├── 0. DEMO ├── Add_annots_owlready2 │ ├── AnnotationsGO_without_url.tsv.tsv │ ├── AnnotationsHP_diseases_without_url.tsv │ ├── AnnotationsHP_genes_without_url.tsv │ ├── owlready2_GOannots.py │ └── owlready2_HPannots.py ├── OPA2VEC_Annotations_url_HPO.tsv ├── OPA2Vec_Annotations_url_HPO_GO.tsv ├── OWL2Vec_entities.txt ├── OpenKE_entities.csv ├── RDF2Vec_OpenKE_GO_annotations.tsv ├── RDF2Vec_OpenKE_HP_annotations.tsv ├── RDF2Vec_entities.txt ├── Step_by_Step.pdf └── opa2vec_entities.txt ├── 1. Embeddings_calculation ├── OpenKE │ ├── base │ │ ├── Base.cpp │ │ ├── Corrupt.h │ │ ├── Random.h │ │ ├── Reader.h │ │ ├── Setting.h │ │ ├── Test.h │ │ ├── Triple.h │ │ └── Valid.h │ ├── config │ │ ├── Config.py │ │ ├── __init__.py │ │ └── __pycache__ │ │ │ ├── Config.cpython-36.pyc │ │ │ ├── Config.cpython-37.pyc │ │ │ ├── __init__.cpython-36.pyc │ │ │ └── __init__.cpython-37.pyc │ ├── models │ │ ├── Analogy.py │ │ ├── ComplEx.py │ │ ├── DistMult.py │ │ ├── HolE.py │ │ ├── Model.py │ │ ├── RESCAL.py │ │ ├── TransD.py │ │ ├── TransE.py │ │ ├── TransH.py │ │ ├── TransR.py │ │ ├── __init__.py │ │ └── __pycache__ │ │ │ ├── Analogy.cpython-36.pyc │ │ │ ├── Analogy.cpython-37.pyc │ │ │ ├── ComplEx.cpython-36.pyc │ │ │ ├── ComplEx.cpython-37.pyc │ │ │ ├── DistMult.cpython-36.pyc │ │ │ ├── DistMult.cpython-37.pyc │ │ │ ├── HolE.cpython-36.pyc │ │ │ ├── HolE.cpython-37.pyc │ │ │ ├── Model.cpython-36.pyc │ │ │ ├── Model.cpython-37.pyc │ │ │ ├── RESCAL.cpython-36.pyc │ │ │ ├── RESCAL.cpython-37.pyc │ │ │ ├── TransD.cpython-36.pyc │ │ │ ├── TransD.cpython-37.pyc │ │ │ ├── TransE.cpython-36.pyc │ │ │ ├── TransE.cpython-37.pyc │ │ │ ├── TransH.cpython-36.pyc │ │ │ ├── TransH.cpython-37.pyc │ │ │ ├── TransR.cpython-36.pyc │ │ │ ├── TransR.cpython-37.pyc │ │ │ ├── __init__.cpython-36.pyc │ │ │ └── __init__.cpython-37.pyc │ ├── release │ │ └── Base.so │ └── res │ │ └── checkpoint ├── Process_KG_TransE_DistMult.py ├── Run_OPA2Vec_embeddings.txt ├── Run_OWL2Vec_embeddings.py ├── Run_OpenKE_Embeddings.py ├── Run_RDF2VEC_embeddings.py ├── opa2vec │ ├── AddAncestors.pl │ ├── AnnotateMetadata.pl │ ├── Dockerfile │ ├── LICENSE │ ├── Prediction_File_1.tsv │ ├── ProcessOntology.groovy │ ├── README.md │ ├── RepresentationModel_pubmed.txt │ ├── getMetadata.groovy │ ├── getclasses.pl │ ├── process_vectors.py │ ├── runOPA2Vec.py │ ├── runWord2Vec.py │ └── runWord2Vec_WITHOUT_pretrain.py ├── owl2vec │ ├── Evaluator.py │ ├── Evaluator.pyc │ ├── Graph_for_OpenKE.py │ ├── Label.py │ ├── Onto_Access.py │ ├── Onto_Annotations.py │ ├── Onto_Projection.py │ ├── RDF2Vec_Embed.py │ ├── RDF2Vec_Embed.pyc │ ├── README.md │ └── __pycache__ │ │ ├── Evaluator.cpython-37.pyc │ │ ├── Label.cpython-37.pyc │ │ ├── Onto_Access.cpython-37.pyc │ │ ├── Onto_Annotations.cpython-37.pyc │ │ ├── Onto_Projection.cpython-37.pyc │ │ └── RDF2Vec_Embed.cpython-37.pyc └── pyrdf2vec │ ├── __init__.py │ ├── __pycache__ │ ├── __init__.cpython-37.pyc │ └── rdf2vec.cpython-37.pyc │ ├── embedders │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-37.pyc │ │ ├── embedder.cpython-37.pyc │ │ └── word2vec.cpython-37.pyc │ ├── embedder.py │ └── word2vec.py │ ├── graphs │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-37.pyc │ │ └── kg.cpython-37.pyc │ └── kg.py │ ├── rdf2vec.py │ ├── samplers │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-37.pyc │ │ ├── frequency.cpython-37.pyc │ │ ├── pagerank.cpython-37.pyc │ │ ├── sampler.cpython-37.pyc │ │ └── uniform.cpython-37.pyc │ ├── frequency.py │ ├── pagerank.py │ ├── sampler.py │ └── uniform.py │ └── walkers │ ├── __init__.py │ ├── __pycache__ │ ├── __init__.cpython-37.pyc │ ├── anonymous.cpython-37.pyc │ ├── community.cpython-37.pyc │ ├── halk.cpython-37.pyc │ ├── ngrams.cpython-37.pyc │ ├── random.cpython-37.pyc │ ├── walker.cpython-37.pyc │ ├── walklets.cpython-37.pyc │ └── weisfeiler_lehman.cpython-37.pyc │ ├── anonymous.py │ ├── halk.py │ ├── ngrams.py │ ├── random.py │ ├── walker.py │ ├── walklets.py │ └── weisfeiler_lehman.py ├── 2. Vector Operations an CS ├── CS_threshold.py ├── Dataset_Pairs_Label.csv ├── Indexes_split │ ├── PairsIndexes__splitTest.txt │ ├── PairsIndexes__splitTrain.txt │ └── Split_70-30.py ├── Vector_operations.py ├── example_Performance_Baseline_Cosine_Similarity.txt └── output_operator.csv ├── 3. Performance ML ├── Indexes_split │ ├── PairsIndexes__splitTest.txt │ ├── PairsIndexes__splitTrain.txt │ └── Split_70-30.py ├── Performance_ML_70-30split.py └── example_Performance_RandomForestHadamard.txt ├── Crossvalidation_10-fold ├── Median-Calculation.py ├── MedianResults_Baseline.py ├── Performance_ML_10fold.py ├── Script threshold_10fold.py ├── Threshold_Baseline_10fold.py ├── _10Fold_indexes │ ├── 10Fold_indexes__crossvalidationTest_Run_1.txt │ ├── 10Fold_indexes__crossvalidationTest_Run_10.txt │ ├── 10Fold_indexes__crossvalidationTest_Run_2.txt │ ├── 10Fold_indexes__crossvalidationTest_Run_3.txt │ ├── 10Fold_indexes__crossvalidationTest_Run_4.txt │ ├── 10Fold_indexes__crossvalidationTest_Run_5.txt │ ├── 10Fold_indexes__crossvalidationTest_Run_6.txt │ ├── 10Fold_indexes__crossvalidationTest_Run_7.txt │ ├── 10Fold_indexes__crossvalidationTest_Run_8.txt │ ├── 10Fold_indexes__crossvalidationTest_Run_9.txt │ ├── 10Fold_indexes__crossvalidationTrain_Run_1.txt │ ├── 10Fold_indexes__crossvalidationTrain_Run_10.txt │ ├── 10Fold_indexes__crossvalidationTrain_Run_2.txt │ ├── 10Fold_indexes__crossvalidationTrain_Run_3.txt │ ├── 10Fold_indexes__crossvalidationTrain_Run_4.txt │ ├── 10Fold_indexes__crossvalidationTrain_Run_5.txt │ ├── 10Fold_indexes__crossvalidationTrain_Run_6.txt │ ├── 10Fold_indexes__crossvalidationTrain_Run_7.txt │ ├── 10Fold_indexes__crossvalidationTrain_Run_8.txt │ ├── 10Fold_indexes__crossvalidationTrain_Run_9.txt │ └── Split_10Fold.py ├── example10fold_Performance_Baseline_Measure1-BMA_Seco2004.txt ├── exampleMedian_Results_RandomForestHadamard.txt └── example_10fold_Performance_RandomForestHadamard.txt ├── Dataset_Pairs_Label.csv ├── README.md ├── SS_Baseline ├── Indexes_split │ ├── PairsIndexes__splitTest.txt │ └── PairsIndexes__splitTrain.txt ├── SSMC Tool │ ├── Configuration.json │ └── SSMC-script.py ├── SSMC output example.csv ├── Threshold_Baseline.py └── example_Performance_Baseline_Measure1-BMA_Seco2004.txt └── curated_Disgenet.csv /0. 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