lib/genome/importers/msk_impact/msk_impact_tsv_importer.rb
module Genome
module Importers
module MskImpact
def self.source_info
{
base_url: 'http://www.ncbi.nlm.nih.gov/pubmed/25801821',
site_url: 'https://www.mskcc.org/msk-impact',
citation: 'Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): A Hybridization Capture-Based Next-Generation Sequencing Clinical Assay for Solid Tumor Molecular Oncology. Cheng, Donavan T., et al. The Journal of Molecular Diagnostics 17.3 (2015): 251-264. PMID: 25801821',
source_db_version: 'May-2015',
source_type_id: DataModel::SourceType.POTENTIALLY_DRUGGABLE,
source_db_name: 'MskImpact',
full_name: 'Memorial Sloan Kettering IMPACT',
source_trust_level_id: DataModel::SourceTrustLevel.EXPERT_CURATED,
license: 'Supplementary data from American Society for Investigative Pathology and the Association for Molecular Pathology copyright publication',
license_link: 'https://jmd.amjpathol.org/action/showPdf?pii=S1525-1578%2815%2900045-8',
}
end
def self.run(tsv_path)
TSVImporter.import tsv_path, MskImpactRow, source_info, header=false do
gene :gene_symbol, nomenclature: 'Gene Symbol' do
category 'CLINICALLY ACTIONABLE'
end
end.save!
end
end
end
end