Difference between revisions of "UniProtKB gpad to WormBase .ace"
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**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 - 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: | **gpad_extra_column.err - a file that indicates: | ||
| − | ***which UniProtKB IDs don't map to WBGene IDs in the gp2protein.wb file | + | ***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 | ||
| + | ****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 PMIDs don't map to a WBPaper ID | ||
***which annotation extensions can't be mapped to the model | ***which annotation extensions can't be mapped to the model | ||
**gp_annotation.ace - the .ace file for upload to citace | **gp_annotation.ace - the .ace file for upload to citace | ||
| − | *The gpad file format is | + | *The gpad file format is documented on the GOC wiki here: |
**http://wiki.geneontology.org/index.php/Final_GPAD_and_GPI_file_format | **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 | **Note that once the parsing script runs and we add an additional column, the column numbers shift one higher in the .err output file | ||
Revision as of 14:19, 22 July 2015
- 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
- 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
- which UniProtKB IDs don't map to WBGene IDs in the gp2protein.wb file, for example:
- 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
