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Re: [SED-ML-discuss] sed-ml language
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From: Lucian S. <lp...@sp...> - 2010-06-08 18:06:33
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Why would SED-ML provide a link to a schema? Doesn't it assume that you already know how to parse (and even simulate!) a file of the particular language? If you want to make sure you're linking to a particular version of a file, I think you want a checksum, not a level description. (Actually, since SEDML only deals with files at the XML level, it doesn't even need the language bit, except as a hint to the SEDML interpreter. The file itself should tell whoever tries to parse it what language it is.) Actually, that brings up an interesting point: can we add the language 'xml' to the list, for when we want to punt and let the simulator decide whether it knows how to parse/simulate a model? -Lucian * Nicolas Le novère <le...@eb...> [2010-06-08 18:36] writes: > 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 > >>> > >>> > >>> ---------------------------------------------------------------------- > >>> -------- 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 > >> > >> > >> > >> > > ---------------------------------------------------------------------------- > > -- > >> 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...(NOT 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 |
