WormBase gene association file

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Generating the WormBase gene association file

In the acedb user account on Tazendra at:/home/acedb/ranjana/GO:

  1. Use ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS211/ONTOLOGY/ eg., to get the latest gene association file generated by WormBase EBI eg., gene_association.WS211.wb.ce.
  2. Use 'grep IEA gene_association.WSXXX.wb.ce > gene_association.wb.electronic to separate the IEAs.
  3. Grep WBPhenotype gene_association.WSXXX.wb.ce > gene_association.wb.rnai2go(to get i.e both Erich's earlier RNAi2GO ones and the new associations based on allele phenotypes that went into WormBase WS186).
  4. copy the right go.go.<date> file from /home/acedb/ranjana/citace_upload/go_curation/go_dumper_files/ to this directory,change name to gene_association.wb.manual.
  5. Cd to the /external_annots directory and download the latest GOA elegans file,for external annots (use 'wget ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/9.C_elegans.goa')
  6. Run the ./wrapper.pl script, note this script generates both go.ace and go.go (gene association format file) in the go_dumper_files directory:
  7. ./wrapper.pl gives the following output: filtering secondary GO IDs into .no_secondary filenames now and outputs NUMBER of ERRORS by COLUMN:
  8. Run strip_errors_and_concatenate.pl, this script also generates the file genecounts that has gene, GO term numbers.

On your local machine:

  1. Work in the tmp directory on Maya:
  2. scp file to Maya
  3. remove 'NOT' annotations from mtm-9, vha-2, vha-3, hsp-60, hsp-12.3, hsp-12.6. (We do not take out NOT annotations anymore)
  4. remove header from the middle of concatenated file in two places (on top of UniProt file too, search for 'gaf-version') and placed on top of file (correct minor mistake in header--space after the $ on one of the lines)
  5. And move the following header from the middle of file to the top of file:

!Version: $Revision: $

!Organism: Caenorhabditis elegans

!date: $Date: $

!From: WormBase

Add these two lines at the bottom of header:

!DataBase_Project_Name: WormBase WS215/WS216

!gaf-version: 2.0

TO upload to the GO consortium:

  1. Remove the header 'gaf 2.0', from the top of the UniProt file
  2. gzip file
  3. Copy file to the tmp directory
  4. CVS_RSH=ssh; export CVS_RSH at terminal to use the RSH program
  5. NOTE-Upload:Stopped using the -z option to during: remove 'z3' from 'qz3'
  6. cvs -q -d :ext:ranjana@ext.geneontology.org:/share/go/cvs checkout go/gene-associations/submission/gene_association.wb.gz
  7. Replace old file with the new gene_association.wb.gz under go/gene-associations/submission/
  8. To check in the new file:
  9. cvs -q -d :ext:ranjana@ext.geneontology.org:/share/go/cvs commit go/gene-associations/submission/gene_association.wb.gz
  10. Outputs new version numbers: new revision: 1.103; previous revision: 1.102

TO update README:

  1. Checkout README and modify to reflect the version change and any other changes:
  2. cvs -q -d :ext:ranjana@ext.geneontology.org:/share/go/cvs checkout go/gene-associations/readme/WormBase.README
  3. Changes:Updated only for release numbers
  4. For manual annotations column 2(DB_Object_ID) all converted into WBGene IDs, i.e WBGeneXXXXXXXX, from Dec, 2009 upload.
  5. Commit new README (this time modified for only WS numbers):
  6. cvs -q -d :ext:ranjana@ext.geneontology.org:/share/go/cvs commit go/gene-associations/readme/WormBase.README
  7. Outputs new version numbers: new revision: 1.54; previous revision: 1.53 (noted only version changes)

Specifications for script that is run by wrapper.pl and generates the gene association file:

Column 6: Reference: In the OA: script looks at 'Accession number' field in the OA, and dumps that entry, if empty, looks at the Paper field and dumps that.

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