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

[Marc Carlson]

Thanks for the feedback Peter.  I have updated the affected manual page 
templates so that future manual pages can be a little clearer.

   Marc


On 05/02/2013 08:47 PM, Peter Langfelder wrote:
> 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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