gmane.science.biology.biomart.general

[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

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

Tide Software — 2013-05-30T11:18:23

_______________________________________________
Users mailing list
Users< at >biomart.org
https://lists.biomart.org/mailman/listinfo/users

[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 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
  [7] LC_PAPER=C                 LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] biomaRt_2.16.0

loaded via a namespace (and not attached):
[1] RCurl_1.95-4.1 XML_3.96-1.1




_______________________________________________
Users mailing list
Users< at >biomart.org
https://lists.biomart.org/mailman/listinfo/users

[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.

Stacktrace:
Exception::Class::Base::new
/ensemblweb/wwwmart/www_71/biomart-perl/cgi-bin/martview:105
ModPerl::ROOT::ModPerl::Registry::ensemblweb_wwwmart_www_71_biomart_2dperl_cgi_2dbin_martview::handler
/localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204
(eval)
/localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204
ModPerl::RegistryCooker::run
/localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:170
ModPerl::RegistryCooker::default_handler
/localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ModPerl/Registry.pm:31
ModPerl::Registry::handler -e:0
(eval) -e:0
_______________________________________________
Users mailing list
Users< at >biomart.org
https://lists.biomart.org/mailman/listinfo/users

[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
_______________________________________________
Users mailing list
Users< at >biomart.org
https://lists.biomart.org/mailman/listinfo/users

[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 configuration 
versions >=  0.5
use strict;
use BioMart::Initializer;
use BioMart::Query;
use BioMart::QueryRunner;

my $confFile = "PATH TO YOUR REGISTRY FILE UNDER biomart-perl/conf/. 
For Biomart Central Registry navigate to
http://www.biomart.org/biomart/martservice?type=registry";
#
# NB: change action to 'clean' if you wish to start a fresh 
configuration
# and to 'cached' if you want to skip configuration step on subsequent 
runs from the same registry
#

my $action='cached';
my $initializer = BioMart::Initializer->new('registryFile'=>$confFile, 
'action'=>$action);
my $registry = $initializer->getRegistry;

my $query = 
BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>'default');


$query->setDataset("hsapiens_gene_ensembl");
$query->addAttribute("ensembl_gene_id");
$query->addAttribute("ensembl_transcript_id");
$query->addAttribute("atlas_celltype");
$query->addAttribute("atlas_diseasestate");
$query->addAttribute("atlas_organismpart");

$query->formatter("TSV");

my $query_runner = BioMart::QueryRunner->new();
############################## GET COUNT ############################
# $query->count(1);
# $query_runner->execute($query);
# print $query_runner->getCount();
#####################################################################


############################## GET RESULTS ##########################
# to obtain unique rows only
# $query_runner->uniqueRowsOnly(1);

$query_runner->execute($query);
$query_runner->printHeader();
$query_runner->printResults();
$query_runner->printFooter();
#####################################################################

_______________________________________________
Users mailing list
Users< at >biomart.org
https://lists.biomart.org/mailman/listinfo/users

[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 configuration 
versions >=  0.5
use strict;
use BioMart::Initializer;
use BioMart::Query;
use BioMart::QueryRunner;

my $confFile = "PATH TO YOUR REGISTRY FILE UNDER biomart-perl/conf/. 
For Biomart Central Registry navigate to
http://www.biomart.org/biomart/martservice?type=registry";
#
# NB: change action to 'clean' if you wish to start a fresh 
configuration
# and to 'cached' if you want to skip configuration step on subsequent 
runs from the same registry
#

my $action='cached';
my $initializer = BioMart::Initializer->new('registryFile'=>$confFile, 
'action'=>$action);
my $registry = $initializer->getRegistry;

my $query = 
BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>'default');


$query->setDataset("hsapiens_gene_ensembl");
$query->addAttribute("ensembl_gene_id");
$query->addAttribute("ensembl_transcript_id");
$query->addAttribute("atlas_celltype");
$query->addAttribute("atlas_diseasestate");
$query->addAttribute("atlas_organismpart");

$query->formatter("TSV");

my $query_runner = BioMart::QueryRunner->new();
############################## GET COUNT ############################
# $query->count(1);
# $query_runner->execute($query);
# print $query_runner->getCount();
#####################################################################


############################## GET RESULTS ##########################
# to obtain unique rows only
# $query_runner->uniqueRowsOnly(1);

$query_runner->execute($query);
$query_runner->printHeader();
$query_runner->printResults();
$query_runner->printFooter();
#####################################################################

_______________________________________________
Users mailing list
Users< at >biomart.org
https://lists.biomart.org/mailman/listinfo/users

[BioMart Users] May 27,2013: CFP from Monthly Double-Blind Peer Reviewed (Refereed/Juried)OA International Journals, available on www.ijrcm.org.in

IJRCM — 2013-05-26T18:26:10

Your email client cannot read this email.
To view it online, please go here:
http://ecruxmailer.co.in/em/display.php?M=468832&C=5b5107f8442e81c1fd51b6e8a550db5d&S=3&L=11&N=2


To stop receiving these
emails:http://ecruxmailer.co.in/em/unsubscribe.php?M=468832&C=5b5107f8442e81c1fd51b6e8a550db5d&L=11&N=3
_______________________________________________
Users mailing list
Users< at >biomart.org
https://lists.biomart.org/mailman/listinfo/users

[BioMart Users] Query multiple datasets in biomart 08

Medvedeva, Olga — 2013-05-22T21:05:46

Hi All,

Is it possible to query multiple datasets as it was in biomart 07? According to the biomart 08 user manual it needs to link 2 sources and index the link. I did exactly as it was described in the manual, using the example data sources, but in the martview I can't query them to consecutively, only separately.

What am I missing?

Thank you,
Olga.


_______________________________________________
Users mailing list
Users< at >biomart.org
https://lists.biomart.org/mailman/listinfo/users

[BioMart Users] Biomart on Mountain Lion

Rashad — 2013-05-22T17:19:27

Hi, 

In case anyone is familiar with running Biomart on mac: 

I have been using Biomart on my Mountain Lion with no problems, benefiting from the mac command line tools package, until I updated the command line tools to the latest version. My understanding is that upon doing that, I had to re-build my Biomart installation using ant. However, this did not work, and the build process fails with the following errors: 
BUILD FAILED
/Users/elbadr/ElbadrFiles/IRCM/DrugNet/Biomart/release-0_8-candidate_6/build.xml:196: IOException in /Users/elbadr/ElbadrFiles/IRCM/DrugNet/Biomart/release-0_8-candidate_6/dist/web/webapps/martapps/_js_includes.jsp - java.io.IOException:
Failed to delete /Users/elbadr/ElbadrFiles/IRCM/DrugNet/Biomart/release-0_8-candidate_6/dist/web/webapps/martapps/_js_includes.jsp while trying to rename /Users/elbadr/ElbadrFiles/IRCM/DrugNet/Biomart/release-0_8-candidate_6/dist/web/webapps/martapps/rep5565059420460101763.tmp

There is no such file, though. This happens at the end of the Build process, and obviously, when running the martconfigurator, it cannot find the classes it needs. 

Regards, 
Rashad _______________________________________________
Users mailing list
Users< at >biomart.org
https://lists.biomart.org/mailman/listinfo/users

[BioMart Users] Biomart on Mountain Lion

El-Badrawi Rachad — 2013-05-22T17:17:55

Hi,

In case anyone is familiar with running Biomart on mac:

I have been using Biomart on my Mountain Lion with no problems, benefiting from the mac command line tools package, until I updated the command line tools to the latest version. My understanding is that upon doing that, I had to re-build my Biomart installation using ant. However, this did not work, and the build process fails with the following errors:
BUILD FAILED
/Users/elbadr/ElbadrFiles/IRCM/DrugNet/Biomart/release-0_8-candidate_6/build.xml:196: IOException in /Users/elbadr/ElbadrFiles/IRCM/DrugNet/Biomart/release-0_8-candidate_6/dist/web/webapps/martapps/_js_includes.jsp - java.io.IOException:
Failed to delete /Users/elbadr/ElbadrFiles/IRCM/DrugNet/Biomart/release-0_8-candidate_6/dist/web/webapps/martapps/_js_includes.jsp while trying to rename /Users/elbadr/ElbadrFiles/IRCM/DrugNet/Biomart/release-0_8-candidate_6/dist/web/webapps/martapps/rep5565059420460101763.tmp

There is no such file, though. This happens at the end of the Build process, and obviously, when running the martconfigurator, it cannot find the classes it needs.

Regards,
Rashad
_______________________________________________
Users mailing list
Users< at >biomart.org
https://lists.biomart.org/mailman/listinfo/users

[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_homolog_perc_id_r1                 % Identity with respect to Mouse gene

Can anyone see what I'm doing wrong ?


Best.

Dubreuil Benjamin
E. Levy Group (The Cell architecture Lab)
Weitzmann Insitute of Science, ISRAEL
Kimmelman Building, 4th floor, room 410
       _______________________________________________
Users mailing list
Users< at >biomart.org
https://lists.biomart.org/mailman/listinfo/users

[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"/><Attribute
name="stableidentifier_identifier"/><Attribute
name="_displayname"/></Dataset></Query>

Any help is much appreciated. Thanks!

[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
_______________________________________________
Users mailing list
Users< at >biomart.org
https://lists.biomart.org/mailman/listinfo/users

[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 wrong.

Thanks a lot for the assistance!
Francesco Mazzarotto
_______________________________________________
Users mailing list
Users< at >biomart.org
https://lists.biomart.org/mailman/listinfo/users

[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.wur.nl/>
           https://madmax.bioinformatics.nl
           http://www.nutrigenomicsconsortium.nl<http://www.nutrigenomicsconsortium.nl/>



_______________________________________________
Users mailing list
Users< at >biomart.org
https://lists.biomart.org/mailman/listinfo/users

[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
_______________________________________________
Users mailing list
Users< at >biomart.org
https://lists.biomart.org/mailman/listinfo/users

[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

[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
_______________________________________________
Users mailing list
Users< at >biomart.org
https://lists.biomart.org/mailman/listinfo/users

[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,
results coming from queries over fungi databases (Fungi genes 17, Fungi
Variations 17,...) will set the *_site* param to "fungi", while bacteria's
queries will send the param to "bacteria"...
Is there any setting in the martRegistry.xml file that I can use as I did
with the Displayed name, the host, database name,... for each used database?

I've tried adding different *exturl *fields (exturl1,exturl2,exturl3,...),
one per each database but it doesn't work.

Any idea?

Thank you and regards,

Rafa Hernández de Diego

Genomics of Gene Expression Lab.
Bioinformatics and Genomics Department
Prince Felipe Research Centre (CIPF)
C/ Eduardo Primo Yúfera 3
46012 Valencia, Spain
_______________________________________________
Users mailing list
Users< at >biomart.org
https://lists.biomart.org/mailman/listinfo/users