├── .ipynb_checkpoints └── SinglePREDICT - ML-checkpoint.ipynb ├── Dockerfile ├── Download and Save Input.ipynb ├── FeatureGeneration.ipynb ├── HumanInteractome.ipynb ├── LICENSE.txt ├── MappingPREDICTGoldstandard.ipynb ├── OMIMHpoAnnotations.ipynb ├── OpenPREDICT - ML.ipynb ├── RDFConversionOfMeshAnnotation-BioPortal.ipynb ├── RDFConversionOfMeshAnnotation.ipynb ├── RDFConversionOfPubchemMapping.ipynb ├── README.md ├── SinglePREDICT - ML.ipynb ├── data ├── conf │ ├── sml.gene.go.conf │ └── sml.omim.hpo.conf ├── external │ ├── human_interactome.tsv │ ├── human_interactome.tsv.gz │ ├── meshAnnotationsFromBioPorttalUsingOMIMDesc.txt │ ├── mim2mesh.tsv │ ├── mim2mesh.tsv.gz │ ├── msb201126-s1.csv │ ├── msb201126-s4.csv │ ├── phenotype_annotation_hpoteam.tab │ ├── phenotype_annotation_hpoteam.tab.gz │ ├── pubchem.tsv │ └── pubchem.tsv.gz ├── features │ ├── diseases-hpo-sim.csv │ ├── diseases-hpo-sim.txt.gz │ ├── diseases-pheno-sim.csv │ ├── diseases-pheno-sim.txt.gz │ ├── drugs-fingerprint-sim.csv │ ├── drugs-fingerprint-sim.txt.gz │ ├── drugs-ppi-sim.csv │ ├── drugs-ppi-sim.txt.gz │ ├── drugs-se-sim.csv │ ├── drugs-se-sim.txt.gz │ ├── drugs-target-go-sim.csv │ ├── drugs-target-go-sim.txt.gz │ ├── drugs-target-seq-sim.csv │ └── drugs-target-seq-sim.txt.gz ├── input │ ├── drugbank-drug-goa.csv │ ├── drugbank-drug-smiles.csv │ ├── drugbank-drug-synonym.csv │ ├── drugbank-drug-target.csv │ ├── drugbank-sider-se.csv │ ├── drugbank-target-seq.csv │ ├── human-interactome.csv │ ├── omim-disease-hpo.csv │ ├── omim-disease-mesh.csv │ └── openpredict-omim-drug.csv ├── ontology │ ├── README.md │ ├── go.owl.gz │ ├── hpo.owl.gz │ ├── plex_tbox_0.1.1.owl │ ├── plex_tbox_0.1.1.ttl │ ├── plex_tbox_0.1.1.xml │ ├── plex_tbox_0.1.2.owl │ ├── plex_tbox_0.1.2.ttl │ └── plex_tbox_0.1.2.xml ├── rdf │ ├── hpo_annotations.nq.gz │ ├── hpo_annotations_metadata.nq │ ├── human_interactome.nq.gz │ ├── human_interactome_metadata.nq │ ├── omim_mesh_annotations.nq.gz │ ├── omim_mesh_annotations_metadata.nq │ ├── omim_mesh_bioportal.nq.gz │ ├── omim_mesh_bioportal_metadata.nq │ ├── plex.ttl │ ├── plex_abox-opredict_0.1.0.ttl │ ├── plex_tbox-imports_and_abox-opredict_0.1.0.ttl │ ├── predict_gold_standard_omim.nq.gz │ ├── predict_gold_standard_omim_metadata.nq │ ├── pubchem_mapping.nq.gz │ ├── pubchem_mapping_metadata.nq │ └── results_disjoint_lr.nq ├── results │ ├── disjoint_lr.csv │ └── nondisjoint_lr.csv └── sparql │ ├── README.md │ ├── drugbank-drug-goa.rq │ ├── drugbank-drug-smiles.rq │ ├── drugbank-drug-synonym.rq │ ├── drugbank-drug-target.rq │ ├── drugbank-sider-sideeffects.rq │ ├── drugbank-target-seq.rq │ ├── human-interactome.rq │ ├── omim-disease-hpo.rq │ ├── omim-disease-mesh-bioportal.rq │ ├── omim-disease-mesh.rq │ └── openpredict-omim-drug.rq ├── known_associations ├── cdataset-gold-standard-omim.txt ├── drugcentral-gold-std-omim.txt ├── predict-gold-standard-omim.txt └── sider-gold-std-omim.txt ├── lib ├── biojava-alignment-4.0.0.jar ├── 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