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Gene Ontology Newsletter - August 2006, Issue No. 2

Kimberly Van Auken vanauken at
Wed Aug 16 11:32:33 PDT 2006

Gene Ontology Newsletter
August 2006, Issue No. 2

In this issue:
1. Paper Highlight: Using GO to Evaluate Interactions and Networks
2. Expansion of Central Nervous System Development Representation
3. Representing Interactions between Organisms
4. Annotation Camp 2006
5. OBO-Edit Released
6. Removing 'unknown' Terms
7. New File in OBO 1.2 Format
8. Upcoming Meetings

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


1. Paper Highlight: Using GO to Evaluate Interactions and Networks
A recent paper from Mike Tyer's laboratory describes curation of all the 
genetic and physical interactions in Saccharomyces cerevisiae that have 
been reported in the primary literature.  Using GO Biological Process 
annotations available at SGD, the authors compare the extent of shared 
annotations between the literature-curated dataset and existing 
high-throughput datasets to show that literature-curated datasets 
greatly enhance gene function prediction.

2. Expansion of Central Nervous System Development Representation
In June 2006, GO curators from MGI (Mouse Genome Informatics) and ZFIN 
(ZebraFish Information Network) collaborated with neuroscientists to 
greatly enhance the representation of central nervous system development 
in the Biological Process aspect of the GO.  Over 500 new terms have 
been added.

3. Representing Interactions between Organisms
PAMGO (Plant-Associated Microbe Gene Ontology) curators and the GO 
Editorial Office have added 123 new terms capturing symbiont-host 
interactions in the 'interactions between organisms' node of the 
Biological Process ontology.

4. Annotation Camp 2006
During the week of July 10-14, 2006, SGD and Stanford University were 
hosts to the third GO Annotation Camp.  Divided into two sessions, the 
first part of camp was attended by GO Consortium members who discussed 
consistent use of evidence codes.  The second part of camp was devoted 
to training new GO curators and/or users in the process of making manual 
annotations from the primary literature.

5. OBO-Edit Released
The ontology editor OBO-Edit (formally known as DAG-Edit) has now been 
released and is available for download from SourceForge.

6. Removing 'unknown' Terms
The unknown terms that currently exist in each branch of the ontology 
will be removed from GO on October 16, 2006.  All annotations to 
'unknown' will be migrated to the corresponding top level terms.

7. New File in OBO 1.2 Format
The GO Consortium will provide an additional ontology file in OBO 1.2 
format as of September 15, 2006.  This file will specify replacement 
terms for obsolete terms in tags rather than comments.

8. Upcoming Meetings
GO Users Meeting:  September 10, 2006, University Tower Hotel, Seattle, 
WA (in conjunction with MGED9)
Genome Informatics Meeting:  September 13-17, 2006, Wellcome Trust 
Genome Campus, Hinxton, UK
ARK-Genomics 6th Farm Animal Functional Genomics Workshop: September 
27th -September 28th 2006, Robinson College, Cambridge, UK
Please contact the Gene Ontology Consortium with any comments or 
suggestions at gohelp at Frequently asked questions may 
appear as tutorials or tips in upcoming newsletters.


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