December 2007 - January 2008 Report

Judy Blake Contacted sea urchin db

- about doing GO annotation: Mike had contact with the Sea Urchin group and they are not ready to annotate yet. They are still assembling the genome. We should contact them again maybe in April or March.

Judy has contacted the group and they said that they are still working on their genome and that we should write to them again in March or April

Action Item: Judy will contact them.

TAIR at PAG

Donghui Li reports that TAIR organised a workshop on community annotation at the Plant and Animal Genome XVI Conference on 13 January 2008, San Diego, CA.

Representatives from three MODs talked about the current status and future plan in regard to community annotation:

TAIR, SGN (SOL Genomics Network) and WormBase.

TAIR and journal community annotation plans

Tanya Berardini has been in discussion with the Plant Journal to see if they would be interested to ask for GO annotations from users when they submit manuscripts. Kate Dreher at TAIR initiated the

conversation. Also Plant Physiology, who are already working with TAIR to accept annotations from authors, is very close to starting accepting community annotations. They also have a draft of the editorial that they will publish to introduce the system and the tool is ready in it's first phase, and now being improved. .

TAIR, Cornell and Sol Genomics Network database

Groups at TAIR and Cornell (including staff trained at Gramene) are working with the Sol Genomics Network database (http://www.sgn.cornell.edu) to convert their manual annotation for submission to the GO consortium. The staff at SOL involved are Dr Naama Menda and Dr Anuradha Pujar.

Nature Connotea tool

Jennifer Deegan attended a talk at EBI on the new Nature Connotea tool. This tool allows scientists to tag publications of interest and group them by topic and label them with text descriptions. Connotea is open source and plugins can easily be written. There is already a plugin for firefox to allow users to label publications with terms from the GO ontologies. Jennifer enquired about whether this might be extended to allow users to label specific parts of the text with GO terms, or in some other way to support community annotations. The speaker (Ian Mulvany) was interested in the idea and said that they would add this to their very long feature request list. However he said that if anyone else wanted to write plugins to for this functionality then Nature would be happy to incorporate the plugins into the main programme to open up the features to all users.