Re: Proposed addition to L3 core
09 Sep '09 14:52
> But, the purpose of species type (and indeed a group in the
> current draft groups proposal) is merely to associate an
> additional identifier with each species object.
What Robert mentioned earlier is that what we call "species" should be
called "pool" because it is a specific subset of a chemical species in a
model. What we now call species type is actually what the chemical species
is. Our current practice is to add all unique chemical species as species
types and annotate these with the appropriate MIRIAM rdf that points to the
authoritative database entry for that chemical species. After this, we can
infer that some "species" is also of that composition (because it is tagged
with that species type).
> This identifier (the identifier of the type) does not itself
> carry semantics.
Indeed, but it can be added with <annotation> and at that point it allows us
to find out which "species" are of this chemical nature. (BTW this same
mechanism could be used to group cell types too, etc. as long as the
<annotation> is to the appropriate URN). Also, an SBO term can be added to
indicate that this is a "simple molecule" (another problematic label, but I
won't go there), or a protein, or a cell type (if/when we create the
appropriate SBO term for that), etc. etc.
> The semantics can only be associated with the type by virtue of connections
that the type object migh have to other resources.
The connections created by speciesType (or groups) are important as they carry
the semantic meaning that these entities all have something in common. The
something in common is what is pointed by the MIRIAM annotation on the
I am not prescribing this use to everyone; but I am proposing that this is a
mechanism that allows us to unequivocally indentify things with their correct
semantics (through MIRIAM), and then indicate which other entities are
special cases of them. This may not be ideal or elegant, but it works right
now with SBML L2 and it will stop working with L3core.
Prof. Pedro Mendes
EPSRC Chair in Computational Systems Biology
University of Manchester
School of Computer Science
Manchester Centre for Integrative Systems Biology
131 Princess St., Manchester, M1 7DN, UK
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