Re: [SED-ML-discuss] Model identifiers

[Nicolas Le N. <n.l...@gm...>]

On 21/03/14 09:50, Oliver Ruebenacker wrote:
>
>       Hello,
>
> On Thu, Mar 20, 2014 at 6:05 AM, Nicolas Le Novere <n.l...@gm... <mailto:n.l...@gm...>> wrote:
>
>     Examples of versionned URIs:
>
>     http://identifiers.org/uniprot/P12345.1
>     http://identifiers.org/uniprot/P12345.89
>     http://identifiers.org/uniprot/P12345
>
>
>    But these all refer to the same protein, while different versions of a model are actually different models, or am I missing something?

Different versions of a Uniprot entry refer to the same protein, but can contain different or even contradictory information. Same with the model. I was merely giving examples of Identifiers.org pointing to versioned information.

>       Best,
>       Oliver
>
>
>
>     On 20/03/14 04:34, David Nickerson wrote:
>      > Hi all,
>      >
>      > In several places in the SED-ML L1V2 specification, notably section
>      > 2.2.2.1, the use of MIRIAM URN's (or URI's) is recommended for
>      > identifying models. BioModels DB identifiers are used as an example of
>      > this "best practice". But as far as I know, following discussion at
>      > COMBINE last year, BioModels DB identifiers are not persistent
>      > identifiers for the same resource - inasmuch as a particular model
>      > (SBML document) identified by a given ID can change between releases
>      > of the BioModels DB.
>      >
>      > If my understanding of this is correct (and it could well be very much
>      > the opposite of correct), then BioModels identifiers suffer the same
>      > problem as models in the Physiome Repository in that you need to know
>      > not only what model to use, but what version of the model to use, in
>      > order to unambiguously identify the model. For models in the Physiome
>      > Repository this would correspond to the actual version in the history
>      > of the model and for BioModels DB it would correspond to the database
>      > release number, I guess.
>      >
>      > Now, the Physiome Repository provides URLs for all versions of a given
>      > model or you can keep the SED-ML document in the same workspace and
>      > use relative URLs to keep everything at the same version. But we have
>      > not yet been able to come up with a useful scheme to add this
>      > repository as a MIRIAM resource.
>      >
>      > Does this mean that there are no useful MIRIAM resources which provide
>      > model identifiers? Should we look at removing that recommendation from
>      > future SED-ML specifications? or, better to look at how we can define
>      > MIRIAM resources which do meet the requirements of the first paragraph
>      > in section 2.2.2.1 of the SED-ML L1V2 specification? Something to
>      > discuss at HARMONY perhaps...
>      >
>      >
>      >
>      > Cheers,
>      > David.
>      >
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>     --
>     Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT
>     Tel: +441223496433 <tel:%2B441223496433>   Mob:+447833147074 <tel:%2B447833147074> n.l...@gm... <mailto:n.l...@gm...>
>     orcid.org//0000-0002-6309-7327 <http://orcid.org//0000-0002-6309-7327> http://lenoverelab.org/perso/lenov/
>     Skype:n.lenovere  twitter:@lenovere http://nlenov.wordpress.com/
>
>
>
>
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>
> --
> Oliver Ruebenacker
> Founder at Relomics Consulting <http://www.relomics.com>
> Be always grateful, but never satisfied.


-- 
Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT
Tel: +441223496433   Mob:+447833147074   n.l...@gm...
orcid.org//0000-0002-6309-7327  http://lenoverelab.org/perso/lenov/
Skype:n.lenovere  twitter:@lenovere  http://nlenov.wordpress.com/