lib/genome/importers/russ_lampel/russ_lampel_tsv_importer.rb
module Genome
module Importers
module RussLampel
def source_info
{
base_url: 'http://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=',
site_url: 'http://www.ncbi.nlm.nih.gov/pubmed/16376820/',
citation: 'The druggable genome: an update. Russ AP, Lampel S. Drug Discov Today. 2005 Dec;10(23-24):1607-10. PMID: 16376820',
source_db_version: '26-Jul-2011',
source_type_id: DataModel::SourceType.GENE,
source_db_name: 'RussLampel',
full_name: 'The druggable genome: an update (Russ & Lampel, 2005)',
license: 'Unknown; data is no longer publicly available from external site, referenced in Elsevier copyright publication',
license_link: 'https://www.sciencedirect.com/science/article/pii/S1359644605036664',
}
end
def self.run(tsv_path)
na_filter = ->(x) { x.upcase == 'N/A' }
TSVImporter.import tsv_path, RussLampelRow, source_info do
gene :gene_stable_id, nomenclature: 'RussLampel Gene Stable Id' do
#name :HumanReadableName, nomenclature :HumanReadableName #TODO: this needs an update to the dsl to allow the nomenclature to work
name :gene_stable_id, nomenclature: 'Ensembl Gene Id', unless: na_filter
name :display_id, nomenclature: 'Display Id', unless: na_filter
name :description, nomenclature: 'Description', unless: na_filter
end
end
end
end
end
end