10 NOV 2009 RefGen Phone Conference (Archived)

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Incorporating new protein family annotations via GAF files

  1. How are you handling externally submitted GAF files right now? Primarily, these are the GAF files from GOA. What is the existing process ? For example:
    • Are there manual and/or automated verifications (redundancies, quality of annotations) before a file from GOA gets integrated in your database?
    • How are existing IEA annotations handled ?
    • What is the frequency of incorporation ?
    • How are the accepted annotations from GOA loaded into the MOD ?
    • What appears in their own GAF files they send to the GO site as the annotation source ?


Proposed SOP for uploading 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 visually: link to DAG (coming this afternoon). For each PAINT ISS, there are two questions to answer:
    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?
  4. Feedback to PAINT curators, or just download the GAF (from GO site soon, from Princeton temporarily)
  5. Final GAFs will be available from central GO site, but are at Princeton for now
    1. 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.
    2. The primary issue is whether you know of any evidence that might contradict the ISS that has been made based on protein family.
    3. Are the two display options for viewing the annotations just discussed adequate for this review process ?
    4. Eventually you may simply incorporate them automatically without manual review
  6. 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
  7. Repeat the above until all questionable annotations have been resolved
  8. Upload the GAF file from the geneontology web site
  9. Load the GAF file into your MOD
  10. Submit comprehensive GAF file for your species as usual

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