February 2007 Monthly Report

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The annotation outreach working group exists to encourage and enable new groups to begin annotating to the Gene Ontology.

In our group meetings we have been working on flowcharts to show a simple SOP on how to begin annotation. The SOP is evolving on:

Rama Balakrishnan has sent emails to users she met at the PAG meeting inviting them to join the go-friends email list. She is starting to make contacts with JGI and may be attending a meeting at JGI.

Fiona McCarthy of AgBase has now joined the working group.

There have been a number of new outreach avenues with GOA in the last month:

1. On Feb 7th 2007 Evelyn gave a seminar at St. Vincents Hospital,Research Centre, Dublin entitled 'Sharing immunological knowledge with Gene Ontology'. Researchers from University College Dublin (UCD), Conway institute also joined the seminar.

2. On Feb 6th Evelyn also discussed a grant collaboration for one GO annotation position at UCD, Ireland with Prof. Cliona O' Farrelly as part of a Science Foundation Ireland (SFI) programme grant application that should have been submitted late February. While there Evelyn also made contact Fiona Roche who although living in Ireland works for the canadian Simon Fraser University, Brinkman Lab, http://www.pathogenomics.sfu.ca/brinkman/ who are setting up an InnateDB initially focussed on human and mouse innate immune genes(Fiona Brinkman -is the lead PI developing this database along with Bob Hancock). They have been incontact with Richard at Immport. Fiona Roche will send Evelyn her 800 innate immune gene list for the GO Immune gene Working group.

3. Emily made contact with 'Avril Coghlan' Wellcome Trust Sanger Institute (Team 71:Gene finding; the TreeFam project; evolution of animal nervous system genes; intron evolution)...as she was sending GO annotation updates via gohelp. Emily invited her to the EBI to see if she would like to learn more about contributing manual GO annotations.

4. In Feb Ruth Lovering(UCL) has submitted the outline proposal for two GO annotation posts to the British Heart Foundation. This grant would allow 2 curators to concentrate on genes important in cardiac related diseases. Ruth Lovering and Varsha Khodiyar are now working 80-100% on GO annotation until the end of their contracts late summer 2007(?)( is that right Ruth?)

5. Ruth Lovering(UCL) visited the Institute of Child Health, London. It was recommended to her to speak to John Harper, a clinician at Great Ormond Street. John Harper has an interest in dermatology and some of his patients have morphoea (localised scleroderma). So they have done microarray analysis on 3 patients using 3 scleroderma leg tissue samples and 3 tissue samples from the unaffected leg. They have a list of 200 genes upregulated and 200 downregulated in all matched samples in all 3 patients. However they don't know how to do next. Varsha Khodiyar(UCL) is enjoying having a go at using GO tools to get something out of the data.

6. Evelyn has been invited to speak at Irish Society of immunology meeting, UCD, Ireland possibly September 2007 and UCD, School of Biology and Environmental Science, possibly March 2007.

7. Emily Dimmer and Rachel Huntley are discussing the 275 standardised subcellular location terms in UniProtKB/Swiss-Prot with Serenella Ferro Rojas, SIB, Geneva and are manually mapping these to GO terms via a new EBI GO mapping tool. This new mapping file will improve the number of IEA subcelullar locations in GOA which are not well covered my other mapping files. A new GO_REF will be created.