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.
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]]
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]]