIF
  • The Simple Interaction File, developed as part of the Cytoscape project.
  • The format describes a graph structure built from a series of interactions between named nodes. The format is primarily used as a simple data import mechanism for Cytoscape.

Web standards

• MathML
  • The Math Markup Language from the World Wide Web Consortium (W3C).
  • The format describes equations.
• OWL
  • The Web Ontology Language from the World Wide Web Consortium (W3C).
  • The format describes ontologies - interconnected structures (such as hierachies or graphs) and the relationships between components of those structures.
• RDF
  • The Resource Description Framework from the World Wide Web Consortium (W3C).
  • The format defines how to declare relationships between objects and metadata describing those relationships.
• XML
  • The Extensible Markup Language from the World Wide Web Consortiium (W3C).
  • The format deefines a text format for describing hierarchical data, such as Web documents. XML is the parent language of XHTML, the strict form of the HTML syntax used for web pages. XML and HTML are both derived from SGML, an earlier ISO standard for document description.