Re: [sbml-annot] On metadata attached to COMBINE standards

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

Hi Nicolas,

After going through this, I get the impression that much of this refers to annotation of the model itself (author, date, organism, system, etc., i.e. metadata of the model) and not so much the content of the model (EC terms, gene ids, etc.). Would this be right?

Cheers,

Neil.

Neil Swainston, PhD
Research Fellow

Manchester Institute of Biotechnology
University of Manchester
Manchester M1 7DN
United Kingdom

On 24 Jul 2013, at 11:47, Nicolas Le Novere <n.l...@gm...>
 wrote:

> Hello all,
> 
> Thank-you to Dagmar for rebooting this effort. I think metadata are 
> becoming ever more important in computational systems biology. I have a 
> slightly different take on the approach though. When we started the 
> discussions about the annotation package, we had a few precise 
> requirements. More appeared during the discussions, as well as grand 
> ambitions. That led to the realisation that maybe we should go towards OWL2 
> etc. and finally to an arrest of the development.
> 
> Since the SBML annotation meeting, two things happened that IMHO change a 
> bit the context and the path we want to take.
> 
> Firstly, there is a general movement to move metadata into the realm of 
> semantic web, and provide them in triple stores, or at least made them 
> available through SPARQL end points. This is for instance going full swing 
> at the EBI, and BioModels Db in involved in the process, meaning that its 
> SBML annotations will be externalised.
> 
> Secondly, the COMBINE/OMEX archive has become a reality, with the 
> development of packages that encapsulate all the files necessary for 
> understanding and processing a model. It has been proposed that the 
> metadata related to the content of an archive be expressed in RDF in a 
> separate file.
> 
> IMHO, this is the proper way to go. If we want all the COMBINE formats 
> (SBML, SED-ML, CellML and soon NeuroML) to share the same metadata, having 
> a format independent specification is much better than duplicating this 
> metadata specification in every language spec. It would also free this 
> metadata specification from the constraints of each particular model format 
> effort. Finally, it could be a proper RDF file (whatever flavour). For 
> instance, we would just have to define which vocabularies to use, rather 
> than defining the structure of the metadata at the XML level, as we do in SBML.
> 
> The consequences is that we should not necessarily have an SBML Level 3 
> package. Instead, we could "fix" the SBML controlled annotations to 
> facilitate its use. All the major developments, that would not go in the 
> Core controlled annotation, would rather be food for the COMBINE archive. 
> BUT, it is important to remember that anything can be included as an SBML 
> annotation. So such a metadata file could always be included in an SBML 
> file (e.g. in the annotation of the model element).
> 
> I think we definitively need sessions in COMBINE to discuss that.
> 
> Cheers
> 
> -- 
> Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT
> Tel: +441223496433   Mob:+447833147074   n.l...@gm...
> orcid.org//0000-0002-6309-7327  http://lenoverelab.org/perso/lenov/
> Skype:n.lenovere  twitter:@lenovere  http://nlenov.wordpress.com/
> 
> 
> 
> 
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