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The Cell Cycle Ontology (CCO) integrates and manages knowledge about the cellular components involved in cell cycle execution and regulation. A number of knowledge representation formalisms, such as OBO, OWL, and RDF are used to capture and represent the knowledge about cell cycle. This knowledge is assembled from a diverse set of already existing resources (such as GO, UniProt, IntAct, GOA, NCBI taxonomy). The integration of the knowledge in a single resource gives an overall picture of the cell cycle process difficult to obtain otherwise.

The following cartoon depicts a bit of knowledge currently stored in CCO for the specific protein SWI4_YEAST. This local neighborhood also shows the type of relations attached to a protein and the different terms (e.g. intracellular localization, interactions, associated process, post-translational modifications, etc).

SWI4_YEAST local neighborhood

The CCO is available in a range of formats  supporting various applications:

  • CCO in OBO format can be loaded in OBO-Edit
  • CCO in OWL format can be loaded in Protege
  • CCO in GML format can be loaded in Cytoscape
  • CCO in DOT format can be loaded in Graphviz
  • CCO in RDF format can be loaded in Protege
  • CCO in RDF format can be loaded into a triple store for SPARQL querying

    • CCO v. 1.02 can be explored in:

  • NCBO BioPortal
  • Ontology Lookup Service
  • Ontology Online
  • DIAMONDS workbench

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    Last Updated on Tuesday, 22 March 2011 10:48
     

    Newsflash

    New release of ONTO-PERL

    ONTO-PERL 1.32 features multiple enhancements
     

    'TurboOrtho - a High Performance Alternative for OrthoMCL' presented at ECCB 2010 as a poster (Ekseth et al.)

    (The software will be released in April 2011)
     
    'Benchmarking triple stores with biological data' presented at SWAT4LS 2010 as a full paper (Mironov et al.)