EcoliWiki:Gene Association File: Difference between revisions
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==Detailed Description== | ==Detailed Description== | ||
There are actually two files that get submitted each month. The <tt>gene association</tt> file and the <tt>gp2protein</tt> file. A detailed description of each can be found in the [[http://www.geneontology.org/GO.contents.doc.shtml GO Consortium's documentation]]. | There are actually two files that get submitted each month. The <tt>gene association</tt> file and the <tt>gp2protein</tt> file. A detailed description of each can be found in the [[http://www.geneontology.org/GO.contents.doc.shtml 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 <tt>gene_assocation.ecocyc.conf</tt> file in the <tt>go/gene-associations/submission/</tt> directory of the [[http://www.geneontology.org/GO.downloads.ftp.cvs.shtml 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=== | ===gene_association.ecocyc=== | ||
The following is the process by which the annotation file is prepared, broken into managable steps. | |||
====Obtain annotations from EcoCyc==== | |||
===gp2protein.ecocyc=== | |||
==See Also== | ==See Also== | ||
* GO Consortium's specification for the GAF - http://www.geneontology.org/GO.format.annotation.shtml | * 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 | * gp2protein file notes - http://wiki.geneontology.org/index.php/Gp2protein | ||
Revision as of 21:07, 8 March 2010
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:
- Obtain annotations from EcoCyc (quarterly)
- Obtain annotations from EcoliWiki (monthly)
- Merge them and resolve name-conflicts
- 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.
Obtain annotations from EcoCyc
gp2protein.ecocyc
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