Updating Cow and Chicken entries to CDS in EMBL/DDBJ/Genabnk and UniProtKB

[Elsik, Christine G]

Hi Evelyn,

I'm working with Baylor on bovine genome analysis and annotation. They haven't
yet released the ~8X assembly on which the automated gene predictions and
manual gene model annotation will be done. This assembly should be available
within weeks, and then Ensembl and NCBI will run their automated gene
prediction pipelines. We will be creating a single consensus gene set, doing
some community gene model annotation, and submitting the final gene set to
GenBank as features on the assembly probably sometime in early 2007. I would
suggest that people wait for the NCBI and Ensembl predictions on the 8X
assembly. Those will probably be available early this Fall. If people want to
get started on those, we can then later easily transfer the GO annotations to
the consensus gene set, because we will know which consensus gene model is
associated with each Ensembl and RefSeq gene model.

all the best,
Chris Elsik


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

> 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
> 
> 



-- 
Christine Elsik
Department of Animal Science
Texas A&M University
2471 TAMU
College Station, TX  77843-2471
phone 979-845-2618
fax 979-845-6970