10 NOV 2009 RefGen Phone Conference (Archived)

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  • GOA: Emily
  • MGI: Li, Mary, Judy, Harold
  • RGD: Stan
  • Flybase: Susan
  • dictyBase: Pascale, Petra
  • TAIR: Donghui
  • AgBase:
  • SGD: Stacia, Julie
  • pombe
  • Ecoli: Jim
  • Wormbase: Ranjana, Kimberly
  • ZFIN:
  • PPOD: Kara, Mike
  • Berkeley: Suzi, Chris

Incorporating new protein family annotations via GAF files

We'd like each group to provide information about how they handle GAF files. The survey is here: http://www.surveymonkey.com/s.aspx?sm=zPTWtTxoC_2f6yC8I_2foXmDDg_3d_3d

Proposed SOP for incorporating GAF files

Steps to the review process (monthly to start):

  1. Start on the central protein family annotation page here: http://wiki.geneontology.org/index.php/GAFs_for_trees-based_annotations
  2. View notes/summary on family: http://wiki.geneontology.org/index.php/PANTHER10977
  3. Review the annotations: from the above page, we will have summaries, visual representations of the annotations, and tables to peruse. In addition to the display options shown now, we are working on an additional view that will show the original experimental annotations, in addition to just the new ones. While reviewing these proposed annotations is up to the MOD, if you do review them, we especially encourage you to answer the following for each PAINT ISS:
    1. Is the annotation consistent with what you know about the gene to date?
    2. Is the inference justified by the relationship of the protein to the proteins from which the inference was drawn?
    • Review of the reference genome GAFs will necessarily be different than GOA. Unlike GOA, which provides a mix of IEA and literature based annotations, these will all be ISS.
    • The primary issue is whether you know of any evidence that might contradict the ISS that has been made based on protein family.
    • Eventually you may simply incorporate them automatically without manual review
  4. Provide feedback to the particular PAINT curator, or if all is well, just download the GAF. Final GAFs will be available from central GO site.
  5. Are there ISS annotations for your species ?
    1. If yes: then if you see mistakes or have questions contact the ref. genome curator who made the inference for corrections. Note the reason for the correction in the annotation guidelines for the future
    2. If no: then you're done
  6. Repeat the above until all questionable annotations have been resolved
  7. Download the GAF file from the geneontology web site
  8. Load the GAF file into your MOD
  9. Submit comprehensive GAF file for your species as usual


  1. Will each family have a different file? Chris says that it would be trivial to concatenate.
  2. (Mary D): problem: there are ISS annotations to 'molecular function' (PAINT bug)
  3. PAINT needs to also include functionality to look for obsolete terms and secondary IDs
  4. Some people would like taxon-specific files; or we could provide a script to parse a specific taxon

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