[Goa_curators] Re: Updating Cow and Chicken entries to CDS in EMBL/DDBJ/Genab

[Fiona McCarthy]

Hi Evelyn,

I really like the IPI idea, I have found the IPI database very useful in a
lot of our work. For this reason I have tried to attach IPI accessions to
many of the 'predicted' proteins that we were initially looking for in
UniParc but I found that not all of the 'predicted' proteins were in IPI.

Could we state that when UniProtKB is unavailable, our first priority will
be to use IPI and then only if the gene product is not in IPI to use
another database ID?

Fiona



Evelyn Camon <camon at ebi.ac.uk> writes:


>Hi
>
>We just had a discussion with Paul Kersey (IPI database)and Abel 
>Ureta-vidal (Ensembl). At that meeting it was suggested that the IPI
ID 
>might be better than the UniParc Id for manual annotation purposes
when 
>UniProtAcessions not available. Might be easier to track accessions 
>after sucessive sequence updates.
>I will investigate if that would work best. Any comments helpful at
this 
>point.
>
>cheers
>Evelyn
>
>Evelyn Camon wrote:
>> Dear Farm Animal Interest Group,
>> 
>> As you may already know the Gene Ontology Annotation (GOA)database
>at 
>> the EBI is the agreed supplier of GO annotation association files
to
>the 
>> GO consortium for the Chicken and Bovine species. As such it is
our 
>> responsibility to ensure that we supply and integrate high
quality 
>> experimentally verified manual GO anotation from external groups 
>> (AgBase, Roslin, others) and create as complete an annotation 
>> association file as possible.
>> 
>> The completed bovine and chicken genome sequences are still in a 
>> preliminary state in the Whole Genome Shotgun (WGS) section of
the 
>> EMBL/GenBank/DDBJ nucleotide databases and therfore not all
protein 
>> coding regions have been annotated. As a result there is no way
for 
>> UniProt to automatically create new entries using normal
procedures
>and 
>> as such the sequences get archived in UniParc instead. This
creates
>a 
>> problem since only UniProtKB identifiers could be annotated in GOA
>in 
>> the past.
>> 
>> We have the following proposal for the farm animal communities:
>> 
>> In order to get the data upgraded into UniProtKB we need
>> 
>> (a) either individuals to submit a third party annotation (TPA)
to 
>> either EMBL or Genbank where they upgrade the annotations to CDS
>(coding 
>> sequence). Then the data will automatically get integrated into 
>> UniProtKB/TrEMBL...
>> 
>> AND/OR
>> 
>> (b) Individuals or ChickGO Consortium make requests to the
>sequencing 
>> centres to update the annotation of these sequences from EST to
CDS. 
>> Once this is done the data will enter the UniProtKB/TrEMBL by
normal 
>> pipeline procedures and will also be available for the UniProtKB 
>> curators to annotate and promote into UniProtKB/Swiss-Prot. The
>TrEMBL 
>> sequences would also then automatically inherit good quality
>electronic 
>> GO annotation from the GOA group via InterPro, Swiss-Prot keywords
>and 
>> Enzyme to GO mappings (and other future planned GO mappings to
>pathways).
>> 
>> Although the above is our preferred route, we acknowledge that it
>might 
>> take some time to implement SO we also propose (c) to temporarily
>allow 
>> the annotation of UniParc identifiers in the protein2GO annotation
>tool 
>> at GOA by Roslin, EBI and AgBase staff and will also consider the 
>> integration of GO annotation to UniParc identifiers from external
>groups 
>> if it is in keeping with GO Consortium guidelines. This is
possible
>as 
>> UniParc identifiers are now STABLE and we can upgrade to
UniProtKB 
>> accesions automatically later.
>> 
>> Also to aid the farm animal proteome GO annotations we are
proposing
>(d) 
>> to transfer automatically, any experimentally verified GO
annotation 
>> between species using ensembl compara(predicts orthologs). This
data 
>> will be evidence coded as IEA(inferred from electronic annotation)
>and 
>> NOT ISS(inferred from sequence similarity) in the GOA database.
>> 
>> We are very interested in hearing your opinions particularly
>concerning 
>> the TPA route of updating the EMBL/GenBank/DDBJ sequence
annotations
>to 
>> solve this problem.
>> 
>> Dave and Fiona could the ChickGO Consortium get in touch with the 
>> sequencing centres???
>> 
>> Kind regards,
>> 
>> Evelyn Camon
>> 
>
>
>-- 
>Evelyn Camon
>GOA Coordinator
>Senior Scientific Curator
>European Bioinformatics Institute
>Tel:01223-494465
>Fax:01223-494468
>E-mail: camon at ebi.ac.uk
>URL: http://www.ebi.ac.uk/goa
>
>_______________________________________________
>Goa_curators mailing list
>Goa_curators at ebi.ac.uk
>http://listserver.ebi.ac.uk/mailman/listinfo/goa_curators



AgBase Biocurator
Department of Basic Sciences
Box 6100
MS 39762-6100 
Mississippi State University
USA
Tel:   (+ 1) 662 325 5859
Fax:  (+ 1) 662 325 1031

http://www.agbase.msstate.edu/