Hi Ernesto, Please check first if you can get it using web GUI. The problem maybe at the source
a On 29/10/10 12:08 PM, "ernesto" <ernesto.l...@crg.es> wrote: Hi, I am trying to use the biomart perl API to access Reactome data for Arabidopsis. The script I've written returns 0 entries. When I repeat the same query but using the BioMart section of Reactome (http://www.reactome.org/cgi-bin/mart) it returns 649 entries. What it's happening or what am I doing wrong? The perl script I've used to access BioMart is: use strict; use BioMart::Initializer; use BioMart::Query; use BioMart::QueryRunner; my $confFile = "/users/bi/elowy/src/biomart-perl/conf/new_registry.xml"; # # 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='clean'; my $initializer = BioMart::Initializer->new('registryFile'=>$confFile, 'action'=>$action); my $registry = $initializer->getRegistry; my $query = BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>'default'); $query->setDataset("reaction"); $query->addFilter("species_selection", ["Arabidopsis thaliana"]); $query->addAttribute("stableidentifier_identifier"); $query->addAttribute("reaction_db_id"); $query->formatter("TSV"); my $query_runner = BioMart::QueryRunner->new(); ############################## GET COUNT ############################ # $query->count(1); # $query_runner->execute($query); # print $query_runner->getCount(); ##################################################################### And the config file of my Perl api is: <MartRegistry><MartURLLocation database="test_reactome_mart" default="1" displayName="REACTOME" host="banon.cshl.edu" includeDatasets="complex,pathway,reaction,interaction" martUser="" name="REACTOME" path="/biomart/martservice" port="5555" redirect="1" serverVirtualSchema="default" visible="1" /></MartRegistry> Thanks, Ernesto Arek Kasprzyk Director, Bioinformatics Operations and Principal Investigator Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Tel: 416-673-8559 Toll-free: 1-866-678-6427 www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.
