problems connecting to Biomart today?
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@jdelasherasedacuk-1189
Last seen 9.3 years ago
United Kingdom
I seem to be unable to use biomaRt today (working fine Friday) but I don't see anything on the Biomart website wbout downtime, so I am not sure if the problem lies at my end. Any ideas? Jose example: library(biomaRt) ensembl=useMart("ensembl") dataset="hsapiens_gene_ensembl" ensembl=useDataset(dataset, mart=ensembl) getBM(attributes="hgnc_curated_gene_name", filters="entrezgene", values=c(1,33), mart=ensembl) I get: Error in getBM(attributes = "hgnc_curated_gene_name", filters = "entrezgene", : Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_61: DBI connect('database=ensembl_mart_61;host=dcc-qa- db.oicr.on.ca;port=3306','bm_web',...) failed: Can't connect to MySQL server on 'dcc-qa-db.oicr.on.ca' (113) at /srv/biomart_server/biomart.org/biomart- perl/lib/BioMart/Configuration/DBLocation.pm line 98 > my sessionInfo() R version 2.11.0 (2010-04-22) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] xtable_1.5-6 GO.db_2.4.1 org.Hs.eg.db_2.4.1 annotate_1.26.0 GOstats_2.14.0 [6] RSQLite_0.9-0 DBI_0.2-5 graph_1.28.0 Category_2.14.0 AnnotationDbi_1.10.1 [11] Biobase_2.8.0 biomaRt_2.4.0 loaded via a namespace (and not attached): [1] genefilter_1.30.0 GSEABase_1.10.0 RBGL_1.26.0 RCurl_1.4-2 splines_2.11.0 survival_2.35-9 [7] tools_2.11.0 XML_3.1-0 -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6507095 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
GO biomaRt GO biomaRt • 1.7k views
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@rhoda-kinsella-3200
Last seen 10.2 years ago
Hi Jose, The reason for this error is that the HGNC curated gene name attribute has been removed. We have also removed HGNC automated filters and attributes as these external references were confusing for users. You can still retrieve the HGNC ID and symbol and also the HGNC transcript name from the database. I hope this helps. Regards Rhoda On 21 Feb 2011, at 12:19, <j.delasheras at="" ed.ac.uk=""> wrote: > I seem to be unable to use biomaRt today (working fine Friday) but I > don't see anything on the Biomart website wbout downtime, so I am > not sure if the problem lies at my end. Any ideas? > > Jose > > example: > > library(biomaRt) > ensembl=useMart("ensembl") > dataset="hsapiens_gene_ensembl" > ensembl=useDataset(dataset, mart=ensembl) > > getBM(attributes="hgnc_curated_gene_name", filters="entrezgene", > values=c(1,33), mart=ensembl) > > I get: > Error in getBM(attributes = "hgnc_curated_gene_name", filters = > "entrezgene", : > Query ERROR: caught BioMart::Exception::Database: Could not connect > to mysql database ensembl_mart_61: DBI > connect('database=ensembl_mart_61;host=dcc-qa- > db.oicr.on.ca;port=3306','bm_web',...) failed: Can't connect to > MySQL server on 'dcc-qa-db.oicr.on.ca' (113) at /srv/biomart_server/ > biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm > line 98 >> > > > my sessionInfo() > > R version 2.11.0 (2010-04-22) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United > Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 > [4] LC_NUMERIC=C LC_TIME=English_United > Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] xtable_1.5-6 GO.db_2.4.1 org.Hs.eg.db_2.4.1 > annotate_1.26.0 GOstats_2.14.0 > [6] RSQLite_0.9-0 DBI_0.2-5 graph_1.28.0 > Category_2.14.0 AnnotationDbi_1.10.1 > [11] Biobase_2.8.0 biomaRt_2.4.0 > > loaded via a namespace (and not attached): > [1] genefilter_1.30.0 GSEABase_1.10.0 RBGL_1.26.0 > RCurl_1.4-2 splines_2.11.0 survival_2.35-9 > [7] tools_2.11.0 XML_3.1-0 > > > -- > Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk > The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 > 6507095 > Institute for Cell & Molecular Biology Fax: +44 (0)131 > 6507360 > Swann Building, Mayfield Road > University of Edinburgh > Edinburgh EH9 3JR > UK > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > _______________________________________________ > 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.
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Quoting Rhoda Kinsella <rhoda at="" ebi.ac.uk="">: > Hi Jose, > The reason for this error is that the HGNC curated gene name > attribute has been removed. We have also removed HGNC automated > filters and attributes as these external references were confusing > for users. You can still retrieve the HGNC ID and symbol and also > the HGNC transcript name from the database. I hope this helps. > Regards > Rhoda Hi Rhoda, anywhere I can check what else has changed? The example I put there was one that gave me teh same error, but what I was after really were the Gene Ontologies, have those been deleted/renamed also?: "go_cellular_component_id", "go_cellular_component__dm_name_1006" "go_biological_process_id", "name_1006" "go_molecular_function_id", "go_molecular_function__dm_name_1006" "goslim_goa_accession", "goslim_goa_description" Jose -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6507095 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
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Hi Jose You can find the lists of filters and attributes available for each species using the following (e.g for the human dataset): http://www.ensembl.org/biomart/martservice?type=filters&dataset=hsapie ns_gene_ensembl http://www.ensembl.org/biomart/martservice?type=attributes&dataset=hsa piens_gene_ensembl I also try to send out an e-mail of changes to the biomart and bioconductor mailing lists after each release. I hope that helps Rhoda On 21 Feb 2011, at 13:15, J.delasHeras@ed.ac.uk wrote: > Quoting Rhoda Kinsella <rhoda@ebi.ac.uk>: > >> Hi Jose, >> The reason for this error is that the HGNC curated gene name >> attribute has been removed. We have also removed HGNC automated >> filters and attributes as these external references were confusing >> for users. You can still retrieve the HGNC ID and symbol and also >> the HGNC transcript name from the database. I hope this helps. >> Regards >> Rhoda > > > Hi Rhoda, > > anywhere I can check what else has changed? > The example I put there was one that gave me teh same error, but > what I was after really were the Gene Ontologies, have those been > deleted/renamed also?: > > "go_cellular_component_id", > "go_cellular_component__dm_name_1006" > > "go_biological_process_id", > "name_1006" > > "go_molecular_function_id", > "go_molecular_function__dm_name_1006" > > "goslim_goa_accession", > "goslim_goa_description" > > Jose > > > -- > Dr. Jose I. de las Heras Email: J.delasHeras@ed.ac.uk > The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 > 6507095 > Institute for Cell & Molecular Biology Fax: +44 (0)131 > 6507360 > Swann Building, Mayfield Road > University of Edinburgh > Edinburgh EH9 3JR > UK > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > Rhoda Kinsella Ph.D. Ensembl Bioinformatician, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK. [[alternative HTML version deleted]]
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@hotz-hans-rudolf-3951
Last seen 4.1 years ago
Switzerland
Hi Jose it is the Biomart server...the web site is up, but you can't do any queries (ie they will produce the same error message as you got through the biomaRt interface). you should contact the Biomart team. Regards, Hans On 02/21/2011 01:19 PM, J.delasHeras at ed.ac.uk wrote: > I seem to be unable to use biomaRt today (working fine Friday) but I > don't see anything on the Biomart website wbout downtime, so I am not > sure if the problem lies at my end. Any ideas? > > Jose > > example: > > library(biomaRt) > ensembl=useMart("ensembl") > dataset="hsapiens_gene_ensembl" > ensembl=useDataset(dataset, mart=ensembl) > > getBM(attributes="hgnc_curated_gene_name", filters="entrezgene", > values=c(1,33), mart=ensembl) > > I get: > Error in getBM(attributes = "hgnc_curated_gene_name", filters = > "entrezgene", : > Query ERROR: caught BioMart::Exception::Database: Could not connect to > mysql database ensembl_mart_61: DBI > connect('database=ensembl_mart_61;host=dcc-qa- db.oicr.on.ca;port=3306','bm_web',...) > failed: Can't connect to MySQL server on 'dcc-qa-db.oicr.on.ca' (113) at > /srv/biomart_server/biomart.org/biomart- perl/lib/BioMart/Configuration/DBLocation.pm > line 98 >> > > > my sessionInfo() > > R version 2.11.0 (2010-04-22) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United > Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 > [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] xtable_1.5-6 GO.db_2.4.1 org.Hs.eg.db_2.4.1 annotate_1.26.0 > GOstats_2.14.0 > [6] RSQLite_0.9-0 DBI_0.2-5 graph_1.28.0 Category_2.14.0 > AnnotationDbi_1.10.1 > [11] Biobase_2.8.0 biomaRt_2.4.0 > > loaded via a namespace (and not attached): > [1] genefilter_1.30.0 GSEABase_1.10.0 RBGL_1.26.0 RCurl_1.4-2 > splines_2.11.0 survival_2.35-9 > [7] tools_2.11.0 XML_3.1-0 > >
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Hi Jose I should also have mentioned in my previous email that if you are having difficulties doing other queries, this may be a server issue at www.biomart.org and you should try running your query against www.ensembl.org marts by setting host=www.ensembl.org. I hope that helps, Regards Rhoda On 21 Feb 2011, at 12:38, Hans-Rudolf Hotz wrote: > Hi Jose > > it is the Biomart server...the web site is up, but you can't do any > queries (ie they will produce the same error message as you got > through the biomaRt interface). you should contact the Biomart team. > > Regards, Hans > > > > On 02/21/2011 01:19 PM, J.delasHeras at ed.ac.uk wrote: >> I seem to be unable to use biomaRt today (working fine Friday) but I >> don't see anything on the Biomart website wbout downtime, so I am not >> sure if the problem lies at my end. Any ideas? >> >> Jose >> >> example: >> >> library(biomaRt) >> ensembl=useMart("ensembl") >> dataset="hsapiens_gene_ensembl" >> ensembl=useDataset(dataset, mart=ensembl) >> >> getBM(attributes="hgnc_curated_gene_name", filters="entrezgene", >> values=c(1,33), mart=ensembl) >> >> I get: >> Error in getBM(attributes = "hgnc_curated_gene_name", filters = >> "entrezgene", : >> Query ERROR: caught BioMart::Exception::Database: Could not connect >> to >> mysql database ensembl_mart_61: DBI >> connect('database=ensembl_mart_61;host=dcc-qa- >> db.oicr.on.ca;port=3306','bm_web',...) >> failed: Can't connect to MySQL server on 'dcc-qa- >> db.oicr.on.ca' (113) at >> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/ >> Configuration/DBLocation.pm >> line 98 >>> >> >> >> my sessionInfo() >> >> R version 2.11.0 (2010-04-22) >> i386-pc-mingw32 >> >> locale: >> [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United >> Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 >> [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] xtable_1.5-6 GO.db_2.4.1 org.Hs.eg.db_2.4.1 annotate_1.26.0 >> GOstats_2.14.0 >> [6] RSQLite_0.9-0 DBI_0.2-5 graph_1.28.0 Category_2.14.0 >> AnnotationDbi_1.10.1 >> [11] Biobase_2.8.0 biomaRt_2.4.0 >> >> loaded via a namespace (and not attached): >> [1] genefilter_1.30.0 GSEABase_1.10.0 RBGL_1.26.0 RCurl_1.4-2 >> splines_2.11.0 survival_2.35-9 >> [7] tools_2.11.0 XML_3.1-0 >> >> > > _______________________________________________ > 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.
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Quoting Rhoda Kinsella <rhoda at="" ebi.ac.uk="">: > Hi Jose > I should also have mentioned in my previous email that if you are > having difficulties doing other queries, this may be a server issue > at www.biomart.org and you should try running your query against > www.ensembl.org marts by setting host=www.ensembl.org. > I hope that helps, > Regards > Rhoda Hi again Rhoda, using the www.ensembl.org as host does allow me to do the queries I needed. Thank you. To clarify, if anybody else was on the same boat as I: library(biomaRt) ensembl=useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org") dataset="hsapiens_gene_ensembl" ensembl=useDataset(dataset, mart=ensembl) attributes1=attributes1=c("entrezgene", "go_cellular_component_id", "go_cellular_component__dm_name_1006") obj=c(949, 3576) getBM(attributes=attributes1, filters="entrezgene", values=obj, mart=ensembl) Jose -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6507095 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
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