├── .github ├── ISSUE_TEMPLATE │ ├── bug.yml │ └── model.yml ├── dependabot.yml ├── release.yml └── workflows │ ├── python-publish.yml │ └── unittests.yml ├── .gitignore ├── CHANGELOG.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── README.md ├── environment.yml ├── make.bat ├── simpler_triples_file.tsv └── source │ ├── api │ ├── base_models │ │ └── index.rst │ ├── corpus │ │ └── index.rst │ ├── datasets │ │ └── index.rst │ ├── evaluation │ │ └── index.rst │ ├── extra │ │ ├── dl2vec.rst │ │ └── owl2vec.rst │ ├── models │ │ └── index.rst │ ├── nn │ │ └── index.rst │ ├── ontology │ │ └── index.rst │ ├── owlapi │ │ └── index.rst │ ├── projection │ │ └── index.rst │ ├── reasoning │ │ └── index.rst │ ├── visualization │ │ └── index.rst │ └── walking │ │ └── index.rst │ ├── appendix │ └── references.rst │ ├── conf.py │ ├── corpus │ └── index.rst │ ├── datasets │ ├── index.rst │ ├── testing_ontology.owl │ ├── training_ontology.owl │ └── validation_ontology.owl │ ├── embedding_el │ └── index.rst │ ├── evaluation │ └── index.rst │ ├── examples │ ├── elmodels │ │ ├── images │ │ │ └── thumb │ │ │ │ ├── sphx_glr_plot_1_elembeddings_thumb.png │ │ │ │ └── sphx_glr_plot_2_elboxembeddings_thumb.png │ │ ├── index.rst │ │ ├── plot_1_elembeddings.ipynb │ │ ├── plot_1_elembeddings.py │ │ ├── plot_1_elembeddings.py.md5 │ │ ├── plot_1_elembeddings.rst │ │ ├── plot_2_elboxembeddings.ipynb │ │ ├── plot_2_elboxembeddings.py │ │ ├── plot_2_elboxembeddings.py.md5 │ │ ├── plot_2_elboxembeddings.rst │ │ └── sg_execution_times.rst │ ├── graph_based │ │ ├── images │ │ │ └── thumb │ │ │ │ └── sphx_glr_plot_1_dl2vec_thumb.png │ │ ├── index.rst │ │ ├── plot_1_dl2vec.ipynb │ │ ├── plot_1_dl2vec.py │ │ ├── plot_1_dl2vec.py.md5 │ │ ├── plot_1_dl2vec.rst │ │ └── sg_execution_times.rst │ ├── index.rst │ └── syntactic │ │ ├── images │ │ └── thumb │ │ │ ├── sphx_glr_plot_1_onto2vec_thumb.png │ │ │ └── sphx_glr_plot_2_opa2vec_thumb.png │ │ ├── index.rst │ │ ├── plot_1_onto2vec.ipynb │ │ ├── plot_1_onto2vec.py │ │ ├── plot_1_onto2vec.py.md5 │ │ ├── plot_1_onto2vec.rst │ │ ├── plot_2_opa2vec.ipynb │ │ ├── plot_2_opa2vec.py │ │ ├── plot_2_opa2vec.py.md5 │ │ ├── plot_2_opa2vec.rst │ │ └── sg_execution_times.rst │ ├── faq │ └── errors │ │ └── index.rst │ ├── graphs │ ├── index.rst │ ├── kge.rst │ ├── projection.rst │ └── random_walks.rst │ ├── imgs │ └── architecture.png │ ├── index.rst │ ├── install │ └── index.rst │ ├── mowl-logo.jpg │ ├── mowl_black_background_colors_2048x2048px.png │ ├── mowl_white_background_colors_2048x2048px.png │ ├── ontology │ ├── MyOntology.owl │ ├── annots.tsv │ ├── index.rst │ ├── my_triples_file.tsv │ └── simpler_triples_file.tsv │ ├── owlapi │ └── index.rst │ ├── pyplots │ └── tsne.py │ └── visualization │ └── index.rst ├── envs ├── environment_3_10.yml ├── environment_3_11.yml ├── environment_3_12.yml ├── environment_3_13.yml ├── environment_dev_3_10.yml ├── environment_dev_3_11.yml ├── environment_dev_3_12.yml └── environment_dev_3_13.yml ├── examples ├── README.rst ├── elmodels │ ├── README.rst │ ├── plot_1_elembeddings.py │ └── plot_2_elboxembeddings.py ├── environment.yml ├── graph_based │ ├── README.rst │ └── plot_1_dl2vec.py └── syntactic │ ├── README.rst │ ├── plot_1_onto2vec.py │ └── plot_2_opa2vec.py ├── experiments ├── README.md ├── box2el │ ├── ppi.py │ └── subsumption.py ├── boxel │ ├── ppi.py │ └── subsumption.py ├── cate │ ├── add_ppi_nodes.py │ ├── data.py │ ├── kg.py │ ├── ppi.py │ └── subsumption.py ├── compute_deductive_closure.py ├── create_subsumption_dataset.py ├── datasets.py ├── download_ontologies.py ├── elbe │ └── ppi.py ├── elembeddings │ ├── ppi.py │ └── subsumption.py ├── environment.yml ├── evaluators.py ├── opa2vec │ ├── ppi.py │ ├── ppi_nn.py │ ├── subsumption.py │ └── subsumption_nn.py ├── owl2vecstar │ ├── ppi.py │ ├── ppi_kg.py │ ├── subsumption.py │ └── subsumption_kg.py └── utils.py ├── extra ├── annotations.py ├── create_dataset.py ├── uni2pandas.py └── utils.py ├── gateway ├── build.gradle ├── gradle │ └── wrapper │ │ ├── gradle-wrapper.jar │ │ └── gradle-wrapper.properties ├── gradlew ├── gradlew.bat ├── settings.gradle └── src │ └── main │ ├── groovy │ └── org │ │ └── mowl │ │ ├── Edge.groovy │ │ └── HelloG.groovy │ ├── java │ ├── Main.java │ └── org │ │ └── mowl │ │ ├── Edge.java │ │ └── MOWLShortFormProvider.java │ └── scala │ └── org │ └── mowl │ ├── CatParser │ └── CatParser.scala │ ├── Hello.scala │ ├── Projectors │ ├── AbstractProjector.scala │ ├── DL2VecProjector.scala │ ├── OWL2VecStarProjector.scala │ ├── TaxonomyProjector.scala │ └── TaxonomyWithRelsProjector.scala │ ├── Types.scala │ ├── Utils.scala │ └── Walking │ ├── DeepWalk.scala │ └── Node2Vec.scala ├── gradle_install.sh ├── mowl ├── __init__.py ├── base_models │ ├── __init__.py │ ├── alcmodel.py │ ├── elmodel.py │ ├── graph_model.py │ ├── model.py │ └── syntactic_model.py ├── corpus │ ├── __init__.py │ └── base.py ├── datasets │ ├── __init__.py │ ├── alc │ │ ├── __init__.py │ │ └── alc_dataset.py │ ├── base.py │ ├── builtin │ │ ├── #family.py# │ │ ├── #gda.py# │ │ ├── __init__.py │ │ ├── family.py │ │ ├── gda.py │ │ ├── gda2.py │ │ ├── hpi.py │ │ ├── ppi_yeast.py │ │ └── subsumption.py │ ├── el │ │ ├── __init__.py │ │ └── el_dataset.py │ └── gci.py ├── error │ ├── __init__.py │ └── messages.py ├── evaluation │ ├── __init__.py │ ├── base.py │ ├── gda.py │ ├── metrics.py │ ├── ppi.py │ ├── predictions.py │ ├── rank_based.py │ └── subsumption.py ├── inference │ ├── __init__.py │ ├── axiom_scoring.py │ ├── base.py │ ├── cosine.py │ ├── el.py │ └── elinfer │ │ ├── gci0.py │ │ └── gci2.py ├── kge │ ├── __init__.py │ └── model.py ├── lib │ ├── apache-mime4j-core-0.7.2.jar │ ├── automaton-1.11-8.jar │ ├── axiom-api-1.2.14.jar │ ├── axiom-c14n-1.2.14.jar │ ├── axiom-dom-1.2.14.jar │ ├── axiom-impl-1.2.14.jar │ ├── caffeine-2.8.6.jar │ ├── checker-qual-3.7.0.jar │ ├── collection-0.7.jar │ ├── commons-beanutils-1.7.0.jar │ ├── commons-beanutils-core-1.8.0.jar │ ├── commons-cli-1.4.jar │ ├── commons-codec-1.15.jar │ ├── commons-collections-3.2.1.jar │ ├── commons-compress-1.20.jar │ ├── commons-configuration-1.6.jar │ ├── commons-csv-1.8.jar │ ├── commons-dbcp-1.3.jar │ ├── commons-digester-1.8.jar │ ├── commons-httpclient-3.1.jar │ ├── commons-io-2.8.0.jar │ ├── commons-lang-2.4.jar │ ├── commons-lang3-3.11.jar │ ├── commons-logging-1.2.jar │ ├── commons-pool-1.5.4.jar │ ├── elk-cli-0.4.3.jar │ ├── elk-distribution-0.4.3.jar │ ├── elk-owl-implementation-0.4.3.jar │ ├── elk-owl-model-0.4.3.jar │ ├── elk-owl-parsing-javacc-0.4.3.jar │ ├── elk-owlapi-0.4.3.jar │ ├── elk-owlapi-standalone-0.4.3-bin.jar │ ├── elk-owlapi-standalone-0.4.3-lib.jar │ ├── elk-owlapi-standalone-0.4.3-src.jar │ ├── elk-protege-0.4.3.jar │ ├── elk-reasoner-0.4.3.jar │ ├── elk-standalone-0.4.3.jar │ ├── elk-util-collections-0.4.3.jar │ ├── elk-util-common-0.4.3.jar │ ├── elk-util-concurrent-0.4.3.jar │ ├── elk-util-hashing-0.4.3.jar │ ├── elk-util-io-0.4.3.jar │ ├── elk-util-logging-0.4.3.jar │ ├── error_prone_annotations-2.4.0.jar │ ├── fluent-hc-4.5.12.jar │ ├── gateway.jar │ ├── geronimo-activation_1.1_spec-1.1.jar │ ├── geronimo-javamail_1.4_spec-1.7.1.jar │ ├── geronimo-stax-api_1.0_spec-1.0.1.jar │ ├── groovy-all-2.4.15.jar │ ├── guava-18.0.jar │ ├── hppcrt-0.7.5.jar │ ├── httpclient-4.5.13.jar │ ├── httpclient-cache-4.5.13.jar │ ├── httpclient-osgi-4.5.12.jar │ ├── httpcore-4.4.13.jar │ ├── httpcore-nio-4.4.13.jar │ ├── httpcore-osgi-4.4.13.jar │ ├── httpmime-4.5.12.jar │ ├── jackson-annotations-2.11.3.jar │ ├── jackson-core-2.11.3.jar │ ├── jackson-databind-2.11.3.jar │ ├── javax.annotation-api-1.3.2.jar │ ├── javax.inject-1.jar │ ├── jaxen-1.1.4.jar │ ├── jcel-core-0.24.1.jar │ ├── jcel-coreontology-0.24.1.jar │ ├── jcel-ontology-0.24.1.jar │ ├── jcel-owlapi-0.24.1.jar │ ├── jcel-reasoner-0.24.1.jar │ ├── jcl-over-slf4j-1.7.30.jar │ ├── jcommander-1.72.jar │ ├── jena-arq-3.17.0.jar │ ├── jena-base-3.17.0.jar │ ├── jena-core-3.17.0.jar │ ├── jena-dboe-base-3.17.0.jar │ ├── jena-dboe-index-3.17.0.jar │ ├── jena-dboe-storage-3.17.0.jar │ ├── jena-dboe-trans-data-3.17.0.jar │ ├── jena-dboe-transaction-3.17.0.jar │ ├── jena-iri-3.17.0.jar │ ├── jena-rdfconnection-3.17.0.jar │ ├── jena-shacl-3.17.0.jar │ ├── jena-shaded-guava-3.17.0.jar │ ├── jena-tdb-3.17.0.jar │ ├── jena-tdb2-3.17.0.jar │ ├── jopt-simple-4.5.jar │ ├── jsonld-java-0.13.2.jar │ ├── jsr305-3.0.1.jar │ ├── libthrift-0.13.0.jar │ ├── log4j-1.2.14.jar │ ├── lucene-core-4.9.0.jar │ ├── opencsv-2.3.jar │ ├── org.apache.servicemix.bundles.javax-inject-1_2.jar │ ├── org.semanticweb.hermit-1.3.8.413.jar │ ├── owlapi-api-4.5.22.jar │ ├── owlapi-apibinding-4.5.22.jar │ ├── owlapi-compatibility-4.5.22.jar │ ├── owlapi-distribution-4.5.22.jar │ ├── owlapi-fixers-4.5.22.jar │ ├── owlapi-impl-4.5.22.jar │ ├── owlapi-oboformat-4.5.22.jar │ ├── owlapi-osgidistribution-4.5.22.jar │ ├── owlapi-parsers-4.5.22.jar │ ├── owlapi-rio-4.5.22.jar │ ├── owlapi-tools-4.5.22.jar │ ├── rdf4j-model-2.4.2.jar │ ├── rdf4j-rio-api-2.4.2.jar │ ├── rdf4j-rio-binary-2.4.2.jar │ ├── rdf4j-rio-datatypes-2.4.2.jar │ ├── rdf4j-rio-jsonld-2.4.2.jar │ ├── rdf4j-rio-languages-2.4.2.jar │ ├── rdf4j-rio-n3-2.4.2.jar │ ├── rdf4j-rio-nquads-2.4.2.jar │ ├── rdf4j-rio-ntriples-2.4.2.jar │ ├── rdf4j-rio-rdfjson-2.4.2.jar │ ├── rdf4j-rio-rdfxml-2.4.2.jar │ ├── rdf4j-rio-trig-2.4.2.jar │ ├── rdf4j-rio-trix-2.4.2.jar │ ├── rdf4j-rio-turtle-2.4.2.jar │ ├── rdf4j-util-2.4.2.jar │ ├── scala-library-2.11.12.jar │ ├── sesame-http-client-2.7.13.jar │ ├── sesame-http-protocol-2.7.13.jar │ ├── sesame-model-2.7.13.jar │ ├── sesame-query-2.7.13.jar │ ├── sesame-queryalgebra-evaluation-2.7.13.jar │ ├── sesame-queryalgebra-model-2.7.13.jar │ ├── sesame-queryparser-api-2.7.13.jar │ ├── sesame-queryparser-serql-2.7.13.jar │ ├── sesame-queryparser-sparql-2.7.13.jar │ ├── sesame-queryresultio-api-2.7.13.jar │ ├── sesame-queryresultio-binary-2.7.13.jar │ ├── sesame-queryresultio-sparqljson-2.7.13.jar │ ├── sesame-queryresultio-sparqlxml-2.7.13.jar │ ├── sesame-queryresultio-text-2.7.13.jar │ ├── sesame-repository-api-2.7.13.jar │ ├── sesame-repository-contextaware-2.7.13.jar │ ├── sesame-repository-dataset-2.7.13.jar │ ├── sesame-repository-event-2.7.13.jar │ ├── sesame-repository-http-2.7.13.jar │ ├── sesame-repository-manager-2.7.13.jar │ ├── sesame-repository-sail-2.7.13.jar │ ├── sesame-repository-sparql-2.7.13.jar │ ├── sesame-rio-api-2.7.13.jar │ ├── sesame-rio-binary-2.7.13.jar │ ├── sesame-rio-datatypes-2.7.13.jar │ ├── sesame-rio-languages-2.7.13.jar │ ├── sesame-rio-n3-2.7.13.jar │ ├── sesame-rio-nquads-2.7.13.jar │ ├── sesame-rio-ntriples-2.7.13.jar │ ├── sesame-rio-rdfjson-2.7.13.jar │ ├── sesame-rio-rdfxml-2.7.13.jar │ ├── sesame-rio-trig-2.7.13.jar │ ├── sesame-rio-trix-2.7.13.jar │ ├── sesame-rio-turtle-2.7.13.jar │ ├── sesame-runtime-2.7.13.jar │ ├── sesame-sail-api-2.7.13.jar │ ├── sesame-sail-federation-2.7.13.jar │ ├── sesame-sail-inferencer-2.7.13.jar │ ├── sesame-sail-memory-2.7.13.jar │ ├── sesame-sail-nativerdf-2.7.13.jar │ ├── sesame-sail-rdbms-2.7.13.jar │ ├── sesame-util-2.7.13.jar │ ├── slf4j-api-1.7.30.jar │ ├── slf4j-simple-1.7.25.jar │ ├── slib-graph-0.9.1.pom │ ├── slib-graph-algo-0.9.1.jar │ ├── slib-graph-io-0.9.1.jar │ ├── slib-graph-model-0.9.1.jar │ ├── slib-graph-model-impl-0.9.1.jar │ ├── slib-graph-utils-0.9.1.jar │ ├── slib-indexer-0.9.1.jar │ ├── slib-sml-0.9.1.jar │ ├── slib-tools-module-0.9.1.jar │ ├── slib-utils-0.9.1.jar │ ├── stax2-api-3.1.1.jar │ ├── woodstox-core-asl-4.1.4.jar │ └── xz-1.6.jar ├── main.py ├── models │ ├── __init__.py │ ├── boxsquaredel │ │ ├── __init__.py │ │ ├── evaluate.py │ │ └── model.py │ ├── elbe │ │ ├── __init__.py │ │ ├── evaluate.py │ │ ├── examples │ │ │ ├── __init__.py │ │ │ ├── model_gda.py │ │ │ └── model_ppi.py │ │ └── model.py │ ├── elembeddings │ │ ├── #evaluate.py# │ │ ├── __init__.py │ │ ├── evaluate.py │ │ ├── examples │ │ │ ├── __init__.py │ │ │ ├── model_gda.py │ │ │ └── model_ppi.py │ │ └── model.py │ ├── falcon │ │ ├── __init__.py │ │ ├── evaluate.py │ │ ├── examples │ │ │ ├── __init__.py │ │ │ ├── model_gda.py │ │ │ └── model_ppi.py │ │ └── module.py │ ├── graph_kge │ │ ├── __init__.py │ │ └── graph_pykeen_model.py │ ├── graph_random_walk │ │ ├── __init__.py │ │ └── random_walk_w2v_model.py │ └── syntactic │ │ ├── __init__.py │ │ └── w2v_model.py ├── nn │ ├── __init__.py │ └── el │ │ ├── __init__.py │ │ ├── boxel │ │ ├── __init__.py │ │ ├── losses.py │ │ └── module.py │ │ ├── boxsquaredel │ │ ├── __init__.py │ │ ├── losses.py │ │ └── module.py │ │ ├── elbe │ │ ├── __init__.py │ │ ├── losses.py │ │ └── module.py │ │ ├── elem │ │ ├── __init__.py │ │ ├── losses.py │ │ └── module.py │ │ └── elmodule.py ├── ontology │ ├── __init__.py │ ├── create.py │ ├── extend.py │ └── normalize.py ├── owlapi │ ├── __init__.py │ ├── adapter.py │ ├── constants.py │ ├── defaults.py │ └── model.py ├── projection │ ├── __init__.py │ ├── base.py │ ├── categorical │ │ ├── __init__.py │ │ ├── edge.py │ │ ├── model.py │ │ └── utils.py │ ├── dl2vec │ │ ├── README.md │ │ ├── __init__.py │ │ ├── model.py │ │ └── tree.py │ ├── edge.py │ ├── factory.py │ ├── owl2vec_star │ │ ├── __init__.py │ │ └── model.py │ ├── taxonomy │ │ ├── __init__.py │ │ └── model.py │ ├── taxonomy_rels │ │ ├── __init__.py │ │ └── model.py │ └── util.py ├── reasoning │ ├── __init__.py │ └── base.py ├── utils │ ├── __init__.py │ ├── data.py │ └── random.py ├── visualization │ ├── __init__.py │ └── base.py └── walking │ ├── __init__.py │ ├── deepwalk │ ├── __init__.py │ └── model.py │ ├── factory.py │ ├── node2vec │ ├── __init__.py │ └── model.py │ └── walking.py ├── pylintrc ├── pyproject.toml ├── readthedocs.yml ├── setup.cfg ├── setup.py ├── test_pytest.sh └── tests ├── __init__.py ├── base_models ├── __init__.py ├── test_elmodel.py ├── test_graph_kge_model.py ├── test_graph_model.py ├── test_graph_random_walks_model.py ├── test_model.py └── test_syntactic_model.py ├── conftest.py ├── corpus ├── __init__.py └── test_base.py ├── datasetFactory.py ├── datasets ├── __init__.py ├── test_alc_dataset.py ├── test_dataset_base.py ├── test_dataset_builtin.py ├── test_el_dataset.py └── test_reindex_dataset.py ├── error ├── __init__.py └── test_error_msgs.py ├── evaluation ├── test_base.py ├── test_el.py ├── test_gda.py ├── test_kg_kge.py ├── test_kg_random_walks.py ├── test_ppi.py ├── test_subsumption.py ├── test_syntactic.py └── utils.py ├── inductive ├── __init__.py ├── test_graph_kge_model.py ├── test_graph_rw_model.py ├── test_semantic_model.py └── test_syntactic_w2v_model.py ├── kge ├── __init__.py └── test_kge.py ├── models ├── __init__.py ├── test_graph_pykeen_model.py └── test_graph_rw_w2v_model.py ├── nn ├── __init__.py ├── fixtures │ ├── __init__.py │ └── elaxioms.py ├── test_boxsquaredel_module.py ├── test_elbe_module.py └── test_elem_module.py ├── ontology ├── __init__.py ├── fixtures │ ├── 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