Contents

$LOAD_PATH.unshift(File.join(File.dirname(__FILE__),'..', '..', '..', '..', 'lib'))
require 'rbbt/sources/biomart'
require 'rbbt/sources/entrez'
require File.join(File.dirname(__FILE__), '../../lib/helpers')

$taxs = [10116]
$scientific_name = "Rattus norvegicus"

$biomart_db = 'rnorvegicus_gene_ensembl'
$biomart_db_germline_variation = 'rnorvegicus_snp'
$biomart_db_somatic_variation = 'rnorvegicus_snp_som'

$biomart_lexicon = [ 
  [ 'Associated Gene Name' , "external_gene_id"], 
  [ 'HGNC symbol', "hgnc_symbol"  ],
  [ 'HGNC automatic gene name', "hgnc_automatic_gene_name"  ],
  [ 'HGNC curated gene name ', "hgnc_curated_gene_name"  ],
]

$biomart_identifiers = [ 
  ['Associated Gene Name' , "external_gene_id"], 
  ['Protein ID' , "protein_id"] , 
  ['UniProt/SwissProt ID' , "uniprot_swissprot"] , 
  ['UniProt/SwissProt Accession' , "uniprot_swissprot_accession"] , 
  ['RefSeq Protein ID' , "refseq_peptide"] , 
  ['RefSeq DNA ID' , "refseq_dna"] , 
  ['EMBL (Genbank) ID' , "embl"] , 
  ['RGD ID' , "rgd"] , 
  ['RGD Symbol' , "rgd_symbol"] , 

  ['Affy rae230a', "affy_rae230a"],
  ['Affy rae230b', "affy_rae230b"],
  ['Affy RaGene', "affy_ragene_1_0_st_v1"],
  ['Affy rat230 2', "affy_rat230_2"],
  ['Affy RaEx', "affy_raex_1_0_st_v1"],
  ['Affy rg u34a', "affy_rg_u34a"],
  ['Affy rg u34b', "affy_rg_u34b"],
  ['Affy rg u34c', "affy_rg_u34c"],
  ['Affy rn u34', "affy_rn_u34"],
  ['Affy rt u34', "affy_rt_u34"],
  ['Agilent WholeGenome',"agilent_wholegenome" ],
  ['Codelink ID ', "codelink"],
]

$namespace = File.basename(File.dirname(File.expand_path(__FILE__)))
load File.join(File.dirname(__FILE__), '../organism_helpers.rb')

Version data entries

3 entries across 3 versions & 1 rubygems

Version	Path
rbbt-sources-1.1.0	share/install/Organism/Rno/Rakefile
rbbt-sources-1.0.1	share/install/Organism/Rno/Rakefile
rbbt-sources-1.0.0	share/install/Organism/Rno/Rakefile