BioMart is a query-oriented data management system developed jointly by the European Bioinformatics Institute (EBI) and Cold Spring Harbor Laboratory (CSHL). ()

Arek Kasprzyk | 17 May 2013 20:22

[BioMart Users] BioMart service restored

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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Mazzarotto, Francesco | 17 May 2013 16:24

[BioMart Users] R crash on getBM query

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:

> sessionInfo()

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

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Groot, Philip de | 17 May 2013 14:59

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

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
I: http://humannutrition.wur.nl

https://madmax.bioinformatics.nl

http://www.nutrigenomicsconsortium.nl

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Alexia Cardona | 17 May 2013 14:11

[BioMart Users] Biomart error

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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Sílvia Bonàs | 17 May 2013 11:38

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

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

--
Sílvia Bonàs

Joint programme IRB Barcelona-BSC

Computational Genomics

Life Sciences, Barcelona Supercomputing Center

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Steffen Durinck | 15 May 2013 22:57

www.biomart.org?

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>

</Dataset>

</Dataset>

</Query>

Cheers,

Steffen

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Rafael Hernández | 14 May 2013 18:35

[BioMart Users] Biomart 0.7 results redirections

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

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Steven Rosanoff | 14 May 2013 14:34

[BioMart Users] Error During perl configure.pl

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

--

-- 
Steven Rosanoff
Software Engineer
EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD, UK
Phone: +44 (0)1223 494565
Email: srosanof <at> ebi.ac.uk

Learn more about EBI at: http://www.ebi.ac.uk

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Widiyana Samudra | 13 May 2013 07:16

[BioMart Users] Salam Sahajetra

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 dengan harga 1,500USD(Lima belas Juta per karton)

Yang paling penting Niat dan ikhlas untuk mencari rezeki semata-mata karena Allah. Insya Allah, Allah akan membantu kita untuk mencari rezeki yang halal dan berkat,saya ingin Anda buat keputusan yang bijak, Anda bisa merubahnya .. Insya Allah '

Apa bila ada berminat atau ada pertanyaan, silahkan balas email terus ke saya berdasarkan alamat di bawah atau silahkan berikan number supaya bisa di hubungi dan saya akan menerangkannya lebih lanjut di telepon: Insya Allah saya mencoba membantu Anda. Semoga ikatan silaturahmi sesama kita diberkati Allah. Selamat berkenalan.

widiyana26 <at> yahoo.com

Yang benar...
WIDIYANA SAMUDRA

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Kristian Gray | 9 May 2013 17:44

[BioMart Users] Problem with HGNC attributes

Hi,

A user has notified us of a problem on the biomart central site. The user has pointed out that for the HGNC dataset,

it is no longer possible to select the "Approved Symbol" attribute as seen in the url below.

http://central.biomart.org/martwizard/#!/Gene_annotation?mart=Hugo+Gene+Nomenclature+%28HGNC%29+%28EBI%2C+UK%29&step=3

On our own biomart server (http://www.genenames.org/biomart/martview) has the "Approved Symbol" set as

default as this is arguably the most important attribute. If this could be correct it would be very much appreciated.

Many thanks,

Kristian Gray
Scientific Programmer
HUGO Gene Nomenclature Committee (HGNC)
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridgeshire
CB10 1SD, UK
fax: +44 (0)1223 494468
email: hgnc <at> genenames.org
http://www.genenames.org

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Sheri Skerget | 8 May 2013 18:50

[BioMart Users] Fwd: Results Export

Hello

For the past few days I have been having problems exporting results. Rather than provide a file for download I get an error message such as the one I have included below. I have tried using different browsers and have restarted my computer since encountering the problem but it persists. Although it says it may be a session problem, I think the site may be having an issue. If it is an issue on my end, please let me know if there is anything I can do to fix the problem.

Thanks!

- Sheri

ERROR: caught BioMart::Exception::Session: new(): failed: load(): couldn't thaw() data using CGI::Session::Serialize::default:thaw(): couldn't thaw. Can't find string terminator "'" anywhere before EOF at (eval 179) line 1336.

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::throw /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Web.pm:364
BioMart::Web::restore_session /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Web.pm:1443
BioMart::Web::handle_request /srv/biomart_server/biomart.org/biomart-perl/cgi-bin/martview:96
(eval) /srv/biomart_server/biomart.org/biomart-perl/cgi-bin/martview:95
ModPerl::ROOT::ModPerl::Registry::srv_biomart_server_biomart_2eorg_biomart_2dperl_cgi_2dbin_martview::handler /usr/lib/perl5/ModPerl/RegistryCooker.pm:204
(eval) /usr/lib/perl5/ModPerl/RegistryCooker.pm:204
ModPerl::RegistryCooker::run /usr/lib/perl5/ModPerl/RegistryCooker.pm:170
ModPerl::RegistryCooker::default_handler /usr/lib/perl5/ModPerl/Registry.pm:31
ModPerl::Registry::handler -e:0
(eval) -e:0

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