ADDITIONAL NOTES ON THE METAB MODELS
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This should be read in conjunction with Takako Igarashi's notes
on producing Pathway diagrams from the METAB modules.

Caenorhabditis elegans metabolism models came from the original soybean
metabolic database, but now soybean models (courtesy of David Grant)
have diverged from worm; although the soybean changes are mainly cosmetic
and give much more detailed information in the text windows.
Takako Igarashi's models for the human signalling pathways
differ from both and have necessitated quite a few changes in the code.
The code versions 4_3 and 4_5 available from Sanger Centre and NCBI
do not support all the things mentioned by Takako, although it
is anticipated that her changes and additions will be merged into
the public code release sometime.

The ?Metabolite class of worm and soybean has been renamed to ?Molecule,
for the signalling pathways. In the latter, steps in a pathway
have been explicitly called ?Step whereas in the worm and soybean
both steps and groups of steps are called ?Pathway. The PathwayDiagram
model uses only these ?Steps in signalling pathways but in the other
two its uses ?Pathway (or in the case of soybean, Reaction_or_Pathway). Again
the signalling PathwayDiagram uses ?Molecule instead of ?Metabolite.
Other tag_names have been changed, such as the replacement of Major_Product
by To_molecule and Major_Reactant has become From_molecule. These latter
changes make the Tag_names more general.

Although it is true that one can change a diagram and save the diagram
by quitting the window on the drop-down menu one can't look at the
saved example of the class PathwayDiagram, since this Class
has been removed from the list available on the arrow on the Class window.

One can't add enzyme to the diagram in worm and soybean
databases because the Tag Enzyme in ?Pathway does not have class 
?Process  mentioned  by Takako. The label for each step on the diagram is
taken from the object name of the Pathway (in this case a step).

Maybe, a change in several places to a TAG2 system for
reactants, products and labels would give a more flexible model set
which could be applied to metabolic, signalling and genetic pathways
in the future.


Sylvia Martinelli