Ontologies for the life sciences [chapter]

Steffen Schulze-Kremer, Barry Smith
2005 Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics  
Where humans can manipulate and integrate the information they receive in subtle and everchanging ways from context to context, computers need structured and context-free background information of a sort which ontologies can help to provide. A domain ontology captures the stable, highly general and commonly accepted core knowledge for an application domain. The domain at issue here is that of the life sciences, in particular molecular biology and bioinformatics. Contemporary life science
more » ... h includes components drawn from physics, chemistry, mathematics, medicine and many other areas, and all of these dimensions, as well as fundamental philosophical issues, must be taken into account in the construction of a domain ontology. Here we describe the basic features of domain ontologies in the life sciences and show how they can be used. Keywords: domain ontology, molecular biology, bioinformatics, philosophy 2. The ontologies employ, or can be instantiated in, or can be easily converted into, a common shared syntax. This may be either the GO syntax, extensions of this syntax, or OWL. This criterion is not met in all of the OBO ontologies currently listed. 3. The ontologies are orthogonal to other ontologies already lodged within OBO. Thus different ontologies, for example ontologies for anatomy and process, can be combined through additional relationships, and the latter can then be used to constrain when terms from different ontologies can be jointly applied to describe one and the same biological entity from distinct perspectives. 4. The ontologies share a unique identifier space. The source of concepts from any ontology can be immediately identified by the prefix of the identifier of each concept. It is, therefore, important that this prefix be unique. 5. The ontologies include textual definitions of their terms. Many biological terms are ambiguous; thus each term should be defined in such a way that its precise meaning within the context of a particular ontology is clear to a human user. Resources on (Bio-)Ontologies The following include information relevant to work on bio-ontologies.  Protégé 2000, an ontology editing software from Stanford Medical Informatics, is at .  On-To-Knowledge: Content-driven Knowledge-Management through Evolving Ontologies is a European funded research project at http://www.ontoknowledge.org.  The previous Bio-Ontologies Workshops and other material on ontologies is compiled by Robert Stevens at http://img.cs.man.ac.uk/stevens.  Cycorp has its own webpage at http://www.cyc.com.  Formal Ontology in Information Systems is an international conference series on ontologies with a webpage at http://www.fois.org.  Barry Smith has an extensive collection of works on ontology development in general and biomedical ontologies in particular at http://ontology.buffalo.edu/smith.
doi:10.1002/047001153x.g408213 fatcat:slqplkfx2fdcll6tnpwnzzxed4