Ideas for publicizing Ref.Genome Annotation Data (Retired)

From GO Wiki
Revision as of 13:39, 25 January 2010 by Rama (talk | contribs)

Jump to: navigation, search

Ideas for Publicizing Ref.Genome Data

Reference Genome Annotation data should be made available at each of the participating groups (for download and display) and should be available in AmiGO in a user-friendly way.

At each MOD

  • How can the MODs (ref.genome project member) highlight the genes that have been annotated for the ref.genome project?
    • What do we want our users to get out of this annotation data?

At AmiGO

AmiGO is the face of GOC and is good place to promote and offer useful displays for ref.genome data.

Here are some ideas. Please feel free to add.

  • We should be able to download a list of genes picked for ref.genome project. In addition users could have an option to filter annotations by species

Some feed back from SGD curators

1) Turns out some of the SGD curators did not realize that ref.genome data was integrated within AmiGO. I strongly recommend that other MODs also bring this up within their group to educate and garner ideas.

2) How to look for ref.genome data in AmiGO? - there is no link on the home page and since ref.genome data is a resource and not a tool, one wouldn't think of clicking on the More tools link.

2a) Perhaps remove this option from the Tools tab and have a separate tab called 'Homolog Annotations' (or somthing that we can agree on. We shdn't use ref.genome as a tab name because it is too jargony and no body will click on it)?

2b) When you click on the "More tools" tab, you get to a page that is titled- "Complete List of AmiGO Software" The word software is too jargony. how about change it to just "GO Tools"? BTW, BLAST should *also* be listed under Tools.

3) If I search for TOP1 (with the genes/proteins radiobutton checked), I get a list of TOP1 genes and the ref.genome ones have a 'star' next to it. But the star is totally lost on the page (very small and not bright enough). We should look into highlighting those with gold stars (good size and bright) or some thing else nice and bright (may be a dendogram icon)

4) Once you click on say the S. cerevisiae TOP1 from the page I mentioned above, you get to the TOP1 details page. http://amigo.geneontology.org/cgi-bin/amigo/gp-details.cgi?gp=SGD:S000005366&session_id=9034amigo1263416858

4a) We all felt that the phrase 'Ref Genome' and then 'Homology under TOP1' is not clear, is confusing and we should come up with some intuitive language to highlight what that link is about. There are two different links in that one line, one going to the annotations of TOP1 homologs and one going to the complete homolog set (list of genes). They should be separated and reworded.

For the Annotations- the link should be reworded to something like (of course other groups shd be consulted on the wording):

    • Annotations for homologs [tab] TOP1 related genes in M.musculus, S. cerevisiae ..etc (keep the colored icons)

hyperlink 'TOP1 related genes' OR

    • Annotations for homologs [tab] Genes similar to TOP1 in M.musculus, S. cerevisiae ..etc

hyperlink 'Genes similar to TOP1' OR just say in one long line-

    • Compare GO annotations for TOP1 and its homologs in M.musculus, S. cerevisiae ..etc (keep the colored icons)

hyperlink "Compare GO annotations for TOP1 and its homologs"

4b) The 'Homology under TOP1' link should possibly be changed to 'List of TOP1 related genes in model organisms'. We could probably use the gold star or what ever icon we decide on this page and consistently wherever applicable to indicate ref.genome project.

5) Ref.Genome genes are not currently highlighted when you come in from a term search. For example when you look at the list of gps associated with say GO:3917 (DNA topoisomerase type I activity), the ref.genome genes are not highlighted with a star on this list. As I mentioned earlier, we should highlight ref.genome genes with a star, wherever it is displayed.

GAF file

  • Should we indicate ref.genome genes with a Y/N column in the GAF file?

Other Venues?