Barry Smith (UB Philosophy)
11/19/07
The Future of Biomedical Informatics
While the bulk of the data obtained through clinical research is still managed on the basis of
local coding schemes which pose severe obstacles to data retrieval and integration, the NIH and
other bodies are increasingly mandating that primary research data should in the future be
published in forms which will ensure that they can be reused by others. We describe one means
to address such mandates through the use of ontologies, which are consensus-based controlled
vocabularies for the description of data. We outline some of the successes of ontology research,
and sketch some of the ontology-based projects in clinical and translational medicine currently
under way in Buffalo.
1. Biomedical Informatics Needs Data
2. The Problem of Local Coding Schemes
3. NIH Policies for Data Reusability and the Growth of Clinical Research Consortia
4. Is SNOMED the Solution?
5. The Gene Ontology
6. The OBO Foundry
7. The National Center for Biomedical Ontology
8. Ontology in Buffalo
References
Bittner, T. & Goldberg, L.J. Spatial location and its relevance for terminological inferences in
bio-ontologies. Bioinformatics 23, 1674-1682 (2007).
Ceusters W, Smith B. Strategies for referent tracking in Electronic Health Records, J Biomed
Inform, 2006;39(3):362-378.
Ceusters W, Smith B. Referent tracking for treatment optimisation in schizophrenic patients: A
case study in applying philosophical ontology to diagnostic algorithms. J Web Semantics, 2006;
4(3): 1-45.
Kumar A, Yip YL, Smith B, Grenon P. Bridging the gap between medical and bioinformatics:
An ontological case study in colon carcinoma, Comput Biol Med, 2006; 36 (7-8): 694-711.
Natale DA, Arighi CN, Barker W, et al. Framework for a Protein Ontology, BMC Bionformatics
(in press).
Smith B, Ceusters W, Kumar A, Rosse R. On carcinomas and other pathological entities, Comp.
Funct. Genomics, 2005;6(7/8):379-387.
Smith B, Ashburner M, Rosse C, et al. The OBO Foundry: Coordinated evolution of ontologies
to support biomedical data integration, Nature Biotechnology 2007; 25 (11): 1251-1255.
http://ontology.buffalo.edu/obofoundry/NBT_OBO.pdf