[BioC] GOTERM in GO.db returns NULL
shidaxia at yahoo.com
Fri Aug 1 22:28:26 CEST 2008
I was using GOTERM in GO.db to get the annotations for the GO terms and a few of them return NULL. But I checked the GO website and using AmiGO, all of them except the last one still exist and have annotations. The last one, according to this (http://fafner.stanford.edu/pipermail/go/2008-January/015594.html), seems to be obsolete. There could be other GO terms like these exist. I'm aware of this could be due to the different version of GO used in the package, but I still want to point out just in case there are other problems.
> GOTERM[["GO:0022904"]] ## respiratory electron transport chain
> GOTERM[["GO:0022900"]] ## electron transport chain
> GOTERM[["GO:GO:0055114"]] ## oxidation reduction
> GOTERM[["GO:0045192"]] ## low-density lipoprotein catabolic process; obsolete?
R version 2.7.0 (2008-04-22)
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:
 tools stats graphics grDevices utils datasets methods base
other attached packages:
 GO.db_2.2.0 AnnotationDbi_1.2.2 RSQLite_0.6-9 DBI_0.2-4 Biobase_2.0.1
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