- From: Michel Dumontier <michel.dumontier@gmail.com>
- Date: Tue, 4 Jun 2013 14:52:33 +0200
- To: Jerven Bolleman <me@jerven.eu>
- Cc: N Juty <juty@ebi.ac.uk>, Joachim Baran <joachim.baran@gmail.com>, Alasdair J G Gray <Alasdair.Gray@manchester.ac.uk>, "public-semweb-lifesci@w3.org" <public-semweb-lifesci@w3.org>
- Message-ID: <CALcEXf5kQ=Ev-g_UzstGrS=Ekt-5zt=dedqdqikz7doAjq905w@mail.gmail.com>
On Tue, Jun 4, 2013 at 2:47 PM, Jerven Bolleman <me@jerven.eu> wrote: > 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? > > easy. provide two matching patterns. m. > 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 > -- Michel Dumontier Associate Professor of Bioinformatics, Carleton University Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group http://dumontierlab.com
Received on Tuesday, 4 June 2013 12:53:21 UTC