Re: Rules (was Re: Ambiguous names. was: Re: URL +1, LSID -1)

In that case, I would recommend  that it is unwise to use Uniprot ids  
as identifiers of protein classes on the semantic web. Doing so would  
encourage exactly the kind of ambiguity that we need to avoid in  
order to write statements that will not confuse semantic web agents  
(including people).

I would suggest instead, that Uniprot not suggest that they represent  
specific classes of proteins, and instead keep them being exactly  
what they are, records containing information about diverse sets of  
entites, which we all admit is very useful. If there is interest in  
formalization for semantic web use at Uniprot, perhaps the focus can  
be instead on the smaller entities on which these records collect  
information.

Let others who are more interested in providing formal definitions  
for proteins work on making definitions that carve out specific  
classes. They can do so in part by pointing at information in the  
Uniprot records and other sources.

-Alan

On Jul 17, 2007, at 4:33 AM, Eric Jain wrote:

> Alan Ruttenberg wrote:
>> To clarify, no, I didn't mean this. I meant that the definition of  
>> Uniprot records are already broad in the sense that sometimes  
>> multiple splice variants are included in a single record, as are  
>> population and disease-causing variants, according to Eric.  
>> Basically I don't know what set of proteins people currently  
>> intend to denote when they use a uniprot id as a protein, and I'm  
>> not entirely certain what the curators intend. So step one would  
>> be an english description of how to figure out what the curator's  
>> intent is, and we could go on from there to define OWL definitions  
>> based on that. I suspect that people currently using Uniprot ids  
>> may be using them in both broader and narrow ways, but we could  
>> leave the discovery of such cases to a reasoner once we had the  
>> basics in place.
>
> People do indeed use UniProtKB identifiers in both broad and narrow  
> ways: The narrow way is to talk about the exact, main sequence that  
> is shown...

I
> In any case, I'm not too optimistic about being able to define our  
> concepts in a strict, yet meaningful way, as often it's practical  
> criteria that are used to decide, e.g. here's what one of our  
> curators has to say on this:
>
> "[Usually] we have one entry per gene. We have several entries for  
> a single gene when description of variations are too complicated to  
> describe in FT lines (of course, this criteria depends on the  
> annotator). For viruses, it is much more messy, due to ribosomal  
> frameshifts."
>
> Formalize that! :-)

Received on Wednesday, 18 July 2007 04:51:15 UTC