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Wed Jul 27 15:46:25 2005 UTC (14 years, 5 months ago) by overbeek
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add evidence codes to protein.cgi

<h1>An Explanation of the SEED Evidence Codes</h1>

Within the SEED, we use evidence codes to reflect significant factors
that go into making assignments of function.  Some of these codes are
computed and reflect information that we consider particularly
useful.  Others are used to reflect experimental evidence of function.

<h2>icw(n): in cluster with</h2>

This code indicates that the PEG occurs in a cluster with <i>n</i>
other genes from the same subsystem (very strong evidence).

<h2>isu: in subsystem unique -- the only entry in a subsystem cell</h2>

This code indicates that the PEG occurs in a subsystem, and it is the
only PEG for that genome that has been assigned the functional role
(i.e., the cell in the spreadsheet contains a single entry).  This
means that, if you wish to change an annotation, you should discuss it
with the owner of the subsystem.

<h2>isd(n): in subsystem duplicates</h2>

This code indicates that the PEG occurs in a subsystem, but it is 
in a cell of the spreadsheet containing duplicates (and it is not
clustered with other genes connected to the same subsystem).
In this case, you may make a change without notifying the owner of the
subsystem, since you are probably disambuating the situation to his

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