The Cell Cycle Ontology: an application
        ontology supporting the Life Sciences

 Erick Antezana1,2 , Mikel Egaña3 , Ward Blondé1,2 , Robert Stevens3 , Bernard
             De Baets4 , Vladimir Mironov5 , and Martin Kuiper5
              1
                Dept. of Plant Systems Biology, VIB, Gent, Belgium
          2
            Dept. of Molecular Genetics, Ghent University, Gent, Belgium
         3
           School of Computer Science, The University of Manchester, UK
4
  Dept. of Applied Mathematics, Biometrics and Process Control, Ghent University,
                                 Gent, Belgium
   5
     Dept. of Biology, Norwegian University of Science and Technology, Norway
                      http://www.CellCycleOntology.org



Abstract
The terms and relationships provided by existing bio-ontologies only capture a
small part of our biological understanding, thus the potential of applying compu-
tational analysis on such information remains limited. The Cell Cycle Ontology
(CCO) is designed to capture detailed information of the cell cycle process by
combining representations from several sources. CCO is an application ontology
that is supplied as an integrated turnkey system for exploratory analysis, ad-
vanced querying, and automated reasoning. CCO supports four model organisms
(Human, Arabidopsis, Baker’s yeast and Fission yeast) with separate ontologies
but also one integrated ontology. CCO holds more that 65000 concepts and more
than 20 types of relationships. CCO comprises data from existing resources such
as the Gene Ontology (GO), the Relations Ontology (RO), the IntAct database
(MI), the NCBI taxonomy, the UniProt knowledge base as well as orthology data.
An automatic pipeline builds CCO from scratch periodically: initially some exist-
ing ontologies (GO, RO, MI, in-house ones) are automatically fetched, integrated
and merged, producing in turn a core cell cycle ontology. Then, organism-specific
protein and gene data are added from UniProt and from the GO Annotation files,
generating four organism-specific ontologies. Those four ontologies are merged
and more terms are included from an ontology built automatically from the Or-
thoMCL execution on the cell cycle proteins. Finally, during the maintenance
phase, a semantic improvement on the OWL version is carried out: ontology
design patterns are included using the Ontology Pre-Processor Language. The
resulting CCO is designed to provide a richer view of the cell cycle regulatory
process, in particular by accommodating the intrinsic dynamics of this process.
CCO is available in: OBOF, RDF, XML, OWL, GML, and DOT. A SPARQL
endpoint allows building complex queries, such as “get the cell cycle related
proteins in A. thaliana participating in the same interaction but having differ-
ent locations”. Visual exploration can be done via the BioPortal, the Ontology
Lookup Service, the Ontology Online service, or the DIAMONDS platform.