Manager 22Sep10

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Discussion topics

From BHB meeting

  1. Report from working group working improve efficiency of propagation of experimental annotations in each protein family: (aka "broad" but the use of the word "broad" is deprecated) -> see ref genome section WG: Pascale, Mike, Kara, Paul, Suzi, Mary, Judy
  2. Report from working group on evidence codes: proof of principle for chain of evidence: WG: Rama (will follow up), Paul, Alex, Suzi, Peter D? other curators? (including Lego proposal)
    • There are some issues with compound evidence for example with ISS and IMP

Ref Genome Group Priorities

  • We had a phone call yesterday (Pascale, Kara, Mike L, Paul, Mike C, Rama) ; see notes 21_SEPT_2010_RefGen_Priorities_Discussion
  • The goal of the reference genome project is to provide detailed functional annotations capturing experimental data (deep) for each and every gene (broad) in the 12 reference genome species where such data is available.
  • To achieve biological coverage for the first goal is to base our approach on known biological/cellular processes - see document: GO textbook approach for annotation.
  • There is a backlog of 431 families that have been curated by MODs over the past 4 years.
  • Given these reference annotations the follow-on goal is to propagate these exp. annotations to other species (including other ref. genomes) based on phylogenetic relationships. The practical issues are:
    • How to improve efficiency of propagation within protein families?
    • What resources are available?
    • Who is responsible for carrying out these ISS annotations?

Annotation Group Priorities

  1. educate annotators; new monthly annotation conference call: Rama to send an email about monthly call.
  2. change annotation jamborees: everyone does the same paper? Plan is to do it the next one in November
  3. loading GAF files - how can we help groups identify appropriate files, procedures
  4. improvements to documentation on the website
  5. 1st phase of QC checks is almost in place, by October probably still working out with Chris how to do soft QC checks, e.g. communicating with groups what they need to do, including keeping track of things that have already been checked; tracking things that have actually been removed (so that we can give some stats for the grant showing actual improvement)
  6. Protein binding : what do we do next?

Other discussion topics

  1. Code for updated ontology terms: can we improve TXN_OH? this is very cryptic. (These are all documented here: http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/doc/GO.curator_dbxrefs).
  2. Software Group/Annotation: Column 16: We need some documentation before groups start populating column 16 with too much heterogenous data. Can we agree to start with cell type information only, document and test that, before having other data types?
    • Approach is to start one data type at a time. Process:

responsibility for the Annotation team

      1. Documentation will first be made available for each data type
      2. Documentation will be reviewed by everyone
      3. Documentation will be integrated on the GOC website
      4. QC scripts will be written for the data
      5. Data will be integrated in the GO dataabse
      6. AmiGO need to be modified to display the data
    • [Action item]: David will send the documentation MGI already has.
    • Existing documentation: [1]