Ontolome

The Ontolome is the complete collection of application ontologies containing no duplicate elements. More formally, an ontolome contains no pair of application ontologies o1 and o2 such that o1 is equal to o2.

Nowadays, there are substantial efforts in the biological community for organizing biological concepts as controlled terminologies or ontologies (mainly domain and application ones). Generally speaking, domain bio-ontologies are organism independent. Nonetheless, in the case of the application ontologies, organism specific data is considered as a relevant component. For instance, the Arabidopsis thaliana ontolome will hold ontologies such as CCO which holds specific protein information of that particular model organim. That specific ontolome can be considered as a fingerprint for Arabidopsis thaliana.

CCO, AO (Apoptosis Ontology) constitute a subset of the ontolome that can be used as alignment/matching artefacts across organisms which in turn will contribute to a sort of comparative ontolomics and gain a better understanding in many aspects (e.g. how species have evolved). This comparative analysis follows the systems biology approach by not only taking gene sequences as comparison artefacts but also taking into account the system entities (processes, interactions, and so on) that play an important role. Moreover, some hypothesis can be generated based on this comparative analysis as well as serve as hypothesis testing platform and evaluate them for consistency with existing knowledge.