Annotation outreach group meeting 16th March 2007
Present- Rama, JenC, Evelyn, Fiona, Pascale, Michelle
Fiona McCarthy's Meeting Proposal
Fiona mentioned about the proposal she is submitting to conduct a conference/symposium on Avian geneome and to get the Avian community together to get a Avian MOD started. Part of this conference would educate people about GO, how to do annotations etc, a GO annotation symposium. Funding rules require that they do it in Mississipi State. There will also be a discussion about the annotation effort in the Chicken genome meeting to be held in Barcelona in April.
Rama: What is the format of this meeting? What is the role of GO?
Fiona- An outreach presentation by GO would be appropriate.
When we seek input/annotations from the community, what is reasonable?
Evelyn mentioned that John Young (Institute of Animal Research) is very proactive and contributes annotations for chicken. He also contacts Fiona about AgBase related questions.
Evelyn mentioned that we should be cautious when we ask the research community to give us annotations or feedback. Chasing bench researchers for providing annotations can end up taking lot of our time. Identifying a paper that has GO annotations and sending it to the annotators is also contributing to the GO. Some people don't bother if they have to make the detailed annotations.
Community Annotation via Wiki
How can we use Wikis to get the community to contribute annotations or data relevant to GO annotations?
Wiki- Fiona mentioned that when users see a blank page on the wiki, they hesitate and don't want to be the first person to contribute.
One way to populate the wiki pages is to use data from GeneRIFs and IHOP so that users can identify papers from that list.
Example GeneRIF url for human CD28 -http://www.ncbi.nlm.nih.gov/ entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_uids=940
Rama and Pascale mentioned that the dictybase and SGD wiki pages are preloaded with basic information about the gene so that their users don't see a blank page.
Action Item- send URLs for those wiki pages to the WG
Evelyn brought up the issue of being able to do batch query that she sent to the go-help desk. People working on human cardiac proteins want to batch download all the GO annotations for these proteins. They are biologists and they don't want to do sql query.
She sent them to Princeton GO slim mapper, but it was too slow.
Suggestion- can the goslim mapper be speeded up?
She sent the user to biomart but that did not do it either.
We need documentation on how to do such a query or how to make a query in Biomart.
Pascale mentioned that they have a good tutorial for Biomart at dictybase that Eric created.
Action item for Pascale- send the URL to the group.
[Jen has brought this to the attention of the User Advocacy group.]
Journals and GO Annotation
Contacting Journals/funding agencies to request/require authors to submit data to GO. David Hill is working on getting people to be clear about the date and format of GO that they used in analysis.
JenC- Flowcharts should be our priority.
Fiona- Who is the audience for these flow charts?
Jen- anybody who wants to start making GO annotations.
Fiona- the first step should be to check if somebody else is annotating that taxonID. Search GOA to see if they are annotating and take it from there. This aspect should be in the flow chart.