[Go] Ontology development - June highlights

[Midori Harris]

Dear GO,

The most recent monthly report on ontology content, for June 2008, is now 
available at:

     http://wiki.geneontology.org/index.php/Jun2008_report

Ontology development highlights from June:

   * Work has begun to overhaul the peptidase/protease activity terms in 
the function ontology. We hope to be able to retire many of the gene 
product terms in this branch 
(http://wiki.geneontology.org/index.php/Proteases).

   * An overhaul of transcription and transcription factors has begun 
(http://wiki.geneontology.org/index.php/Transcription).

   * As before, function-process links are still being gathered for 
electron transport and metabolic pathways. Function-process main page: 
http://wiki.geneontology.org/index.php/Function-Process_Links.

   * Last month we announced that 'regulates' F-P links will be made; we're 
now working on a more detailed announcement aimed especially at tool 
developers (first announcement in May newsletter: 
http://www.geneontology.org/newsletter/archive/200805.shtml)

   * The overhaul of signal transduction process terms continues 
(http://wiki.geneontology.org/index.php/Signaling).

   * Drug tranpsorters have come into focus, as part of the ongoing work on 
transport and transporters 
(http://wiki.geneontology.org/index.php/Transporters).

As noted in recent months, the function-process work will continue, as 
will the signaling overhaul, taxon links, and quality control work 
connected with the regulation terms. In July, we plan to work on thee 
terms and relationships in the metabolism branch of the process ontology.

Our plans for implementing cross-products based on Chris' new suggestion 
are unchanged (see 
http://wiki.geneontology.org/index.php/Cross_Product_Guide and files in 
the go/scratch/xps/ directory), as are plans to improve the metabolism 
branch with respect to structure and consistency with ChEBI.

As usual, details of small- and medium-scale changes are available in the 
SourceForge Curator Requests tracker. Please contact us if you want to 
help out with ontology work in a particular area, or if you have any 
comments or questions about what's going on.

Ontology Development wiki:
http://wiki.geneontology.org/index.php/Ontology_Development

SourceForge Curator Requests tracker:
https://sourceforge.net/tracker/?group_id=36855&atid=440764

Midori & David
on behalf of GO's ontology developers