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Posts: 307
Location:
Cambridge UK
Registered:
February 2005
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Posts: 469
Registered:
October 2003
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Re: [Biomodels-net-discuss] Using SBO term to annotate SBML Unit and UnitDefinition
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02 Dec '10 00:53
 
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Hello,
Units per se should not be part of SBO I think. By the way, I do not think
the SBO term represented the unit of time, but the time itself, as in
SBML's csymbol time.
There are various unit ontologies. One can mention
the Measurement Unit Ontology:
http://forge.morfeo-project.org/wiki_en/index.php/Units_of_measurement_ontology
http://idi.fundacionctic.org/muo/muo-vocab.html
the W3C unit ontology:
http://www.w3.org/2007/ont/unit
But more importantly, OBO has its own unit ontology. It used to be a bit
simplistic, but it now joined PATO and is pretty comprehensive and well
maintained:
http://bioportal.bioontology.org/visualize/44519
I would go for this one.
On 24/11/10 14:14, Nicolas Rodriguez wrote:
> Hello,
>
> We have annotated, in jsbml, one of our unit with the SBO Term 345,
> which is/was time (now obsolete).
> We were wondering if this specific term could be replace with a term
> that is a child of 'temporal measure' (SBO 346) ?
>
> And as a more general question, could SBO be used to annotate
> Unit/UnitDefinition or should we use an other ontology ?
>
> Thanks,
> Nico
>
>
> ------------------------------------------------------------------------------
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--
Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC,
Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468,
Skype:n.lenovere, AIM:nlenovere, MSN:nlenovere@hotmail.com(NOT email)
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/, @lenovere
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Posts: 273
Registered:
June 2006
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Re: [Biomodels-net-discuss] Using SBO term to annotate SBML Unit and UnitDefinition
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02 Dec '10 08:56
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Hello everybody,
Ok, does this mean, we should or we should not automatically annotate
predefined units with the help of MIRIAM? At least for L/V combinations,
for which MIRIAM is defined?
I mean, on the one hand, it cold be very nice to include a MIRIAM
annotation for those units, for which we precisely know beforehand what
is meant.
On the other hand, this is not necessarily part of the SBML specification.
What do people mean?
Cheers
Andreas
--
Dipl.-Bioinform. Andreas Dräger
Eberhard Karls University Tübingen
Center for Bioinformatics (ZBIT)
Sand 1
72076 Tübingen
Germany
Phone: +49-7071-29-70436
Fax: +49-7071-29-5091
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Posts: 307
Location:
Cambridge UK
Registered:
February 2005
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Re: [Biomodels-net-discuss] Using SBO term to annotate SBML Unit and UnitDefinition
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02 Dec '10 14:28
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Le 02/12/2010 08:53, Nicolas Le novère a écrit :
> Hello,
>
> Units per se should not be part of SBO I think. By the way, I do not think
> the SBO term represented the unit of time, but the time itself, as in
> SBML's csymbol time.
>
> There are various unit ontologies. One can mention
>
> the Measurement Unit Ontology:
> http://forge.morfeo-project.org/wiki_en/index.php/Units_of_measurement_ontology
> http://idi.fundacionctic.org/muo/muo-vocab.html
>
> the W3C unit ontology:
> http://www.w3.org/2007/ont/unit
>
> But more importantly, OBO has its own unit ontology. It used to be a bit
> simplistic, but it now joined PATO and is pretty comprehensive and well
> maintained:
> http://bioportal.bioontology.org/visualize/44519
>
> I would go for this one.
Is any of the above ontologies is in miriam ?
I did a search in miriam for unit, it returns plenty of results but
nothing look likes any of these 3 propositions.
Nico
> On 24/11/10 14:14, Nicolas Rodriguez wrote:
>> Hello,
>>
>> We have annotated, in jsbml, one of our unit with the SBO Term 345,
>> which is/was time (now obsolete).
>> We were wondering if this specific term could be replace with a term
>> that is a child of 'temporal measure' (SBO 346) ?
>>
>> And as a more general question, could SBO be used to annotate
>> Unit/UnitDefinition or should we use an other ontology ?
>>
>> Thanks,
>> Nico
>>
>>
>> ------------------------------------------------------------------------------
>> Increase Visibility of Your 3D Game App& Earn a Chance To Win $500!
>> Tap into the largest installed PC base& get more eyes on your game by
>> optimizing for Intel(R) Graphics Technology. Get started today with the
>> Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs.
>> http://p.sf.net/sfu/intelisp-dev2dev
>> _______________________________________________
>> BioModels.net Discussion Mailing List
>> Biomodels-net-discuss@lists.sourceforge.net
>> Setting: https://lists.sourceforge.net/lists/listinfo/biomodels-net-discuss
>> Website: http://www.biomodels.net
>
____________________________________________________________
To manage your jsbml-development list subscription, visit
https://utils.its.caltech.edu/mailman/listinfo/jsbml-development
For a web interface to the jsbml-development mailing list, visit
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For questions or feedback about the jsbml-development list,
contact sbml-team@caltech.edu
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Posts: 307
Location:
Cambridge UK
Registered:
February 2005
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Re: [Biomodels-net-discuss] Using SBO term to annotate SBML Unit and UnitDefinition
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02 Dec '10 14:30
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Le 02/12/2010 16:56, Andreas Draeger a écrit :
> Hello everybody,
>
> Ok, does this mean, we should or we should not automatically annotate
> predefined units with the help of MIRIAM? At least for L/V combinations,
> for which MIRIAM is defined?
>
> I mean, on the one hand, it cold be very nice to include a MIRIAM
> annotation for those units, for which we precisely know beforehand what
> is meant.
>
> On the other hand, this is not necessarily part of the SBML specification.
>
> What do people mean?
> But more importantly, OBO has its own unit ontology. It used to be a bit
> simplistic, but it now joined PATO and is pretty comprehensive and well
> maintained:
> http://bioportal.bioontology.org/visualize/44519
>
> I would go for this one.
That mean that we can annotate unit, if we want to, with the above ontology.
But as I asked in a separate email, I am not sure this ontology is in
miriam at the moment, so it might be difficult to
use miriam annotation until it is.
Nico
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