[Fwd: Updating Cow and Chicken entries to CDS in EMBL/DDBJ/Genabnk and UniPro

[Fiona McCarthy]

Hi Evelyn,

Thank you for raising this point. As you know this is something that we at
AgBase have been working towards for some time now. Since not everyone may
be aware, the problem for farm animals with sequenced genomes is that many
of the proteins are ‘predicted’ based on electronic ORF prediction
algorithms. As Evelyn has already stated these entries are initially found
as UniParc entries rather than UniProtKB entries. The good news is that
this situation is changing and already this year the number of chicken
proteins not represented in UniProtKB has decreased from 70% to 50% of the
estimated total chicken genes.

I think that if we want individuals to submit a third party
structural-genomic annotation (TPA) to either EMBL or Genbank we will need
to make the exact procedure very clear. I have already tried this route
with Genbank but was unable to make any progress because there was no
clear mechanism in place to change ‘predicted’ entries once they had been
submitted by the sequencing consortium. Maybe this will be easier now that
NCBI has genome champions.

Your suggestion to temporarily allow the annotation of UniParc identifiers
in the protein2GO annotation tool at GOA is a good one but from my direct
experience with UniParc IDs I can tell you that it is *very* time
consuming for annotators to track down the UniParc IDs. I think this is
because the UniParc database is so very large and cannot be parsed by
species.

The way the gene association files are set up the gene product identifier
can be from any public database. In fact, GOA has gene association linked
to Ensembl and Vega IDs (I did not check for Genbank IDs) so the precedent
exists for using different database IDs. 

I think the issue is that we need
more flexibility in the use of IDs. Since the protein2GO tool cannot
handle every ID, the issue may be that we need to be able to map between
different IDs and this is something that I think would benefit many
communities.

regards,

Fiona

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


>
>
>-------- Original Message --------
>Subject: Updating Cow and Chicken entries to CDS in EMBL/DDBJ/Genabnk 
>and UniProtKB
>Date: Thu, 13 Jul 2006 11:39:29 +0100
>From: Evelyn Camon <camon at ebi.ac.uk>
>To: farmanimals at genome.stanford.edu, Jen Clark
><jenclark at ebi.ac.uk>, 
>     camon at ebi.ac.uk, jane at ebi.ac.uk
>
>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
>
>
>-- 
>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
>



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