This is one of the possible Use Cases.
1. Abstract
This use case covers scenarios where rules are needed to extend the expressive power of OWL for use in large biomedical ontologies.
2. Status
Proposed by Christine Golbreich (and posted by IanHorrocks on her behalf). It is based on experience with real applications in the biomedical domain.
3. Benefits of Interchange
Large-scale terminologies, classifications and ontologies have been developed for many years in various biomedical domains. These resources have the potential to contribute to the Semantic Web for the Life Sciences.
4. Requirements on the RIF
- Interoperability between ontologies through OWL standard is necessary to allow reasoning across connected domains e.g. pathology, genes, anatomy.
- As most of the ontologies use union or existential in rhs, OWL-DLP expressiveness is not enough.
- OWL DL expressiveness is required.
- OWL DL reasoining services (consistency checking, classification) are crucial for the quality assurance of such large-scale biomedical ontologies.
In conclusion, many biomedical ontologies are represented in OWL DL, so a Web rule language should be compatible with OWL DL.
5. Narratives
Life Sciences have a long tradition of controlled vocabularies. Large-scale terminologies, classifications and ontologies have been developed for many years in various biomedical domains. These resources have the potential to contribute to the Semantic Web for the Life Sciences. Several actual biomedical ontologies, e.g. The Foundational Model of Anatomy (FMA), the Medical Subject Headings (MeSH), the Gene Ontology™, the National Cancer Institute Thesaurus are converted to OWL. The conversion of other ontologies to OWL is also been investigated, including the UMLS® Metathesaurus® and Semantic Network and other ones e.g., SNOMED-CT, GALEN are represented in other DLs. New biomedical ontologies are now directly developed in OWL e.g.; BioPax an ontology for biological pathway information. For example, the FMA is the most complete ontology of human canonical anatomy. It contains more than 72,000 concepts and more than two million instantiations of 150 relations. 2/3 of the FMA (i.e. a subset of 40000 concepts) including about 40000 subclass axioms, with existential and union in rhs and other OWL constructors has been represented in OWL DL [17]. The FMA is used in several actual applications e.g. the Virtual Soldier project Virtual Soldier project (http://www.virtualsoldier.net/) [16].
- Rubin DL, Dameron O, Bashir Y, Grossman D, Dev P and Musen MA, Using ontologies linked with geometric models to reason about penetrating injuries. American Med Info J, 2005 (AMIA)
- C. Golbreich, S. Zhang, O. Bodenreider Foundational Model of Anatomy in OWL: experience and perspectives, OWL Experiences and Directions Workshop, collocated with the International Conference on Rule Markup Languages for the Semantic Web, Galway, Ireland, 2005 (extended version submitted)