Cornelius Rosse, Anand Kumar, Jose LV Mejino Jr, Daniel L
Cook, Landon T Detwilern and Barry Smith,
“A
Strategy for Improving and Integrating Biomedical Ontologies”,
Proceedings of AMIA Symposium 2005, Washington DC, 639–643.
The integration of biomedical terminologies is indispensable to the process
of information integration. When terminologies are linked merely through the
alignment of their leaf terms, however, differences in context and ontological
structure are ignored. Making use of the SNAP and SPAN ontologies, we show how
three reference domain ontologies can be integrated at a higher level, through
what we shall call the OBR framework (for: Ontology of Biomedical Reality). OBR
is designed to facilitate inference across the boundaries of domain ontologies
in anatomy, physiology and pathology.
Barry Smith, Werner
Ceusters, Anand Kumar and Cornelius Rosse, “On
Carcinomas and Other Pathological Entities”, Comparative and Functional
Genomics, forthcoming.
Tumors, abscesses, cysts, scars, fractures are familiar types of what we
shall call pathological continuant entities. The instances of such types exist
always in or on anatomical structures, which thereby become transformed into
pathological anatomical structures of corresponding types: a fractured tibia, a
blistered thumb, a carcinomatous colon. In previous work on biomedical
ontologies we showed how the provision of formal definitions for relations such
as is_a, part_of and transformation_of can facilitate the integration of such
ontologies in ways which have the potential to support new kinds of automated
reasoning. We here extend this approach to the treatment of pathologies,
focusing especially on those pathological continuant entities which arise when
organs become affected by carcinomas.
Includes a revised and
corrected
classification of biomedical entities.