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On Mon, 2011-04-04 at 08:51 -0700, 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.

Hi Ben, thanks for your email you raise some important issues.

> 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?

While many of the annotations can be addressed using e.g. MIRIAM
resources (species, reactions) the thorny issue, at the moment, is the
concept of COBRA style GENE ASSOCIATION. There are different ways of
addressing this, depending on your point of view. Ours is one, while
this thread has most other points of view expressed at some point.

> 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?).

I'm not an expert in this, but as far as I am aware people are looking
to address this in a more general way. At the moment we don't consider
this, but it would definitely be a future consideration.

> 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.

As far as general annotation goes, yes, translation and initial
annotation is difficult and I'm certain there is an interest in
developing tools for this. The rest of the model structure (bounds,
objective function etc) is relatively easy to implement/translate.

> 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?

Absolutely, forking is to be avoided at all costs. In my opinion, as new
tools are developed that allow for the faster reconstruction of genome
scale models, the situation is only intensifying.

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--
Dr Brett G. Olivier
Researcher in Computational Systems Biology

Life Sciences
Centrum voor Wiskunde en Informatica (CWI), Amsterdam


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