Re: [SED-ML-discuss] sed-ml language

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Preferably, I would like to keep the level / version stuff out of SED-ML at
all ... it is such a pain to do things like ChangeXML in the first place ...
having to potentially translate it to different levels/ versions seems
daunting. Thats why when I use the feature, I will use the archive format
to ensure its the right combo, and no one updates the model under my hand
... 

Still the symbols we can use are specified within the urn:sedml:symbol
scheme, right? (Presumably on some accessible format somewhere akin to how
we deal with the MIRIAM scheme right now). So I think this definition should
be independent of level and versions of the model ... at least for now I
don't see a reason I would want to define a symbol for one level / version
combination that I would not like to use in another. 

Frank

> -----Original Message-----
> From: Nicolas Le novère [mailto:le...@eb...]
> Sent: Tuesday, June 08, 2010 10:33 AM
> To: Frank Bergmann
> Cc: sed...@li...
> Subject: Re: [SED-ML-discuss] sed-ml language
> 
> The need is that different versions/levels can have different
> elements/symbols/way of doing things. If we provide links to schemas, we
> must differentiate between alternatives. Would-you always point to the
> latest SBML definition, like L3V1, even if the file is an L2V4?
> 
> On 08/06/10 18:26, Frank Bergmann wrote:
> > I still don't see the need, but if others do that is fine with me. Why
> > would I reject a model, just because now the resource is pointing to
> > an SBML Level
> > 3 document, when the SED-ML document was expecting an l2v4 one?
> >
> > Cheers
> > Frank
> >
> >> -----Original Message-----
> >> From: Nicolas Le novère [mailto:le...@eb...]
> >> Sent: Tuesday, June 08, 2010 10:23 AM
> >> To: sed...@li...
> >> Subject: Re: [SED-ML-discuss] sed-ml language
> >>
> >> What about a system providing info for the ones who want it but allow
> >> for
> >> fuzziness:
> >>
> >> urn:sedml:language:cellml:version-1.1
> >> urn:sedml:language:neuroml:version-1.8
> >> urn:sedml:language:sbml:level-2-version-4
> >>
> >> ?
> >>
> >> On 08/06/10 18:11, Frank T. Bergmann wrote:
> >>> Hello Dagmar,
> >>>
> >>> this is an interesting idea. However, I would prefer not to bring in
> >>> the level / version of the model into SED-ML. For example, no matter
> >>> what SBML model you are pointing to many software packages will be
> >>> able
> >> to support it.
> >>> Moreover when you point at a model for example with a BioModel URN
> >>> your version number can change under your hand. So how about we
> >> simplify it to:
> >>>
> >>> urn:sedml:language:cellml
> >>> urn:sedml:language:neuroml
> >>> urn:sedml:language:sbml
> >>> urn:sedml:language:vcml
> >>>
> >>> from then on we could easily get level and version information from
> >>> the actual source file.
> >>>
> >>> Thanks
> >>> Frank
> >>>
> >>>> -----Original Message-----
> >>>> From: Dagmar Waltemath [mailto:dag...@un...]
> >>>> Sent: Tuesday, June 08, 2010 9:28 AM
> >>>> To: sed...@li...
> >>>> Subject: [SED-ML-discuss] sed-ml language
> >>>>
> >>>> Hello...
> >>>>
> >>>> I was looking at the language references.
> >>>> We decided to store the language of each model we use in the SED-ML
> >>>> file. And we want to use a common urn scheme for that:
> >>>> urn:sedml:language:X.
> >>>>
> >>>> We will have to  specify the X for each language that we know
> >>>> thinks about using SED-ML, so far I have CellML, NeuroML, SBML and
> VCML.
> >>>> Same for the different versions of those languages.
> >>>>
> >>>> The information will be provided online. The idea is to provide
> >>>> information on the language/version name, as well as a reference to
> >>>> the according specification and format definition, and to the
> >>>> citation that explains the format, if those things are existing.
> >>>>
> >>>> I attach a table with a number of languages and versions, and the
> >>>> above mentioned information.
> >>>> It would be great if you could
> >>>>
> >>>> 1) correct and complete the table
> >>>> 2) let me know if you are aware of further languages/versions we
> >>>> should include.
> >>>>
> >>>> Thanks.
> >>>> Dagmar
> >>>
> >>>
> >>> --------------------------------------------------------------------
> >>> --
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> >>
> >>
> >> --
> >> Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-
> >> Trust Genome Campus, Hinxton CB101SD UK, Mob:+447833147074,
> >> Tel:+441223494521
> >>
> Fax:468,Skype:n.lenovere,AIM:nlenovere,MSN:nle...@ho...(N
> >> OT email) http://www.ebi.ac.uk/~lenov/,
> >> http://www.ebi.ac.uk/compneur/, @lenovere
> >>
> >>
> >>
> >>
> > ----------------------------------------------------------------------
> > ------
> > --
> >> ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad
> >> Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit.
> >> See the prize list and enter to win:
> >> http://p.sf.net/sfu/thinkgeek-promo
> >> _______________________________________________
> >> SED-ML-discuss mailing list
> >> SED...@li...
> >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> >
> 
> 
> --
> Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-
> Trust Genome Campus, Hinxton CB101SD UK, Mob:+447833147074,
> Tel:+441223494521
> Fax:468,Skype:n.lenovere,AIM:nlenovere,MSN:nle...@ho...(N
> OT email) http://www.ebi.ac.uk/~lenov/,
> http://www.ebi.ac.uk/compneur/, @lenovere
> 