gmane.science.biology.biomart.general

[BioMart Users] [biomaRt] Finding Orthologs genes between Human and Mouse - problem with getBM to retrieve some attributes

Benjamin Dubreuil — 2013-05-22T08:47:10

Hi folks,

I'm having a problem with getBM function.
I would like to retrieve the orthologs genes between Human and Mouse, with their percentage of identity to one another, their orthology relationship and their common ancestor.

I did this, and it works fine :

[1] 22886     3

But when I'm adding some attributes, I get an error : 

Error in `[.data.frame`(result, , attributes) : 
  undefined columns selected


I've checked the attributes names, I didnt make any typos:
                  name                                                  description
1                    ensembl_gene_id                                          Ensembl Gene ID
567                mmusculus_homolog_ensembl_gene           Mouse Ensembl Gene ID
573                mmusculus_homolog_orthology_type          Homology Type
574                mmusculus_homolog_subtype                     Ancestor
575                mmusculus_homolog_perc_id                      % Identity with respect to query gene
576                mmusculus_homolo

Re: [BioMart Users] General query - "Error has occurred"

Arek Kasprzyk — 2013-05-21T07:31:05

Hi Raffael,

The Reactome mart has been recently offline. I am cc'ing Robin Haw who runs
this project. Robin, do you know  if/when this service going to be restored?

cheers,
a



On 20 May 2013 17:19, Rafael Alcántara <rafael.alcantara< at >ebi.ac.uk> wrote:

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[BioMart Users] General query - "Error has occurred"

Rafael Alcántara — 2013-05-20T15:19:39

Hi,

I am trying to get Reactome pathway IDs from a given Reactome reaction
ID - i.e. any pathways in which the reaction might be involved - but get
unexpected results.

We use the biomart web service, which returns no results at all for
REACT_1524 (pyruvate kinase). I expect to get at least REACT_1383
(glycolysis).

On the other hand, the same query issued from the web front end gives me
a message "Error has occurred". The bookmark of the query is this:

http://central.biomart.org/martwizard/#!/Interaction_and_pathways?mart=Reactome+(OICR%2C+Canada%3B+EBI%2C+UK%3B+NYU+Medical+Center%2C+USA)&datasets=pathway&step=4&id_list_filters%5B%5D=reaction_id_list&id_list_filters%5B%5D=REACT_1524&id_list_filters%5B%5D=Reaction+stable+ID(s)+(e.g.+REACT_533)&attributes=stableidentifier_identifier%2C_displayname

The XML sent in the query is this:
<!DOCTYPE Query><Query client="true" processor="TSV" limit="-1"
header="1"><Dataset name="pathway" config="pathway_config"><Filter
name="reaction_id_list" value="REACT_1524"/><A

Re: [BioMart Users] Problem with HGNC attributes

Rhoda Kinsella — 2013-05-20T10:46:00

Hi Arek
HGNC is a separate project and they produce their own BioMart databases (see link that Kris added below). Therefore this issue is not related to the Ensembl mart databases or Ensembl release.
Hope that helps
Rhoda

On 9 May 2013, at 20:36, Arek Kasprzyk <arek.kasprzyk< at >gmail.com> 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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Re: [BioMart Users] Error During perl configure.pl

Syed Haider — 2013-05-18T12:16:29

cvs update on ths should fix it

biomart-perl/lib/BioMart/Configuration/URLLocation.pm




On 14 May 2013 13:34, Steven Rosanoff <srosanof< at >ebi.ac.uk> wrote:

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Re: [BioMart Users] BioMart service restored

Groot, Philip de — 2013-05-17T19:38:46

Hi Arek,



The service worked perfectly fine now. Thank you!



Regards,



Dr. Philip de Groot Ph.D.
Bioinformatics Researcher

Wageningen University / TIFN
Nutrigenomics Consortium
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
PO Box 8129, 6700 EV Wageningen
Visiting Address: Erfelijkheidsleer: De Valk, Building 304
Dreijenweg 2, 6703 HA  Wageningen
Room: 0052a
T: +31-317-485786
F: +31-317-483342
E-mail:   Philip.deGroot< at >wur.nl<mailto:Philip.deGroot< at >wur.nl>
Internet: http://www.nutrigenomicsconsortium.nl<http://www.nutrigenomicsconsortium.nl/>
             http://humannutrition.wur.nl/
             https://madmax.bioinformatics.nl/
________________________________
From: Arek Kasprzyk [arek.kasprzyk< at >gmail.com]
Sent: 17 May 2013 20:22
To: users< at >biomart.org
Cc: Francesco; alexia.cardona< at >gmail.com; Groot, Philip de; silvia.bonas< at >bsc.es; Rafael Hernández
Subject: BioMart service restored


Dear All,
It seems that one of our amazon instances blocked the other for some odd reason. This has

[BioMart Users] BioMart service restored

Arek Kasprzyk — 2013-05-17T18:22:05

Dear All,
It seems that one of our amazon instances blocked the other for some odd
reason. This has now been rectified and the service is restored. Please
report any further problems and accept our apologies for the disruption in
the BioMart service.


a
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Re: [BioMart Users] Biomart error

Alexia Cardona — 2013-05-17T16:00:30

I found a temporary solution to this by using an archive instead of the
biomart.org server today which seems to be experiencing some problems
today.  Use an archive instead eg:
mart <- useMart(host="jan2013.archive.ensembl.org", biMBL",
dataset="hsapiens_gene_ensembl")




On Fri, May 17, 2013 at 1:11 PM, Alexia Cardona <alexia.cardona< at >gmail.com>wrote:

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Re: [BioMart Users] R crash on getBM query

Thomas Maurel — 2013-05-17T15:22:08

Dear Francesco,

I can't see what's wrong with your query.
Since the query is working fine on the biomart interface on ensembl.org (see screenshot below), this might be a bug coming from the biomaRt package. I would advise you to email the bioconductor list: bioconductor< at >r-project.org

Hope this helps,
Regards,
Thomas
On 17 May 2013, at 15:24, Mazzarotto, Francesco wrote:


--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK
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[BioMart Users] R crash on getBM query

Mazzarotto, Francesco — 2013-05-17T14:24:51

Good afternoon,
I am contacting you for an information:
Every time I try to get information on a SNP using biomaRt, the R console crashes. The session info are:

R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base


And the commands that I use are:

library(biomaRt)
snp.db = useMart("ENSEMBL_MART_SNP",host="www.ensembl.org",dataset="hsapiens_snp")
variant = list(9,133271654)
var_info = getBM(c("chr_name","chrom_start","allele","minor_allele","minor_allele_freq"),c("chr_name","chrom_start"),variant,snp.db)

R always crashes at this point, also on other computers. I am using R 3.0.1 and the biomaRt package is up to date.

I really don't understand if this is a problem of the server or if I am doing something

[BioMart Users] Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_69

Groot, Philip de — 2013-05-17T12:59:57

Hi,

I tried to do a query using biomaRt and ran into the following issue:

Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_69: DBI connect('database=ensembl_mart_69;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

Looks like a configuration issue on your side?

Regards,

Dr. Philip de Groot
Bioinformatician / Microarray analysis expert

Wageningen University / TIFN
Netherlands Nutrigenomics Center (NNC)
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
PO Box 8129, 6700 EV Wageningen
Visiting Address:
"De Valk" ("Erfelijkheidsleer"),
Building 304,
Verbindingsweg 4, 6703 HC Wageningen
Room: 0052a
T: 0317 485786
F: 0317 483342
E-mail: Philip.deGroot< at >wur.nl<mailto:Philip.deGroot< at >wur.nl>
I:         http://humannutrition.wur.nl<http://humannutrition.

[BioMart Users] Biomart error

Alexia Cardona — 2013-05-17T12:11:19

Dear all,
there seems to be an error in the biomart connection.  Can anyone look into
this please?

Error:
Error in getBM(c("ensembl_gene_id", "ensembl_transcript_id", "ensembl_exon :
  Query ERROR: caught BioMart::Exception::Database: Could not connect to
matabase ensembl_mart_69: DBI
connect('database=ensembl_mart_69;host=bm_myst=3306','bmweb',...) failed:
Host '54.225.80.241' is blocked because of manection errors; unblock with
'mysqladmin flush-hosts' at /srv/
biomart_servmart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line
98


Code example:

#load Bioconductor
source("http://bioconductor.org/biocLite.R")
#load package GenomeGraphs
library(GenomeGraphs)

mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
makeGeneRegion(start=105800000, end=107800000, strand="+", chromosome="7",
biomart=mart)

Thanks
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[BioMart Users] Blocked connection to biomart --> variant retrieval

Sílvia Bonàs — 2013-05-17T09:38:14

Dear colleagues,

I usually use biomaRt from R. I am using the following mart:

*snp <- useMart("snp",dataset="hsapiens_snp") *

I did not notice any problem to look at the list of attributes or filters
from that mart. However, if I want to retrieve the following data I got
that error.

*data <-
getBM(c("refsnp_id","chrom_start"),filters=c("chr_name","chrom_start"),values=list(chrom_start=DAT$BP,chr_name=DAT$chr),mart=snp)
*

Error en getBM(c("refsnp_id", "chrom_start"), filters = c("chr_name",  :
  Query ERROR: caught BioMart::Exception::Database: Could not connect to
mysql database snp_mart_69: DBI
connect('database=snp_mart_69;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*


Thank you for attention.

Kind regards

Re: [BioMart Users] inter dataset query not working onwww.biomart.org?

Thomas Maurel — 2013-05-16T09:05:23

Dear Steffen,

I am sorry, we had a bug in the ensembl mart release 69 were the second dataset wasn't working properly.
This was fixed in the ensembl mart release 70 but since biomart central is still pointing to the release 69 databases the bug is still there.
You can use the up to date ensembl mart on ensembl.org until biomart central get updated.

Hope this helps,
Thomas
On 15 May 2013, at 21:57, Steffen Durinck wrote:


--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK

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[BioMart Users] inter dataset query not working on www.biomart.org?

Steffen Durinck — 2013-05-15T20:57:42

Hi All,

The query below returns a result when used at the Ensembl BioMart server
but not against www.biomart.org  (v0.7).  Is there an issue with inter
dataset queries like these at www.biomart.org?

<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query>
<Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0'
datasetConfigVersion = '0.6' header='1' requestid= "biomaRt">
<Dataset name = 'hsapiens_gene_ensembl'>
<Attribute name = 'hgnc_symbol'/>
<Attribute name = 'chromosome_name'/>
<Attribute name = 'start_position'/>
<Filter name = 'hgnc_symbol' value = 'TP53' />
</Dataset>
<Dataset name = 'mmusculus_gene_ensembl' >
<Attribute name = 'chromosome_name'/>
<Attribute name = 'start_position'/>
</Dataset>
</Query>

Cheers,
Steffen
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[BioMart Users] Biomart 0.7 results redirections

Rafael Hernández — 2013-05-14T16:35:47

Hi biomart devs,

I've configured Biomart v0.7 to work with different databases such as
Ensembl Genes 70, Ensembl Bacteria 17, Ensembl Fungi 17...
Everything works fine but when I get a list of genes or transcripts and I
click on the links, Biomart try to send me to Ensembl but without success.

In the *settings.conf* file, I changed the redirection with the *exturl* field
adding my own URL which send the request to a cgi perl script. This script
send users to the correct Ensembl version.
i.e. If the user queries the Ensembl Fungi Genes 17 using Biomart and
obtains a list of genes, when clicking one of those genes, the idea is that
Biomart send the request to the *redirect *script with a param
"_site=fungi". The redirection script will read the value of the *_site* param
and send the request to the correct Ensembl site.
Eg. *my_server_url**/*cgi/
redirect.pl?_site=fungi&_trail=/Gallus_gallus/Gene/Summary?db=core;g=ENSGALG00000014600

My question is, How can I map each database with its own URL? In this way,

[BioMart Users] Error During perl configure.pl

Steven Rosanoff — 2013-05-14T12:34:00

Hello,

I started getting a weird error message while trying to run the 
configure.pl on my registry file. I checked the registry file and 
everything looks fine. I tried to archive cached registires and run it 
with the --clean command but get the same error. Any ideas where to start?


Warning: Use of "require" without parentheses is ambiguous at (eval 113) 
line 1.
Bareword found where operator expected at (eval 113) line 1, near 
"888110DD34A1D613C5E6EF76903DF9CC"
         (Missing operator before DD34A1D613C5E6EF76903DF9CC?)
Reversed /= operator at (eval 113) line 1.

ERROR something wrong with your registry: could not load module 
BioMart::Dataset::Set-Cookie: 
X-Mapping-gbooldlg=888110DD34A1D613C5E6EF76903DF9CC;path=/: Search 
pattern not terminated at (eval 113) line 1.


regards,
Steve

[BioMart Users] Salam Sahajetra

Widiyana Samudra — 2013-05-13T05:16:32

Assalamualaikum Wr.Wb...

Sebelum dan sesudahnya saya ingin memperkenalkan diri saya,nama saya WIDIYANA SAMUDRA berasal dari Indonesia dan bekerja di London (United Kingdom), ingin berkenalan dengan anda di sana.
Saya ingin menawarkan satu peluang bisnis yang begitu bagus,dan  bagi Anda yang berminat dengan bisnis ... Inilah kesempatan Anda,kapan lagi kalau bukan sekarang bukan.???
Produk ini di namakan (MULITE CLEANSER) kegunaannya untuk mencuci barangan yang sangat berharga sekali seperti batu intan permata yg masih mentah.
Dan pada waktu yang sama perusahaan di tempat saya bekerja membutuhkan MULITE CLEANSER dimana mineral tersbut tersedia dari operator yg di Indonesia.
Jadi bagi anda yang berminat dengan bisnis ini, saya ingin Anda menjadi Agent untuk menjual produk tersebut ke pada perusahaan tempat saya bekerja, (Anda membeli produk tersebut dari operator yang di Indonesia terlebih dahulu dengan harga 500USD(Lima Juta Rupiah) per karton dan dijualnya kembali ke pada perusahaan  di tempat saya bekerja d

Re: [BioMart Users] Problem with biomaRt::getSequence

Steffen Durinck — 2013-05-10T15:57:23

Thanks Arek,

I check the query in R and it is indeed working again!

Cheers,
Steffen


On Thu, May 9, 2013 at 12:29 PM, Arek Kasprzyk <arek.kasprzyk< at >gmail.com>wrote:

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Re: [BioMart Users] Problem with HGNC attributes

Arek Kasprzyk — 2013-05-09T19:36:37

Hi Krisitian,
we are happy to fix it if this is available in the latest Ensembl release.
Rhoda, could you confirm?


a


On 9 May 2013 16:44, Kristian Gray <hgnc< at >genenames.org> wrote:

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Re: [BioMart Users] Fwd: Results Export

Arek Kasprzyk — 2013-05-09T19:31:13

Hi Sheri,
there was an issue with a missing mysql tmp directory. Could you check if
your problem still persist?


a


On 8 May 2013 17:50, Sheri Skerget <sskerget< at >asu.edu> wrote:

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