[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
More information about the Bioconductor
mailing list