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SBML Discussions » sbml-discuss » SBML L2v2 specification vote #4: References to controlled vocabularies
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Mike Hucka


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

>>>>> 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.)

      

SubjectPosterDate
Read Message   SBML L2v2 specification vote #4: References to con... Mike Hucka13 Dec '05 14:21
Read Message   Re: SBML L2v2 specification vote #4: References t... Ralph.Gauges15 Dec '05 06:57
Read Message   Re: SBML L2v2 specification vote #4: References to... hugh.d.spence15 Dec '05 10:02
Read Message   Re: SBML L2v2 specification vote #4: References to... Ralph.Gauges16 Dec '05 00:27
Read Message   Re: SBML L2v2 specification vote #4: References to... Nicolas Le Novere16 Dec '05 10:11
Read Message   Re: SBML L2v2 specification vote #4: References to... Sven Sahle19 Dec '05 04:53
Read Message   Re: SBML L2v2 specification vote #4: References to... hugh.d.spence16 Dec '05 10:56
Read Message   Re: SBML L2v2 specification vote #4: References to... Howard16 Dec '05 11:43
Read Message   Re: SBML L2v2 specification vote #4: References to... hugh.d.spence19 Dec '05 04:00
Read Message   Re: SBML L2v2 specification vote #4: References to... Howard19 Dec '05 09:19
Read Message   Re: SBML L2v2 specification vote #4: References to... Martin Ginkel21 Dec '05 12:26
Read Message   Re: SBML L2v2 specification vote #4: References to... Howard21 Dec '05 15:30
Read Message   Re: SBML L2v2 specification vote #4: References t... Nicolas Le Novere16 Dec '05 01:27
Read Message   Re: SBML L2v2 specification vote #4: References t... Mike Hucka20 Dec '05 11:31
Read Message   Re: SBML L2v2 specification vote #4: References t... Nicolas Le Novere20 Dec '05 16:05
Read Message   Re: SBML L2v2 specification vote #4: References t... Mike Hucka20 Dec '05 19:42
Read Message   Re: SBML L2v2 specification vote #4: References t... bshapiro15 Dec '05 12:15
Read Message   Re: SBML L2v2 specification vote #4: References t...  Mike Hucka20 Dec '05 19:50
Read Message   Re: SBML L2v2 specification vote #4: References t... Ben Bornstein21 Dec '05 09:25
Read Message   RE: SBML L2v2 specification vote #4: References to... Ralph.Gauges17 Dec '05 09:11
Read Message   RE: SBML L2v2 specification vote #4: References to... Nicolas Le Novere19 Dec '05 08:52
Read Message   RE: SBML L2v2 specification vote #4: References to... Mike Hucka20 Dec '05 15:11
Read Message   Re: SBML L2v2 specification vote #4: References to... Ralph.Gauges21 Dec '05 02:04
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka02 Jan '06 23:33
Read Message   Re: SBML L2v2 specification vote #4: References to... Nicolas Le Novere03 Jan '06 00:21
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka03 Jan '06 15:30
Read Message   Re: SBML L2v2 specification vote #4: References to... Nicolas Le Novere04 Jan '06 03:08
Read Message   Re: SBML L2v2 specification vote #4: References to... Nicolas Le Novere06 Jan '06 10:37
Read Message   Re: SBML L2v2 specification vote #4: References to... Martin Ginkel05 Jan '06 01:44
Read Message   Re: SBML L2v2 specification vote #4: References to... Nicolas Le Novere03 Jan '06 00:50
Read Message   Re: SBML L2v2 specification vote #4: References to... hugh.d.spence05 Jan '06 05:29
Read Message   Re: SBML L2v2 specification vote #4: References to... Nicolas Le Novere05 Jan '06 11:01
Read Message   Re: SBML L2v2 specification vote #4: References to... hugh.d.spence06 Jan '06 02:48
Read Message   Re: SBML L2v2 specification vote #4: References to... Nicolas Le Novere06 Jan '06 10:32
Read Message   Re: SBML L2v2 specification vote #4: References to... hugh.d.spence03 Jan '06 04:30
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka03 Jan '06 20:55
Read Message   Re: SBML L2v2 specification vote #4: References to... bshapiro03 Jan '06 12:52
Read Message   Re: SBML L2v2 specification vote #4: References to... Stefan Hoops03 Jan '06 14:16
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka03 Jan '06 15:39
Read Message   Re: SBML L2v2 specification vote #4: References to... Nicolas Le Novere04 Jan '06 03:02
Read Message   Re: SBML L2v2 specification vote #4: References to... Stefan Hoops04 Jan '06 09:46
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka03 Jan '06 14:24
Read Message   Re: SBML L2v2 specification vote #4: References to... Nicolas Le Novere04 Jan '06 02:55
Read Message   Re: SBML L2v2 specification vote #4: References to... Howard19 Dec '05 09:22
Read Message   Re: SBML L2v2 specification vote #4: References to... Ralph.Gauges20 Dec '05 01:48
Read Message   Re: SBML L2v2 specification vote #4: References to... Howard20 Dec '05 11:13
Read Message   RE: SBML L2v2 specification vote #4: References to... Mike Hucka20 Dec '05 19:56
Read Message   Re: SBML L2v2 specification vote #4: References to... bshapiro20 Dec '05 20:18
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka20 Dec '05 23:55
Read Message   Re: SBML L2v2 specification vote #4: References to... hugh.d.spence21 Dec '05 02:18
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka21 Dec '05 05:48
Read Message   Re: SBML L2v2 specification vote #4: References to... bshapiro21 Dec '05 11:35
Read Message   Re: SBML L2v2 specification vote #4: References to... Howard21 Dec '05 15:44
Read Message   Re: SBML L2v2 specification vote #4: References to... Stefan Hoops22 Dec '05 07:30
Read Message   Re: SBML L2v2 specification vote #4: References to... Howard22 Dec '05 09:22
Read Message   Re: SBML L2v2 specification vote #4: References to... Stefan Hoops22 Dec '05 10:12
Read Message   Re: SBML L2v2 specification vote #4: References to... Pedro Mendes22 Dec '05 10:23
Read Message   Re: SBML L2v2 specification vote #4: References to... Howard22 Dec '05 11:18
Read Message   Re: SBML L2v2 specification vote #4: References to... zucker22 Dec '05 11:54
Read Message   Re: SBML L2v2 specification vote #4: References to... Howard22 Dec '05 12:13
Read Message   Re: SBML L2v2 specification vote #4: References to... Ralph.Gauges23 Dec '05 01:02
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka02 Jan '06 20:49
Read Message   Partial compliance [was] SBML L2v2 specification ... Nicolas Le Novere03 Jan '06 00:08
Read Message   Re: SBML L2v2 specification vote #4: References to... bshapiro22 Dec '05 12:05
Read Message   Re: SBML L2v2 specification vote #4: References to... Howard22 Dec '05 12:21
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka23 Dec '05 09:07
Read Message   Re: SBML L2v2 specification vote #4: References to... Howard23 Dec '05 10:07
Read Message   Re: SBML L2v2 specification vote #4: References to... Nicolas Le Novere22 Dec '05 05:23
Read Message   Re: SBML L2v2 specification vote #4: References to... Stefan Hoops22 Dec '05 08:25
Read Message   Re: SBML L2v2 specification vote #4: References to... Nicolas Le Novere22 Dec '05 10:19
Read Message   Re: SBML L2v2 specification vote #4: References to... Stefan Hoops22 Dec '05 10:31
Read Message   Re: SBML L2v2 specification vote #4: References to... bshapiro22 Dec '05 10:58
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka22 Dec '05 12:29
Read Message   Re: SBML L2v2 specification vote #4: References to... Darren J Wilkinson23 Dec '05 12:12
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka23 Dec '05 15:46
Read Message   Re: SBML L2v2 specification vote #4: References to... Hiroyuki Kuwahara24 Dec '05 22:01
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka03 Jan '06 00:33
Read Message   Re: SBML L2v2 specification vote #4: References to... Hiroyuki Kuwahara04 Jan '06 10:27
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka04 Jan '06 11:49
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka02 Jan '06 22:23
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka02 Jan '06 20:20
Read Message   Re: SBML L2v2 specification vote #4: References to... Howard21 Dec '05 10:29
Read Message   Re: SBML L2v2 specification vote #4: References to... Sven Sahle22 Dec '05 01:56
Read Message   RE: SBML L2v2 specification vote #4: References to... Nicolas Le Novere21 Dec '05 10:08
Read Message   RE: SBML L2v2 specification vote #4: References to... zucker21 Dec '05 11:02
Read Message   Re: SBML L2v2 specification vote #4: References to... Ralph.Gauges22 Dec '05 02:53
Read Message   Re: SBML L2v2 specification vote #4: References to... Ralph.Gauges22 Dec '05 02:57
Read Message   Re: SBML L2v2 specification vote #4: References to... Stefan Hoops22 Dec '05 08:10
Read Message   RE: SBML L2v2 specification vote #4: References to... Herbert Sauro22 Dec '05 13:08
Read Message   Re: SBML L2v2 specification vote #4: References to... zucker23 Dec '05 22:28
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka26 Dec '05 09:11
Read Message   Results of SBML L2v2 specification survey vote #4 Mike Hucka04 Jan '06 23:37
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