Parent Directory
| 
Revision Log
Revision 1.4 - (view) (download) (as text)
| 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 : |
| MCS Webmaster | ViewVC Help |
| Powered by ViewVC 1.0.3 |