New GO Progress Report Script

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Revision as of 18:51, 6 March 2014 by Vanaukenk (talk | contribs)
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GO is now requiring quarterly progress reports, with the first one due at the meeting this month (2014-03-16).

We've been wanting to provide a more details progress report for GO for some time now, so this is a good opportunity to do that.

Here's one idea for C. elegans manual annotations:

Input files:

  • gp2protein.wb
  • gp_association.wb
  1. Ignore all lines with IEA evidence code
  2. Replace UniProtKB identifiers in Column 2 with WBGene ID using gp2protein.wb
  3. Remove (i.e. ignore for further reporting) any resulting lines that are exact duplicate lines of annotation

Then determine:

  1. Total number of unique annotations
  2. Total number of unique WBGenes
  3. For each of the values in qualifier Column 4 count number of annotations for a given evidence code in Column 7 and number of annotations with an entry in Column 12
  4. Sort results according to unique entries in Column 10 (i.e., each contributing group)
  5. Also report on any lines where the UniProtKB identifier cannot be converted to a WBGene

For an idea of the kind of table I'm hoping to be able to produce, here's a link to Zfin's progress report from December 2013: