Question: Biomart server down?
0
gravatar for Alistair Rust
8.3 years ago by
Alistair Rust20 wrote:
Hi, I've had an R script playing nicely with biomaRt for a while Today there seem to be a few wee problems. Is the result of the server being down in Toronto? SessionInfo, a simple test and output below. I downloaded and installed the 2.8.0 version of biomaRt this morning. Also tried the 2.9.0 development version with the same results. Cheers Alistair Team113: Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK > sessionInfo() R version 2.11.1 (2010-05-31) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=C [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.8.0 loaded via a namespace (and not attached): [1] RCurl_1.4-2 XML_3.1-0 Simple test from the R script on the BioConductor biomaRt webpage ======== library(biomaRt) listMarts() ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") affyids=c("202763_at","209310_s_at","207500_at") getBM(attributes=c('affy_hg_u133_plus_2', 'entrezgene'), filters = 'affy_hg_u133_plus_2', values = affyids, mart = ensembl) ========= Output ========= V1 1 2 <html><head> 3 <meta http-equiv="Content-Type" content="text/html;" charset="utf-8"> 4 <title>ERROR: The requested URL could not be retrieved</title> 5 <style type="text/css">
genetics cancer biomart • 829 views
ADD COMMENTlink modified 8.3 years ago by Rhoda Kinsella660 • written 8.3 years ago by Alistair Rust20
Answer: Biomart server down?
0
gravatar for Rhoda Kinsella
8.3 years ago by
Rhoda Kinsella660 wrote:
Hi Alistair You can set your host to www.ensembl.org and use the Ensembl Biomart databases there. Regards Rhoda On 20 May 2011, at 15:44, Alistair Rust wrote: > Hi, > > I've had an R script playing nicely with biomaRt for a while > Today there seem to be a few wee problems. Is the result > of the server being down in Toronto? > > SessionInfo, a simple test and output below. I downloaded > and installed the 2.8.0 version of biomaRt this morning. > Also tried the 2.9.0 development version with the same > results. > > Cheers > > Alistair > > Team113: Experimental Cancer Genetics, > Wellcome Trust Sanger Institute, > Hinxton, Cambridge, UK > > >> sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=C > [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.8.0 > > loaded via a namespace (and not attached): > [1] RCurl_1.4-2 XML_3.1-0 > > > Simple test from the R script on the BioConductor biomaRt webpage > ======== > library(biomaRt) > > listMarts() > > ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") > > affyids=c("202763_at","209310_s_at","207500_at") > > getBM(attributes=c('affy_hg_u133_plus_2', 'entrezgene'), filters = > 'affy_hg_u133_plus_2', values = affyids, mart = ensembl) > ========= > > > > Output > ========= > > V1 > > 1 http://www.w3.org/TR/html4/strict.dtd> > 2 > <html><head> > 3 <meta http-equiv="Content-Type" content="text/"> html; > charset=utf-8> > 4 ERROR: The requested URL could not be > retrieved > 5 <style> type=text/css>
ADD COMMENTlink written 8.3 years ago by Rhoda Kinsella660
Hi Rhoda, Yep, indeed adding the following bit of magic into my simple test script did the trick for that. listMarts(mart, host="www.ensembl.org") The 'real' script I'm working with however uses a R package that is hardcoded to run off the Biomart.org databases. Though it looks as if things are now back as my test script seems to run without complaining... Best Alistair On Fri, May 20, 2011 at 3:58 PM, Rhoda Kinsella <rhoda@ebi.ac.uk> wrote: > Hi Alistair > You can set your host to www.ensembl.org and use the Ensembl Biomart > databases there. > Regards > Rhoda > > > > On 20 May 2011, at 15:44, Alistair Rust wrote: > > Hi, >> >> I've had an R script playing nicely with biomaRt for a while >> Today there seem to be a few wee problems. Is the result >> of the server being down in Toronto? >> >> SessionInfo, a simple test and output below. I downloaded >> and installed the 2.8.0 version of biomaRt this morning. >> Also tried the 2.9.0 development version with the same >> results. >> >> Cheers >> >> Alistair >> >> Team113: Experimental Cancer Genetics, >> Wellcome Trust Sanger Institute, >> Hinxton, Cambridge, UK >> >> >> sessionInfo() >>> >> R version 2.11.1 (2010-05-31) >> x86_64-unknown-linux-gnu >> >> locale: >> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=C >> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] biomaRt_2.8.0 >> >> loaded via a namespace (and not attached): >> [1] RCurl_1.4-2 XML_3.1-0 >> >> >> Simple test from the R script on the BioConductor biomaRt webpage >> ======== >> library(biomaRt) >> >> listMarts() >> >> ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") >> >> affyids=c("202763_at","209310_s_at","207500_at") >> >> getBM(attributes=c('affy_hg_u133_plus_2', 'entrezgene'), filters = >> 'affy_hg_u133_plus_2', values = affyids, mart = ensembl) >> ========= >> >> >> >> Output >> ========= >> >> V1 >> >> 1 > http://www.w3.org/TR/html4/strict.dtd> >> 2 >> <html><head> >> 3 <meta http-equiv="Content-Type" content="text/html;">> charset=utf-8> >> 4 ERROR: The requested URL could not be >> retrieved >> 5 <style>> type=text/css>
ADD REPLYlink written 8.3 years ago by Alistair Rust20
Hi Alistair Glad it now works. Regards Rhoda On 20 May 2011, at 16:41, Alistair Rust wrote: > Hi Rhoda, > > Yep, indeed adding the following bit of magic into my simple test > script did the trick for that. > > listMarts(mart, host="www.ensembl.org") > > The 'real' script I'm working with however uses a R package that is > hardcoded > to run off the Biomart.org databases. > > Though it looks as if things are now back as my test script seems to > run > without > complaining... > > Best > > Alistair > > > On Fri, May 20, 2011 at 3:58 PM, Rhoda Kinsella <rhoda at="" ebi.ac.uk=""> > wrote: > >> Hi Alistair >> You can set your host to www.ensembl.org and use the Ensembl Biomart >> databases there. >> Regards >> Rhoda >> >> >> >> On 20 May 2011, at 15:44, Alistair Rust wrote: >> >> Hi, >>> >>> I've had an R script playing nicely with biomaRt for a while >>> Today there seem to be a few wee problems. Is the result >>> of the server being down in Toronto? >>> >>> SessionInfo, a simple test and output below. I downloaded >>> and installed the 2.8.0 version of biomaRt this morning. >>> Also tried the 2.9.0 development version with the same >>> results. >>> >>> Cheers >>> >>> Alistair >>> >>> Team113: Experimental Cancer Genetics, >>> Wellcome Trust Sanger Institute, >>> Hinxton, Cambridge, UK >>> >>> >>> sessionInfo() >>>> >>> R version 2.11.1 (2010-05-31) >>> x86_64-unknown-linux-gnu >>> >>> locale: >>> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >>> [5] LC_MONETARY=C LC_MESSAGES=C >>> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] biomaRt_2.8.0 >>> >>> loaded via a namespace (and not attached): >>> [1] RCurl_1.4-2 XML_3.1-0 >>> >>> >>> Simple test from the R script on the BioConductor biomaRt webpage >>> ======== >>> library(biomaRt) >>> >>> listMarts() >>> >>> ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") >>> >>> affyids=c("202763_at","209310_s_at","207500_at") >>> >>> getBM(attributes=c('affy_hg_u133_plus_2', 'entrezgene'), filters = >>> 'affy_hg_u133_plus_2', values = affyids, mart = ensembl) >>> ========= >>> >>> >>> >>> Output >>> ========= >>> >>> V1 >>> >>> 1 >> http://www.w3.org/TR/html4/strict.dtd> >>> 2 >>> <html><head> >>> 3 <meta http-equiv="Content-Type">>> content=text/html; >>> charset=utf-8> >>> 4 ERROR: The requested URL could >>> not be >>> retrieved >>> 5 <style>>> type=text/css>
ADD REPLYlink written 8.3 years ago by Rhoda Kinsella660
On website http://www.ensembl.org/biomart/martview/a711f46360c68acaec8 8385696d09186/a711f46360c68acaec88385696d09186 I want to get the REGULATORY FEATURES It seems not work. Dataset Count unavailable On Fri, May 20, 2011 at 4:58 PM, Rhoda Kinsella <rhoda at="" ebi.ac.uk=""> wrote: > Hi Alistair > You can set your host to www.ensembl.org and use the Ensembl Biomart > databases there. > Regards > Rhoda > > > On 20 May 2011, at 15:44, Alistair Rust wrote: > >> Hi, >> >> I've had an R script playing nicely with biomaRt for a while >> Today there seem to be a few wee problems. ?Is the result >> of the server being down in Toronto? >> >> SessionInfo, a simple test and output below. ?I downloaded >> and installed the 2.8.0 version of biomaRt this morning. >> Also tried the 2.9.0 development version with the same >> results. >> >> Cheers >> >> Alistair >> >> Team113: Experimental Cancer Genetics, >> Wellcome Trust Sanger Institute, >> Hinxton, Cambridge, UK >> >> >>> sessionInfo() >> >> R version 2.11.1 (2010-05-31) >> x86_64-unknown-linux-gnu >> >> locale: >> [1] LC_CTYPE=en_GB.UTF-8 ? ? ? LC_NUMERIC=C >> [3] LC_TIME=en_GB.UTF-8 ? ? ? ?LC_COLLATE=en_GB.UTF-8 >> [5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=C >> [7] LC_PAPER=en_GB.UTF-8 ? ? ? LC_NAME=C >> [9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >> >> other attached packages: >> [1] biomaRt_2.8.0 >> >> loaded via a namespace (and not attached): >> [1] RCurl_1.4-2 XML_3.1-0 >> >> >> Simple test from the R script on the BioConductor biomaRt webpage >> ======== >> library(biomaRt) >> >> listMarts() >> >> ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") >> >> affyids=c("202763_at","209310_s_at","207500_at") >> >> getBM(attributes=c('affy_hg_u133_plus_2', 'entrezgene'), filters = >> 'affy_hg_u133_plus_2', values = affyids, mart = ensembl) >> ========= >> >> >> >> Output >> ========= >> >> ? ? V1 >> >> 1 > http://www.w3.org/TR/html4/strict.dtd> >> 2 >> <html><head> >> 3 ? ? ? ? ? ? ? ? ? ? ? ?<meta http-equiv="Content-Type" content="text/html;">> charset=utf-8> >> 4 ? ? ? ? ? ? ? ? ? ? ? ? ERROR: The requested URL could not be >> retrieved >> 5 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? <style>> type=text/css>
ADD REPLYlink written 8.3 years ago by Fabrice Tourre970
Hi Fabrice Unfortunately we have never been able to have a functional count for the regulation mart as restrictions in the 0.7 Biomart code as well as the complexity of the regulation schema does not allow it. The rest of the mart does work as expected. Regards Rhoda On 20 May 2011, at 16:08, Fabrice Tourre wrote: > On website http://www.ensembl.org/biomart/martview/a711f46360c68acae c88385696d09186/a711f46360c68acaec88385696d09186 > > I want to get the REGULATORY FEATURES > > It seems not work. > > Dataset Count unavailable > > > On Fri, May 20, 2011 at 4:58 PM, Rhoda Kinsella <rhoda at="" ebi.ac.uk=""> > wrote: >> Hi Alistair >> You can set your host to www.ensembl.org and use the Ensembl Biomart >> databases there. >> Regards >> Rhoda >> >> >> On 20 May 2011, at 15:44, Alistair Rust wrote: >> >>> Hi, >>> >>> I've had an R script playing nicely with biomaRt for a while >>> Today there seem to be a few wee problems. Is the result >>> of the server being down in Toronto? >>> >>> SessionInfo, a simple test and output below. I downloaded >>> and installed the 2.8.0 version of biomaRt this morning. >>> Also tried the 2.9.0 development version with the same >>> results. >>> >>> Cheers >>> >>> Alistair >>> >>> Team113: Experimental Cancer Genetics, >>> Wellcome Trust Sanger Institute, >>> Hinxton, Cambridge, UK >>> >>> >>>> sessionInfo() >>> >>> R version 2.11.1 (2010-05-31) >>> x86_64-unknown-linux-gnu >>> >>> locale: >>> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >>> [5] LC_MONETARY=C LC_MESSAGES=C >>> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] biomaRt_2.8.0 >>> >>> loaded via a namespace (and not attached): >>> [1] RCurl_1.4-2 XML_3.1-0 >>> >>> >>> Simple test from the R script on the BioConductor biomaRt webpage >>> ======== >>> library(biomaRt) >>> >>> listMarts() >>> >>> ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") >>> >>> affyids=c("202763_at","209310_s_at","207500_at") >>> >>> getBM(attributes=c('affy_hg_u133_plus_2', 'entrezgene'), filters = >>> 'affy_hg_u133_plus_2', values = affyids, mart = ensembl) >>> ========= >>> >>> >>> >>> Output >>> ========= >>> >>> V1 >>> >>> 1 >> http://www.w3.org/TR/html4/strict.dtd> >>> 2 >>> <html><head> >>> 3 <meta http-equiv="Content-Type">>> content=text/html; >>> charset=utf-8> >>> 4 ERROR: The requested URL could >>> not be >>> retrieved >>> 5 <style>>> type=text/css>
ADD REPLYlink written 8.3 years ago by Rhoda Kinsella660
Is it possible to download? For example: Filters Feature Type : RegulatoryFeature Attributes: Feature Set Feature Type Chromosome Name Start (bp) End (bp) On Fri, May 20, 2011 at 5:18 PM, Rhoda Kinsella <rhoda at="" ebi.ac.uk=""> wrote: > Hi Fabrice > Unfortunately we have never been able to have a functional count for the > regulation mart as restrictions in the 0.7 Biomart code as well as the > complexity of the regulation schema does not allow it. The rest of the mart > does work as expected. > Regards > Rhoda > > > On 20 May 2011, at 16:08, Fabrice Tourre wrote: > >> On website >> http://www.ensembl.org/biomart/martview/a711f46360c68acaec88385696d 09186/a711f46360c68acaec88385696d09186 >> >> I want to get the REGULATORY FEATURES >> >> It seems not work. >> >> Dataset Count unavailable >> >> >> On Fri, May 20, 2011 at 4:58 PM, Rhoda Kinsella <rhoda at="" ebi.ac.uk=""> wrote: >>> >>> Hi Alistair >>> You can set your host to www.ensembl.org and use the Ensembl Biomart >>> databases there. >>> Regards >>> Rhoda >>> >>> >>> On 20 May 2011, at 15:44, Alistair Rust wrote: >>> >>>> Hi, >>>> >>>> I've had an R script playing nicely with biomaRt for a while >>>> Today there seem to be a few wee problems. ?Is the result >>>> of the server being down in Toronto? >>>> >>>> SessionInfo, a simple test and output below. ?I downloaded >>>> and installed the 2.8.0 version of biomaRt this morning. >>>> Also tried the 2.9.0 development version with the same >>>> results. >>>> >>>> Cheers >>>> >>>> Alistair >>>> >>>> Team113: Experimental Cancer Genetics, >>>> Wellcome Trust Sanger Institute, >>>> Hinxton, Cambridge, UK >>>> >>>> >>>>> sessionInfo() >>>> >>>> R version 2.11.1 (2010-05-31) >>>> x86_64-unknown-linux-gnu >>>> >>>> locale: >>>> [1] LC_CTYPE=en_GB.UTF-8 ? ? ? LC_NUMERIC=C >>>> [3] LC_TIME=en_GB.UTF-8 ? ? ? ?LC_COLLATE=en_GB.UTF-8 >>>> [5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=C >>>> [7] LC_PAPER=en_GB.UTF-8 ? ? ? LC_NAME=C >>>> [9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C >>>> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>>> >>>> other attached packages: >>>> [1] biomaRt_2.8.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] RCurl_1.4-2 XML_3.1-0 >>>> >>>> >>>> Simple test from the R script on the BioConductor biomaRt webpage >>>> ======== >>>> library(biomaRt) >>>> >>>> listMarts() >>>> >>>> ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") >>>> >>>> affyids=c("202763_at","209310_s_at","207500_at") >>>> >>>> getBM(attributes=c('affy_hg_u133_plus_2', 'entrezgene'), filters = >>>> 'affy_hg_u133_plus_2', values = affyids, mart = ensembl) >>>> ========= >>>> >>>> >>>> >>>> Output >>>> ========= >>>> >>>> ? ?V1 >>>> >>>> 1 >>> http://www.w3.org/TR/html4/strict.dtd> >>>> 2 >>>> <html><head> >>>> 3 ? ? ? ? ? ? ? ? ? ? ? ?<meta http-equiv="Content-Type">>>> content=text/html; >>>> charset=utf-8> >>>> 4 ? ? ? ? ? ? ? ? ? ? ? ? ERROR: The requested URL could not be >>>> retrieved >>>> 5 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? <style>>>> type=text/css>
ADD REPLYlink written 8.3 years ago by Fabrice Tourre970
Hi Fabrice Yes this should be possible if you select a particular regulatory feature (e.g. feature type -> Gene Associated). I would suggest that you take a look at the web interface at http://www.ensembl.org/biomart/martview/ and try to construct a query by selecting filters such as region filter and one or more filter from the regulatory feature filter section (i.e. feature type or cell type) and then go to the attributes section and select the attributes you require from the corresponding regulatory feature attribute page. You can then take a look at the xml for that query by clicking the xml button and use the internal names in the construction of your query using the biomaRt package. Regards Rhoda On 20 May 2011, at 16:35, Fabrice Tourre wrote: > Is it possible to download? For example: > > > Filters Feature Type : > RegulatoryFeature > Attributes: > Feature Set > Feature Type > Chromosome Name > Start (bp) > End (bp) > > > On Fri, May 20, 2011 at 5:18 PM, Rhoda Kinsella <rhoda at="" ebi.ac.uk=""> > wrote: >> Hi Fabrice >> Unfortunately we have never been able to have a functional count >> for the >> regulation mart as restrictions in the 0.7 Biomart code as well as >> the >> complexity of the regulation schema does not allow it. The rest of >> the mart >> does work as expected. >> Regards >> Rhoda >> >> >> On 20 May 2011, at 16:08, Fabrice Tourre wrote: >> >>> On website >>> http://www.ensembl.org/biomart/martview/a711f46360c68acaec88385696 d09186/a711f46360c68acaec88385696d09186 >>> >>> I want to get the REGULATORY FEATURES >>> >>> It seems not work. >>> >>> Dataset Count unavailable >>> >>> >>> On Fri, May 20, 2011 at 4:58 PM, Rhoda Kinsella <rhoda at="" ebi.ac.uk=""> >>> wrote: >>>> >>>> Hi Alistair >>>> You can set your host to www.ensembl.org and use the Ensembl >>>> Biomart >>>> databases there. >>>> Regards >>>> Rhoda >>>> >>>> >>>> On 20 May 2011, at 15:44, Alistair Rust wrote: >>>> >>>>> Hi, >>>>> >>>>> I've had an R script playing nicely with biomaRt for a while >>>>> Today there seem to be a few wee problems. Is the result >>>>> of the server being down in Toronto? >>>>> >>>>> SessionInfo, a simple test and output below. I downloaded >>>>> and installed the 2.8.0 version of biomaRt this morning. >>>>> Also tried the 2.9.0 development version with the same >>>>> results. >>>>> >>>>> Cheers >>>>> >>>>> Alistair >>>>> >>>>> Team113: Experimental Cancer Genetics, >>>>> Wellcome Trust Sanger Institute, >>>>> Hinxton, Cambridge, UK >>>>> >>>>> >>>>>> sessionInfo() >>>>> >>>>> R version 2.11.1 (2010-05-31) >>>>> x86_64-unknown-linux-gnu >>>>> >>>>> locale: >>>>> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >>>>> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >>>>> [5] LC_MONETARY=C LC_MESSAGES=C >>>>> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C >>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices utils datasets methods >>>>> base >>>>> >>>>> other attached packages: >>>>> [1] biomaRt_2.8.0 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] RCurl_1.4-2 XML_3.1-0 >>>>> >>>>> >>>>> Simple test from the R script on the BioConductor biomaRt webpage >>>>> ======== >>>>> library(biomaRt) >>>>> >>>>> listMarts() >>>>> >>>>> ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") >>>>> >>>>> affyids=c("202763_at","209310_s_at","207500_at") >>>>> >>>>> getBM(attributes=c('affy_hg_u133_plus_2', 'entrezgene'), filters = >>>>> 'affy_hg_u133_plus_2', values = affyids, mart = ensembl) >>>>> ========= >>>>> >>>>> >>>>> >>>>> Output >>>>> ========= >>>>> >>>>> V1 >>>>> >>>>> 1 >>>> http://www.w3.org/TR/html4/strict.dtd> >>>>> 2 >>>>> <html><head> >>>>> 3 <meta http-equiv="Content-Type">>>>> content=text/html; >>>>> charset=utf-8> >>>>> 4 ERROR: The requested URL could >>>>> not be >>>>> retrieved >>>>> 5 >>>>> <style>>>>> type=text/css>
ADD REPLYlink written 8.3 years ago by Rhoda Kinsella660
Rhoda, Not works for me. I used feature type -> RegulatoryFeature. The xml file is fellow. I cannot download anything form the web sites. Filters Feature Type : RegulatoryFeature Attributes: Feature Set Feature Type Chromosome Name Start (bp) End (bp) <query virtualschemaname="default" formatter="TSV" header="0" uniquerows="0" count="" datasetconfigversion="0.6"> <dataset name="hsapiens_feature_set" interface="default"> <filter name="regulatory_feature_type_name" value="RegulatoryFeature"/> <attribute name="fs_display_label_1048"/> <attribute name="feature_type_name_1048"/> <attribute name="seq_region_name_1048"/> <attribute name="seq_region_start_1048"/> <attribute name="seq_region_end_1048"/> <attribute name="cell_type_name_1048"/> </dataset> </query>
ADD REPLYlink written 8.3 years ago by Fabrice Tourre970
Hi Fabrice, You can put this into a biomaRt query as follows for example: >mart = useMart('functional_genomics', dataset='hsapiens_feature_set') >feat = getBM(c('fs_display_label_1048','feature_type_description_1048 ','seq_region_start_1048','seq_region_end_1048'),filters='chromosome_n ame',values='22',mart=mart) > head(feat) fs_display_label_1048 feature_type_description_1048 1 2 DNase1 - CD4 Enriched Sites DNase1 Hypersensitive Site 3 DNase1 - CD4 Enriched Sites DNase1 Hypersensitive Site 4 DNase1 - CD4 Enriched Sites DNase1 Hypersensitive Site 5 DNase1 - CD4 Enriched Sites DNase1 Hypersensitive Site 6 DNase1 - CD4 Enriched Sites DNase1 Hypersensitive Site seq_region_start_1048 seq_region_end_1048 1 NA NA 2 51221960 51222408 3 51195540 51195777 4 51175647 51175790 5 51173065 51173230 6 51171513 51171699 Steffen On Fri, May 20, 2011 at 9:04 AM, Fabrice Tourre <fabrice.ciup at="" gmail.com=""> wrote: > Rhoda, > Not works for me. > I used ?feature type -> RegulatoryFeature. The xml file is fellow. I > cannot download anything form the web sites. > > Filters Feature Type : > ? ?RegulatoryFeature > Attributes: > ? ?Feature Set > ? ?Feature Type > ? ?Chromosome Name > ? ?Start (bp) > ? ?End (bp) > > > > <query ?virtualschemaname="default" formatter="TSV" header="0"> uniqueRows = "0" count = "" datasetConfigVersion = "0.6" > > > ? ? ? ?<dataset name="hsapiens_feature_set" interface="default"> > ? ? ? ? ? ? ? ?<filter name="regulatory_feature_type_name" value="RegulatoryFeature"/> > ? ? ? ? ? ? ? ?<attribute name="fs_display_label_1048"/> > ? ? ? ? ? ? ? ?<attribute name="feature_type_name_1048"/> > ? ? ? ? ? ? ? ?<attribute name="seq_region_name_1048"/> > ? ? ? ? ? ? ? ?<attribute name="seq_region_start_1048"/> > ? ? ? ? ? ? ? ?<attribute name="seq_region_end_1048"/> > ? ? ? ? ? ? ? ?<attribute name="cell_type_name_1048"/> > ? ? ? ?</dataset> > </query> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 8.3 years ago by Steffen Durinck540
Steffen, Thank you very much. It works. I am interesting to RegulatoryFeatures. I am strange why the region in your example cannot be found in these files. ftp://ftp.ensembl.org/pub/release-62/functional_genomics/homo_sapiens/ ftp://ftp.ensembl.org/pub/release-62/functional_genomics/homo_sapiens/ RegulatoryFeatures_CD4.Chr22.gff.gz I just think the items get by bioMart will be the same as in the ftp directory functional_genomics. But it is not. Do I have misunderstand something? Thanks. On Fri, May 20, 2011 at 8:19 PM, Steffen Durinck <durinck.steffen at="" gene.com=""> wrote: > Steffen
ADD REPLYlink written 8.3 years ago by Fabrice Tourre970
Hi Fabrice Please contact helpdesk at ensembl.org who will be able to help you with your query. Regards Rhoda On 20 May 2011, at 21:06, Fabrice Tourre wrote: > Steffen, > > Thank you very much. It works. > > I am interesting to RegulatoryFeatures. I am strange why the region in > your example cannot be found in these files. > > ftp://ftp.ensembl.org/pub/release-62/functional_genomics/homo_sapiens/ > ftp://ftp.ensembl.org/pub/release-62/functional_genomics/homo_sapien s/RegulatoryFeatures_CD4.Chr22.gff.gz > > I just think the items get by bioMart will be the same as in the ftp > directory functional_genomics. But it is not. Do I have misunderstand > something? > > Thanks. > > On Fri, May 20, 2011 at 8:19 PM, Steffen Durinck > <durinck.steffen at="" gene.com=""> wrote: >> Steffen > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Rhoda Kinsella Ph.D. Ensembl Bioinformatician, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK.
ADD REPLYlink written 8.3 years ago by Rhoda Kinsella660
Rhoda, I have written to helpdesk at ensembl.org two days ago. But no response, maybe need more time to wait. Could you give me some words about why the items get by bioMart is not the same as in the ftp directory functional_genomics? If I can download the file from FTP sites, it will be more easy than using biomaRt. ftp://ftp.ensembl.org/pub/release-62/functional_genomics/homo_sapiens/ ftp://ftp.ensembl.org/pub/release-62/functional_genomics/homo_sapiens/ RegulatoryFeatures_CD4.Chr22.gff.gz On Mon, May 23, 2011 at 9:19 AM, Rhoda Kinsella <rhoda at="" ebi.ac.uk=""> wrote: > Hi Fabrice > Please contact helpdesk at ensembl.org who will be able to help you with your > query. > Regards > Rhoda > > > On 20 May 2011, at 21:06, Fabrice Tourre wrote: > >> Steffen, >> >> Thank you very much. It works. >> >> I am interesting to RegulatoryFeatures. I am strange why the region in >> your example cannot be found in these files. >> >> ftp://ftp.ensembl.org/pub/release-62/functional_genomics/homo_sapiens/ >> >> ftp://ftp.ensembl.org/pub/release-62/functional_genomics/homo_sapie ns/RegulatoryFeatures_CD4.Chr22.gff.gz >> >> I just think the items get by bioMart will be the same as in the ftp >> directory functional_genomics. But it is not. Do I have misunderstand >> something? >> >> Thanks. >> >> On Fri, May 20, 2011 at 8:19 PM, Steffen Durinck >> <durinck.steffen at="" gene.com=""> wrote: >>> >>> Steffen >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > Rhoda Kinsella Ph.D. > Ensembl Bioinformatician, > European Bioinformatics Institute (EMBL-EBI), > Wellcome Trust Genome Campus, > Hinxton > Cambridge CB10 1SD, > UK. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 8.2 years ago by Fabrice Tourre970
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