[BioC] GO evidence codes in org.Xx.egGO

Peter Langfelder peter.langfelder at gmail.com
Fri May 3 05:47:44 CEST 2013


Hello,

the help information for org.Xx.egGO appears to be incomplete - the help says

The Evidence element contains a code indicating what kind of
     evidence supports the association of the GO identifier to the
     Entrez Gene id. The evidence codes in use include:

     IMP: inferred from mutant phenotype
     IGI: inferred from genetic interaction
     IPI: inferred from physical interaction
     ISS: inferred from sequence similarity
     IDA: inferred from direct assay
     IEP: inferred from expression pattern
     IEA: inferred from electronic annotation
     TAS: traceable author statement
     NAS: non-traceable author statement
     ND: no biological data available
     IC: inferred by curator

According to the GO web site at
http://www.geneontology.org/GO.evidence.shtml, there are many more
codes (22, to be precise). It would be great if the codes could be
listed in the help file, or at least if the help explicitly said that
this is not the full listing of possible codes and referred the reader
the web site for more details.

Incidentally, the help for GO[BP,CC,MF]OFFSPRING also contains a typo: it says

    The format is an R object mapping the GO MF terms to all offspring
     terms, where an ancestor term is a more specific GO term that is
     preceded by the given GO term in the DAG (in other words, the
     children and all their children, etc.).

The word "ancestors" should be replaced by "offspring".

Thanks,

Peter



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