Re: Identifiers (was Notes from today's meeting)

Hi All,

The problem with the current suggested solution is that it does not account
for a mix of identifiers in a dataset.
This is because in RDF we have resources not data items.

So in case of uniprot.org we have lots of identifiers in a single dataset.
Identifying annotation, ranges, go terms etc... etc...
The modeling does not support that common use case of having multiple
identifier sources in a single dataset.

So if I have a dataset like this .

uniprot:P12345 a up:Protein ;
                       up:enzyme ec:1.2.3.4 .
ec:1.2.3.4 a up:Enzyme .

How do I describe correctly the fact that a user should expect both
identifiers of the type 1.2.3.4 and P12345?

Also look beyond the boundaries of life science. What happens when you add
geo or physical data?

Regards,
Jerven



On Tue, Jun 4, 2013 at 1:45 PM, N Juty <juty@ebi.ac.uk> wrote:

> Hi,
>
> The GO abbreviations and cross-referencing list is one of a few possible
> lists that could be used, but there would be overlap and inconsistencies in
> coverage and namespace assignments, especially when using more than one
> such list to bridge any gaps. A lot of these lists are also 'static', with
> no real way to add new information.
>
> If we went down the route of a global 'authority', I would hope
> Identifiers.org would be a good candidate; we have gone to a lot of effort
> in collating data from a variety of such cross-referencing lists. Right now
> we are working on incorporating namespace, resource, regex information,
> etc. from Michel's extensive list: https://docs.google.com/**
> spreadsheet/ccc?key=**0AmzqhEUDpIPvdFR0UFhDUTZJdnNYd**nJwdHdvNVlJR1E#gid=0<https://docs.google.com/spreadsheet/ccc?key=0AmzqhEUDpIPvdFR0UFhDUTZJdnNYdnJwdHdvNVlJR1E#gid=0>
>
> In addition, since Identifiers.org has a dedicated curation team, we
> regard ourselves as being quite responsive and proactive...
>
> cheers
>
> Nick
>
>
>
>
>
> On 04/06/13 12:12, Joachim Baran wrote:
>
>> Hello,
>>
>>
>> On 2013-06-04, at 5:27 AM, Alasdair J G Gray <
>> Alasdair.Gray@manchester.ac.**uk <Alasdair.Gray@manchester.ac.uk><mailto:
>> Alasdair.Gray@**manchester.ac.uk <Alasdair.Gray@manchester.ac.uk>>>
>> wrote:
>>
>>> Again, there is a scoping problem. Prefixes are locally scoped and must
>>> be defined.
>>>
>>   At least in life sciences, there are the Gene Ontology abbreviations
>> for cross-referenced databases: http://www.geneontology.org/**
>> doc/GO.xrf_abbs <http://www.geneontology.org/doc/GO.xrf_abbs>
>>
>>   That document defines a wide range of prefixes, base URIs and URI
>> templates for resolving relevant identifiers, and provides regexps for
>> validating the syntax of identifiers.
>>
>>   I think that the GO xrefs are extremely useful and would be on Michel's
>> side on including them.
>>
>> Best wishes,
>> Joachim
>>
>
>
> --
> ------------------------------**--------------------------
> Nick Juty
> Database Curator
> European Bioinformatics Institute
> Cambridge, United Kingdom
> ------------------------------**--------------------------
>
>


-- 
Jerven Bolleman
me@jerven.eu