[Annotation] Annotating Viral Proteins

[Gwinn Giglio, Michelle]

Jason,

You are 100% correct in you assessment of the "activation of immune
response" term, it should not be used for a viral protein acting on a host.
I suggest instead the term "induction by symbiont of host immune response"
GO:0052559.  This term is part of a large node of the biological process
tree developed by the PAMGO (Plant-Associated Microbe Gene Ontology) working
group.  Terms in this area focus on interactions between microbes and their
hosts, and more broadly any kind of symbiotic interaction (pathogenic and
non-pathogenic, with a host or without).  I realize that viruses are not
technically "organisms" and might not therefore be thought of as symbionts
in the traditional sense.  But I think the general consensus is to treat
viruses as organisms for the purposes of GO annotation.

Please check out the area of the tree where the above term is found.
Hopefully it will have the kinds of terms you need.  Also, you should know
that there are many virus specific terms in the GO that are in need of
revision.  This has been on our "to do" list for a while and will likely be
the subject of upcoming content working groups.  We'd be happy to have your
input on those as well.

If you see any problems in the symbiosis areas of the tree don't hesitate to
send in suggestions/comments to the SourceForge tracker.  Please let me know
if you have any questions.

Thanks very much,

Michelle


-------------------------------
Michelle Giglio
Institute for Genome Sciences
University of Maryland School of Medicine



On 1/30/09 11:43 AM, "vanauken at caltech.edu" <vanauken at caltech.edu> wrote:

> Dear Jason,
> 
> Thanks for writing to the GO.
> 
> I am forwarding your email on to the GO annotation mailing list, as there
> are a number of people in GO who work on annotating host-pathogen
> interactions and they likely can give you good advice on annotating viral
> proteins.
> 
> If you are interested, information about subscribing to this list is
> available here:
> 
> http://geneontology.org/GO.mailing.lists.shtml?all
> 
> 
> Best,
> --Kimberly Van Auken
> Database Curator, WormBase
> 
> www.wormbase.org
> www.geneontology.org
> 
> 
> 
>> Date: Fri, 30 Jan 2009 06:54:59 -0800 (PST)
>> To: gohelp at genome.stanford.edu
>> Subject: GO Help query (from Jason Pokorny)
>> From: jpokorny at mcw.edu
>> 
>> contactName: Jason Pokorny
>> contactEmail: jpokorny at mcw.edu
>> contactText: I have a viral protein (Vaccinia Virus H3) that has been
>> shown to be antigentic to the host during infection.  I want to assign
>> this protein to a biological process, but I can't determine the best term.
>>  I though that "activation of immune response GO:0002253" may be
>> appropriate.  However, I feel this term was intended for cellular proteins
>> where the cell is the host of the infection and not for the proteins in
>> the infectious agent.  Any advice?  Thanks.
>> 
>> 
> 
> 
> _______________________________________________
> Annotation mailing list
> Annotation at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/annotation