Annotation 26Feb10

Organizing the wiki pages

• annotation documentation
• annotation discussion working groups
• action items from emails, meetings, jamborees

Annotations based on Inter-ontology links

(Rama) Chris (and the ontology group) have generated several annotations/inferences based on inter-ontology links. Val has started commenting on (SF) some of these annotations. I think it is our responsibility to let groups know if this is a priority and if they shd be doing this now. http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/gaf-inference/

Format of Ref.genome jamboree calls

• the chair of discussions needs to ensure that SourceForge items are

populated from the action items that come out of the discussion. Either the chair should do this directly, or ensure interested parties do this. Pascale and I have agreed to follow up on the SLIT2/NIPBL discussions

• chairs need to provide/or nominate someone to provide/prepare a quick

overview of the functions that the gene is thought to carry out - and see if this aligns with the annotation set being displayed in GONUTs

• any items that could be converted into QC items should be noted (e.g.

taxon-specific checks, or co-annotation guidelines)

• annotation issues need to be forwarded to the annotation list (either by

the chair, or nominated curator)

• Pascale, could the PAINT folk have an early look at the annotation set

generated, and summarize the transfers that they would propose making on the generated set? As Daniel is currently creating a bulk annotation uploader that accepts GAF formatted files, perhaps we could ask if GONUTs could spit them out as well - so that PAINT could directly upload the most up-to-date RefGen annotation set from the jamboree - would this help you and Kara?

• I thought that having Anita on the call for SLIT2 was invaluable. It

would be fantastic if we could have such experts at other calls - who could clarify some of the more complex issues curators had been having with certain papers/methods/terms.

• a GO ontology developer needs to attend the whole of the call.
• all groups need to be willing to volunteer a curator to either take

minutes or chair a discussion (i.e. it shouldn't always be Pascale or I).

Perhaps these suggestions could be posted somewhere along with the current format of the calls - and we could invite other curators to make suggestions. Could you do this? I think that if we/other curators feel that there is value from these calls, we need to strongly encourage groups to actively participate and support these calls; even the current (sub-optimal) organization takes up a surprising amount of time - from suggesting targets to settting up calls, pestering for people to add annotations, requesting GONUTs features from Jim/Daniel. Perhaps we three could each take on the organisation of one jamboree a year? What are your thoughts?

Organizing the Wiki pages

I'm just adding notes to various sections on the GO wiki that came out of the NIPBL discussion. And I was wondering about whether you would mind if we looked into the organisation of these wiki pages? For instance, it might be nice to have a page that groups all evidence code discussions together (I've created a new page on use of ISS) and these pages could be indicated as being a bit broader than for just the uses of the Reference Genomes group? In addition, I've asked Rachael if she could generate a page that indicates where curators should use caution with certain types of experimental methods (from the CHIP discussion during the call), at the moment it appears this best fits on the Reference Genome index page - but perhaps these are more general guidelines for all curation groups? (we should certainly indicate this information came out of a RefGen call however) Also, I'm looking at a couple of discussion points that mentionned how PAINT could contribute to annotation consistency discussions - could I create a page that lists requests from RefGen for PAINT? I really don't want to mess around with these pages with out checking with you first. I know that you were also looking at having pages which indexed pages according to guidelines, QC, action items and unresolved issues - which I think is a great idea. It would be lovely if we could tag certain sections on a page - that would automatically list the section in another page...does anyone know how this could be done?