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'with' field contents for IPI annotations

Evelyn Camon camon at
Wed Mar 1 06:55:37 PST 2006

I'm afraid that part is out of my realm I will bring the issue 
up with Eleanor Whitfield a Senior Swiss-Prot curator who also is 
currently working with Alternative splicing database and Michele Magrane 
who coordinates the Swiss-Prot anotations at the EBI and also is 
responsible for the mouse curation effort here.

I will carry on this conversation with David offline now
but if other Consortium folks have an interest in this topic please 
holler directly to magrane at


David Hill wrote:
> 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 
> better.
> David
> 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.

Evelyn Camon
GOA Coordinator
Senior Scientific Curator
European Bioinformatics Institute
E-mail: camon at

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