Skip Navigation


Briefings in Bioinformatics Advance Access originally published online on December 12, 2007
Briefings in Bioinformatics 2008 9(1):75-90; doi:10.1093/bib/bbm059
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (PDF) Freely available
Right arrow All Versions of this Article:
9/1/75    most recent
bbm059v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (10)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Rubin, D. L.
Right arrow Articles by Noy, N. F.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Rubin, D. L.
Right arrow Articles by Noy, N. F.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2007. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Biomedical ontologies: a functional perspective

Daniel L. Rubin, Nigam H. Shah and Natalya F. Noy

Corresponding author. Daniel L. Rubin, Stanford Center for Biomedical Informatics Research, Stanford, CA, USA. Tel: 650 723 6979; Fax: 650 725 7944; E-mail: rubin{at}med.stanford.edu

The information explosion in biology makes it difficult for researchers to stay abreast of current biomedical knowledge and to make sense of the massive amounts of online information. Ontologies—specifications of the entities, their attributes and relationships among the entities in a domain of discourse—are increasingly enabling biomedical researchers to accomplish these tasks. In fact, bio-ontologies are beginning to proliferate in step with accruing biological data. The myriad of ontologies being created enables researchers not only to solve some of the problems in handling the data explosion but also introduces new challenges. One of the key difficulties in realizing the full potential of ontologies in biomedical research is the isolation of various communities involved: some workers spend their career developing ontologies and ontology-related tools, while few researchers (biologists and physicians) know how ontologies can accelerate their research. The objective of this review is to give an overview of biomedical ontology in practical terms by providing a functional perspective—describing how bio-ontologies can and are being used. As biomedical scientists begin to recognize the many different ways ontologies enable biomedical research, they will drive the emergence of new computer applications that will help them exploit the wealth of research data now at their fingertips.

Keywords: ontologies, annotation, data analysis

Submitted: June 26, 2007. Received (in revised form): November 7, 2007.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Brief BioinformHome page
A. Lysenko, M. M. Hindle, J. Taubert, M. Saqi, and C. J. Rawlings
Data integration for plant genomics--exemplars from the integration of Arabidopsis thaliana databases
Brief Bioinform, November 1, 2009; 10(6): 676 - 693.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
L. French, S. Lane, T. Law, L. Xu, and P. Pavlidis
Application and evaluation of automated semantic annotation of gene expression experiments
Bioinformatics, June 15, 2009; 25(12): 1543 - 1549.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
V. Praz and P. Bucher
CleanEx: new data extraction and merging tools based on MeSH term annotation
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D880 - D884.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
H. Michael, J. Hogan, A. Kel, O. Kel-Margoulis, F. Schacherer, N. Voss, and E. Wingender
Building a knowledge base for systems pathology
Brief Bioinform, December 10, 2008; (2008) bbn038v1.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
A.M. Willemsen, G.A. Jansen, J.C. Komen, S. van Hooff, H.R. Waterham, P.M.T. Brites, R.J.A. Wanders, and A.H.C. van Kampen
Organization and integration of biomedical knowledge with concept maps for key peroxisomal pathways
Bioinformatics, August 15, 2008; 24(16): i21 - i27.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. Schulz, H. Stenzhorn, and M. Boeker
The ontology of biological taxa
Bioinformatics, July 1, 2008; 24(13): i313 - i321.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.