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About CCO and GexKB PDF Print E-mail

Application ontologies (APO) ingegrate divers types of knowledge pertainig to a rather specialized domain of discourse. This site hosts two projects making use of application ontologies aiming at integrating and managing knowledge about the cellular components involved in the two important domains of scientific research - 1) The Cell Cycle Ontology (CCO) and 2) The Gene Expression Knowledge Base (GexKB) which includes three application ontologies, Gene Expression Ontology (GeXO), Regulation of Gene Expression (ReXO) and Regulation of Transcription Ontology (ReTO). A number of knowledge representation formalisms, such as OBO, OWL, and RDF are used to capture and represent the knowledge over the domain in question. 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 domain difficult to obtain otherwise.

The APOs listed above are 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 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 (deprecated) can be additionally explored in:

  • NCBO BioPortal
  • Ontology Lookup Service
  • Ontology Online
  • DIAMONDS workbench
  • Last Updated on Tuesday, 12 June 2012 18:49


    Doctoral Degree for Aravind Venkatesan On 13th Feb 2014, Aravind Venkatesan successfully defended his Ph.D. thesis "Application of Semantic Web Technology to establish knowledge management and discovery in the Life Sciences"  and was awarded the title of Doctor in Sciences by NTNU.

    BioGateway 2.00
    Major revision
    1. Local URIs replaced with external resolvable URIs
    2. Data from SwissProt extended to UniProt
    3. Data from IntAct added
    4. Scope limited to 147 Reference Proteomes
    5. Inferred triples limited to those supported explicitly by the ontology plus 'priority over is_a'
    Genes2GO: Gene Ontology matrix builder
    Genes2GO builds a binary matrix with genes and GO IDs/Terms.

    Cell Cycle Ontology v.2.01 and Gene Expression Knowledge Base V.1.01
    Streamlined modelling of post-translational protein modifications which makes querying for modifications straightforward (e.g. query APO4)

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