Ontologies

Ontologies are specifications of domain concepts and their relationships. They are essential building blocks of well-designed knowledge-based systems.

Although being high-level representations of abstract knowledge models, ontologies yet have to be mapped to some kind of object model in order to be used in an executable system.

http://smi-web.stanford.edu/people/holger/publications/OOPSLA99-Metadata.html

Definition

An ontology is an explicit specification of some topic.

For our purposes, it is a formal and declarative representation which includes the vocabulary (or names) for referring to the terms in that subject area and the logical statements that describe what the terms are, how they are related to each other, and how they can or cannot be related to each other.

Ontologies therefore provide a vocabulary for representing and communicating knowledge about some topic and a set of relationships that hold among the terms in that vocabulary.

Guides for Ontology

 Ontology Development 101: A Guide to Creating Your First Ontology

Ontology projects

 Some Ongoing KBS/Ontology Projects and Groups at University of Texas
 John Bateman's ontology portal at University of Bremen

Features

 ontology annotations
 ontology contents
 ontology network
 ontology related nodes

Websites

 ontologies/OntologyResources.php" class="spip_out">MGED > Ontology Working Group
 OBO, Open Biological Ontologies

References

 Yue L, Reisdorf WC. Pathway and ontology analysis: emerging approaches connecting transcriptome data and clinical endpoints. Curr Mol Med. 2005 Feb;5(1):11-21. PMID: #15720266#

 Bard JB, Rhee SY. Ontologies in biology: design, applications and future challenges. Nat Rev Genet. 2004 Mar;5(3):213-22. PMID: #14970823#