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12.2 years ago by
Lina Hultin-Rosenberg80 wrote:
Dear list, I have retrieved GO terms for lists of human genes using biomaRt, and I am now using the packages goTools and GO to get further information about the terms. I discovered that one of the terms extracted with biomaRt, GO:0060070, does not exist in goTools and GO. Does anyone know what might be the problem? I would guess this has to do with the version of the Gene Ontology db used, but it would of course be most convenient if the different packages used the same GO version. This are the calls I do and the answer I get: >GOTERM$"GO:0060070" NULL >getGoCategory("GO:0060070") Error in get(x, envir, mode, inherits) : variable "GO:0060070" was not found Error in Ontology(get(id, env = GOTERM)) : error in evaluating the argument 'object' in selecting a method for function 'Ontology' And this is the output from sessionInfo(): >sessionInfo() R version 2.5.0 (2007-04-23) i386-pc-mingw32 locale: LC_COLLATE=Swedish_Sweden.1252;LC_CTYPE=Swedish_Sweden.1252;LC_MONETAR Y= Swedish_Sweden.1252;LC_NUMERIC=C;LC_TIME=Swedish_Sweden.1252 attached base packages: [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" other attached packages: goTools GO annotate Biobase biomaRt RCurl XML "1.8.0" "1.16.0" "1.14.1" "1.14.0" "1.10.0" "0.8-0" "1.7-1" Any help or comments would be greatly appreciated! Best regards, Lina Rosenberg Karolinska Biomics Center ADD COMMENTlink modified 12.2 years ago by Seth Falcon7.4k • written 12.2 years ago by Lina Hultin-Rosenberg80 Answer: GO terms not found in goTools and GO 0 12.2 years ago by Seth Falcon7.4k Seth Falcon7.4k wrote: Wolfgang Huber <huber at="" ebi.ac.uk=""> writes: > Dear Lena, > > the point to realize is that biomaRt queries an online database (you > didn't tell us which one you use), while the GO package is assembled and > packaged by friendly curators in Seattle every couple of months. > > According to this site > http://www.ebi.ac.uk/ego/DisplayGoTerm?id=GO:0060070 > your term was last modified 2007-03-16, which could explain why it is > not yet in the latest GO package (version 1.17.0). > > If you want an consistent set of GO terms throughout, please use the > humanLLmappings (soon to be humanEGmappings) package for gene-GO > associations, not biomaRt. If you use biomaRt, you need to spend more > effort dealing with the dynamic nature of genome annotation (this is not > our fault, this is the state of the science). Good advice. I want to clarify one detail: We are working on new Entrez Gene based organism specific annotation packages for human, mouse and rat. They are intended as New And Improved versions of <organism>LLMappings. We have not finalized how we will name them, and almost surely they will not be humanEGmappings. I will start a thread on bioc-devel today with some proposed naming schemas for those that are interested. Best, + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org ADD COMMENTlink written 12.2 years ago by Seth Falcon7.4k Thank you so much for the information! I did not now exactly how the different packages worked, now I know and understand better the problems I ran into. I use biomart ensembl for the GO queries. Best regards, Lina Seth Falcon skrev: > Wolfgang Huber <huber at="" ebi.ac.uk=""> writes: > >> Dear Lena, >> >> the point to realize is that biomaRt queries an online database (you >> didn't tell us which one you use), while the GO package is assembled and >> packaged by friendly curators in Seattle every couple of months. >> >> According to this site >> http://www.ebi.ac.uk/ego/DisplayGoTerm?id=GO:0060070 >> your term was last modified 2007-03-16, which could explain why it is >> not yet in the latest GO package (version 1.17.0). >> >> If you want an consistent set of GO terms throughout, please use the >> humanLLmappings (soon to be humanEGmappings) package for gene-GO >> associations, not biomaRt. If you use biomaRt, you need to spend more >> effort dealing with the dynamic nature of genome annotation (this is not >> our fault, this is the state of the science). > > Good advice. I want to clarify one detail: > > We are working on new Entrez Gene based organism specific annotation > packages for human, mouse and rat. They are intended as New And > Improved versions of <organism>LLMappings. We have not finalized how > we will name them, and almost surely they will not be humanEGmappings. > I will start a thread on bioc-devel today with some proposed naming > schemas for those that are interested. > > Best, > > + seth > ADD REPLYlink written 12.2 years ago by Lina Hultin-Rosenberg80 Answer: GO terms not found in goTools and GO 0 12.2 years ago by EMBL European Molecular Biology Laboratory Wolfgang Huber13k wrote: Dear Lena, the point to realize is that biomaRt queries an online database (you didn't tell us which one you use), while the GO package is assembled and packaged by friendly curators in Seattle every couple of months. According to this site http://www.ebi.ac.uk/ego/DisplayGoTerm?id=GO:0060070 your term was last modified 2007-03-16, which could explain why it is not yet in the latest GO package (version 1.17.0). If you want an consistent set of GO terms throughout, please use the humanLLmappings (soon to be humanEGmappings) package for gene-GO associations, not biomaRt. If you use biomaRt, you need to spend more effort dealing with the dynamic nature of genome annotation (this is not our fault, this is the state of the science). Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber Lina Hultin-Rosenberg ha scritto: > Dear list, > > I have retrieved GO terms for lists of human genes using biomaRt, and I > am now using the packages goTools and GO to get further information > about the terms. I discovered that one of the terms extracted with > biomaRt, GO:0060070, does not exist in goTools and GO. Does anyone know > what might be the problem? I would guess this has to do with the version > of the Gene Ontology db used, but it would of course be most convenient > if the different packages used the same GO version. > > This are the calls I do and the answer I get: > > >GOTERM$"GO:0060070" > NULL > > >getGoCategory("GO:0060070") > Error in get(x, envir, mode, inherits) : variable "GO:0060070" was not found > Error in Ontology(get(id, env = GOTERM)) : > error in evaluating the argument 'object' in selecting a method > for function 'Ontology' > > > And this is the output from sessionInfo(): > > >sessionInfo() > R version 2.5.0 (2007-04-23) > i386-pc-mingw32 > > locale: > LC_COLLATE=Swedish_Sweden.1252;LC_CTYPE=Swedish_Sweden.1252;LC_MONET ARY= > Swedish_Sweden.1252;LC_NUMERIC=C;LC_TIME=Swedish_Sweden.1252 > > attached base packages: > [1] "tools" "stats" "graphics" "grDevices" "utils" > "datasets" "methods" "base" > > other attached packages: > goTools GO annotate Biobase biomaRt RCurl XML > "1.8.0" "1.16.0" "1.14.1" "1.14.0" "1.10.0" "0.8-0" "1.7-1" > > Any help or comments would be greatly appreciated! > > Best regards, > > Lina Rosenberg > Karolinska Biomics Ce --