Title

On gene ontology and function annotation

Authors

Debnath Pal^1,2

Affiliation

¹Bioinformatics Centre, ²Supercomputer Education Research Centre, Indian Institute of Science, Bangalore 560 012.

E-mail*

dpal@serc.iisc.ernet.in; * Corresponding author

Phone

+91-80-2293-2901

Fax

+91-80-2360-2648

Article Type

Views & Challenges

Date

received February 15, 2006; accepted February 21, 2006; published online February 21, 2006

The effort of function annotation does not merely involve associating a gene with some structured vocabulary that describes action. Rather the details of the actions, the components of the actions, the larger context of the actions are important issues that are of direct relevance, because they help understand the biological system to which the gene/protein belongs. Currently Gene Ontology (GO) Consortium offers the most comprehensive sets of relationships to describe gene/protein activity. However, its choice to segregate gene ontology to subdomains of molecular function, biological process and cellular component is creating significant limitations in terms of future scope of use. If we are to understand biology in its total complexity, comprehensive ontologies in larger biological domains are essential. A vigorous discussion on this topic is necessary for the larger benefit of the biological community. I highlight this point because larger-bio-domain ontologies cannot be simply created by integrating subdomain ontologies. Relationships in larger bio-domain-ontologies are more complex due to larger size of the system and are therefore more labor intensive to create. The current limitations of GO will be a handicap in derivation of more complex relationships from the high throughput biology data.

Keywords

gene; ontology; function; annotation; vocabulary

Citation

Pal, Bioinformation 1(3): 97-98 (2006)

Edited by

N. Srinivasan

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.