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1 : overbeek 1.1 <h1>An Explanation of the SEED Evidence Codes</h1>
2 :    
3 :     Within the SEED, we use evidence codes to reflect significant factors
4 :     that go into making assignments of function. Some of these codes are
5 :     computed and reflect information that we consider particularly
6 :     useful. Others are used to reflect experimental evidence of function.
7 :    
8 :     <h2>icw(n): in cluster with</h2>
9 :    
10 :     This code indicates that the PEG occurs in a cluster with <i>n</i>
11 : overbeek 1.2 other genes from the same subsystem (very strong evidence). There may
12 :     be several of these for a PEG (up to one for each subsystem the PEG
13 :     occurs in).
14 : overbeek 1.1
15 :     <h2>isu: in subsystem unique -- the only entry in a subsystem cell</h2>
16 :    
17 :     This code indicates that the PEG occurs in a subsystem, and it is the
18 :     only PEG for that genome that has been assigned the functional role
19 :     (i.e., the cell in the spreadsheet contains a single entry). This
20 :     means that, if you wish to change an annotation, you should discuss it
21 :     with the owner of the subsystem.
22 :    
23 : overbeek 1.3 <h2>idu(n): in subsystem duplicates</h2>
24 : overbeek 1.1
25 :     This code indicates that the PEG occurs in a subsystem, but it is
26 :     in a cell of the spreadsheet containing duplicates (and it is not
27 :     clustered with other genes connected to the same subsystem).
28 :     In this case, you may make a change without notifying the owner of the
29 :     subsystem, since you are probably disambuating the situation to his
30 :     benefit.
31 : overbeek 1.3
32 :     <h2>IDA: Inferred from Direct Assay</h2>
33 :    
34 :     Curators should read what the GO group mean by this (http://www.geneontology.org/GO.evidence.shtml), but since
35 :     we are not yet consistently adopting the GO ontology, we will take this to mean
36 :     a direct assay establishing the functional role or roles we assign.
37 :    
38 :     <h2>IGI: Inferred from Genetic Interaction</h2>
39 :    
40 : overbeek 1.4 Please refer to the <a href="http://www.geneontology.org/GO.evidence.shtml">GO site</a> to get a detailed discussion
41 : overbeek 1.3 of how they would like this used (and then use your best judgement).
42 :    
43 :     <h2> TAS: traceable author statement </h2>
44 :    
45 : overbeek 1.4 Please refer to the <a href="http://www.geneontology.org/GO.evidence.shtml">GO site</a> to get a detailed discussion
46 : overbeek 1.3 of how they would like this used (and then use your best judgement).
47 :    

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