Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

Splice variant identifiers introduced in GOA species specific files

Alan Ruttenberg alanruttenberg at gmail.com
Tue May 23 11:49:16 PDT 2006


Hello Daniel.

I don't know the specific model you are referring to for annotating  
splice variant identifiers. Could you point me at an example?

When you say you will "we will transfer the annotation to the master  
isoform ID". Does the master isoform ID refer to a specific isoform,  
or to the set of all isoforms. If either of these cases it sounds  
like doing so would introduce incorrect information - i.e. specific  
or global annotation where, in fact, something specific or global is  
not known. Is there a clear way to distinguish those cases where  
specific information about an isoform is known versus those in which  
specific information is not known?

Thanks,

-Alan

On May 22, 2006, at 9:25 AM, Daniel Barrell wrote:

> Hi,
>
> In the new GOA release due out later this week we will start to  
> annotate
> to known splice variants in the species specific files:
>
> gene_association.goa_arabidopsis.gz
> gene_association.goa_chicken.gz
> gene_association.goa_cow.gz
> gene_association.goa_human.gz
> gene_association.goa_mouse.gz
> gene_association.goa_rat.gz
> gene_association.goa_zebrafish.gz
>
> This means we better reflect the IPI
> (http://www.ebi.ac.uk/IPI/IPIhelp.html) datasets that the above files
> are based upon.
>
> This change means that we have had to change the way we deal with  
> manual
> annotations in these files.  For cases where the curator has not
> annotated to the isoform ID directly we will transfer the  
> annotation to
> the master isoform ID.
>
> These changes do not affect the UniProt or PDB sets.  If you have any
> further questions about the implication of these changes than  
> please do
> not hesitate to contact me.
>
> Regards
>
> Dan Barrell, GOA
>
> -- 
>
> Daniel Barrell
> EMBL - The EBI
> Wellcome Trust Genome Campus
> Hinxton, Cambridge CB10 1SD
> Phone: +44 (0)1223 492551
> Email: dbarrell at ebi.ac.uk
>
>
> --
> This message is from the GOFriends moderated mailing list.  A list  
> of public
> announcements and discussion of the Gene Ontology (GO) project.
> Problems with the list?           E-mail: owner- 
> gofriends at geneontology.org
> Subscribing   send   "subscribe"   to   gofriends- 
> request at geneontology.org
> Unsubscribing send   "unsubscribe"  to  gofriends- 
> request at geneontology.org
> Web:          http://www.geneontology.org/


--
This message is from the GOFriends moderated mailing list.  A list of public
announcements and discussion of the Gene Ontology (GO) project.
Problems with the list?           E-mail: owner-gofriends at geneontology.org
Subscribing   send   "subscribe"   to   gofriends-request at geneontology.org
Unsubscribing send   "unsubscribe"  to  gofriends-request at geneontology.org
Web:          http://www.geneontology.org/



More information about the go-friends mailing list