data

overview

This directory contains the 'raw' files from various sources necessary for g2p harvesting.

contents

• pmkb_interpretations.json

  • manual download
  • raw interpretations from cornell linda at standardmolecular dot com

• molecularmatch_trials.json

  • pre-harmonization download of molecularmatch trials
  • recreate via python harvester.py --silos file --harvesters molecularmatch_trials --phases harvest

• cgi

  • cgi_biomarkers_per_variant.tsv
  • catalog_of_validated_oncogenic_mutations.tsv
  • manual download
  • raw evidence

• allAnnotatedVariants.txt, allActionableVariants.txt

  • download by clicking link, or going to oncokb.org/#/dataAccess
  • used to run harvester on oncokb
  • 'oncokb_' prefix added to files for clarity

• data_mutations_extended_1.0.1.txt,data_clinical_1.0.1.txt

  • manual registration and download
  • cohort for GENIE analysis notebook

• harvester/cosmic_lookup_table.tsv

  • manual download
  • pre processing done by harvester/Makefile including harvester/oncokb_all_actionable_variants.tsv

• msk_impact_2017/*

  • manual download from 'Download Data' button at top of page
  • cohort for GENIE analysis notebook

• non_alt_loci_set.json

  • wget ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/json/non_alt_loci_set.json
  • gene symbol validation