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'with' field contents for IPI annotations

David Hill dph at
Wed Mar 1 06:47:14 PST 2006

Not sure it this is out of our realm, but it would be really cool if we 
could somehow notify SwissProt folks when we come across Trembl records 
that represent isoforms. Then we could work together to get the most 
precise info possible. In the end I think it would make both resources 


Evelyn Camon wrote:

> Hi David,
> The main sequence does not always represent isoform 1 but it usually 
> does. TrEMBL records create problems for us also and so we annotate 
> isoforms only when they are Swiss-Prot records. I am ccing 
> Michele/Eleanor to confirm. At the time you look at a TrEMBL record 
> the sequence might represent a specific isoform...later it will be 
> merged with other entries and a different perhaps longer sequence 
> might be chosen as the representative sequence in the Swiss-Prot 
> record. The TrEMBL identifier might then become secondary to this new 
> accession I am not aware of a way of linking the new isoform ids to 
> the old TrEMBL accessions but it may be possible???? Michele or 
> Eleanor can confirm. I believe once an isoform ID is assigned it is 
> stable??(Ele).
> Some minutes of our discussion on the topic for your information.
> Evelyn
> ****************
> The information that is manually annotated to UniProtKB/Swiss-Prot 
> record represents the characterisation of all splicing variants. 
> However each splicing variant is designated a unique isoform id e.g 
> (P12345.1)and it is possible using a script to separate the sequences 
> into those that represent the individual isoforms.
> Up to Novemeber 2005 GOA had no method of annotating directly to 
> splice variants and so all possible annotations were assigned to the 
> main protein accession i.e P12345. This meant that it was impossible 
> for biologists to extract the specific variant GO annotation. The 
> ability to annotate to splice variants allows GOA also to 
> experimentally validate the splicing variants as in UniProtKB they are 
> not all experimentally verified.
> DECISION at GOA Meeting 7-11-2005
> If you know specific variant GO annotation then annotate to the 
> variant/isoform accession(P12345.1).
> If you don't know which specific variant GO annotation should apply 
> then annotate to the main entry(P12345). These are ok to generally 
> transfer to other species by ISS.
> If you know specific isoform has a match in another species then can 
> transfer by ISS from isoform to isoform (wait until David updates tool)
> Notes: No need to try an summarise GO annotation to higher level terms 
> from specific variants in main entry. Eleanor made point that 
> isoform.1 is not always the sequence on display in UniProtKb.
> ****************
> David Hill wrote:
>> Actually, if an author is looking at a specific isoform, it is 
>> usually easy to tell which Uniprot-# it goes with by looking at the 
>> sequence. The probelm I run across is when the isoform corresponds to 
>> a Trembl record. Is that record just rolled into the generic uniprot 
>> id or does it actually become associated with the correct isoform?
>> David
>>> We will also accept UniProt Isoform Ids (P00001.1, P00001.2) if you 
>>> can figure out which is the correct one in the paper and its has an 
>>> id in UniProt..bit of an awkward one at the moment.

David P. Hill, Ph.D.
Senior Scientific Curator
Mouse Genome Informatics
Gene Ontology Consortium
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609-1500

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