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Hi Ben,

You're absolutely right to point out the overlap between existing annotations, the Constraint Based models extension, and the approach used by the COBRA Toolbox.

We've recently released a proposal for extending the use of annotations in Level 3:

http://precedings.nature.com/documents/5610/version/1

This extension should cover some of the things that you mentioned (for example, the provenance of who updated what when and why). It's also clear that some things (such as metabolite charge and formula) may be better specified as an annotation rather than dealt with separately in the Constraint Based models extension. Brett and Frank are familiar with the Annotation proposal (in fact, Frank contributed to its development), so between us we should come up with a sensible solution that reduces overlap in each of the proposed packages.

A more difficult question is integration with COBRA. In my experience, the COBRA guys are not necessarily that forthcoming regarding developing and contributing to standardisation efforts. Although, to be fair, I see that a member of the COBRA team will be attending the Harmony meeting in a few weeks, which would be an ideal place to discuss (and rectify) this divergence of formats. Even if the COBRA guys were not that forthcoming, as you suggested, writing a parser to convert from SBML3 <--> COBRA wouldn't be too much of a job - all of the necessary fields are present in Frank and Brett's proposal.

Cheers,

Neil.

Neil Swainston
Experimental Officer

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

On 4 Apr 2011, at 16:51, Ben Heavner wrote:

>
> As an end user of community-curated metabolic reconstructions (and the COBRA toolbox), I would benefit from additional discussion of an issue raised in your proposal - existing annotation methods.
>
> In particular, what is the best way to add additional annotation to such reconstructions? Are there any aspects of such annotation that are unique to Constraint Based models?
>
> Models I've used would benefit from much more annotation - for example, literature references for each species and reaction, or a history of their review and addition to reconstructions (ie, who looked at it, when, and why was it added?).
>
> As computational approaches to evaluating constraint based models advance (or regulatory networks are developed for use with metabolic networks), it seems likely that there will be increasing demand for other forms of annotation.
>
> As you've noted in your proposal, the existing COBRA approach is to create a unique SBML dialect that depends on specific entities in the <notes> element. COBRA will need significant code revision to deal with different approaches to annotation. Or, it will require a translator from standard SBML to COBRA-SBML. Now that COBRA is on sourceforge, creating and disseminating such software may be more feasible, if there is interest.
>
> It seems that a fork between SBML and COBRA-SBML has already happened. It would be great if COBRA and SBML3 could get back on the same page. Perhaps this extension can facilitate that?
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