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

[Richard A. <ra...@st...>]

So say for SBML, level 3 has 'localParameter' elements in kinetic laws  
which are I believe new in level 3.
  If I have a SEDML file that has some changeXML elements to apply to  
a model in level 2 version 4, which change the values of parameters in  
a kinetic law, the XPath expression to apply the change will have to  
be different depending on whether the retrieved model is level 2v4 or  
level 3. In this case, the SEDML file is tied to a particular SBML  
version (unless we introduce into SEDML some concept of alternative  
changeXML elements for different model versions).

So if we're not in control of the model (e.g., we're accessing it from  
a remote repository), then it seems we have to have some idea of what  
version of a model the SEDML file applies to.

Cheers
  Richard


> 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...(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
>
>



-- 
Dr Richard Adams
Software Development Team Leader,
Centre For Systems Biology Edinburgh
University of Edinburgh
Tel: 0131 650 8285
email : ric...@ed...

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