h4ste / trec-pm Goto Github PK

Hi
First of all thanks for sharing your code. Actually, I wanted to reproduce the results of your paper and wanted to know from where and how to obtain the data and misc files to reproduce the results.

First ,thank you for your code,I want to implement your model, but I don't know much about java. So I want to know your model scores in Clincial,I know this is very presumptuous, but I am really anxious, sorry.

First of all, thank you for sharing the code!
I tried to follow the setup steps. However, the knowledge base resource files are required. I tried to collect the files for COSMIC. The configuration file lists the following files:

 cosmic {
    base-path = ${data.external-base-path}"/cosmic"
    drug-target-path = ${data.cosmic.base-path}"/cosmic_drug_gene.csv"
    cancer-gene-census-path = ${data.cosmic.base-path}"/cancer_gene_census.csv"
    resistance-mutations-path = ${data.cosmic.base-path}"/cosmic_resistance_mutations.tsv"
  }

The cosmic_resistance_mutations.tsv seems to be the exact file you can download from https://cancer.sanger.ac.uk/cosmic/download, no issue here. The cancer_gene_census.csv seems to be available at https://cancer.sanger.ac.uk/census.
But where does the cosmic_drug_gene.csv file come from? I found https://www.cancerrxgene.org/translation/Feature/152#vp but this would only give information about one gene at a time and there are quite some settings that what data you get.

Could you please give instructions as how to create the resource files the way you did? Thank you!