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Dear Colleague,

We wish to follow up on an issue that was raised at the COMBINE meeting in
Edinburgh, 2010. For reference, you can view the slides here:
http://sbml.org/images/c/c5/Juty_combine_SBO_2010-10-07.pdf

Current SBO status:
SBO is currently composed of 6 branches. (We are aware of the problems with
the names of some of these, and will send a message soon regarding the issue).

* entity: An object of reality whose evolution is modeled or represented

* interaction: An event or a relationship involving entities

* participant role: A role played by an entity in an interaction

* mathematical expression: A construct used to assign a value to a variable
or the evolution of a variable

* quantitative parameter: A parameter used in a mathematical expression

* modeling framework: A reference framework in which to interpret a model


Summary of the issue:
The current SBO structure is used to describe the *data* components of a
model, pathway, etc. But some of the constructs in the formats using SBO
are meant to encode/represent elements of the *metadata*. For instance,
there are no SBO terms corresponding to SBML 'notes', SBML 'annotation',
SBGN 'annotation', 'unit of information', etc.


Proposal:
We believe that these metadata concepts cannot be incorporated in any of
the existing SBO branches, and therefore propose the addition of a new
branch to SBO, aimed at dealing with such peripheral, but increasingly
important, information.

We welcome your feedback at this stage, and will communicate back any
consensus opinion.

Sincerely,

SBO Team
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