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Gene Ontology Newsletter - November issue

Ranjana Kishore ranjana at its.caltech.edu
Fri Nov 17 14:37:48 PST 2006


Gene Ontology Newsletter
November 2006, Issue No. 3

In this issue:
1. The Reference Genome Project
2. Paper Highlight: Human Breast and Colorectal Cancers
3. OBO-EDIT Tip: Graph Viewer
4. Developing the Sequence Ontology (SO)
5. Improvements to Representing Immunology
6.~QGene of the Quarter~R Announcement
7. Upcoming Meetings

Below are brief descriptions of each of the news items. The full text of 
the newsletter can be viewed online:

HTML: http://www.geneontology.org/newsletter/current-newsletter.shtml
PDF: http://www.geneontology.org/newsletter/current-newsletter.pdf

1. The Reference Genome Project
Recently the GO consortium initiated the reference genome project to 
provide GO annotations for a set of twelve model organisms. Curators 
from the different model organism databases are working as a team to 
annotate human disease genes and their orthologs or similar genes in the 
other genomes.

2. Paper Highlight: Human Breast and Colorectal Cancers
A recent paper from Sjoblom et al. identified 189 genes that were 
mutated in the genomes of human breast and colorectal cancer tumors. The 
authors utilize GO annotations for mutational studies to query common 
mechanisms of pathology underlying both tumors.

3. OBO-EDIT Tip: Graph Viewer
The OBO-Edit Graph Viewer Plugin is a new way of visualising the GO 
tree. It uses the open source GraphViz package to draw parts of an 
OBO-Edit ontology as a user-configurable graph.

4. Developing the Sequence Ontology (SO)
In September the SO group held a workshop to develop areas of the 
ontology relating to mobile elements and kinds of replicons. Several 
important changes were made to the ontology.

5. Improvements to Representing Immunology
Improvements have been implemented in the representation of immunology 
in the biological process ontology. These aim to provide a comprehensive 
representation of immunological processes, improve the organization of 
immunology-related terms, and revise poorly formulated terms already 
present.

6. ~QGene of the Quarter~R Announcement
A gene from the reference genome project~Rs current annotation list will 
be highlighted in the next issue.

7. Upcoming Meetings

Plant and Animal Genome XV Conference
January 13-17, 2007
http://www.intl-pag.org

GO and PAMGO workshop
January 14, 2007
http://www.intl-pag.org/15/15-gene-ontology.html
Town and Country Convention Center, San Diego, California

Please contact the Gene Ontology Consortium with any comments or 
suggestions at gohelp at geneontology.org. Frequently asked questions may 
appear as tutorials or tips in upcoming newsletters.



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announcements and discussion of the Gene Ontology (GO) project.
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