Skip Navigation



Bioinformatics Advance Access published online on June 20, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl334
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrowOA All Versions of this Article:
22/16/2020    most recent
btl334v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
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 PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Myhre, S.
Right arrow Articles by Lægreid, A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Myhre, S.
Right arrow Articles by Lægreid, A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2006 The Author(s)
Received April 7, 2006
Revised May 30, 2006
Accepted June 12, 2006

Article

Additional Gene Ontology structure for improved biological reasoning

Simen Myhre 1 *, Henrik Tveit 2 *, Torulf Mollestad 3, and Astrid Lægreid 1 *

1 Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7489 Trondheim, Norway
2 Department of Computer and Information Science, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
3 Department of Computer and Information Science, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway; SAS Institute AS Norway, Pb 2666 Solli, NO-0203 Oslo, Norway


  Abstract

Motivation: The Gene Ontology (GO) is a widely used terminology for gene product characterisation in e.g. interpretation of biology underlying microarray experiments. The current GO defines term relationships within each of the independent subontologies: molecular function, biological process and cellular component. However, it is evident that there also exist biological relationships between terms of different subontologies. Our aim was to connect the three subontologies to enable GO to cover more biological knowledge, enable a more consistent use of GO, and provide new opportunities for biological reasoning.

Results: We propose a new structure, the Second Gene Ontology Layer, capturing biological relations not directly reflected in the present ontology structure. Given molecular functions, these paths identify biological processes where the molecular functions are involved and cellular components where they are active. The current Second Layer contains 6271 validated paths, covering 54% of the molecular functions of GO and can be used to render existing gene annotation sets more complete and consistent. Applying Second Layer paths to a set of 4223 human genes, increased biological process annotations by 24% compared to publicly available annotations and reproduced 30% of them.

Availability: The Second Gene Ontology is publicly available through the GO Annotation Toolbox (GOAT.no): http://www.goat.no.

Associate Editor: Jonathan Wren

*These authors contributed equally.


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
 Nucleic Acids ResHome page
S. Gotz, J. M. Garcia-Gomez, J. Terol, T. D. Williams, S. H. Nagaraj, M. J. Nueda, M. Robles, M. Talon, J. Dopazo, and A. Conesa
High-throughput functional annotation and data mining with the Blast2GO suite
Nucleic Acids Res., June 1, 2008; 36(10): 3420 - 3435.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
E. Antezana, M. Egana, B. De Baets, M. Kuiper, and V. Mironov
ONTO-PERL: An API for supporting the development and analysis of bio-ontologies
Bioinformatics, March 15, 2008; 24(6): 885 - 887.
[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.