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Hi Kieran,

This is a rather interesting issue. Although I'm not convinced by your
examples. I'm sorry, but this is important because there are various
proper solutions to handle this situation, depending on what you are
actually trying to achieve.

> Thanks for your mail, and I appreciate your point. However, the reason behind this would not be to reduce the annotation burden (rather the opposite!)
If that would take more time, so why not just annotating the models of
interest in the first place? Like that, there is no need to invent
anything new and you save time. I don't understand.

> * big model #1 is annotated with bells and whistles, and we create an updated version #2, also fully annotated. Now suppose someone does analysis on 1; the question is how we map these results onto the new network. Ideally, of course, metabolites (say) in each model would be annotated with the same ChEBI. But if we realise that the wrong ChEBI was used (and we don't rely on IDs), then any relationship between the models has been lost.
Why one would update a model (I understand "make it better") and after
that still work on the older version? And, in the case both actions
(update and analysis) were done concurrently, can't you run a similar
analysis on 2 afterwards?

> * we decide to merge two big models #A and #B into one really big "consensus" model #C. A and B are not necessarily well-annotated. We'd like to ask questions like "how many reactions from A are present in C?" but are lacking the mapping needed.
If you are lacking the mapping, nobody will ever be able to answer this
question. This mapping can either be achieved by properly annotating A
and B, or by adding a new kind of annotation in C.
Now the big question is: which one is the easiest/fastest/cheapest?
According to what you said in your first sentence, I'm not sure to
understand why you are trying to come up with a new annotation scheme...

Fundamentally, I still think the best is to annotate the models A and B
instead of annotating (only) C (and if you do annotate A and B, C will
come fully annotated for free). This is for the simple fact that, if
one, later, wants to use A and D for something else, he/she will need to
redo part of the work you already did...

Anyway, for this kind of case, I would suggest you to have a look at the
"comp" extension for SBML L3
(http://sbml.org/Community/Wiki/SBML_Level_3_Proposals/Hierarchical_Model_Composition).


Best regards.

--
Camille Laibe
BioModels.net Coordinator
European Bioinformatics Institute, Cambridge (UK)
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