Bio-medical Ontologies Maintenance and Change Management

64 A.S. Sidhu and M. Bellgard
3.4 Protein Ontology as a Structured Hierarchy
Protein Ontology consists of a hierarchical classification of concepts discussed
above represented as classes, from general to specific. In PO, the notions classification,
reasoning, and consistency are applied by defining new concepts from defined
generic concepts. The concepts derived from generic concepts are placed precisely
into the class hierarchy of Protein Ontology to completely represent information
defining a protein complex, as depicted in the figure above. More details about
Protein Ontology are available on the website (http://www.proteinontology.info/).
4 Summary
An ontology for Protein Domain must contain terms or concepts relevant to protein
synthesis, describing Protein Sequence, Structure and Function and relationships
between them. In this chapter, we address this issue by providing clear and
unambiguous definitions of all major biological concepts of the protein synthesis
process and the relationships between them through Protein Ontology or PO
(Sidhu et al., 2007). PO provides a unified controlled vocabulary both for annotation
data types and for annotation data. As complete protein information has to be
obtained from diverse protein sources, it becomes necessary to compose ontology
(corresponding to the diverse sources) that can serve the proteomics domain.
Instead of creating a new ontology right from scratch containing the terms that
are new to the proteomics domain, it is preferable to create an ontology by reusing
terms of existing protein data sources and composing them to form a protein ontology.
The information in protein data sources change rapidly. Organizations
introduce new terminology or expand the terminology they use in the data they
publish. When such an update occurs, any ontology derived from these data
sources also needs to change. An ideal solution to the synchronization problem
between protein data sources and protein ontology when protein data sources are
updated is to have a tool that automatically triggers a systematic update to the ontology
when its sources change. Such a tool requires an algebraic foundation
based upon which the updates can be systematically handled.
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