Forums

One could answer it depends on the tools. Because it depends on what
you want to do with the sboTerm. If you use the sboTerm of a
speciesReference to generate a SBGN graph, I would select the
sboTerm. If you want to process a kineticLaw and your tool can
understand the mathML I would go for the mathML. If you want to
convert a continuous model into discrete, I would choke and refuse the
model as inconsistent.

On Thu, 15 Dec 2005, Ralph Gauges wrote:

> Hi,
>
> unfortunatelly I was not there at the discussion in Boston, so I have a
> question that might has probably been discussed before.
> What happens if e.g. an sboTerm states that the kineticLaw is "irreversible
> first order mass action" but the formula is Michaelis-Menten? Which do I
> take? Same thing goes for SpeciesReferences. Is is an error if a
> SpeciesReference that is in the listOfProducts has an sboTerm that states
> that it is an inhibitor? How should inconsistencies like this be handled?
>
> Thanks
>
> Ralph
>
>
> Michael Hucka wrote:
>
>> The topic of this vote is: REFERENCES TO CONTROLLED VOCABULARIES
>>
>> The URL for the voting page is:
>> http://www.surveymonkey.com/s.asp?u=207211607892
>>
>> Additional background is available in the minutes from the
>> October SBML Forum meeting at
>> http://www.sbml.org/forums/index.php?t=msg&th=713&rid=2
>>
>> The SBML Level 2 Version Specification is at:
>> http://sbml.org/wiki/sbml-level-2-version-2.pdf
>>
>> This survey involves multiple questions.
>>
>> One of the proposed additions in SBML Level 2 Version 2 is
>> an attribute that would permit directly annotating certain
>> SBML elements with links to resources such as controlled
>> vocabulary terms. The need for such a capability in SBML is
>> widely acknowledged.
>>
>> The proposal for SBML Level 2 Version 2 is to add an
>> attribute to the elements Model, Rule, KineticLaw,
>> Parameter, SpeciesReference, and Constraint. This is
>> proposed to be called 'sboTerm' and its data type would be a
>> URI. The set of values that can be assigned to this
>> attribute would be limited to a specific ontology, the
>> Systems Biology Ontology (SBO), developed and maintained
>> independently from SBML.
>>
>> Under the proposal as currently formulated, the URI value of
>> an 'sboTerm' attribute on any given element in a model must
>> refer to a single SBO term that best defines the entity
>> represented by the SBML element in question. An example of
>> the type of relationship intended is:
>>
>> KineticLaw in reaction R1 is a
>> first-order irreversible mass action rate law
>>
>> Note the careful use of the words "defines" and "entity
>> represented by the SBML element" in the paragraph above.
>> The relationship between the SBML element and the URI is:
>>
>> the "thing" represented by this SBML element *is an*
>> instance of the "thing" represented by the referenced
>> SBO term
>>
>> One of the requirements to be imposed on SBO will be that it
>> is constructed in such a way that not more than one term is
>> appropriate as a value of an 'sboTerm' attribute. SBO will
>> not encode biological and biochemical concepts already
>> encoded by other ontologies.
>>
>> 'sboTerm' supersedes the previously proposed definitionURL
>> as first proposed in the discussion referenced here:
>> http://www.sbml.org/forums/index.php?t=tree&goto=2323&rid=0
>> http://www.sbml.org/forums/index.php?t=tree&goto=2237&rid=0
>> http://www.sbml.org/forums/index.php?t=tree&goto=2343&rid=0
>>
>> Here are the questions:
>>
>> 1) Do you think the introduction of the 'sboTerm' attribute
>> as described above is a good idea for SBML Level 2
>> Version 2?
>>
>> 2) In which XML namespace should the attribute 'sboTerm'
>> reside?
>> a) The new level 2 version 2 namespace,
>> "http://www.sbml.org/sbml/level2/version2". In this
>> case, the attribute would appear in an SBML document
>> simply as 'sboTerm', in the same way as other SBML
>> elements appear.
>>
>> b) The SBO namespace. In this case, the attribute would
>> have to appear with a namespace prefix in an SBML
>> document.
>>
>> (Note that this question is not about whether having to
>> use a namespace prefix is pleasant or unpleasant; the
>> question is about whether the 'sboTerm' attribute should
>> be considered part of the SBML namespace.)
>>
>> 3) The 'sboTerm' attribute is not a general purpose
>> mechanism for linking SBML elements to particular
>> resource like controlled vocabulary terms. It is now
>> widely believed in the SBML community that SBML needs
>> such a mechanism. Andrew Finney and Nicolas Le Novere
>> proposed a scheme here:
>> http://www.sbml.org/forums/index.php?t=tree&goto=1435&rid=0
>> http://www.sbml.org/forums/index.php?t=tree&goto=1436&rid=0
>>
>> The specification for this scheme is available here:
>> http://www.ebi.ac.uk/compneur-srv/sbml/proposals/AnnotationURI.pdf
>>
>> The Finney-Le Novere scheme would supersede the use of
>> the CellML metadata scheme defined in SBML Level 2
>> Version 1, and the use of the CellML metadata scheme
>> would be deprecated in SBML Level 2 Version 2.
>>
>> Do you think the Finney-Le Novere scheme should be part
>> of Level 2 Version 2?
>>
>>
>> Please cast your vote by using the voting page at
>> http://www.surveymonkey.com/s.asp?u=207211607892
>>
>> Andrew and Mike
>>
>>
>>
>

--
Nicolas LE NOVÈRE, Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223 494 521, Fax: +44(0)1223 494 468, Mob: +33(0)689218676
http://www.ebi.ac.uk/~lenov AIM screen name: nlenovere