unimart web Service not available
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@guest-user-4897
Last seen 10.2 years ago
Hi everybody, since this weekend I can't no longer connect to uniprot Biomart services via biomaRt (which worked pretty fine before) receiving the following error: > uni <- useMart("unimart",dataset="uniprot") Fehler in useMart("unimart", dataset = "uniprot") : Incorrect BioMart name, use the listMarts function to see which BioMart databases are available In fact, unimart is missing from listMarts(). I tried with R 2.14.1 and biomaRt_2.10.0 and also R 3.0.1 and biomaRt 2.16.0 leading to the same result. Any suggestions what is going on? Thanks a lot for your help, Kathrin -- output of sessionInfo(): > sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.10.0 loaded via a namespace (and not attached): [1] RCurl_1.95-3 XML_3.95-0.1 -- Sent via the guest posting facility at bioconductor.org.
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@steffen-durinck-4894
Last seen 10.2 years ago
Hi Kathrin, It looks like the BioMart server got upgraded and now includes the latest Ensembl version 71. They might have forgotten to add unimart in this upgrade and to find out we need to email the BioMart users list at users@biomart.org I will do this and get back to you to let you know what is going on. Hopefully they can re-add unimart or provide us with an alternate URL to send our queries to. Best, Steffen On Mon, May 27, 2013 at 3:20 AM, Kathrin Otte [guest] < guest@bioconductor.org> wrote: > > Hi everybody, > > since this weekend I can't no longer connect to uniprot Biomart services > via biomaRt (which worked pretty fine before) receiving the following error: > > > uni <- useMart("unimart",dataset="uniprot") > Fehler in useMart("unimart", dataset = "uniprot") : > Incorrect BioMart name, use the listMarts function to see which BioMart > databases are available > > In fact, unimart is missing from listMarts(). I tried with R 2.14.1 and > biomaRt_2.10.0 and also R 3.0.1 and biomaRt 2.16.0 leading to the same > result. > > Any suggestions what is going on? > > Thanks a lot for your help, > Kathrin > > -- output of sessionInfo(): > > > sessionInfo() > R version 2.14.1 (2011-12-22) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C > [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 > [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.10.0 > > loaded via a namespace (and not attached): > [1] RCurl_1.95-3 XML_3.95-0.1 > > -- > Sent via the guest posting facility at bioconductor.org. > [[alternative HTML version deleted]]
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Hi Kathrin, Unimart will be re-added to the central BioMart service soon, for now you can query the Uniprot BioMart service directly by doing: unimart = useMart("unimart",dataset="uniprot",host="www.ebi.ac.uk ",path="/uniprot/biomart/martservice") Best, Steffen On Tue, May 28, 2013 at 4:20 PM, Steffen Durinck <sdurinck@gmail.com> wrote: > Hi Kathrin, > > It looks like the BioMart server got upgraded and now includes the latest > Ensembl version 71. > They might have forgotten to add unimart in this upgrade and to find out > we need to email the BioMart users list at users@biomart.org > I will do this and get back to you to let you know what is going on. > Hopefully they can re-add unimart or provide us with an alternate URL to > send our queries to. > > Best, > Steffen > > > On Mon, May 27, 2013 at 3:20 AM, Kathrin Otte [guest] < > guest@bioconductor.org> wrote: > >> >> Hi everybody, >> >> since this weekend I can't no longer connect to uniprot Biomart services >> via biomaRt (which worked pretty fine before) receiving the following error: >> >> > uni <- useMart("unimart",dataset="uniprot") >> Fehler in useMart("unimart", dataset = "uniprot") : >> Incorrect BioMart name, use the listMarts function to see which BioMart >> databases are available >> >> In fact, unimart is missing from listMarts(). I tried with R 2.14.1 and >> biomaRt_2.10.0 and also R 3.0.1 and biomaRt 2.16.0 leading to the same >> result. >> >> Any suggestions what is going on? >> >> Thanks a lot for your help, >> Kathrin >> >> -- output of sessionInfo(): >> >> > sessionInfo() >> R version 2.14.1 (2011-12-22) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 >> [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] biomaRt_2.10.0 >> >> loaded via a namespace (and not attached): >> [1] RCurl_1.95-3 XML_3.95-0.1 >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> > > [[alternative HTML version deleted]]
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