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Currently, a large number of repository models place "definitional
mathematics"(i.e. mathematical definitions which may be useful to understand
the model, but are not strictly part of the model) in the mathematics, inside
MathML inside the component. This means that tools cannot distinguish between
such definitional equations and the equations that actually form part of the
model.

Therefore, I am proposing that definitional mathematics be moved into the
metadata, and that elements be added to a future version of the cmeta
specification that allows for definitions similar to the following:

<rdf:Description rdf:about="#component_element_id">
<cmeta:definitions rdf:parseType="Resource">
<rdf:Bag>
<rd:li rdf:parseType="Resource">
<cmeta:variable name="x" reference="#another_variable_element_id" />
<cmeta:variable name="y" reference="#another_variable_element_id" />
<cmeta:variable name="z" reference="#yet_another_variable_element_id"
/>
<mathml:math>
<eq/>
<ci> x </ci>
<apply>
<plus/>
<ci> y </ci>
<ci> z </ci>
</apply>
</mathml:math>
</rdf:li>
</rdf:Bag>
</cmeta:definition>
</rdf:Description>

Please let me know if you can think of a better way to handle this, or if you
have any comments.

Best regards,
Andrew Miller


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>From matt.halstead at auckland.ac.nz Mon May 2 13:28:11 2005
From: matt.halstead at auckland.ac.nz (Matt Halstead)
Date: Mon May 2 13:30:59 2005
Subject: [cellml-discussion] Definitional mathematics in metadata
In-Reply-To:
<1114994395.427576db34879 AT www.bioeng.auckland.ac.nz>
References:
<1114994395.427576db34879 AT www.bioeng.auckland.ac.nz>
Message-ID:
<af78fd5e352de44006fa0c9d2a1e3ba8 AT auckland.ac.nz>

Well, I think some people might argue that it is part of the model,
since the model simply reflects what is described in a publication and
not necessarily a particular part of that which is useful for
simulation. Your argument is that they detract from the parts that can
be used for simulation, or that they make it difficult to actually
build simulations?

Also, apart from some rdf errors, such as cmeta:definitions should be
a property not a resource, having a chunk of mathml inside RDF is not
valid RDF.

I think you need to propose something a bit more detailed on what
constitutes definitional mathematics and why it needs to be moved out
of a particular model definition. It may or may not suit metadata, but
we should postpone the syntax for representing that.


On 2/05/2005, at 12:39 PM, Andrew Miller wrote:

> Currently, a large number of repository models place "definitional
> mathematics"(i.e. mathematical definitions which may be useful to
> understand
> the model, but are not strictly part of the model) in the mathematics,
> inside
> MathML inside the component. This means that tools cannot distinguish
> between
> such definitional equations and the equations that actually form part
> of the
> model.
>
> Therefore, I am proposing that definitional mathematics be moved into
> the
> metadata, and that elements be added to a future version of the cmeta
> specification that allows for definitions similar to the following:
>
> <rdf:Description rdf:about="#component_element_id">
> <cmeta:definitions rdf:parseType="Resource">
> <rdf:Bag>
> <rd:li rdf:parseType="Resource">
> <cmeta:variable name="x"
> reference="#another_variable_element_id" />
> <cmeta:variable name="y"
> reference="#another_variable_element_id" />
> <cmeta:variable name="z"
> reference="#yet_another_variable_element_id" />
> <mathml:math>
> <eq/>
> <ci> x </ci>
> <apply>
> <plus/>
> <ci> y </ci>
> <ci> z </ci>
> </apply>
> </mathml:math>
> </rdf:li>
> </rdf:Bag>
> </cmeta:definition>
> </rdf:Description>
>
> Please let me know if you can think of a better way to handle this, or
> if you
> have any comments.
>
> Best regards,
> Andrew Miller
>
>
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> cellml-discussion AT cellml.org
> http://www.cellml.org/mailman/listinfo/cellml-discussion

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• [cellml-discussion] Definitional mathematics in metadata, Andrew Miller, 05/02/2005
  • [cellml-discussion] Definitional mathematics in metadata, Warren Hedley, 05/04/2005
    • RE: [cellml-discussion] Definitional mathematics in metadata, Alan Garny, 05/04/2005

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