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<h1>What Is Meant by a SEED Function?</h1>

A <i>functional role</i> is a basic, undefined concept meaning roughly
"an atomic role that could be played by a gene".  Sorry.
A <i>function</i> or alternatively a <i>gene function</i> expresses
the connection between a PEG and one or more functional roles.  In
addition, we have grafted on the ability to attach key-value pairs to
a function; these are thought of as attributes of the gene.
In this document, we formulate a set of conventions that we will try
to use consistently.  In some cases, we have historically already
violated these conventions, but not too seriously (we hope).
<h2>The Case of a Multi-domain, Multifunctional Gene</h2>
When a gene has a sequence of domains that play distinct functional
roles, we express the function of the gene as
<br> <pre>
     Role1 / Role2 / ... / RoleN
That is, we use " / " as an operator separating distinct functional
roles.  Note that the slash must have spaces on both sides.  This
seems to be a common usage that we have noticed in both Swissprot and
UniProt functions.
<h2>The Case of a Single Domain Playing Multiple Roles</h2>
In many cases we have a gene that has a broad specificity. and we
think of the gene as multifunctional.  In this case, we use
<br> <pre>
     Role1 @ Role2 @ ... @ RoleN
That is, we use " @ " as an operator separating distinct functional
roles.  Note that the "@" must have spaces on both sides.
<h2>The Case of an Ambiguous Function</h2>
Consider a gene that is believed to be either a malate dehydrogenase
or a lactate dehydrogenase, or maybe both.  In this case we need to
express <i>this gene is one of these functions, but I cannot
disambiguate them</i>.  To express this, we use
<br> <pre>
     Role1; Role2; ...; RoleN
Note that we require a space following the semi-colon, but not preceeding
it.  The distinction between the use of " @ " and "; " is that with
the former we are asserting the presence of all of the functional
roles; with the semicolon we are simply saying that any of the
functional roles may or may not be present (a much weaker notion).

<h2>Attaching Key-Value Pairs in the Expression of Function</h2>

Consider the case in which we have a gene that includes an intein.  To
be concrete, let's talk about
<br> <pre>
     Translation initiation factor B ! intein-containing
Using " ! " allows one to attach a key-value pair to the feature.
When discussing boolean key-value pairs, we allow ommision of the
value (thus, <i>intein-containing</i> is thought of as a key
expressing a boolean condition; when it is used, it means "this gene
is <i>intein-containing</i>".  Technically, when the value is omitted,
it defaults to 1.
When you actually want to append a key-value pair with a value other
than 1, use a " ^ " to separate the key and value.  Thus,
<br> <pre>
     Translation initiation factor C ! intein-containing ^ 3
attaches the key-value pair <i>(intein-containing,3)</i> to the gene
for which the function is being asserted.  The SEED includes other
mechanisms for attaching key-value pairs to features (adding key-value
pairs to files in the <i>Attributes</i> subdirectory), but these are not easily
used by annotators; they are for making "batch" assertions.
This mechanism is used solely as a convenience for inputting key-value
pairs.  When the function of the gene is displayed, it will not
include the list of pairs.  By convention, the <i>protein page</i>
used for displaying genes gives the attached key-value pairs as a
separate part of the display.  These key-value pairs can be used to
express attributes like essentiality, virulence, expression values,
and so forth.
<b>Technical Note: </b>
the assertion of key-value pairs in gene functions overrides the
"batch sources".  That is, a key has at most one value for a given
PEG, and that value will come from the assigned_functions file, if
present.  Finally, the use of
<br> <pre>
     Role ! K ^
has the effect of removing the key-value pair with a key of <i>K</i>.

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