Abstract
The National Center for Biomedical Ontology (NCBO) BioPortal provides common access for browsing and querying a large set of ontologies that are commonly used in biomedical communities. One of our missions is to align lexical features (i.e., textual definitions) that are commonly used in these ontologies across different representation formats with standard tags and to represent them in a standard way to the users. The Simple Knowledge Organization System (SKOS) is a recommendation of the World-Wide-Web Consortium (W3C) for a common data model for sharing and linking knowledge organization systems on the Semantic Web. The BioPortal is in the process of adopting SKOS in the backend representation for its content. During this process, we discovered that there exists a set of commonly-used lexical features shared by the biomedical ontologies that SKOS does not yet represent. In this paper, we discuss our proposed SKOS extensions to cover this set of commonly used lexical features, the rationales, and the detailed description of each proposed construct.
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
LexGrid: The Lexical Grid (2009), https://cabig-kc.nci.nih.gov/Vocab/KC/index.php/LexGrid
ISOcat - data category registry (October 2011), http://www.isocat.org
AGROVOC Thesaurus, Food and Agriculture Organization of the United Nations (FAO), http://www.fao.org/agrovoc
NCBO Bioportal, http://bioportal.bioontology.org/
Bodenreider, O.: Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support. In: Geissbuhler, A., Kulikowski, C. (eds.) IMIA Yearbook of Medical Informatics, vol. 47, pp. 67–79. International Medical Informatics Association (2008)
Chute, C.G.: The Copernican Era of Healthcare Terminology: A Re-Centering of Health Information Systems. In: AMIA Annual Symposium, pp. 68–73 (1998)
Chute, C.G.: Clinical Classification and Terminology: Some History and Current Observations. JAMIA 7(3), 298–303 (2000)
Library of congress subject headings, the library of congress cataloging distribution service, http://www.loc.gov/cds/lcsh.html
NASA Taxonomy, http://nasataxonomy.jpl.nasa.gov/fordevelopers/
Noy, N.F., Shah, N.H., Whetzel, P.L., Dai, B., Dorf, M., Griffith, N., Jonquet, C., Rubin, D.L., Storey, M.D., Chute, C.G., Musen, M.A.: Bioportal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Research 37, 170–173 (2009)
The open biomedical ontologies, http://www.obofoundry.org/
OWL 2 web ontology language structural specification and functional-style syntax, http://www.w3.org/TR/owl2-syntax/
The RDF vocabulary, http://www.w3.org/1999/02/22-rdf-syntax-ns
SKOS vocabulary, http://www.w3.org/2006/07/SWD/SKOS/reference/20090315/skos.rdf
SKOS XL vocabulary, http://www.w3.org/2006/07/SWD/SKOS/reference/20090315/skos-xl.rdf
SPARQL Query Language for RDF, www.w3.org/TR/rdf-sparql-query/
Tao, C., Pathak, J., Solbrig, H.R., Wei, W., Chute, C.G.: Common terminology guidelines for representing biomedical ontologies in semantic web notations. Journal of Biomedical Informaitcs (submitted)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Tao, C., Noy, N.F., Solbrig, H.R., Shah, N.H., Musen, M.A., Chute, C.G. (2012). Proposed SKOS Extensions for BioPortal Terminology Services. In: Pan, J.Z., et al. The Semantic Web. JIST 2011. Lecture Notes in Computer Science, vol 7185. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-29923-0_23
Download citation
DOI: https://doi.org/10.1007/978-3-642-29923-0_23
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-29922-3
Online ISBN: 978-3-642-29923-0
eBook Packages: Computer ScienceComputer Science (R0)