Using GO 1.6.5 the following code produces a list of GO terms that are annotated as being connected with a certain LL id, but have their "Ontology" slot listed as "NA" (presumably because they are missing from GOTERM and the other GO* objects): library(GO) ll2go <- as.list.environment(GOLOCUSID2GO) tmp <- lapply(ll2go, function (x) sapply(x, function(x) ifis.na(x$Ontology)){ print(x$GOID) })) Perhaps a more recent file was used to build GOLOCUSID2GO than was used to build the remaining GO annotations? Jeff. (Here's the list of missing terms) GO:0001880 GO:0001881 GO:0001883 GO:0001886 GO:0030968 GO:0030970 GO:0030971 GO:0035199 GO:0035211 GO:0035214 GO:0035215 GO:0035224 GO:0035226 GO:0035227 GO:0035229 GO:0035232 GO:0035233 GO:0035234 GO:0043185 GO:0043190 GO:0043197 GO:0043198 GO:0048488 GO:0048489 GO:0051082 GO:0051087 GO:0051089 GO:0051092 GO:0051097 GO:0051101 GO:0051106

Funny you should ask... yes we just noticed this. It seems to be a problem somewhere in the data we obtained. It is most likely that we will drop these - they can often be hand curated, but hands are the one thing we are very short of...so anyone looking for something constructive to do...we have lots of basic mundane things (on which more excting and less mundane things can be built) that are not getting done. Robert On Wed, Oct 27, 2004 at 01:36:18PM -0700, jeffrey rasmussen wrote: > Using GO 1.6.5 the following code produces a list of GO terms that are > annotated as being connected with a certain LL id, but have their > "Ontology" slot listed as "NA" (presumably because they are missing from > GOTERM and the other GO* objects): > > library(GO) > ll2go <- as.list.environment(GOLOCUSID2GO) > tmp <- lapply(ll2go, function (x) sapply(x, function(x) > ifis.na(x$Ontology)){ print(x$GOID) })) > > Perhaps a more recent file was used to build GOLOCUSID2GO than was used to > build the remaining GO annotations? > > Jeff. > > (Here's the list of missing terms) > > GO:0001880 > GO:0001881 > GO:0001883 > GO:0001886 > GO:0030968 > GO:0030970 > GO:0030971 > GO:0035199 > GO:0035211 > GO:0035214 > GO:0035215 > GO:0035224 > GO:0035226 > GO:0035227 > GO:0035229 > GO:0035232 > GO:0035233 > GO:0035234 > GO:0043185 > GO:0043190 > GO:0043197 > GO:0043198 > GO:0048488 > GO:0048489 > GO:0051082 > GO:0051087 > GO:0051089 > GO:0051092 > GO:0051097 > GO:0051101 > GO:0051106 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+