Abstract
Ontology is the talk of the day in the medical informatics community. Its relevant role in the design and implementation of information systems in health care is now widely acknowledged. In this paper we present two case studies showing ontologies “at work” in the genomic domain and in the clinical context. First we show how ontologies and genomic controlled vocabularies can be effectively applied to help in a genomic approach towards the comprehension of fundamental biological processes and complex cellular patho-physiological mechanisms, and hence in biological knowledge mining and discovery. Subsequently, as far as the clinical context is concerned, we emphasize the relevance of ontologies in order to maintain semantic consistency of patient data in a continuity of care scenario. In conclusion we advocate that a deep analysis of the structure and the concepts present at different granular level – from genes to organs – is needed in order to bridge this different domains and to unify bio-medical knowledge in a single paradigm.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Gruber, T.R.: A translation approach to portable ontologies. Knowledge Acquisition 5(2), 199–220 (1993)
Guarino, N.: Formal ontology and information systems. In: Guarino, N. (ed.) Formal Ontology in Information Systems. Proceedings of FOIS 1998, IOS Press, Amsterdam (1998)
Available on-line at http://www.jfsowa.com/ontology/ontoshar.htm (Last access June 1, 2005)
Available on-line at http://ontology.buffalo.edu/ontology [PIC].pdf (Last access: June 1, 2005)
Kumar, A., Smith, B., Novotny, D.D.: Biomedical Informatics and Granularity, Available on-line at http://ontologist.com (Last access: June 1, 2005)
Schuler, G.D.: Pieces of the puzzle: expressed sequence tags and the catalog of human genes. J. Mol. Med. 75, 694–698 (1997)
National Center for Biotechnology Information (NCBI), UniGene system, Available from http://www.ncbi.nlm.nih.gov/UniGene/ (Last access: June 1, 2005)
Maglott, D., Ostell, J., Pruitt, K.D., Tatusova, T.: Entrez Gene: gene-centered information at NCBI. Nucleic Acids Research 33, D54–D58 (2005)
National Center for Biotechnology Information (NCBI). Entrez Gene database. Available from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene (Last access: June 1, 2005)
Apweiler, R., Bairoch, A., Wu, C.H., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M.J., Natale, D.A., O’Donovan, C., Redaschi, N., Yeh, L.S.: UniProt: the Universal Protein Knowledgebase. Nucleic Acids Research 32, 115–119 (2004)
UniProt the universal protein resource. Available from http://www.pir.uniprot.org/ (Last access: June 1, 2005)
Kanehisa, M., Goto, S.: KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research 28(1), 27–30 (2000)
Kyoto Encyclopedia of Genes and Genomes – KEGG. Available from http://www.genome.ad.jp/kegg/ (Last access: June 1, 2005)
Online Mendelian Inheritance in Man – OMIM. Available from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM (Last access: June 1, 2005)
Sonnhammer, E.L.L., Eddy, S.R., Durbin, R.: PFAM: A comprehensive database of protein domain families based on seed alignments. Proteins 28, 405–420 (1997)
MGED NETWORK. Ontology Working Group (OWG). Available from http://mged.sourceforge.net/ontologies/ (Last access: June 1, 2005)
The Gene Ontology Consortium, Gene ontology: tool for the unification of biology. Nat. Gen. 25, 25–29 (2000)
Smith, B., Williams, J., Schulze-Kremer, S.: The ontology of the gene ontology. In: AMIA Annu. Symp. Proc. pp. 609–13 (2003)
Guffanti, A., Reid, J.F., Alcalay, M., Gyorgy, S.: The meaning of it all: Web-based resources for large-scale functional annotation and visualization of DNA microarray data. Trends in Genetics 18, 589–592 (2002)
Masseroli, M., Pinciroli, F.: Using Gene Ontology and genomic controlled vocabularies to analyze high-throughput gene lists. To appear on Computers in Biology and Medicine
Task Force of the Working Group on Heart Failure of the European Society of Cardiology. The treatment of heart failure. European Heart J. 18, 736–753 (1997)
Beale, T.: Archetypes: Constraint-based Domain Models for Future-proof Information System. Available at http://www.openehr.org/downloads/archetypes/archetypes_new.pdf (Last access: June 1, 2005)
Masolo, C., Gangemi, A., Guarino, N., Oltramari, A., Schneider, L.: Wonder Web Deliverable D17. The WonderWeb Library of Foundational Ontologies (2002)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Pisanelli, D.M., Pinciroli, F., Masseroli, M. (2005). The Ontological Lens: Zooming in and out from Genomic to Clinical Level. In: Oliveira, J.L., Maojo, V., Martín-Sánchez, F., Pereira, A.S. (eds) Biological and Medical Data Analysis. ISBMDA 2005. Lecture Notes in Computer Science(), vol 3745. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11573067_5
Download citation
DOI: https://doi.org/10.1007/11573067_5
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-29674-4
Online ISBN: 978-3-540-31658-9
eBook Packages: Computer ScienceComputer Science (R0)