RefGenome11Nov08 Phone Conference (Archived)

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Pascale, Petra, Emily, Ruth, Judy, Li, Kimberly, Seth, Siddhartha,

GOC meeting

For those who were not present, minutes are here: 20th_GO_Consortium_Meeting_Minutes#Reference_Genome

Annotation tracker Software update

see prototype at:

  • problem with the 32-bit and the 64-bit software talking to each other
  • Sidd will try to get a machine at Northwestern
  • Question: what's the difference between search for gene name and search for target? Target was only for for the human gene; gene name was to search for gene names, using wild cards etc.
  • when will this be ready to use?
  • Current status

New AmiGO version incorporating Reference Genome project genes

see beta version :

    • Need correct Orthosets


Curation Targets

  • Any comments? (thanks Harold for the suggestions for Dec)

Improving annotation documentation

(from GOC minutes) There is a general issue of not being able to find documentation and when it's appropriate to use a term. Particularly since some of this information is spread between the wiki, GO web page, meeting minutes, annotation camp minutes, etc. This often leads to inconsistent usage - "binding" and "regulation" terms were brought up as examples.

Although the definition provides the core usage, it often is not enough. Many people voiced support for examples of how to use the term, with PMIDs, as well as examples of cases when you wouldn't want to use it. Seth and Debby suggested links to GONUTS from AmiGO. Having a wiki would not limit the amount of space that's available. If there are links to a wiki page, they need to be propagated through to all children terms. A few were concerned about displaying this publicly but in general, there was support for making it public, particularly since E. coli is trying to have the community annotate.

The current documentation for GO is in many places and spans many many pages. It was agreed that there needed to be a central, consolidated repository for the documentation that was easily accessible and searchable. Jen brought up that these types of project works best when there is one person in charge of the technology and individuals take responsibility for sending that person up-to-date content. The GO editorial office can have oversight but would need input from all the groups. Peter pointed out that the RefGenome group already has a forum where examples and counterexamples with references are brought up and would be a natural group for providing documentation content.


  • Amelia is the point person for the documentation project.
  • New content driven by Kara and Pascale as they go through the trees for the RefGenome project and see the usage of the terms
  • Debby and Brenley will be in charge of salvaging and consolidation of existing documentation
  • everyone will send appropriate examples and counter-examples with PMIDs to the GO editorial office to add as comments to the GO terms and definitions
  • All documentation will be indexed and searchable on GONUTS (Seth, Amelia)

Annotation issues

  1. Annotation consistency: x protein binding and with : Becky, David
  2. Annotation consistency: Using IEP : Emily, Pascale, Ruth, Stacia

Review action items

  1. Everyone should add to Annotation_consistency:_'Response_to'_terms how they use the response to terms (evidence codes and typical supporting experiment)
  2. Everyone who have comments about a potential HTP annotation tag should add them here: Annotation_consistency:_HTP.
  3. Debby: Put in a SourceForge request that definitions of terms for oligomerization, dimerization, protein complex assembly etc. should be clarified as to their use and annotations using these terms be checked and, if necessary, changed.
  4. Emily and Debby: Clarify GO:0006730 one-carbon compound metabolic process and GO:0019438 aromatic compound biosynthetic process - these terms were added by the HAMAP and InterPro groups. Both of those processes involve enzymes that use a folic acid derivative as a coenzyme, but Debbie didn't think that FolE (which catalyzes the first committed step in folic acid biosynthetic) should be annotated to those processes.
  5. Victoria: Make a SourceForge request to clarify the definitions of unfolded/misfolded protein binding and add chaperone activity as a synonym to both of the terms. Also add ‘de novo’ synonym to ‘unfolded protein binding’.
  6. All (ongoing): Annotation Quality control: Please pick an ortholog set from the Curation Targets table [1] see also Annotation_QC for some general documentation and previous issues
  7. All (ongoing): Annotation Quality control: Have a look at the SF items and see if the ortholog from your organism is correctly annotated ("comprehensive"). Let lead curator for that set know that you're done.

Next conference call

Tuesday December 9, 2008, (1 PM CDT, 11 AM PDT, 7 PM BST)

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