TY - JOUR
T1 - Terminology representation guidelines for biomedical ontologies in the semantic web notations
AU - Tao, Cui
AU - Pathak, Jyotishman
AU - Solbrig, Harold R.
AU - Wei, Wei Qi
AU - Chute, Christopher G.
N1 - Funding Information:
This research is partially supported by the National Center for Biomedical Ontologies (NCBO) under the NIH Grant #N01-HG04028 and the NSF under Grant #0937060 to the Computing Research Association for the CIFellows Project. The authors thank Drs. Mark Musen, Natasha Noy, and Nigam Shah for their valuable suggestions during the preparation of the paper.
PY - 2013/2
Y1 - 2013/2
N2 - Terminologies and ontologies are increasingly prevalent in healthcare and biomedicine. However they suffer from inconsistent renderings, distribution formats, and syntax that make applications through common terminologies services challenging. To address the problem, one could posit a shared representation syntax, associated schema, and tags. We identified a set of commonly-used elements in biomedical ontologies and terminologies based on our experience with the Common Terminology Services 2 (CTS2) Specification as well as the Lexical Grid (LexGrid) project. We propose guidelines for precisely such a shared terminology model, and recommend tags assembled from SKOS, OWL, Dublin Core, RDF Schema, and DCMI meta-terms. We divide these guidelines into lexical information (e.g. synonyms, and definitions) and semantic information (e.g. hierarchies). The latter we distinguish for use by informal terminologies vs. formal ontologies. We then evaluate the guidelines with a spectrum of widely used terminologies and ontologies to examine how the lexical guidelines are implemented, and whether our proposed guidelines would enhance interoperability.
AB - Terminologies and ontologies are increasingly prevalent in healthcare and biomedicine. However they suffer from inconsistent renderings, distribution formats, and syntax that make applications through common terminologies services challenging. To address the problem, one could posit a shared representation syntax, associated schema, and tags. We identified a set of commonly-used elements in biomedical ontologies and terminologies based on our experience with the Common Terminology Services 2 (CTS2) Specification as well as the Lexical Grid (LexGrid) project. We propose guidelines for precisely such a shared terminology model, and recommend tags assembled from SKOS, OWL, Dublin Core, RDF Schema, and DCMI meta-terms. We divide these guidelines into lexical information (e.g. synonyms, and definitions) and semantic information (e.g. hierarchies). The latter we distinguish for use by informal terminologies vs. formal ontologies. We then evaluate the guidelines with a spectrum of widely used terminologies and ontologies to examine how the lexical guidelines are implemented, and whether our proposed guidelines would enhance interoperability.
KW - Biomedical ontology
KW - OWL
KW - Ontology representation guidelines
KW - RDF
KW - Terminology
KW - W3C
UR - http://www.scopus.com/inward/record.url?scp=84873129066&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84873129066&partnerID=8YFLogxK
U2 - 10.1016/j.jbi.2012.09.003
DO - 10.1016/j.jbi.2012.09.003
M3 - Article
C2 - 23026232
AN - SCOPUS:84873129066
SN - 1532-0464
VL - 46
SP - 128
EP - 138
JO - Journal of Biomedical Informatics
JF - Journal of Biomedical Informatics
IS - 1
ER -