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

[camon at ebi.ac.uk]

Hi Fiona,

Thanks for the mails.

Yes I agree I will talk to David Binns(GOA tool developer) about upgrading
the GOA annotation tool to permit the manual GO annotation of IPI ids
related to chicken and cow sequences so that the curators can continue
capturing information in the literature. Could you report via e-mail the
gene products that don't have IPI ids to goa_curators at ebi.ac.uk. Paul
Kersey seemed to believe they should all pretty much have IPI ids. Of
course not all authors of scientific papers submit their sequences to
genbank/embl too which is another problem. But we can submit these to the
journal scanning curator at UniProtKB.

cheers,

Evelyn

> 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
>
>
>
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>
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>
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