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initial versions of some tutorials

<h1>Support for Metabolic Reconstructions in the NMPDR</h1>
by Ross Overbeek


The term metabolic reconstruction was created by Evgeni Selkov to
describe his early efforts to predict the metabolic capabilities of
an organism from partially sequenced genomes.  I remember discussing
this concept in some detail at least a year before the first
completely sequenced genome became available (he was working on
analysis of <i>Mycoplasma capricolum</i>, and organism that we thought
might become the first completely sequenced genome).
Since those early days, the concept has taken on a variety of more
specialized meanings.  This was natural, since reconstruction of
metabolic networks was clearly an important topic, and many groups
have begun to address the problem.  In the context of the NMPDR, we
distinguish two versions of metabolic reconstructions: informal
metabolic reconstructions and formal metabolic
<h2>What Is an Informal Metabolic Reconstruction?</h2>

An <b>informal metabolic reconstruction</b>, as we use the term,

the set of pathways present in the organism,
the functional roles of each pathway that can be connected to specific
genes, and
the functional roles that are believed to be present, but which cannot
yet be connected to specific genes.
Within <a href=./1KG.html>The Project to Annotate 1000 Genomes</a>,
the notion of pathway was generalized to <b>subsystem</b>.  Subsystems
can be pathways, but they could also be a collection of functional
roles that implement a nonmetabolic process.  A subsystem is given a
fairly abstract definition -- it is simply a set of functional roles.
Hence, an informal metabolic reconstruction for an organism amounts to
a set of subsystems that are believed to be present (actually, we
specifiy which of several possible <i>variants</i> of each subsystem
is present), the functional roles that make up these subsystems, and
how those functional roles connect to genes.
<h2>A Specific Informal Metabolic Reconstruction</h2>

It is, perhaps, easier if we consider an example: go to the home page
of the NMPDR, click on <b>Subsystem Summary</b>, select an organism
(say, <i>Staphylococcus aureus subsp. aureus MRSA252</i>), and click
on <b>Show Subsystems</b>.  Now look carefully at what is displayed:

There are some main sections headers like <b>Amino Acids and
Derivatives</b>.  Sometimes, there are second-level breakdowns in this
minimal classification such as <b>Alanine, serine, and glycine</b>.
The classification framework at this point is pretty minimal.
Within classification sections, there are subsystems like
<b>Asp-Glu-tRNA(Asn-Gln)_transamidation</b>, and so forth.  Links from
to the routines to display the details of each subsystem can be
followed to see what funcgtional roles are included, who constructed
it, how the genes cluster on different chromosomes, and so forth.
Below the name of each subsystem, we include the genes that have been
connected to roles from the subsystem.  You can explore the individual
genes by taking the provided links.
In the context of the NMPDR, this is what we mean by an informal
metabolic reconstruction.  This basic information becomes the
underlying data from which specific properties of the organism can be
predicted.  One specific goal of gthe NMPDR is to make these informal
metabolic reconstructions as comprehensive as possible.

<h2>What Is a Formal Reconstructions?</h2>

By the term <b>formal metabolic reconstruction</b> we mean a detailed
encoding of the metabolic reaction network.  There are different
possible representations that might be chosen, but they are all
equivalent.  One must represent the reactions that the organism might
support.  For each reaction, one must include the substrates and
products, whether or not the reaction is reversible, the enzymatic
function that catalyzes the reaction, and which proteins in the
organism implement the enzymatic role. 
Again, let us consider an example: go to the home page
of the NMPDR, click on <b>Subsystem Summary</b>, select an organism
(say, <i>Staphylococcus aureus subsp. aureus MRSA252</i>), and click
on <b>Show Reactions</b>.  In this display, you see the reactions, and
by clicking on the link you will be able to go to KEGG for a more
detailed depiction of the reaction.
A formal reconstruction represents the starting point for modeling
efforts.  Our goal at the NMPDR is to make our compilations of
reactions for each organism easily accessible, to maintain links to
KEGG (which offers an excellent encoding of reactions and compounds, as
well as metabolic reconstructions).
It should be noted that our initial offerings represent starting
points that we intend to constantly improve.

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