Error GO.db package "term is not member of any ontology"
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Ana Conesa ▴ 340
@ana-conesa-2156
Last seen 10.3 years ago
Dear all, I am working with the package GO.db (version 2.3.5) to retrieve information from GO terms and I find a large number of my GO IDs that apparently are not in the database, i.e. I get the following error: Error in getGOParents(x) : GO:0090153 is not a member of any ontology But this term can be found at the Amigo site as "regulation of sphingolipid biosynthetic process". And there are many more in this situation. I is this a problem of GO database versions?. How could I find within R these l"lost" terms? Thank you in advance Ana -- Ana Conesa Bioinformatics and Genomics Department Centro de Investigaciones Principe Felipe Avda. Autopista Saler 16, 46012 Valencia, Spain Phone: +34 96 328 96 80 Fax: +34 96 328 97 01 http://bioinfo.cipf.es/aconesa http://www.blast2go.org
GO GO • 1.9k views
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@sean-davis-490
Last seen 4 months ago
United States
On Fri, Apr 9, 2010 at 8:50 AM, Ana Conesa <aconesa at="" cipf.es=""> wrote: > Dear all, > > I am working with the package GO.db (version 2.3.5) to retrieve information > from GO terms and I find a large number of my GO IDs that apparently are not > in the database, i.e. I get the following error: > > Error in getGOParents(x) : GO:0090153 is not a member of any ontology > > But this term can be found at the Amigo site as "regulation of sphingolipid > biosynthetic process". And there are many more in this situation. I > > is this a problem of GO database versions?. How could I find within R these > l"lost" terms? Hi, Ana. You'll probably need to provide a reproducible example and the output of sessionInfo() to get direct help. However, this works fine for me: > library(GO.db) > get('GO0090153',GOTERM) GOID: GO:0090153 Term: regulation of sphingolipid biosynthetic process Ontology: BP Definition: Any process that modulates the rate, frequency or extent of sphingolipid biosynthesis. Sphingolipid biosynthesis is the chemical reactions and pathways resulting in the formation of sphingolipids, any of a class of lipids containing the long-chain amine diol sphingosine or a closely related base (a sphingoid). > sessionInfo() R version 2.11.0 Under development (unstable) (2009-11-13 r50424) i386-apple-darwin10.2.0 locale: [1] en_US/en_US/C/C/en_US/en_US attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] GO.db_2.4.1 RSQLite_0.8-4 DBI_0.2-5 [4] AnnotationDbi_1.9.8 Biobase_2.7.3 Sean
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Thanks Sean for your fast reply This is my sessionInfo() > sessionInfo() R version 2.10.0 (2009-10-26) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GO.db_2.3.5 RSQLite_0.7-1 DBI_0.2-4 [4] annotate_1.24.1 AnnotationDbi_1.8.2 Biobase_2.6.1 loaded via a namespace (and not attached): [1] xtable_1.5-5 > get('GO0090153',GOTERM) Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : value for "GO0090153" not found > Any hint? Ana On Friday 09 April 2010 15:03:20 Sean Davis wrote: > get('GO0090153',GOTERM) -- Ana Conesa Bioinformatics and Genomics Department Centro de Investigaciones Principe Felipe Avda. Autopista Saler 16, 46012 Valencia, Spain Phone: +34 96 328 96 80 Fax: +34 96 328 97 01 http://bioinfo.cipf.es/aconesa http://www.blast2go.org ========================================== FIRST INTERNATIONAL COURSE IN AUTOMATED FUNCTIONAL ANNOTATION AND DATA MINING Valencia/Orlando, September/October 2009 http://bioinfo.cipf.es/blast2gocourse
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What is the exact command you are running that generates the error? Present it in a way that another person not using your computer can generate it. On Fri, Apr 9, 2010 at 9:17 AM, Ana Conesa <aconesa@cipf.es> wrote: > Thanks Sean for your fast reply > > This is my sessionInfo() > > > > sessionInfo() > R version 2.10.0 (2009-10-26) > x86_64-pc-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GO.db_2.3.5 RSQLite_0.7-1 DBI_0.2-4 > [4] annotate_1.24.1 AnnotationDbi_1.8.2 Biobase_2.6.1 > > loaded via a namespace (and not attached): > [1] xtable_1.5-5 > > get('GO0090153',GOTERM) > Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : > value for "GO0090153" not found > > > > > Any hint? > > Ana > > > > On Friday 09 April 2010 15:03:20 Sean Davis wrote: > > get('GO0090153',GOTERM) > > > > -- > Ana Conesa > Bioinformatics and Genomics Department > Centro de Investigaciones Principe Felipe > Avda. Autopista Saler 16, > 46012 Valencia, Spain > Phone: +34 96 328 96 80 > Fax: +34 96 328 97 01 > http://bioinfo.cipf.es/aconesa > http://www.blast2go.org > ========================================== > FIRST INTERNATIONAL COURSE IN AUTOMATED > FUNCTIONAL ANNOTATION AND DATA MINING > Valencia/Orlando, September/October 2009 > http://bioinfo.cipf.es/blast2gocourse > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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I think she gives the command below. There is a problem with the form of the call to get(); the keys are of the form GO:0090153, while the key used is missing the colon. So even if the term did exist in the GO.db package, it wouldn't be found using that key. However, I think the real reason this term isn't found is that it is a new term, added after the current version of the GO.db was produced. If you look at the term information on the AmiGO website, the source is stated to be ascb_2009. Since the GO.db package is now 6 months out of date, I wouldn't be surprised if this term were added after we built this package last. Best, Jim Vincent Carey wrote: > What is the exact command you are running that generates the error? Present > it in a way that another person not using your computer can generate it. > > On Fri, Apr 9, 2010 at 9:17 AM, Ana Conesa <aconesa at="" cipf.es=""> wrote: > >> Thanks Sean for your fast reply >> >> This is my sessionInfo() >> >> >>> sessionInfo() >> R version 2.10.0 (2009-10-26) >> x86_64-pc-linux-gnu >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] GO.db_2.3.5 RSQLite_0.7-1 DBI_0.2-4 >> [4] annotate_1.24.1 AnnotationDbi_1.8.2 Biobase_2.6.1 >> >> loaded via a namespace (and not attached): >> [1] xtable_1.5-5 >>> get('GO0090153',GOTERM) >> Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : >> value for "GO0090153" not found >> >> Any hint? >> >> Ana >> >> >> >> On Friday 09 April 2010 15:03:20 Sean Davis wrote: >>> get('GO0090153',GOTERM) >> >> >> -- >> Ana Conesa >> Bioinformatics and Genomics Department >> Centro de Investigaciones Principe Felipe >> Avda. Autopista Saler 16, >> 46012 Valencia, Spain >> Phone: +34 96 328 96 80 >> Fax: +34 96 328 97 01 >> http://bioinfo.cipf.es/aconesa >> http://www.blast2go.org >> ========================================== >> FIRST INTERNATIONAL COURSE IN AUTOMATED >> FUNCTIONAL ANNOTATION AND DATA MINING >> Valencia/Orlando, September/October 2009 >> http://bioinfo.cipf.es/blast2gocourse >> >> _______________________________________________ >> 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 >> > > [[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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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Dear Jim and Vicent, Yes, I guess this is the thing. I was wondering if there was a more up-to-date GO.db package... If case you find it interesting, I found around 200 terms not present in the current GO.db... (see attached) Thanks again Ana On Friday 09 April 2010 17:19:25 James W. MacDonald wrote: > I think she gives the command below. > > There is a problem with the form of the call to get(); the keys are of > the form GO:0090153, while the key used is missing the colon. So even if > the term did exist in the GO.db package, it wouldn't be found using that > key. > > However, I think the real reason this term isn't found is that it is a > new term, added after the current version of the GO.db was produced. > > If you look at the term information on the AmiGO website, the source is > stated to be ascb_2009. Since the GO.db package is now 6 months out of > date, I wouldn't be surprised if this term were added after we built > this package last. > > Best, > > Jim > > Vincent Carey wrote: > > What is the exact command you are running that generates the error? > > Present it in a way that another person not using your computer can > > generate it. > > > > On Fri, Apr 9, 2010 at 9:17 AM, Ana Conesa <aconesa at="" cipf.es=""> wrote: > >> Thanks Sean for your fast reply > >> > >> This is my sessionInfo() > >> > >>> sessionInfo() > >> > >> R version 2.10.0 (2009-10-26) > >> x86_64-pc-linux-gnu > >> > >> locale: > >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > >> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > >> [9] LC_ADDRESS=C LC_TELEPHONE=C > >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > >> > >> attached base packages: > >> [1] stats graphics grDevices utils datasets methods base > >> > >> other attached packages: > >> [1] GO.db_2.3.5 RSQLite_0.7-1 DBI_0.2-4 > >> [4] annotate_1.24.1 AnnotationDbi_1.8.2 Biobase_2.6.1 > >> > >> loaded via a namespace (and not attached): > >> [1] xtable_1.5-5 > >> > >>> get('GO0090153',GOTERM) > >> > >> Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : > >> value for "GO0090153" not found > >> > >> Any hint? > >> > >> Ana > >> > >> On Friday 09 April 2010 15:03:20 Sean Davis wrote: > >>> get('GO0090153',GOTERM) > >> > >> -- > >> Ana Conesa > >> Bioinformatics and Genomics Department > >> Centro de Investigaciones Principe Felipe > >> Avda. Autopista Saler 16, > >> 46012 Valencia, Spain > >> Phone: +34 96 328 96 80 > >> Fax: +34 96 328 97 01 > >> http://bioinfo.cipf.es/aconesa > >> http://www.blast2go.org > >> ========================================== > >> FIRST INTERNATIONAL COURSE IN AUTOMATED > >> FUNCTIONAL ANNOTATION AND DATA MINING > >> Valencia/Orlando, September/October 2009 > >> http://bioinfo.cipf.es/blast2gocourse > >> > >> _______________________________________________ > >> 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 > > > > [[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 -- Ana Conesa Bioinformatics and Genomics Department Centro de Investigaciones Principe Felipe Avda. Autopista Saler 16, 46012 Valencia, Spain Phone: +34 96 328 96 80 Fax: +34 96 328 97 01 http://bioinfo.cipf.es/aconesa http://www.blast2go.org ========================================== FIRST INTERNATIONAL COURSE IN AUTOMATED FUNCTIONAL ANNOTATION AND DATA MINING Valencia/Orlando, September/October 2009 http://bioinfo.cipf.es/blast2gocourse ========================================== -------------- next part -------------- Error in getGOParents(x) : GO:0004299 is not a member of any ontology Error in getGOParents(x) : GO:0005837 is not a member of any ontology Error in getGOParents(x) : GO:0008575 is not a member of any ontology Error in getGOParents(x) : GO:0030693 is not a member of any ontology Error in getGOParents(x) : GO:0044281 is not a member of any ontology Error in getGOParents(x) : GO:0006803 is not a member of any ontology Error in getGOParents(x) : GO:0006118 is not a member of any ontology Error in getGOParents(x) : GO:0044283 is not a member of any ontology Error in getGOParents(x) : GO:0044282 is not a member of any ontology Error in getGOParents(x) : GO:0071103 is not a member of any ontology Error in getGOParents(x) : GO:0006441 is not a member of any ontology Error in getGOParents(x) : GO:0006510 is not a member of any ontology Error in getGOParents(x) : GO:0004680 is not a member of any ontology Error in getGOParents(x) : GO:0004682 is not a member of any ontology Error in getGOParents(x) : GO:0070925 is not a member of any ontology Error in getGOParents(x) : GO:0071554 is not a member of any ontology Error in getGOParents(x) : GO:0006512 is not a member of any ontology Error in getGOParents(x) : GO:0003754 is not a member of any ontology Error in getGOParents(x) : GO:0090066 is not a member of any ontology Error in getGOParents(x) : GO:0071174 is not a member of any ontology Error in getGOParents(x) : GO:0071173 is not a member of any ontology Error in getGOParents(x) : GO:0015482 is not a member of any ontology Error in getGOParents(x) : GO:0003773 is not a member of any ontology Error in getGOParents(x) : GO:0071212 is not a member of any ontology Error in getGOParents(x) : GO:0071216 is not a member of any ontology Error in getGOParents(x) : GO:0071496 is not a member of any ontology Error in getGOParents(x) : GO:0071514 is not a member of any ontology Error in getGOParents(x) : GO:0003763 is not a member of any ontology Error in getGOParents(x) : GO:0090092 is not a member of any ontology Error in getGOParents(x) : GO:0003929 is not a member of any ontology Error in getGOParents(x) : GO:0003926 is not a member of any ontology Error in getGOParents(x) : GO:0045045 is not a member of any ontology Error in getGOParents(x) : GO:0008605 is not a member of any ontology Error in getGOParents(x) : GO:0003936 is not a member of any ontology Error in getGOParents(x) : GO:0005065 is not a member of any ontology Error in getGOParents(x) : GO:0071555 is not a member of any ontology Error in getGOParents(x) : GO:0070972 is not a member of any ontology Error in getGOParents(x) : GO:0071539 is not a member of any ontology Error in getGOParents(x) : GO:0070993 is not a member of any ontology Error in getGOParents(x) : GO:0008248 is not a member of any ontology Error in getGOParents(x) : GO:0006371 is not a member of any ontology Error in getGOParents(x) : GO:0070897 is not a member of any ontology Error in getGOParents(x) : GO:0005551 is not a member of any ontology Error in getGOParents(x) : GO:0030508 is not a member of any ontology Error in getGOParents(x) : GO:0003685 is not a member of any ontology Error in getGOParents(x) : GO:0004239 is not a member of any ontology Error in getGOParents(x) : GO:0003901 is not a member of any ontology Error in getGOParents(x) : GO:0004681 is not a member of any ontology Error in getGOParents(x) : GO:0004600 is not a member of any ontology Error in getGOParents(x) : GO:0042027 is not a member of any ontology Error in getGOParents(x) : GO:0045034 is not a member of any ontology Error in getGOParents(x) : GO:0004229 is not a member of any ontology Error in getGOParents(x) : GO:0008567 is not a member of any ontology Error in getGOParents(x) : GO:0003928 is not a member of any ontology Error in getGOParents(x) : GO:0004213 is not a member of any ontology Error in getGOParents(x) : GO:0006804 is not a member of any ontology Error in getGOParents(x) : GO:0070918 is not a member of any ontology Error in getGOParents(x) : GO:0071359 is not a member of any ontology Error in getGOParents(x) : GO:0071310 is not a member of any ontology Error in getGOParents(x) : GO:0003208 is not a member of any ontology Error in getGOParents(x) : GO:0003206 is not a member of any ontology Error in getGOParents(x) : GO:0003205 is not a member of any ontology Error in getGOParents(x) : GO:0003231 is not a member of any ontology Error in getGOParents(x) : GO:0003229 is not a member of any ontology Error in getGOParents(x) : GO:0003321 is not a member of any ontology Error in getGOParents(x) : GO:0044212 is not a member of any ontology Error in getGOParents(x) : GO:0090100 is not a member of any ontology Error in getGOParents(x) : GO:0061008 is not a member of any ontology Error in getGOParents(x) : GO:0003333 is not a member of any ontology Error in getGOParents(x) : GO:0070997 is not a member of any ontology Error in getGOParents(x) : GO:0090079 is not a member of any ontology Error in getGOParents(x) : GO:0071375 is not a member of any ontology Error in getGOParents(x) : GO:0071495 is not a member of any ontology Error in getGOParents(x) : GO:0003158 is not a member of any ontology Error in getGOParents(x) : GO:0003401 is not a member of any ontology Error in getGOParents(x) : GO:0003254 is not a member of any ontology Error in getGOParents(x) : GO:0090218 is not a member of any ontology Error in getGOParents(x) : GO:0071445 is not a member of any ontology Error in getGOParents(x) : GO:0003407 is not a member of any ontology Error in getGOParents(x) : GO:0090087 is not a member of any ontology Error in getGOParents(x) : GO:0060986 is not a member of any ontology Error in getGOParents(x) : GO:0071378 is not a member of any ontology Error in getGOParents(x) : GO:0060969 is not a member of any ontology Error in getGOParents(x) : GO:0060968 is not a member of any ontology Error in getGOParents(x) : GO:0071466 is not a member of any ontology Error in getGOParents(x) : GO:0090224 is not a member of any ontology Error in getGOParents(x) : GO:0003338 is not a member of any ontology Error in getGOParents(x) : GO:0060993 is not a member of any ontology Error in getGOParents(x) : GO:0090181 is not a member of any ontology Error in getGOParents(x) : GO:0090101 is not a member of any ontology Error in getGOParents(x) : GO:0071385 is not a member of any ontology Error in getGOParents(x) : GO:0071384 is not a member of any ontology Error in getGOParents(x) : GO:0071383 is not a member of any ontology Error in getGOParents(x) : GO:0071158 is not a member of any ontology Error in getGOParents(x) : GO:0090068 is not a member of any ontology Error in getGOParents(x) : GO:0071156 is not a member of any ontology Error in getGOParents(x) : GO:0000051 is not a member of any ontology Error in getGOParents(x) : GO:0090077 is not a member of any ontology Error in getGOParents(x) : GO:0003341 is not a member of any ontology Error in getGOParents(x) : GO:0003352 is not a member of any ontology Error in getGOParents(x) : GO:0003228 is not a member of any ontology Error in getGOParents(x) : GO:0003209 is not a member of any ontology Error in getGOParents(x) : GO:0003230 is not a member of any ontology Error in getGOParents(x) : GO:0071256 is not a member of any ontology Error in getGOParents(x) : GO:0070988 is not a member of any ontology Error in getGOParents(x) : GO:0071322 is not a member of any ontology Error in getGOParents(x) : GO:0090130 is not a member of any ontology Error in getGOParents(x) : GO:0044179 is not a member of any ontology Error in getGOParents(x) : GO:0070938 is not a member of any ontology Error in getGOParents(x) : GO:0090162 is not a member of any ontology Error in getGOParents(x) : GO:0030161 is not a member of any ontology Error in getGOParents(x) : GO:0090109 is not a member of any ontology Error in getGOParents(x) : GO:0044215 is not a member of any ontology Error in getGOParents(x) : GO:0044216 is not a member of any ontology Error in getGOParents(x) : GO:0044217 is not a member of any ontology Error in getGOParents(x) : GO:0044182 is not a member of any ontology Error in getGOParents(x) : GO:0004263 is not a member of any ontology Error in getGOParents(x) : GO:0019131 is not a member of any ontology Error in getGOParents(x) : GO:0030188 is not a member of any ontology Error in getGOParents(x) : GO:0004192 is not a member of any ontology Error in getGOParents(x) : GO:0004218 is not a member of any ontology Error in getGOParents(x) : GO:0004295 is not a member of any ontology Error in getGOParents(x) : GO:0008133 is not a member of any ontology Error in getGOParents(x) : GO:0003818 is not a member of any ontology Error in getGOParents(x) : GO:0004277 is not a member of any ontology Error in getGOParents(x) : GO:0004215 is not a member of any ontology Error in getGOParents(x) : GO:0050425 is not a member of any ontology Error in getGOParents(x) : GO:0030601 is not a member of any ontology Error in getGOParents(x) : GO:0004214 is not a member of any ontology Error in getGOParents(x) : GO:0004228 is not a member of any ontology Error in getGOParents(x) : GO:0003816 is not a member of any ontology Error in getGOParents(x) : GO:0004281 is not a member of any ontology Error in getGOParents(x) : GO:0008464 is not a member of any ontology Error in getGOParents(x) : GO:0004186 is not a member of any ontology Error in getGOParents(x) : GO:0016512 is not a member of any ontology Error in getGOParents(x) : GO:0004240 is not a member of any ontology Error in getGOParents(x) : GO:0090174 is not a member of any ontology Error in getGOParents(x) : GO:0003804 is not a member of any ontology Error in getGOParents(x) : GO:0004286 is not a member of any ontology Error in getGOParents(x) : GO:0030189 is not a member of any ontology Error in getGOParents(x) : GO:0004230 is not a member of any ontology Error in getGOParents(x) : GO:0004276 is not a member of any ontology Error in getGOParents(x) : GO:0016919 is not a member of any ontology Error in getGOParents(x) : GO:0030602 is not a member of any ontology Error in getGOParents(x) : GO:0004246 is not a member of any ontology Error in getGOParents(x) : GO:0004217 is not a member of any ontology Error in getGOParents(x) : GO:0003815 is not a member of any ontology Error in getGOParents(x) : GO:0004237 is not a member of any ontology Error in getGOParents(x) : GO:0008451 is not a member of any ontology Error in getGOParents(x) : GO:0004289 is not a member of any ontology Error in getGOParents(x) : GO:0008125 is not a member of any ontology Error in getGOParents(x) : GO:0003812 is not a member of any ontology Error in getGOParents(x) : GO:0008067 is not a member of any ontology Error in getGOParents(x) : GO:0008581 is not a member of any ontology Error in getGOParents(x) : GO:0003817 is not a member of any ontology Error in getGOParents(x) : GO:0071267 is not a member of any ontology Error in getGOParents(x) : GO:0071265 is not a member of any ontology Error in getGOParents(x) : GO:0004238 is not a member of any ontology Error in getGOParents(x) : GO:0008423 is not a member of any ontology Error in getGOParents(x) : GO:0017114 is not a member of any ontology Error in getGOParents(x) : GO:0005061 is not a member of any ontology Error in getGOParents(x) : GO:0004231 is not a member of any ontology Error in getGOParents(x) : GO:0008132 is not a member of any ontology Error in getGOParents(x) : GO:0006125 is not a member of any ontology Error in getGOParents(x) : GO:0016804 is not a member of any ontology Error in getGOParents(x) : GO:0004254 is not a member of any ontology Error in getGOParents(x) : GO:0003160 is not a member of any ontology Error in getGOParents(x) : GO:0003157 is not a member of any ontology Error in getGOParents(x) : GO:0003159 is not a member of any ontology Error in getGOParents(x) : GO:0042315 is not a member of any ontology Error in getGOParents(x) : GO:0050517 is not a member of any ontology Error in getGOParents(x) : GO:0042576 is not a member of any ontology Error in getGOParents(x) : GO:0008472 is not a member of any ontology Error in getGOParents(x) : GO:0004287 is not a member of any ontology Error in getGOParents(x) : GO:0030019 is not a member of any ontology Error in getGOParents(x) : GO:0030191 is not a member of any ontology Error in getGOParents(x) : GO:0003803 is not a member of any ontology Error in getGOParents(x) : GO:0030192 is not a member of any ontology Error in getGOParents(x) : GO:0005155 is not a member of any ontology Error in getGOParents(x) : GO:0004278 is not a member of any ontology Error in getGOParents(x) : GO:0004178 is not a member of any ontology Error in getGOParents(x) : GO:0003802 is not a member of any ontology Error in getGOParents(x) : GO:0017165 is not a member of any ontology Error in getGOParents(x) : GO:0004182 is not a member of any ontology
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On 04/09/2010 08:30 AM, Ana Conesa wrote: > Dear Jim and Vicent, > > Yes, I guess this is the thing. I was wondering if there was a more up-to-date > GO.db package... > If case you find it interesting, I found around 200 terms not present in the > current GO.db... (see attached) The GO.db has just been rebuilt for the forthcoming release. It's available through biocLite when using R-2.11.0 pre-release. I get > get("GO:0090153", GOTERM) GOID: GO:0090153 Term: regulation of sphingolipid biosynthetic process Ontology: BP Definition: Any process that modulates the rate, frequency or extent of sphingolipid biosynthesis. Sphingolipid biosynthesis is the chemical reactions and pathways resulting in the formation of sphingolipids, any of a class of lipids containing the long-chain amine diol sphingosine or a closely related base (a sphingoid). with > packageDescription("GO.db")$Version [1] "2.4.1" and > GO_dbInfo() name 1 GOSOURCENAME 2 GOSOURCEURL 3 GOSOURCEDATE 4 DBSCHEMA 5 GOEGSOURCEDATE 6 GOEGSOURCENAME 7 GOEGSOURCEURL 8 DBSCHEMAVERSION value 1 Gene Ontology 2 ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/ 3 20100320 4 GO_DB 5 2010-Mar1 6 Entrez Gene 7 ftp://ftp.ncbi.nlm.nih.gov/gene/DATA 8 2.1 Martin > Thanks again > > Ana > > > > On Friday 09 April 2010 17:19:25 James W. MacDonald wrote: >> I think she gives the command below. >> >> There is a problem with the form of the call to get(); the keys are of >> the form GO:0090153, while the key used is missing the colon. So even if >> the term did exist in the GO.db package, it wouldn't be found using that >> key. >> >> However, I think the real reason this term isn't found is that it is a >> new term, added after the current version of the GO.db was produced. >> >> If you look at the term information on the AmiGO website, the source is >> stated to be ascb_2009. Since the GO.db package is now 6 months out of >> date, I wouldn't be surprised if this term were added after we built >> this package last. >> >> Best, >> >> Jim >> >> Vincent Carey wrote: >>> What is the exact command you are running that generates the error? >>> Present it in a way that another person not using your computer can >>> generate it. >>> >>> On Fri, Apr 9, 2010 at 9:17 AM, Ana Conesa <aconesa at="" cipf.es=""> wrote: >>>> Thanks Sean for your fast reply >>>> >>>> This is my sessionInfo() >>>> >>>>> sessionInfo() >>>> >>>> R version 2.10.0 (2009-10-26) >>>> x86_64-pc-linux-gnu >>>> >>>> locale: >>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] GO.db_2.3.5 RSQLite_0.7-1 DBI_0.2-4 >>>> [4] annotate_1.24.1 AnnotationDbi_1.8.2 Biobase_2.6.1 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] xtable_1.5-5 >>>> >>>>> get('GO0090153',GOTERM) >>>> >>>> Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : >>>> value for "GO0090153" not found >>>> >>>> Any hint? >>>> >>>> Ana >>>> >>>> On Friday 09 April 2010 15:03:20 Sean Davis wrote: >>>>> get('GO0090153',GOTERM) >>>> >>>> -- >>>> Ana Conesa >>>> Bioinformatics and Genomics Department >>>> Centro de Investigaciones Principe Felipe >>>> Avda. Autopista Saler 16, >>>> 46012 Valencia, Spain >>>> Phone: +34 96 328 96 80 >>>> Fax: +34 96 328 97 01 >>>> http://bioinfo.cipf.es/aconesa >>>> http://www.blast2go.org >>>> ========================================== >>>> FIRST INTERNATIONAL COURSE IN AUTOMATED >>>> FUNCTIONAL ANNOTATION AND DATA MINING >>>> Valencia/Orlando, September/October 2009 >>>> http://bioinfo.cipf.es/blast2gocourse >>>> >>>> _______________________________________________ >>>> 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 >>> >>> [[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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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Hi, Ana, The most current version is 2.4.1 (which is what Sean Davis used to fetch the GO:0090153 information). Installing the dev-R (2.11.0) will allow you to install and use this newer version of GO.db. Once you install R2.11.0, start R and enter source("http://bioconductor.org/biocLite.R") biocLite("GO.db") The source code can be found here: http://www.bioconductor.org/packages/2.6/data/annotation/html/GO.db.ht ml I check the first 5 term on your list, they are not GO terms. At least I cannot find them in AmiGo. Are you sure those "GO" terms really exist? Chao-Jen On 04/09/10 08:30, Ana Conesa wrote: > Dear Jim and Vicent, > > Yes, I guess this is the thing. I was wondering if there was a more up-to-date > GO.db package... > If case you find it interesting, I found around 200 terms not present in the > current GO.db... (see attached) > Thanks again > > Ana > > > > On Friday 09 April 2010 17:19:25 James W. MacDonald wrote: > >> I think she gives the command below. >> >> There is a problem with the form of the call to get(); the keys are of >> the form GO:0090153, while the key used is missing the colon. So even if >> the term did exist in the GO.db package, it wouldn't be found using that >> key. >> >> However, I think the real reason this term isn't found is that it is a >> new term, added after the current version of the GO.db was produced. >> >> If you look at the term information on the AmiGO website, the source is >> stated to be ascb_2009. Since the GO.db package is now 6 months out of >> date, I wouldn't be surprised if this term were added after we built >> this package last. >> >> Best, >> >> Jim >> >> Vincent Carey wrote: >> >>> What is the exact command you are running that generates the error? >>> Present it in a way that another person not using your computer can >>> generate it. >>> >>> On Fri, Apr 9, 2010 at 9:17 AM, Ana Conesa <aconesa@cipf.es> wrote: >>> >>>> Thanks Sean for your fast reply >>>> >>>> This is my sessionInfo() >>>> >>>> >>>>> sessionInfo() >>>>> >>>> R version 2.10.0 (2009-10-26) >>>> x86_64-pc-linux-gnu >>>> >>>> locale: >>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] GO.db_2.3.5 RSQLite_0.7-1 DBI_0.2-4 >>>> [4] annotate_1.24.1 AnnotationDbi_1.8.2 Biobase_2.6.1 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] xtable_1.5-5 >>>> >>>> >>>>> get('GO0090153',GOTERM) >>>>> >>>> Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : >>>> value for "GO0090153" not found >>>> >>>> Any hint? >>>> >>>> Ana >>>> >>>> On Friday 09 April 2010 15:03:20 Sean Davis wrote: >>>> >>>>> get('GO0090153',GOTERM) >>>>> >>>> -- >>>> Ana Conesa >>>> Bioinformatics and Genomics Department >>>> Centro de Investigaciones Principe Felipe >>>> Avda. Autopista Saler 16, >>>> 46012 Valencia, Spain >>>> Phone: +34 96 328 96 80 >>>> Fax: +34 96 328 97 01 >>>> http://bioinfo.cipf.es/aconesa >>>> http://www.blast2go.org >>>> ========================================== >>>> FIRST INTERNATIONAL COURSE IN AUTOMATED >>>> FUNCTIONAL ANNOTATION AND DATA MINING >>>> Valencia/Orlando, September/October 2009 >>>> http://bioinfo.cipf.es/blast2gocourse >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@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@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Chao-Jen Wong Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., M1-B514 PO Box 19024 Seattle, WA 98109 206.667.4485 cwon2@fhcrc.org [[alternative HTML version deleted]]
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Hi Ana, Ana Conesa wrote: > Dear Jim and Vicent, > > Yes, I guess this is the thing. I was wondering if there was a more up-to-date > GO.db package... > If case you find it interesting, I found around 200 terms not present in the > current GO.db... (see attached) It's not particularly interesting, since it is expected. As Martin Morgan notes in another email, this particular GO term (and likely most if not all 200 that you found) are available in the newest version of the GO.db package. We have to tread a fine line between reproducibility and being up-to-date. If we are constantly updating packages, then it is impossible for our end users to get consistent results, as the underlying data are constantly in a state of flux. On the other hand, if we never update things, then we simply push data that is completely outdated and fairly useless. As a compromise, we update all our annotation packages every six months, along with the release of the new version of Bioconductor. We feel this is a good compromise between reproducibility and currentness of data. If an end user wants to completely reproduce earlier results, she can simply use the version of BioC that was used to generate those earlier results. If on the other hand, she wants the most current results, those can be obtained using the most current release. However, as you have found, near the release date the current data packages start to show their age (and we will be releasing the new version of BioC in just a few weeks). Best, Jim > Thanks again > > Ana > > > > On Friday 09 April 2010 17:19:25 James W. MacDonald wrote: >> I think she gives the command below. >> >> There is a problem with the form of the call to get(); the keys are of >> the form GO:0090153, while the key used is missing the colon. So even if >> the term did exist in the GO.db package, it wouldn't be found using that >> key. >> >> However, I think the real reason this term isn't found is that it is a >> new term, added after the current version of the GO.db was produced. >> >> If you look at the term information on the AmiGO website, the source is >> stated to be ascb_2009. Since the GO.db package is now 6 months out of >> date, I wouldn't be surprised if this term were added after we built >> this package last. >> >> Best, >> >> Jim >> >> Vincent Carey wrote: >>> What is the exact command you are running that generates the error? >>> Present it in a way that another person not using your computer can >>> generate it. >>> >>> On Fri, Apr 9, 2010 at 9:17 AM, Ana Conesa <aconesa at="" cipf.es=""> wrote: >>>> Thanks Sean for your fast reply >>>> >>>> This is my sessionInfo() >>>> >>>>> sessionInfo() >>>> R version 2.10.0 (2009-10-26) >>>> x86_64-pc-linux-gnu >>>> >>>> locale: >>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] GO.db_2.3.5 RSQLite_0.7-1 DBI_0.2-4 >>>> [4] annotate_1.24.1 AnnotationDbi_1.8.2 Biobase_2.6.1 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] xtable_1.5-5 >>>> >>>>> get('GO0090153',GOTERM) >>>> Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : >>>> value for "GO0090153" not found >>>> >>>> Any hint? >>>> >>>> Ana >>>> >>>> On Friday 09 April 2010 15:03:20 Sean Davis wrote: >>>>> get('GO0090153',GOTERM) >>>> -- >>>> Ana Conesa >>>> Bioinformatics and Genomics Department >>>> Centro de Investigaciones Principe Felipe >>>> Avda. Autopista Saler 16, >>>> 46012 Valencia, Spain >>>> Phone: +34 96 328 96 80 >>>> Fax: +34 96 328 97 01 >>>> http://bioinfo.cipf.es/aconesa >>>> http://www.blast2go.org >>>> ========================================== >>>> FIRST INTERNATIONAL COURSE IN AUTOMATED >>>> FUNCTIONAL ANNOTATION AND DATA MINING >>>> Valencia/Orlando, September/October 2009 >>>> http://bioinfo.cipf.es/blast2gocourse >>>> >>>> _______________________________________________ >>>> 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 >>> [[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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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