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Name		Name	Last commit message	Last commit date
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tools		tools
00_download_data.py		00_download_data.py
01a_WikiData_Nodes.ipynb		01a_WikiData_Nodes.ipynb
01b_WikiData_Edges.ipynb		01b_WikiData_Edges.ipynb
01c_WikiData_Cleanup.ipynb		01c_WikiData_Cleanup.ipynb
01d_WikiData_Compute.ipynb		01d_WikiData_Compute.ipynb
02a_Reactome_DB_Queries.ipynb		02a_Reactome_DB_Queries.ipynb
02b_Reactome_Process_Queries.ipynb		02b_Reactome_Process_Queries.ipynb
03_WikiData_Reactome_Merge.ipynb		03_WikiData_Reactome_Merge.ipynb
04_InterPro_and_Ensembl.ipynb		04_InterPro_and_Ensembl.ipynb
05a_GO_Annotations.ipynb		05a_GO_Annotations.ipynb
05b_Other_Ontologies.ipynb		05b_Other_Ontologies.ipynb
05c_Computing_GO_Regulation_Edges.ipynb		05c_Computing_GO_Regulation_Edges.ipynb
06_HPO_Annotations.ipynb		06_HPO_Annotations.ipynb
07a_NCATS_Inxight_Drugs_DB_and_DC.ipynb		07a_NCATS_Inxight_Drugs_DB_and_DC.ipynb
07b_Resolving_Chemical_Identifiers.ipynb		07b_Resolving_Chemical_Identifiers.ipynb
08_CTD.ipynb		08_CTD.ipynb
09_GAUSS_Geneset_to_Phenotype.ipynb		09_GAUSS_Geneset_to_Phenotype.ipynb
10a_Disease_Pheno_Cleanup_parse_owls.ipynb		10a_Disease_Pheno_Cleanup_parse_owls.ipynb
10b_Diseae_Phenotype_Cleanup_Preliminary_DOID_cleaning.ipynb		10b_Diseae_Phenotype_Cleanup_Preliminary_DOID_cleaning.ipynb
10c_Diseae_Phenotype_Cleanup_do_hp_node_merging.ipynb		10c_Diseae_Phenotype_Cleanup_do_hp_node_merging.ipynb
10d_Diseae_Phenotype_Cleanup_deduplication.ipynb		10d_Diseae_Phenotype_Cleanup_deduplication.ipynb
10e_Diseae_Phenotype_Cleanup_adding_edges.ipynb		10e_Diseae_Phenotype_Cleanup_adding_edges.ipynb
11_Reactions_and_Regulation.ipynb		11_Reactions_and_Regulation.ipynb
12a_Preprocessing-Semmantic_Compression.ipynb		12a_Preprocessing-Semmantic_Compression.ipynb
12b_Preprocessing-Semmantic_Hierarchy_Mapping.ipynb		12b_Preprocessing-Semmantic_Hierarchy_Mapping.ipynb
12c_Preprocessing-Pruning.ipynb		12c_Preprocessing-Pruning.ipynb
12d_Preprocessing-Abbreviations_and_Biolink.ipynb		12d_Preprocessing-Abbreviations_and_Biolink.ipynb
13a_Model_Prep_Holdout_Set.ipynb		13a_Model_Prep_Holdout_Set.ipynb
13b_Model_Prep_Metapath_Membership_Analysis.ipynb		13b_Model_Prep_Metapath_Membership_Analysis.ipynb
13c_Model_Prep_Hyperparam_tuning.ipynb		13c_Model_Prep_Hyperparam_tuning.ipynb
13c_Model_Prep_Hyperparam_tuning_1000to1.ipynb		13c_Model_Prep_Hyperparam_tuning_1000to1.ipynb
13c_Model_Prep_Hyperparam_tuning_10to1.ipynb		13c_Model_Prep_Hyperparam_tuning_10to1.ipynb
13c_Model_Prep_Hyperparam_tuning_1to1.ipynb		13c_Model_Prep_Hyperparam_tuning_1to1.ipynb
14a_Model_Eval_10fold_CV.ipynb		14a_Model_Eval_10fold_CV.ipynb
14a_Model_Eval_10fold_CV_1000to1.ipynb		14a_Model_Eval_10fold_CV_1000to1.ipynb
14a_Model_Eval_10fold_CV_10to1.ipynb		14a_Model_Eval_10fold_CV_10to1.ipynb
14a_Model_Eval_10fold_CV_1to1.ipynb		14a_Model_Eval_10fold_CV_1to1.ipynb
14b_Model_Eval_Holdout_1to1.ipynb		14b_Model_Eval_Holdout_1to1.ipynb
14b_Model_Eval_Holdout_Set.ipynb		14b_Model_Eval_Holdout_Set.ipynb
14b_Model_Eval_Holdout_Set_1000to1.ipynb		14b_Model_Eval_Holdout_Set_1000to1.ipynb
14b_Model_Eval_Holdout_Set_10to1.ipynb		14b_Model_Eval_Holdout_Set_10to1.ipynb
14b_combine_1,10,100,1000to1_plots_Figure4.ipynb		14b_combine_1,10,100,1000to1_plots_Figure4.ipynb
15_Final_Model_Training.ipynb		15_Final_Model_Training.ipynb
16a_Model_results_analysis.ipynb		16a_Model_results_analysis.ipynb
16a_Results_Metolazone_Fig8.ipynb		16a_Results_Metolazone_Fig8.ipynb
16b_Model_results_analysis_DMDB.ipynb		16b_Model_results_analysis_DMDB.ipynb
16d_Model_results_analysis_Reframe_neg.ipynb		16d_Model_results_analysis_Reframe_neg.ipynb
16e_Model_results_analysis_alzheimers.ipynb		16e_Model_results_analysis_alzheimers.ipynb
17_Target_Analysis.ipynb		17_Target_Analysis.ipynb
18_Target_Analysis-DrugCentral.ipynb		18_Target_Analysis-DrugCentral.ipynb
19a_PAPER_MRN_Paper_Figure3a_3b.ipynb		19a_PAPER_MRN_Paper_Figure3a_3b.ipynb
19b_PAPER_MRN_Paper_Figure3c.ipynb		19b_PAPER_MRN_Paper_Figure3c.ipynb
graph_plots.py		graph_plots.py

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