SOP for GO citace and GO consortium data uploads

Old SOP for generating a gene association file

In the acedb user account on Tazendra at:/home/acedb/ranjana/GO: --Use ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS211/ONTOLOGY/gene_association.WS211.wb.ce

--use'grep IEA gene_association.WSXXX.wb.ce>gene_association.wb.electronic to separate the IEAs.

--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).

--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.

--new GOA elegans file, from 04.02.12, for external annots (use 'wget ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/9.C_elegans.goa')

--Run the ./wrapper.pl script Output will include the various error types

--Run ./strip_errors_and_concatenate.pl

Scp the generated gene association file to a local machine for post-processing and upload to the GOC In the tmp directory on Maya: --scp file to Maya

--removed '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)

--removed 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)

--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

--Remove the header 'gaf 2.0', from the top of the UniProt file

--gzip file

--Copy file to the tmp directory

Use SVN commands to upload to the GO, also update README file every upload.