Re: [Biomodels-net-discuss] [sbml-annot] BioModels.net qualifier discussion

[Neil S. <nei...@ma...>]

Hi Nicolas,

Agree with all of that. Including the e-mail address issue.

One thing I would add though, that in some cases the use of literals is valid when the values that they specify are immutable. A given species will always have a specified formula, for example.

Cheers,

Neil.

Neil Swainston
Experimental Officer

Manchester Centre for Integrative Systems Biology
Manchester Interdisciplinary Biocentre
University of Manchester
Manchester M1 7DN
United Kingdom

On 17 Jan 2011, at 16:00, Nicolas Le novère wrote:

> On 17/01/11 15:48, Neil Swainston wrote:
> 
>> I'm not sure that we do exclusively specify links to metadata in SBML. Take
>> the following example...
>> 
>> <rdf:RDF
>> xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"xmlns:dc="http://purl.org/dc/elements/1.1/"xmlns:dcterms="http://purl.org/dc/terms/"xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#"xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
>> <rdf:Description rdf:about="#metaid_recon1_1">
>> <dc:creator>
> 
>> "Neil" and "Swainston" and "2011-01-11" aren't links to metadata, they are
>> metadata. We already support the use of literals in the Core annotation.
> 
> Yes ...  you are right of course. I guess I just never considered those attribution annotation as proper parts of the "generic" RDF scheme. And accordingly they are very problematic. For instance, the e-mail addresses become invalid quickly. As soon as ORCID (http://www.orcid.org/) is adopted by the world and we have proper authors repository, I hope the creator and modifier bits will just point to orcids.
> 
>> Essentially, I'm not following your point on abandoning RDF when it comes
>> to specifying literals such as molecular weight or whatever. I'd have
>> thought that adding an entirely new way of specifying these independently
>> of RDF would be confusing.
> 
> I bow. RDFa would be the way to go.
> 
>> > But who will maintain the vocabularies? The formula, charge and ...
>> molecular weight, hydrodynamic radius, polarity, size, shape, conductivity,
>> etc. ?
>> 
>> Excellent question. I don't know. My thought is that these would be MIRIAM
>> qualifiers like any other. Like you point out, *someone* has to keep track
>> of them and their meanings.
> 
> This is done already. By PATO and others. The same way we use vCard and DCTERMS, we should use external vocabularies IMHO.
> 
> 
> -- 
> Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC,
> Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468,
> Skype:n.lenovere, AIM:nlenovere, twitter:@lenovere
> http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/
>