Skip Navigation

This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
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 (29)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Yeh, I.
Right arrow Articles by Altman, R. B.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Yeh, I.
Right arrow Articles by Altman, R. B.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics Vol. 19 no. 2 2003
Pages 241-248
© 2003 Oxford University Press

Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO)

Iwei Yeh 1, Peter D. Karp 1, Natalya F. Noy 1 and Russ B. Altman 1,*

1 Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
2 Bioinformatics Research Group, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
3 Stanford Medical Informatics, Stanford University, Stanford, CA 94305-5479, USA

Received on December 27, 2001 ; revised on May 13, 2002 and July 15, 2002 ; accepted on July 24, 2002

Motivation: A critical element of the computational infrastructure required for functional genomics is a shared language for communicating biological data and knowledge. The Gene Ontology (GO; http://www.geneontology.org) provides a taxonomy of concepts and their attributes for annotating gene products. As GO increases in size, its ongoing construction and maintenance becomes more challenging. In this paper, we assess the applicability of a Knowledge Base Management System (KBMS), Protégé-2000, to the maintenance and development of GO.

Results: We transferred GO to Protégé-2000 in order to evaluate its suitability for GO. The graphical user interface supported browsing and editing of GO. Tools for consistency checking identified minor inconsistencies in GO and opportunities to reduce redundancy in its representation. The Protégé Axiom Language proved useful for checking ontological consistency. The PROMPT tool allowed us to track changes to GO. Using Protégé-2000, we tested our ability to make changes and extensions to GO to refine the semantics of attributes and classify more concepts.

Availability: Gene Ontology in Protégé-2000 and the associated code are located at http://smi.stanford.edu/projects/helix/gokbms/. Protégé-2000 is available from http://protege.stanford.edu.

Contact: russ.altman{at}stanford.edu

* To whom correspondence should be addressed.


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
 J. Am. Med. Inform. Assoc.Home page
F. Bakhshi-Raiez, R. Cornet, and N. F. de Keizer
Development and Application of a Framework for Maintenance of Medical Terminological Systems
J. Am. Med. Inform. Assoc., September 1, 2008; 15(5): 687 - 700.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. Myhre, H. Tveit, T. Mollestad, and A. Laegreid
Additional Gene Ontology structure for improved biological reasoning
Bioinformatics, August 15, 2006; 22(16): 2020 - 2027.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Gene Ontology Consortium
The Gene Ontology (GO) project in 2006
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D322 - D326.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. Akagi, T. Suzuki, R. M. Stephens, N. A. Jenkins, and N. G. Copeland
RTCGD: retroviral tagged cancer gene database
Nucleic Acids Res., January 1, 2004; 32(90001): D523 - 527.
[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.