10 NOV 2009 RefGen Phone Conference (Archived)

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Uploading 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 ?
  2. Review of the reference genome GAFs will necessarily be different. 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.
    • Can this review be carried out monthly ?
    • Are the two display options for viewing the annotations just discussed adequate for this review process ?
    • Will it be a group or a particular curator who does the reviewing ?
  3. Steps to the (temporary?) review process (frequency?)
    1. Review the annotations visually
    2. Are there ISS annotations for your species ?
      • 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
      • If no: then you're done
    3. Repeat the above until all questionable annotations have been resolved
    4. Upload the GAF file from the geneontology web site
    5. Load the GAF file into your MOD
    6. Submit comprehensive GAF file for you species as usual

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