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Posts: 961
Registered: October 2003
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Re: SBML L2v2 specification vote #4: References to controlled vocabularies
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20 Dec '05 19:50

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>>>>> On 15 Dec 2005, "Bruce E Shapiro, PhD" <bshapiro@caltech.edu> wrote:
bshapiro> Sorry if I missed something, but what are the
bshapiro> arguments for/against using the same or a
bshapiro> different namespace here? I don't even recall
bshapiro> this part of the discussion in Boston (must have
bshapiro> been snoozin). Bruce
You know, to be truthful, I don't think there was a lot of
discussion; I think the point was simply raised and then we
went on to something else, figuring it would be resolved
later.
I am not sure there are strong arguments either way. In
(a), the element is a part of SBML, and applications would
not need to do anything different about the handling of the
symbol. It would be an additional field on objects, and
properly part of SBML.
An argument for (b) might that taking the sboTerm attribute
out of the SBML namespace would encapsulate the things
dealing with SBO, which perhaps is conceptually cleaner.
It would be really good if the proponents of each approach
would pipe up with some comments on this point.
MH
>> The topic of this vote is: REFERENCES TO CONTROLLED
>> VOCABULARIES
>>
>> 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.)
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