An Explanation of the SEED Evidence Codes

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.

icw(n): in cluster with

This code indicates that the PEG occurs in a cluster with n other genes from the same subsystem (very strong evidence). There may be several of these for a PEG (up to one for each subsystem the PEG occurs in).

isu: in subsystem unique -- the only entry in a subsystem cell

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.

idu(n): in subsystem duplicates

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 benefit.

IDA: Inferred from Direct Assay

Curators should read what the GO group mean by this (http://www.geneontology.org/GO.evidence.shtml), but since we are not yet consistently adopting the GO ontology, we will take this to mean a direct assay establishing the functional role or roles we assign.

IGI: Inferred from Genetic Interaction

Please refer to the GO site to get a detailed discussion of how they would like this used (and then use your best judgement).

TAS: traceable author statement

Please refer to the GO site to get a detailed discussion of how they would like this used (and then use your best judgement).