UniProtKB gpad to WormBase .ace

• The gpad file that contains all of the C. elegans annotations currently in Protein2GO is produced by UniProtKB on a weekly basis.
  • A new file is available every Monday.
  • The file is located here: ftp://ftp.ebi.ac.uk/pub/contrib/goa/ and is named: gp_association.6239_wormbase.gz

• Download the file from the UniProtKB ftp link and put it on tazendra here (in the appropriate year and month directory):
  • /home/acedb/kimberly/citace_upload/go/gpad2ace
  • for example: /home/acedb/kimberly/citace_upload/go/gpad2ace/2015_February

• To convert the gpad file to a .ace file you'll need:
  • gp2protein.wb file that maps UniProtKB IDs to WBGenes
  • go_gpad_parser.pl

• The go_gpad_parse.pl generates three files:
  • gpad_extra_column - a file that adds the WBGene ID as an extra column (a new column 2) to the gpad file
  • gpad_extra_column.err - a file that indicates:
    • which UniProtKB IDs don't map to WBGene IDs in the gp2protein.wb file, for example:
      • IDs that correspond to a transposon or retrotransposon reverse transcriptase
        • Q9TZX4
      • IDs that correspond to non-elegans species, used for ISS annotations or the occasional annotation extension
    • which PMIDs don't map to a WBPaper ID
    • which annotation extensions can't be mapped to the model
  • gp_annotation.ace - the .ace file for upload to citace

• The gpad file format is documented on the GOC wiki here:
  • http://wiki.geneontology.org/index.php/Final_GPAD_and_GPI_file_format
  • Note that once the parsing script runs and we add an additional column, the column numbers shift one higher in the .err output file