Cell Cycle Ontology

The Cell Cycle Ontology, or CCO, project aims to extend the existing ontologies for cell cycle knowledge, to build a resource that integrates and manages knowledge about the cell cycle components and regulatory aspects in OBO and OWL. This knowledge is assembled from a diverse set of already existing resources (GO, IntAct, BIND, NCBI taxonomy, UniProt, and so forth): the combination of the knowledge will give an overall picture of the cell division process. Not only enriched by the combination of resources, Ontology Design Patterns will be appplied in the OWL version of CCO to provide a fine-grained and expressive knowledge model of the cell cycle. Users will be able to do expressive queries and hypotheses validation against the system.

Each element has a unique identifier of the form CCO:cnnnnnnn. CCO indicates that the concept belongs to the CCO ontology (CCO is also known as the ontology namespace), c denotes de sub-namespace: C (cellular component), P (biological process), F (molecular function), R (reference), T (taxon), I (interaction), B (bio-molecular entity), U (Upper ontology (computer science)), N (instance). Finally, nnnnnnn consists of 7 numerical characters.

Among the languages used for representating the knowledge in CCO, OWL-DL (Description_logics) has been chosen because of its expression power, a well developed theory and consistent semantics. Reasoning packages, such as RACER, KAON2, Pellet and/or FaCT++ are being used for classifying, checking consistencies and making implicit information explicit. In addition, such reasoning can reveal inconsistencies, hidden dependencies, redundancies and misclassifications. As a result, the CCO becomes more robust.

Availability
CCO is available (http://www.CellCycleOntology.org) in several different formats:


 * OBO,
 * OWL,
 * XML,
 * DOT, and
 * GML.

Besides, this application ontology is available for four different model organisms:


 * Arabidopsis thaliana,
 * Saccharomyces cerevisiae,
 * Schizosaccharomyces pombe, and
 * Homo sapiens.

Status
Currently, CCO is being cleaned and improved (many more terms are being added as well as relationships). The ontology in OBO format can be edited using OBO-Edit and the OWL version can also be edited using Protégé. All kinds of curation request and suggestions are very welcome. The project is under constant development, and future plans include other databases, more expressive OWL (using Ontology Design Patterns), better querying interfaces, fuzzy relationships, text mining-based enrichment, and more.