ensembl biomart

0

Entering edit mode

Javier Díez ▴ 50

@javier-diez-2075

Last seen 10.2 years ago

Hi, Do you know how could I query the *martdb.ensembl.org* server, instead of the default server biomart.org ( I think this is the default server, isn't it?). Best Javi [[alternative HTML version deleted]]

biomaRt biomaRt • 1.8k views

ADD COMMENT • link updated 15.9 years ago by steffen@stat.Berkeley.EDU ▴ 600 • written 16.0 years ago by Javier Díez ▴ 50

0

Entering edit mode

Wolfgang Huber ★ 13k

@wolfgang-huber-3550

Last seen 3 months ago

EMBL European Molecular Biology Laborat…

15/12/2008 17:09 Javier D?ez scripsit > Hi, > Do you know how could I query the *martdb.ensembl.org* server, instead of > the default server biomart.org ( I think this is the default server, isn't > it?). > Best > Javi > Have you tried typing ? useMart and reading it? The default value for 'host' is "http://www.biomart.org/biomart/martservice" Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber

ADD COMMENT • link 16.0 years ago Wolfgang Huber ★ 13k

0

Entering edit mode

That's indeed the default host as it is the central registry which keeps track of the available BioMarts and from there a dispatch happens to other hosts depending on the BioMart you use. You probably wanted to access the 52 version of Ensembl which is not yet available from biomart.org. 52 was released last week and it takes a few days to get that update into the central registry. Try this: > listMarts(host="www.ensembl.org/biomart/martservice") biomart version 1 ENSEMBL_MART_ENSEMBL Ensembl 52 2 ENSEMBL_MART_SNP Variation 52 > mart = useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", host="www.ensembl.org/biomart/martservice") Cheers, Steffen > 15/12/2008 17:09 Javier D?ez scripsit >> Hi, >> Do you know how could I query the *martdb.ensembl.org* server, instead >> of >> the default server biomart.org ( I think this is the default server, >> isn't >> it?). >> Best >> Javi >> > > Have you tried typing > > ? useMart > > and reading it? > > > The default value for 'host' is > "http://www.biomart.org/biomart/martservice" > > Best wishes > Wolfgang > > ------------------------------------------------------------------ > Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber > > _______________________________________________ > 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 >

ADD REPLY • link 16.0 years ago steffen@stat.Berkeley.EDU ▴ 600

0

Entering edit mode

BioMart seems to be down for me at the moment - can't even access http://www.biomart.org/news.html. So out of curiosity I tried your code but got the following error. > listMarts(host="www.ensembl.org/biomart/martservice") biomart version 1 ENSEMBL_MART_ENSEMBL Ensembl 52 2 ENSEMBL_MART_SNP Variation 52 3 ENSEMBL_MART_VEGA Vega 33 > mart = useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", host="http://www.ensembl.org/biomart/martservice") Error in file(file, "r") : cannot open the connection In addition: Warning message: In file(file, "r") : InternetOpenUrl failed: 'The URL is invalid' Could you please tell me if I am doing something wrong. thanks, Sebastien > sessionInfo() R version 2.8.0 beta (2008-10-05 r46601) i386-pc-mingw32 locale: LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_M ONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia. 1252 attached base packages: [1] splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_1.16.0 GOstats_2.8.0 Category_2.8.1 genefilter_1.22.0 survival_2.34-1 RBGL_1.18.0 annotate_1.20.1 [8] xtable_1.5-4 graph_1.20.0 mouse4302.db_2.2.5 GDD_0.1-13 annaffy_1.14.0 KEGG.db_2.2.5 GO.db_2.2.5 [15] RSQLite_0.7-1 DBI_0.2-4 AnnotationDbi_1.4.1 limma_2.16.3 affyPLM_1.18.0 preprocessCore_1.4.0 gcrma_2.14.1 [22] matchprobes_1.14.0 affy_1.20.0 Biobase_2.2.1 loaded via a namespace (and not attached): [1] affyio_1.10.1 cluster_1.11.11 GSEABase_1.4.0 RCurl_0.92-0 XML_1.94-0.1 steffen at stat.berkeley.edu wrote: > That's indeed the default host as it is the central registry which keeps > track of the available BioMarts and from there a dispatch happens to other > hosts depending on the BioMart you use. > > You probably wanted to access the 52 version of Ensembl which is not yet > available from biomart.org. 52 was released last week and it takes a few > days to get that update into the central registry. > > Try this: > > >> listMarts(host="www.ensembl.org/biomart/martservice") >> > biomart version > 1 ENSEMBL_MART_ENSEMBL Ensembl 52 > 2 ENSEMBL_MART_SNP Variation 52 > > >> mart = useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", >> > host="www.ensembl.org/biomart/martservice") > > > Cheers, > Steffen > > >> 15/12/2008 17:09 Javier D?ez scripsit >> >>> Hi, >>> Do you know how could I query the *martdb.ensembl.org* server, instead >>> of >>> the default server biomart.org ( I think this is the default server, >>> isn't >>> it?). >>> Best >>> Javi >>> >>> >> Have you tried typing >> >> ? useMart >> >> and reading it? >> >> >> The default value for 'host' is >> "http://www.biomart.org/biomart/martservice" >> >> Best wishes >> Wolfgang >> >> ------------------------------------------------------------------ >> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >> >> _______________________________________________ >> 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 > >

ADD REPLY • link 15.9 years ago Sebastien Gerega ▴ 370

0

Entering edit mode

Hi Sebastien, I don't get the same error, but I am also unable to connect. However, using the MySQL interface does appear to work: > listDatasets(useMart("ensembl_mart_52", mysql=T)) connected to: ensembl_mart_52 dataset version 1 aaegypti_gene_ensembl AaegL1 2 agambiae_gene_ensembl AgamP3 3 btaurus_gene_ensembl Btau_4 4 celegans_gene_ensembl WS190 5 cfamiliaris_gene_ensembl BROADD2 6 cintestinalis_gene_ensembl JGI2 7 cporcellus_gene_ensembl cavPor3 8 csavignyi_gene_ensembl CSAV2.0 9 dmelanogaster_gene_ensembl BDGP5.4 10 dnovemcinctus_gene_ensembl ARMA [snip] Best, Jim Sebastien Gerega wrote: > BioMart seems to be down for me at the moment - can't even access > http://www.biomart.org/news.html. > So out of curiosity I tried your code but got the following error. > > listMarts(host="www.ensembl.org/biomart/martservice") > biomart version > 1 ENSEMBL_MART_ENSEMBL Ensembl 52 > 2 ENSEMBL_MART_SNP Variation 52 > 3 ENSEMBL_MART_VEGA Vega 33 > > mart = useMart("ENSEMBL_MART_ENSEMBL", > dataset="hsapiens_gene_ensembl", > host="http://www.ensembl.org/biomart/martservice") > Error in file(file, "r") : cannot open the connection > In addition: Warning message: > In file(file, "r") : InternetOpenUrl failed: 'The URL is invalid' > > Could you please tell me if I am doing something wrong. > thanks, > Sebastien > > > sessionInfo() > R version 2.8.0 beta (2008-10-05 r46601) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC _MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australi a.1252 > > > attached base packages: > [1] splines tools stats graphics grDevices utils > datasets methods base > other attached packages: > [1] biomaRt_1.16.0 GOstats_2.8.0 Category_2.8.1 > genefilter_1.22.0 survival_2.34-1 RBGL_1.18.0 > annotate_1.20.1 [8] xtable_1.5-4 graph_1.20.0 > mouse4302.db_2.2.5 GDD_0.1-13 annaffy_1.14.0 > KEGG.db_2.2.5 GO.db_2.2.5 [15] RSQLite_0.7-1 > DBI_0.2-4 AnnotationDbi_1.4.1 limma_2.16.3 > affyPLM_1.18.0 preprocessCore_1.4.0 gcrma_2.14.1 [22] > matchprobes_1.14.0 affy_1.20.0 Biobase_2.2.1 > loaded via a namespace (and not attached): > [1] affyio_1.10.1 cluster_1.11.11 GSEABase_1.4.0 RCurl_0.92-0 > XML_1.94-0.1 > > steffen at stat.berkeley.edu wrote: >> That's indeed the default host as it is the central registry which keeps >> track of the available BioMarts and from there a dispatch happens to >> other >> hosts depending on the BioMart you use. >> >> You probably wanted to access the 52 version of Ensembl which is not yet >> available from biomart.org. 52 was released last week and it takes a few >> days to get that update into the central registry. >> >> Try this: >> >> >>> listMarts(host="www.ensembl.org/biomart/martservice") >>> >> biomart version >> 1 ENSEMBL_MART_ENSEMBL Ensembl 52 >> 2 ENSEMBL_MART_SNP Variation 52 >> >> >>> mart = useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", >>> >> host="www.ensembl.org/biomart/martservice") >> >> >> Cheers, >> Steffen >> >> >>> 15/12/2008 17:09 Javier D?ez scripsit >>> >>>> Hi, >>>> Do you know how could I query the *martdb.ensembl.org* server, instead >>>> of >>>> the default server biomart.org ( I think this is the default server, >>>> isn't >>>> it?). >>>> Best >>>> Javi >>>> >>>> >>> Have you tried typing >>> >>> ? useMart >>> >>> and reading it? >>> >>> >>> The default value for 'host' is >>> "http://www.biomart.org/biomart/martservice" >>> >>> Best wishes >>> Wolfgang >>> >>> ------------------------------------------------------------------ >>> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >>> >>> _______________________________________________ >>> 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 >> >> > > _______________________________________________ > 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 Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662

ADD REPLY • link 15.9 years ago James W. MacDonald 67k

0

Entering edit mode

Dear Sebastien, you're not doing something wrong, there seems to be an issue with how www.ensembl.org/biomart/martservice is configured, and the friendly people at EBI and Ensembl are working on fixing it - we'll keep you updated. Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber 18/12/2008 03:46 Sebastien Gerega scripsit > BioMart seems to be down for me at the moment - can't even access > http://www.biomart.org/news.html. > So out of curiosity I tried your code but got the following error. >> listMarts(host="www.ensembl.org/biomart/martservice") > biomart version > 1 ENSEMBL_MART_ENSEMBL Ensembl 52 > 2 ENSEMBL_MART_SNP Variation 52 > 3 ENSEMBL_MART_VEGA Vega 33 >> mart = useMart("ENSEMBL_MART_ENSEMBL", > dataset="hsapiens_gene_ensembl", > host="http://www.ensembl.org/biomart/martservice") > Error in file(file, "r") : cannot open the connection > In addition: Warning message: > In file(file, "r") : InternetOpenUrl failed: 'The URL is invalid' > > Could you please tell me if I am doing something wrong. > thanks, > Sebastien > >> sessionInfo() > R version 2.8.0 beta (2008-10-05 r46601) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC _MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australi a.1252 > > > attached base packages: > [1] splines tools stats graphics grDevices utils > datasets methods base > other attached packages: > [1] biomaRt_1.16.0 GOstats_2.8.0 Category_2.8.1 > genefilter_1.22.0 survival_2.34-1 RBGL_1.18.0 > annotate_1.20.1 [8] xtable_1.5-4 graph_1.20.0 > mouse4302.db_2.2.5 GDD_0.1-13 annaffy_1.14.0 > KEGG.db_2.2.5 GO.db_2.2.5 [15] RSQLite_0.7-1 > DBI_0.2-4 AnnotationDbi_1.4.1 limma_2.16.3 > affyPLM_1.18.0 preprocessCore_1.4.0 gcrma_2.14.1 [22] > matchprobes_1.14.0 affy_1.20.0 Biobase_2.2.1 > loaded via a namespace (and not attached): > [1] affyio_1.10.1 cluster_1.11.11 GSEABase_1.4.0 RCurl_0.92-0 > XML_1.94-0.1 > > steffen at stat.berkeley.edu wrote: >> That's indeed the default host as it is the central registry which keeps >> track of the available BioMarts and from there a dispatch happens to >> other >> hosts depending on the BioMart you use. >> >> You probably wanted to access the 52 version of Ensembl which is not yet >> available from biomart.org. 52 was released last week and it takes a few >> days to get that update into the central registry. >> >> Try this: >> >> >>> listMarts(host="www.ensembl.org/biomart/martservice") >>> >> biomart version >> 1 ENSEMBL_MART_ENSEMBL Ensembl 52 >> 2 ENSEMBL_MART_SNP Variation 52 >> >> >>> mart = useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", >>> >> host="www.ensembl.org/biomart/martservice") >> >> >> Cheers, >> Steffen >> >> >>> 15/12/2008 17:09 Javier D?ez scripsit >>> >>>> Hi, >>>> Do you know how could I query the *martdb.ensembl.org* server, instead >>>> of >>>> the default server biomart.org ( I think this is the default server, >>>> isn't >>>> it?). >>>> Best >>>> Javi >>>> >>>> >>> Have you tried typing >>> >>> ? useMart >>> >>> and reading it? >>> >>> >>> The default value for 'host' is >>> "http://www.biomart.org/biomart/martservice" >>> >>> Best wishes >>> Wolfgang >>> >>> ------------------------------------------------------------------ >>> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >>>

ADD REPLY • link 15.9 years ago Wolfgang Huber ★ 13k

0

Entering edit mode

steffen@stat.Berkeley.EDU ▴ 600

@steffenstatberkeleyedu-2907

Last seen 10.2 years ago

We'll have to wait till the Ensembl version is updated to version 52 on the central service at biomart.org. I'll investigate why we can't use the alternate host I suggested earlier. Cheers, Steffen > Hi Steffen, > listMarts(host="www.ensembl.org/biomart/martservice") works, but not > useMart, that returns this error message: >>Error in file(file, "r") : cannot open the connection >>In addition: Warning message: >>In file(file, "r") : cannot open: HTTP status was '404 Not Found' > Best > Javi > > On Wed, Dec 17, 2008 at 6:11 AM, <steffen at="" stat.berkeley.edu=""> wrote: > >> That's indeed the default host as it is the central registry which keeps >> track of the available BioMarts and from there a dispatch happens to >> other >> hosts depending on the BioMart you use. >> >> You probably wanted to access the 52 version of Ensembl which is not yet >> available from biomart.org. 52 was released last week and it takes a >> few >> days to get that update into the central registry. >> >> Try this: >> >> > listMarts(host="www.ensembl.org/biomart/martservice") >> biomart version >> 1 ENSEMBL_MART_ENSEMBL Ensembl 52 >> 2 ENSEMBL_MART_SNP Variation 52 >> >> > mart = useMart("ENSEMBL_MART_ENSEMBL", >> dataset="hsapiens_gene_ensembl", >> host="www.ensembl.org/biomart/martservice") >> >> >> Cheers, >> Steffen >> >> > 15/12/2008 17:09 Javier D?ez scripsit >> >> Hi, >> >> Do you know how could I query the *martdb.ensembl.org* server, >> instead >> >> of >> >> the default server biomart.org ( I think this is the default server, >> >> isn't >> >> it?). >> >> Best >> >> Javi >> >> >> > >> > Have you tried typing >> > >> > ? useMart >> > >> > and reading it? >> > >> > >> > The default value for 'host' is >> > "http://www.biomart.org/biomart/martservice" >> > >> > Best wishes >> > Wolfgang >> > >> > ------------------------------------------------------------------ >> > Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >> > >> > _______________________________________________ >> > 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 >> > >> >> >

ADD COMMENT • link 15.9 years ago steffen@stat.Berkeley.EDU ▴ 600

0

Entering edit mode

Hi Javier and Steffen, Ensembl has been updated to version 52 on the central service at biomart.org. In the mean time, I will look into why the martservice is not working at ensembl.org/biomart Regards, Rhoda On 19 Dec 2008, at 03:38, steffen at stat.Berkeley.EDU wrote: > We'll have to wait till the Ensembl version is updated to version 52 > on > the central service at biomart.org. > > I'll investigate why we can't use the alternate host I suggested > earlier. > > Cheers, > Steffen > > >> Hi Steffen, >> listMarts(host="www.ensembl.org/biomart/martservice") works, but not >> useMart, that returns this error message: >>> Error in file(file, "r") : cannot open the connection >>> In addition: Warning message: >>> In file(file, "r") : cannot open: HTTP status was '404 Not Found' >> Best >> Javi >> >> On Wed, Dec 17, 2008 at 6:11 AM, <steffen at="" stat.berkeley.edu=""> wrote: >> >>> That's indeed the default host as it is the central registry which >>> keeps >>> track of the available BioMarts and from there a dispatch happens to >>> other >>> hosts depending on the BioMart you use. >>> >>> You probably wanted to access the 52 version of Ensembl which is >>> not yet >>> available from biomart.org. 52 was released last week and it >>> takes a >>> few >>> days to get that update into the central registry. >>> >>> Try this: >>> >>>> listMarts(host="www.ensembl.org/biomart/martservice") >>> biomart version >>> 1 ENSEMBL_MART_ENSEMBL Ensembl 52 >>> 2 ENSEMBL_MART_SNP Variation 52 >>> >>>> mart = useMart("ENSEMBL_MART_ENSEMBL", >>> dataset="hsapiens_gene_ensembl", >>> host="www.ensembl.org/biomart/martservice") >>> >>> >>> Cheers, >>> Steffen >>> >>>> 15/12/2008 17:09 Javier D?ez scripsit >>>>> Hi, >>>>> Do you know how could I query the *martdb.ensembl.org* server, >>> instead >>>>> of >>>>> the default server biomart.org ( I think this is the default >>>>> server, >>>>> isn't >>>>> it?). >>>>> Best >>>>> Javi >>>>> >>>> >>>> Have you tried typing >>>> >>>> ? useMart >>>> >>>> and reading it? >>>> >>>> >>>> The default value for 'host' is >>>> "http://www.biomart.org/biomart/martservice" >>>> >>>> Best wishes >>>> Wolfgang >>>> >>>> ------------------------------------------------------------------ >>>> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >>>> >>>> _______________________________________________ >>>> 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 Rhoda Kinsella Ph.D. Ensembl Bioinformatician, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK.

ADD REPLY • link 15.9 years ago Rhoda Kinsella ▴ 660

Login before adding your answer.