Submit GO annotations
What is needed to submit GO annotations to the GOC
GO annotations are disseminated in a 17 column tab de-limited GAF 2.0 format. But the following bits of information are sufficient to complete/make a GAF file. You can choose to construct a GAF file using the documentation or simply contact the GOC at go-helpdesk@mailman.stanford.edu for step-by-step assistance.
Minimum information needed to make a GAF file:
- Stable IDs for the gene products or objects that are being annotated. If the gene product IDs are not in UniProt or NCBI, please submit the IDs to one of these databases
- GO ID that each gene product can be associated with
- Evidence that allows you to make the association
- Reference (published paper or reference describing the methodology used to make the geneproductToGOterm association)
- taxon_id for the gene products for which the associations are made
Checklist for GAF
Following details have to be considered before taking annotations from a new group.
- If a group contacts GOC offering GO annotations, you want to ask them if they are willing to serve as the species owner (do they have resources, support to maintain the annotations for the species etc). For example MGI is the species owner for mouse. If they are able to serve as the species owner, then they have to provide us the following along with the GO annotations.
- A stanza for the GO.xrefs file (http://www.geneontology.org/cgi-bin/xrefs.cgi). Add the stanza to the GO.xrf_abbs file which is in CVS and the webpage automatically picks it up for display. Example stanza show below.
abbreviation: SGD
database: Saccharomyces Genome Database
object: Identifier for SGD Loci
synonym: SGDID
example_id: SGD:S000006169
local_id_syntax: ^S[0-9]{9}$
generic_url: http://www.yeastgenome.org/
url_syntax: http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=[example_id]
url_example: http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=S000006169
- A config file that provides email address, URL for the website etc. This file is checked into the 'submission' directory (http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/gene-associations/submission/). Make sure the contact Email address in the config file is the same as in the GAF file.
project_name=Saccharomyces Genome Database (SGD) contact_email=sgd-helpdesk@lists.stanford.edu project_url=http://www.yeastgenome.org/ funding_source=NHGRI of US National Institutes of Health, HG001315 email_report=sgd-go-curator@genome.stanford.edu
- gp2protein file