gmane.science.biology.biomart.general

Re: [BioMart Users] Fwd: biomart and perl API

Arek Kasprzyk — 2013-05-31T14:09:47

Hello,
it seems like your path points to rc6. The rc6 is a java version of the
BioMart code and you are trying to run the Perl one? Please make sure to
include biomart-perl libs in your path


a


On 28 May 2013 11:28, arubio <arubio< at >correo.ugr.es> wrote:

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Re: [BioMart Users] biomaRt "ensembl" database error

Arek Kasprzyk — 2013-05-30T16:06:05

Ok, doubled MySQL max connections now. Hopefully this should keep us going
for a while


a


On 30 May 2013 16:55, Arek Kasprzyk <arek.kasprzyk< at >gmail.com> wrote:

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Re: [BioMart Users] biomaRt "ensembl" database error

Arek Kasprzyk — 2013-05-30T15:55:19

Hi Stefan,
Apologies for this disruption. It should be fixed now. We have been
experiencing quite a heavy traffic recently. I'll look into fixing this a
bit more permanently

a


On 30 May 2013 16:38, Stefan Kroeger <kroeger< at >informatik.hu-berlin.de>wrote:

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Re: [BioMart Users] biomaRt "ensembl" database error

Stefan Kroeger — 2013-05-30T15:47:51

ah okay,  it works

big thanks
Stefan


2013/5/30 Steffen Durinck <sdurinck< at >gmail.com>

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Re: [BioMart Users] biomaRt "ensembl" database error

Steffen Durinck — 2013-05-30T15:41:46

Hi Stefan.

It looks like they are having some issues at the central BioMart service.
 You can query ensembl directly doing:

ensembl=useMart("ENSEMBL_MART_ENSEMBL",host="www.ensembl.org
",dataset="mmusculus_gene_ensembl")

Cheers,
Steffen


On Thu, May 30, 2013 at 8:38 AM, Stefan Kroeger <
kroeger< at >informatik.hu-berlin.de> wrote:

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[BioMart Users] biomaRt "ensembl" database error

Stefan Kroeger — 2013-05-30T15:38:15

Hi can anybody confirm my current problems on ensembl biomaRt service?

Executing the following query I get an DB error message.

require(biomaRt)
ensembl <- useMart("ensembl", dataset = "mmusculus_gene_ensembl")
biomart_data <- getBM(
      attributes=c("ensembl_gene_id",
      "ensembl_transcript_id",
      "entrezgene",
      "mgi_symbol"),
      filter="entrezgene",
      values=c("1","2"),
      mart=ensembl)

Error in getBM(attributes = c("ensembl_gene_id", "ensembl_transcript_id",
:
  Query ERROR: caught BioMart::Exception::Database: Could not connect to
mysql database ensembl_mart_71: DBI
connect('database=ensembl_mart_71;host=bm_mysql;port=3306','bmweb',...)
failed: Host '54.225.80.241' is blocked because of many connection errors;
unblock with 'mysqladmin flush-hosts' at /srv/biomart_server/
biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98

[BioMart Users] New Release of UniProt Biomart

Steven Rosanoff — 2013-05-30T11:38:12

FYI,

The newest release of the UniProt Biomart is now available and can be 
accessed using the link below.

http://www.ebi.ac.uk/uniprot/biomart/martview/

Regards,
Steve

Re: [BioMart Users] Query multiple datasets in biomart 08

Arek Kasprzyk — 2013-05-30T11:32:31

Hi Olga,
The short answer to your question is "I am not sure". I remember BioMart
being tested for this scenario early in the development cycle but I don't
think we have ever used in reality so I am not sure what the state of this
functionality is right now and if it works at all TBH.

I am hoping somebody from the list maybe able to give you more meaningful
answer

a





On 24 May 2013 14:06, Medvedeva, Olga <medvop< at >upmc.edu> wrote:

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[BioMart Users] Automatyczne pozyskiwanie danych w tym danych osobowych z ogólnodostępnych stron WWW.

Tide Software — 2013-05-30T11:18:23

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Re: [BioMart Users] Bug in BioMart 0.7 when search term contains the string 'only'

Bob MacCallum — 2013-05-29T09:47:16

Just to follow up that on the surface this smells like an SQL
injection issue but thankfully it is not.

https://github.com/i-dcc/biomart-server/blob/master/lib/BioMart/Query.pm#L1302-L1314

On Wed, May 29, 2013 at 9:31 AM, Arek Kasprzyk <arek.kasprzyk< at >gmail.com> wrote:
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Re: [BioMart Users] biomaRt: connection error - flush-hosts needed ?

Oliver Burren — 2013-05-29T08:38:13

It's fixed. Thanks a lot  for the speedy resolution.

O

On 29/05/13 09:28, Arek Kasprzyk wrote:

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Re: [BioMart Users] Bug in BioMart 0.7 when search term contains the string 'only'

Arek Kasprzyk — 2013-05-29T08:31:34

Hi Jayson,
thanks for reporting this. I am sure your workaround will be useful for a
lot of people


a


On 29 May 2013 06:48, Jayson Harshbarger <jayson< at >gsc.riken.jp> wrote:

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Re: [BioMart Users] biomaRt: connection error - flush-hosts needed ?

Arek Kasprzyk — 2013-05-29T08:28:08

Hi Oliver,
the issue should be resolved now.

a


On 29 May 2013 08:39, Oliver Burren <oliver.burren< at >cimr.cam.ac.uk> wrote:

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Re: [BioMart Users] biomaRt: connection error - flush-hosts needed ?

Oliver Burren — 2013-05-29T08:06:16

Hi Rhoda,

Yup I saw in a previous post that you had said that was a potential 
workaround  and tried that.

 > ensembl <- useMart('ENSEMBL_MART_ENSEMBL',host="www.ensembl.org")
 > ensembl <- useDataset("hsapiens_gene_ensembl",mart=ensembl)
 > gene.details<-getGene(id='ENSG00000163599', 
type="ensembl_gene_id",mart=ensembl)
Error in martCheck(mart, "ensembl") :
   This function only works when used with the ensembl BioMart.

So rather than rewrite a complicated function to use getBM I was going 
to be patient... although it leads to the question as to why getGene() 
function isn't supported on www.ensembl.org or is this just a feature of 
biomaRt ?

Thanks for you help though.

O

On 29/05/13 08:59, Rhoda Kinsella wrote:

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Re: [BioMart Users] biomaRt: connection error - flush-hosts needed ?

Rhoda Kinsella — 2013-05-29T07:59:54

HI Oliver
Until this issue is resolved at www.biomart.org, you can point your host to www.ensembl.org/biomart/martservice/ to get your data.
Hope that helps
Regards
Rhoda


On 29 May 2013, at 08:39, Oliver Burren <oliver.burren< at >cimr.cam.ac.uk> wrote:


Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton,
Cambridge,
CB10 1SD



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[BioMart Users] biomaRt: connection error - flush-hosts needed ?

Oliver Burren — 2013-05-29T07:39:59

Hi,

Not sure that this is the correct place to post but getting the 
following error using biomaRt with following code. I notice that the 
host being returned is for the BioMart portal hence why I'm posting here 
and not directly to Steffen.

Thanks for any help you can provide.

Olly Burren

#connect to BioMart
library(biomaRt)
ensembl <- useMart('ensembl')
ensembl <- useDataset("hsapiens_gene_ensembl",mart=ensembl)
gene.details<-getGene(id='ENSG00000163599', 
type="ensembl_gene_id",mart=ensembl)
Error in getBM(attributes = attrib, filters = type, values = id, mart = 
mart) :
   Query ERROR: caught BioMart::Exception::Database: Could not connect 
to mysql database ensembl_mart_71: DBI 
connect('database=ensembl_mart_71;host=bm_mysql;port=3306','bmweb',...) 
failed: Host '54.225.80.241' is blocked because of many connection 
errors; unblock with 'mysqladmin flush-hosts' at 
/srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm 
line 98


sessionInfo()
R version 3.0.1 (2013-05-

[BioMart Users] Bug in BioMart 0.7 when search term contains thestring 'only'

Jayson Harshbarger — 2013-05-29T05:48:19

Hello BioMart devs and users,

It took me some time to realize this but if a user uses the text 'only' in
any filter BioMart will show an error (copied below).  I've verified that
this is not specific to my installation.  In my case I have a field where
some entries contain the text 'only' (example 'XXX_only').  The only work
around I've discovered is to replace the 'only' text with a wildcard
(example: 'XXX_onl%').  I realize 0.7 is is an old version but there are
still many installations out there so I felt I should point this out.
 Forgive me if this is already known.

Jayson Harshbarger

ERROR: caught BioMart::Exception: non-BioMart die(): Can't locate object
method "setExcluded" via package "BioMart::Configuration::ValueFilter" at
/ensemblweb/wwwmart/www_71/biomart-perl/lib/BioMart/Query.pm line 1371.

If you repeatedly get directed to this error page, there may be a problem
with your current session parameters. To clear your session and start with
a clean slate, please click the*New* button below.

Sta

Re: [BioMart Users] unimart missing?

Arek Kasprzyk — 2013-05-28T23:53:26

Hi Steffen,
There appears to be a small technical problem with the Unimart's registry
that is preventing us from adding it to the Central Portal. I have already
notified Steven (cc'ed on this email) and I am currently awaiting his
response. As soon as this is corrected Unimart will be re-instated


a


On 29 May 2013 00:24, Steffen Durinck <sdurinck< at >gmail.com> wrote:

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[BioMart Users] unimart missing?

Steffen Durinck — 2013-05-28T23:24:58

Dear list,

It looks like unimart is missing from the registry. Was this intentionally
left out for this release?

Best,
Steffen
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[BioMart Users] biomart and perl API

arubio — 2013-05-28T10:25:24

Hello, I installed the biomart following the steps described in 
http://www.biomart.org/download.html

I need to run the code i show at the end of this mail, in a .pl flie,  
from the command line (prompt) and i get the error:

###########
Can't locate BioMart/Initializer.pm in < at >INC (< at >INC contains: 
/home/arubio/Ensembl/bioperl-1.2.3 /home/arubio/Ensembl/ensembl/modules 
/home/arubio   /Ensembl/ensembl-compara/modules 
/home/arubio/Ensembl/ensembl-variation/modules 
/home/arubio/Ensembl/ensembl-functgenomics/modules 
/home/arubio/Biomart/biomart-rc6 /usr/local/lib64/perl5 
/usr/local/share/perl5 /usr/lib64/perl5/vendor_perl 
/usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at 
bio.pl line 5.
BEGIN failed--compilation aborted at bio.pl line 5.
###########

I have include  "PERL5LIB=${PERL5LIB}:${HOME}/Biomart/biomart-rc6"  in 
bashrc file.

What can i do?

thanks



bio.pl->>>>

# An example script demonstrating the use of BioMart API.
# This perl API representation is only available for conf

[BioMart Users] Fwd: biomart and perl API

arubio — 2013-05-28T10:28:09


Hello, I installed the biomart following the steps described in 
http://www.biomart.org/download.html

I need to run the code i show at the end of this mail, in a .pl flie,  
from the command line (prompt) and i get the error:

###########
Can't locate BioMart/Initializer.pm in < at >INC (< at >INC contains: 
/home/arubio/Ensembl/bioperl-1.2.3 /home/arubio/Ensembl/ensembl/modules 
/home/arubio   /Ensembl/ensembl-compara/modules 
/home/arubio/Ensembl/ensembl-variation/modules 
/home/arubio/Ensembl/ensembl-functgenomics/modules 
/home/arubio/Biomart/biomart-rc6 /usr/local/lib64/perl5 
/usr/local/share/perl5 /usr/lib64/perl5/vendor_perl 
/usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at 
bio.pl line 5.
BEGIN failed--compilation aborted at bio.pl line 5.
###########

I have include  "PERL5LIB=${PERL5LIB}:${HOME}/Biomart/biomart-rc6"  in 
bashrc file.

What can i do?

thanks



bio.pl->>>>

# An example script demonstrating the use of BioMart API.
# This perl API representation is only available for co