Cell Cycle Ontology

OWL stands for Web Ontology Language. OWL is a knowledge representation language divided in three flavors: OWL-Full, OWL-DL and OWL-Lite, being OWL-Full the most expressive one and OWL-Lite the least one. OWL Full is not tractable. OWL-DL offers a lot of expresivity retaining tractability, which means that reasoning can be applied, and hence OWL-DL has been chosen for CCO.

OWL-DL queries on CCO

OWL-DL queries against CCO and over the web can be done using the OWLDoc server provided by the CO-ODE project. To do so, load either cco_A_thaliana.oppl.owl or cco_S_pombe.oppl.owl in the "load" slot. Once loaded, DL queries can be executed in the "DL queries" section (using Manchester OWL syntax), for example, if we want to know which proteins participate in "Cell Cycle":

        participates_in some CCO_P0000066

If we want to know which proteins are located in the mitochondrion, we would use the following expression:

CCO_U0000005 and ((located_in some (part_of some CCO_C0000325)) or (located_in some CCO_C0000325))

Expressions of any complexity can be used. Due to performance issues session with the other two organisms (H. sapiens and S. cerevisiae) are not recommended.

OWL-DL queries can also be performed loading any ontology in Protégé 4 and using the DL query tab.