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.

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