Just to clarify, I did not mean to imply that we are not accurate. A better choice of words might be to say that we are slightly less current (updating twice a year instead of continuously). But that this is a deliberate decision which allows us to have annotations that are versioned, synchronized relative to each other, and time-stamped. In turn, this trade-off should aid in making research more reproducible. Marc Marc Carlson wrote: > Hi Tim, > > I suspect that you are not doing anything wrong. GO changes > frequently. And this term is simply not present in the GO package that > is online right now. The GO.db package is a snapshot of GO that matches > the GO to gene mappings from the other .db packages that were also made > at the same time. So to update it, I actually have to update all of the > packages so that everything will be in sync. And we actually do this at > least twice a year (with each release of Bioconductor). Amigo is a web > based platform and so that should usually be more current. Whether or > not that is an improvement over what we do depends on whether you want > to place more emphasis on reproducibility or accuracy. > > > Marc > > > > > > Tim Smith wrote: > >> Hi, >> >> I was trying a simple lookup - essentially looking up the Terms for specific GO IDs (GO:0048663 & GO:0060579). I reporduce the code and error I get: >> >> >>> library("GO.db") >>> Term(GOTERM[["GO:0048663"]]) >>> >>> >> [1] "neuron fate commitment" >> >> >>> Term(GOTERM[["GO:0060579"]]) >>> >>> >> Error in function (classes, fdef, mtable) : >> unable to find an inherited method for function "Term", for signature "NULL" >> I checked in AmiGO and both the terms are listed. Am I doing something wrong? >> thanks! >> PS: My sessionInfo is: >> --------------------------------------- >> >> >> >>> sessionInfo() >>> >>> >> R version 2.9.1 (2009-06-26) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] biomaRt_2.0.0 GO.db_2.2.11 GOstats_2.10.0 >> [4] graph_1.22.2 Category_2.10.1 org.Hs.eg.db_2.2.11 >> [7] RSQLite_0.7-1 DBI_0.2-4 AnnotationDbi_1.6.1 >> [10] Biobase_2.4.1 >> >> loaded via a namespace (and not attached): >> [1] annotate_1.22.0 genefilter_1.24.2 GSEABase_1.6.1 RBGL_1.20.0 >> [5] RCurl_0.98-1 splines_2.9.1 survival_2.35-4 tools_2.9.1 >> [9] XML_2.5-3 xtable_1..5-5 >> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >