diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..35c75e2 --- /dev/null +++ b/.gitignore @@ -0,0 +1,55 @@ +# History files +.Rhistory +.Rapp.history + +# Session Data files +.RData + +# User-specific files +.Ruserdata + +# Example code in package build process +*-Ex.R + +# Output files from R CMD build +/*.tar.gz + +# Output files from R CMD check +/*.Rcheck/ + +# RStudio files +.Rproj.user/ +*.Rproj + +# produced vignettes +vignettes/*.html +vignettes/*.pdf + +# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3 +.httr-oauth + +# knitr and R markdown default cache directories +*_cache/ +/cache/ + +# Temporary files created by R markdown +*.utf8.md +*.knit.md + +# R Environment Variables +.Renviron + +# pkgdown site +docs/ + +# translation temp files +po/*~ + +# jupyter checkpoints +*/.ipynb_checkpoints/* + +# other temp files +*.~lock* +.idea/ +.DS_Store +*__pycache__* diff --git a/README.md b/README.md new file mode 100644 index 0000000..6163fd7 --- /dev/null +++ b/README.md @@ -0,0 +1,11 @@ +# RPath +
+ +
+ +Source code and data presented in "Causal reasoning over knowledge graphs leveraging multimodal transcriptomic signatures for drug discovery". + +## Structure + +- `data`: contains the four transcriptomic datasets used in the paper as well as the two KGs. Furthermore, it contains the drug-disease pairs studied in clinical trials which are used as positive pairs for the validation of the RPath algorithm. +- `src`: contains the code to run the algorithm and its validation as well as to preprocess the datasets. It is divided between `data_preprocess` and `notebooks`. Notebooks contains the core of the analysis and validation. diff --git a/data/gold-standard/clinical-trial.json b/data/gold-standard/clinical-trial.json new file mode 100644 index 0000000..ba6c27b --- /dev/null +++ b/data/gold-standard/clinical-trial.json @@ -0,0 +1,9936 @@ +{ + "pubchem.compound:10071196_mondo:0004975": 3, + "pubchem.compound:10071196_mondo:0012048": 5, + "pubchem.compound:10071196_mondo:0005180": 12, + "pubchem.compound:10071196_mondo:0005090": 5, + "pubchem.compound:10077130_mondo:0005015": 1, + "pubchem.compound:10077130_mondo:0005068": 7, + "pubchem.compound:10077130_mondo:0005311": 4, + "pubchem.compound:10114_mondo:0002049": 1, + "pubchem.compound:10133_mondo:0018544": 1, + "pubchem.compound:10133_mondo:0005148": 1, + "pubchem.compound:10133_mondo:0004790": 2, + "pubchem.compound:10133_mondo:0021187": 1, + "pubchem.compound:10133_mondo:0009958": 1, + "pubchem.compound:10133_mondo:0019609": 1, + "pubchem.compound:10133_mondo:0019064": 1, + 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