GOTERM in GO.db returns NULL
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Shi, Tao ▴ 720
@shi-tao-199
Last seen 7.1 years ago
Hi list, 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. ...Tao > GOTERM[["GO:0022904"]] ## respiratory electron transport chain NULL > GOTERM[["GO:0022900"]] ## electron transport chain NULL > GOTERM[["GO:GO:0055114"]] ## oxidation reduction NULL > GOTERM[["GO:0045192"]] ## low-density lipoprotein catabolic process; obsolete? NULL > > sessionInfo() R version 2.7.0 (2008-04-22) 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] tools stats graphics grDevices utils datasets methods base other attached packages: [1] 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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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 6.0 years ago
United States
Hi Shi, I can confirm that this is just because GO is continuously changing, and because our last snapshot of it was in the Spring. GO will be updated very soon (for the fall release). As always, thanks for letting me know about any possible issues that crop up. Marc Shi, Tao wrote: > Hi list, > > 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. > > ...Tao > > > >> GOTERM[["GO:0022904"]] ## respiratory electron transport chain >> > NULL > >> GOTERM[["GO:0022900"]] ## electron transport chain >> > NULL > >> GOTERM[["GO:GO:0055114"]] ## oxidation reduction >> > NULL > >> GOTERM[["GO:0045192"]] ## low-density lipoprotein catabolic process; obsolete? >> > NULL > >> sessionInfo() >> > R version 2.7.0 (2008-04-22) > 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] tools stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GO.db_2.2.0 AnnotationDbi_1.2.2 RSQLite_0.6-9 DBI_0.2-4 Biobase_2.0.1 > > _______________________________________________ > 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 >
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