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 Ontology Server provided by the CO-ODE project. To do so, click on any of the following links (each link is a predefined session with the necessary settings):

• cco_A_thaliana.oppl.owl.
• cco_S_pombe.oppl.owl.

The query, written in Manchester OWL syntax, should be pasted in the "DL Query" slot. For example, if we want to know which proteins participate in the interaction CCO_I0000041 (van3-drp1a-1 direct interaction), we would use the following expression:

participates_in some CCO_I0000041

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.