EcoliWiki:Gene Association File

See text for description.

Overview

EcoliWiki and EcoCyc contribute to the Gene Ontology (GO) by monthly submitting our annotations.

The two sites' annotations are prepared by the EcoliWiki team (mostly [[User:DanielRenfro|Daniel,) and submitted via CVS to the GO Consortium. The figure at right shows the four basic steps to this process:

1. Obtain annotations from EcoCyc (quarterly)
2. Obtain annotations from EcoliWiki (monthly)
3. Merge them and resolve name-conflicts
4. Submit to the GO

Detailed Description

There are actually two files that get submitted each month. The gene association file and the gp2protein file. A detailed description of each can be found in the GO Consortium's documentation.

header information

Occasionally the header information in the gene_association file needs to be updated. This information can be found in the gene_assocation.ecocyc.conf file in the go/gene-associations/submission/ directory of the GO CVS.

To change this information, just edit the file from the CVS checkout and resubmit it. It will get prepended to the gene_assocation file automatically.

gene_association.ecocyc

The following is the process by which the annotation file is prepared, broken into managable steps.

Setup the environment

<source lang="bash">#!/bin/bash

1. -------------------------------------------------------------------------------
3. gaf_gp2protein.ecoliwiki.sh Daniel Renfro 01/2010
5. This script sets up a working directory for the montly creation of the
6. gene-associations file and the gp2protein file for EcoliWiki.
8. -------------------------------------------------------------------------------

working_dir=$(date "+%Y-%m-%d")

1. prefix="/usr/local/phpwikibots/trunk/PDB_Table" # absolute path bad.

prefix=`dirname "$0"` # relative path good.

1. make the working directory

mkdir $working_dir cd $working_dir

1. make some necessary directory

echo "Creating directories..." mkdir ontology mkdir doc

1. download the stuff from GO

echo "Downloading files from the Gene Ontology..." ncftp ftp://ftp.geneontology.org/pub/go/software/utilities/ <<END_SCRIPT get filter-gene-association.pl get check-abbr-ga-file.pl quit END_SCRIPT ncftp ftp://ftp.geneontology.org/pub/go/ontology <<END_SCRIPT get gene_ontology_edit.obo quit END_SCRIPT ncftp ftp://ftp.geneontology.org/pub/go/doc/ <<END_SCRIPT get GO.xrf_abbs quit END_SCRIPT

1. put the files in the right places

mv gene_ontology_edit.obo ontology mv GO.xrf_abbs doc

1. set the permissions on the executable files.

chmod +x check-abbr-ga-file.pl filter-gene-association.pl

echo "setup complete."

</source>

See Also

• GO Consortium's specification for the GAF - http://www.geneontology.org/GO.format.annotation.shtml
• gp2protein file notes - http://wiki.geneontology.org/index.php/Gp2protein