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,
2005:6(7);
379-387.
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.
The ontology of anatomical and pathological structures formulated in the above
is now being incorporated into the
Ontology for General Medical Science (OGMS):
Richard H. Scheuermann, Werner Ceusters, and Barry
Smith, “Toward
an Ontological Treatment of Disease and Diagnosis”, Proceedings of the 2009
AMIA Summit on Translational Bioinformatics, 2009, 116-120.
Many existing biomedical vocabulary standards rest on incomplete,
inconsistent or confused accounts of basic terms pertaining to diseases,
diagnoses, and clinical phenotypes. Here we outline what we believe to be a
logically and biologically coherent framework for the representation of such
entities and of the relations between them. We defend a view of disease as
involving in every case some physical basis within the organism that bears a
disposition toward the execution of pathological processes. We present our view
in the form of a list of terms and definitions designed to provide a consistent
starting point for the representation of both disease and diagnosis in
information systems in the future.