├── .coveragerc ├── .editorconfig ├── .eslintrc ├── .github ├── workflow-templates │ ├── romanolab-ci-build.yml │ ├── romanolab-ci-python-package.yml │ └── romanolab-ci-python-test.yml └── workflows │ ├── ci-app-build.yml │ ├── ci-doc-build.yml │ ├── ci-python-test.yml │ └── main.yml ├── .gitignore ├── .prettierrc ├── .stylelintrc ├── .vscode ├── .ropeproject │ ├── config.py │ └── objectdb ├── extensions.json ├── launch.json └── settings.json ├── CONFIG-default.yaml ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── SECURITY.md ├── comptox.rdf ├── comptox_ai ├── __init__.py ├── aop │ ├── __init__.py │ ├── aop.py │ └── aopwiki.py ├── build │ ├── __init__.py │ ├── db.py │ ├── load_graph_db.py │ ├── post_install.py │ └── scripts │ │ ├── fetch_chemical_lists.py │ │ ├── make_maccs_fingerprints.py │ │ └── translate_chemical_lists.py ├── chemical_featurizer │ └── generate_vectors.py ├── cypher │ ├── __init__.py │ ├── file_operations.py │ └── queries.py ├── db │ ├── __init__.py │ ├── graph_db.py │ └── io.py ├── doc │ ├── README.md │ ├── aop.py │ ├── compare.py │ ├── data_schema.py │ ├── databases.py │ ├── db_queries.py │ ├── entity_types.py │ ├── graph_concepts.py │ ├── graph_db.py │ ├── installing.py │ └── usage.py ├── feature_sets.py ├── graph │ ├── ARCHIVE.py │ ├── __init__.py │ ├── edge.py │ ├── feature_matrix.py │ ├── graph.py │ ├── io.py │ ├── metrics.py │ ├── node.py │ ├── path.py │ ├── subgraph.py │ ├── utils.py │ └── vertex.py ├── graph_algorithm │ ├── __init__.py │ ├── _base.py │ ├── _shortest_path.py │ ├── _subgraphs.py │ ├── sampling.py │ └── similarity.py ├── math_utils │ ├── __init__.py │ └── ks.py ├── ml │ ├── __init__.py │ ├── decagon.py │ ├── gcn.py │ ├── graphsage.py │ ├── nn.py │ └── train_test_split_edges.py ├── ontology │ ├── __init__.py │ └── ontology.py ├── scripts │ ├── __init__.py │ ├── build-ontology │ │ ├── 1_add_individuals.py │ │ ├── 2_merge_aopwiki.py │ │ └── merge_ctd.py │ ├── fetch_chemical_data.py │ ├── get_chemical_lists.py │ ├── make_graph_dataset.py │ ├── make_qsar.py │ ├── make_static_data_index.py │ ├── make_tabular_dataset.py │ ├── merge_chemical_data.md │ └── parse_chemical_synonyms.py └── utils │ ├── __init__.py │ ├── config_utils.py │ ├── qsar.py │ └── utils.py ├── comptox_test.owl ├── deploy.sh ├── docs ├── Makefile ├── README.md ├── make.bat ├── notes │ └── helpful_queries.txt ├── runtime.txt ├── source │ ├── _static │ │ ├── css │ │ │ └── main.css │ │ ├── img │ │ │ ├── ComptoxAI_logo_type.png │ │ │ ├── aop_fertility.jpg │ │ │ ├── comptox_ai.svg │ │ │ ├── favicon.ico │ │ │ ├── helo-fish-.jpg │ │ │ ├── icon.png │ │ │ ├── neo_aop.png │ │ │ ├── ontology.png │ │ │ └── protege.png │ │ ├── js │ │ │ ├── main.js │ │ │ └── main.js.map │ │ └── mathjax │ │ │ └── es5 │ │ │ ├── a11y │ │ │ ├── assistive-mml.js │ │ │ ├── complexity.js │ │ │ ├── explorer.js │ │ │ ├── semantic-enrich.js │ │ │ └── sre.js │ │ │ ├── adaptors │ │ │ └── liteDOM.js │ │ │ ├── core.js │ │ │ ├── input │ │ │ ├── asciimath.js │ │ │ ├── mml.js │ │ │ ├── mml │ │ │ │ ├── entities.js │ │ │ │ └── extensions │ │ │ │ │ ├── mml3.js │ │ │ │ │ └── mml3.sef.json │ │ │ ├── tex-base.js │ │ │ ├── tex-full.js │ │ │ ├── tex.js │ │ │ └── tex │ │ │ │ └── extensions │ │ │ │ ├── action.js │ │ │ │ ├── all-packages.js │ │ │ │ ├── ams.js │ │ │ │ ├── amscd.js │ │ │ │ ├── autoload.js │ │ │ │ ├── bbox.js │ │ │ │ ├── boldsymbol.js │ │ │ │ ├── braket.js │ │ │ │ ├── bussproofs.js │ │ │ │ ├── cancel.js │ │ │ │ ├── cases.js │ │ │ │ ├── centernot.js │ │ │ │ ├── color.js │ │ │ │ ├── colortbl.js │ │ │ │ ├── colorv2.js │ │ │ │ ├── configmacros.js │ │ │ │ ├── empheq.js │ │ │ │ ├── enclose.js │ │ │ │ ├── extpfeil.js │ │ │ │ ├── gensymb.js │ │ │ │ ├── html.js │ │ │ │ ├── mathtools.js │ │ │ │ ├── mhchem.js │ │ │ │ ├── newcommand.js │ │ │ │ ├── noerrors.js │ │ │ │ ├── noundefined.js │ │ │ │ ├── physics.js │ │ │ │ ├── require.js │ │ │ │ ├── setoptions.js │ │ │ │ ├── tagformat.js │ │ │ │ ├── textcomp.js │ │ │ │ ├── textmacros.js │ │ │ │ ├── unicode.js │ │ │ │ ├── upgreek.js │ │ │ │ └── verb.js │ │ │ ├── latest.js │ │ │ ├── loader.js │ │ │ ├── mml-chtml.js │ │ │ ├── mml-svg.js │ │ │ ├── node-main.js │ │ │ ├── output │ │ │ ├── chtml.js │ │ │ ├── chtml │ │ │ │ └── fonts │ │ │ │ │ ├── tex.js │ │ │ │ │ └── woff-v2 │ │ │ │ │ ├── MathJax_AMS-Regular.woff │ │ │ │ │ ├── MathJax_Calligraphic-Bold.woff │ │ │ │ │ ├── MathJax_Calligraphic-Regular.woff │ │ │ │ │ ├── MathJax_Fraktur-Bold.woff │ │ │ │ │ ├── MathJax_Fraktur-Regular.woff │ │ │ │ │ ├── MathJax_Main-Bold.woff │ │ │ │ │ ├── MathJax_Main-Italic.woff │ │ │ │ │ ├── MathJax_Main-Regular.woff │ │ │ │ │ ├── MathJax_Math-BoldItalic.woff │ │ │ │ │ ├── MathJax_Math-Italic.woff │ │ │ │ │ ├── MathJax_Math-Regular.woff │ │ │ │ │ ├── MathJax_SansSerif-Bold.woff │ │ │ │ │ ├── MathJax_SansSerif-Italic.woff │ │ │ │ │ ├── MathJax_SansSerif-Regular.woff │ │ │ │ │ ├── MathJax_Script-Regular.woff │ │ │ │ │ ├── MathJax_Size1-Regular.woff │ │ │ │ │ ├── MathJax_Size2-Regular.woff │ │ │ │ │ ├── MathJax_Size3-Regular.woff │ │ │ │ │ ├── MathJax_Size4-Regular.woff │ │ │ │ │ ├── MathJax_Typewriter-Regular.woff │ │ │ │ │ ├── MathJax_Vector-Bold.woff │ │ │ │ │ ├── MathJax_Vector-Regular.woff │ │ │ │ │ └── MathJax_Zero.woff │ │ │ ├── svg.js │ │ │ └── svg │ │ │ │ └── fonts │ │ │ │ └── tex.js │ │ │ ├── sre │ │ │ └── mathmaps │ │ │ │ ├── base.json │ │ │ │ ├── ca.json │ │ │ │ ├── da.json │ │ │ │ ├── de.json │ │ │ │ ├── en.json │ │ │ │ ├── es.json │ │ │ │ ├── fr.json │ │ │ │ ├── hi.json │ │ │ │ ├── it.json │ │ │ │ ├── nb.json │ │ │ │ ├── nemeth.json │ │ │ │ ├── nn.json │ │ │ │ └── sv.json │ │ │ ├── startup.js │ │ │ ├── tex-chtml-full-speech.js │ │ │ ├── tex-chtml-full.js │ │ │ ├── tex-chtml.js │ │ │ ├── tex-mml-chtml.js │ │ │ ├── tex-mml-svg.js │ │ │ ├── tex-svg-full.js │ │ │ ├── tex-svg.js │ │ │ └── ui │ │ │ ├── lazy.js │ │ │ ├── menu.js │ │ │ └── safe.js │ ├── about.rst │ ├── conf.py │ ├── contact.rst │ ├── contents.rst │ ├── docs │ │ ├── db.rst │ │ ├── generated │ │ │ ├── comptox_ai.graph.Graph.rst │ │ │ └── comptox_ai.graph.io.rst │ │ ├── graph.rst │ │ ├── graph_algorithm.rst │ │ ├── index.rst │ │ ├── misc.rst │ │ └── ml.rst │ ├── includes │ │ └── toc_css.rst │ ├── install.rst │ ├── posts │ │ └── why-comptoxai.rst │ ├── templates │ │ ├── api.html │ │ ├── browse.html │ │ ├── class.rst │ │ ├── data.html │ │ ├── footer.html │ │ ├── head.html │ │ ├── index.html │ │ ├── layout.html │ │ └── navbar.html │ ├── themes │ │ └── comptox-ai │ │ │ ├── static │ │ │ ├── css │ │ │ │ ├── custom.css │ │ │ │ └── vendor │ │ │ │ │ └── bootstrap.min.css │ │ │ ├── fonts │ │ │ │ ├── cmunrm-webfont.woff │ │ │ │ ├── cmunsx-webfont.woff │ │ │ │ └── cmuntt-webfont.woff │ │ │ └── js │ │ │ │ └── vendor │ │ │ │ ├── bootstrap.bundle.min.js │ │ │ │ └── bootstrap.min.js │ │ │ └── theme.conf │ └── use │ │ ├── aop.rst │ │ ├── comptox.rst │ │ ├── data_schema.rst │ │ ├── databases.rst │ │ ├── db_queries.rst │ │ ├── entity_types.rst │ │ ├── graph_concepts.rst │ │ ├── graph_db.rst │ │ ├── index.rst │ │ ├── tutorials.rst │ │ ├── useful_queries.rst │ │ └── web_api.rst └── use_cases │ ├── aop_expansion.ipynb │ ├── dioxin_immune-system.ipynb │ ├── estrogen_aops │ └── aop_exploration.py │ ├── pfoa │ └── immune_effects.py │ └── qsar_dataset_generation.ipynb ├── environment.yml ├── package.json ├── scripts ├── chemical_distance.py ├── etl_invitrodb.py ├── get_highest_degrees.py ├── import_rdf_data.py ├── output │ ├── pfhxs_similarities_cityblock.txt │ ├── pfhxs_similarities_cityblock_PFAS-ONLY.txt │ ├── pfhxs_similarities_jaccard.txt │ ├── pfhxs_similarities_jaccard_PFAS-ONLY.txt │ ├── top_chemicals.csv │ └── top_diseases.csv ├── pfhxs │ ├── PFHxS_assay-preliminary-results.xlsx │ ├── get_datasets.py │ ├── get_datasets2.py │ ├── make_tables.py │ └── train_classifier.py └── remove_nones.sh ├── setup.py ├── tests ├── __init__.py ├── badconfig.txt ├── example_vector_table_original_chemical_ids_as_index.pkl ├── example_vector_table_smiles_as_index.pkl ├── phecode_icd10_map_list_saaedits (1).xlsx ├── sample_db.json ├── test_chemical_featurizer.py ├── test_db.py ├── test_io.py.txt ├── test_ontology.py └── unavailconfig.txt └── web ├── .eslintignore ├── .eslintrc ├── .gitignore ├── ecosystem.config.js ├── package-lock.json ├── package.json └── packages ├── api ├── app.js ├── assets │ ├── data.json │ └── qsar_params_data.json ├── config.js ├── helpers │ └── response.js ├── middleware │ └── neo4jSessionCleanup.js ├── models │ ├── chemicals.js │ ├── datasets.js │ ├── graphs.js │ ├── neo4j │ │ ├── graph.js │ │ ├── node.js │ │ ├── nodetype.js │ │ ├── path.js │ │ ├── relationship.js │ │ └── relationshiptype.js │ ├── nodes.js │ ├── paths.js │ └── relationships.js ├── mymol.mol ├── neo4j.js ├── neo4j │ └── dbUtils.js ├── package.json └── routes │ ├── chemicals.js │ ├── datasets.js │ ├── graphs.js │ ├── index.js │ ├── nodes.js │ ├── paths.js │ └── relationships.js └── app ├── .gitignore ├── README.md ├── package.json ├── public ├── favicon.ico ├── index.html ├── manifest.json └── robots.txt ├── scripts └── build-custom.js └── src ├── App.css ├── App.js ├── App.test.js ├── BatchQuery.js ├── HowToUse.js ├── components ├── ChemicalSearch.js ├── DatasetBuilder.js ├── ExpandNetwork.js ├── NodeLabel.js ├── NodeResult.js ├── NodeResults.js ├── NodeSearch.js ├── NodeSearchWidget.js ├── PathSearch.js ├── RelationshipSearch.js ├── ShortestPath.js └── marvin │ ├── client-settings.js │ ├── client.js │ └── example_mol.mol ├── data ├── chemical_list_data.json ├── data.json └── qsar_params_data.json ├── features ├── comptoxApiSlice.js ├── modulesSlice.js ├── nodeSlice.js ├── pathSlice.js ├── relationshipSlice.js └── structureSlice.js ├── fonts ├── cmunrm-webfont.woff ├── cmunsx-webfont.woff └── cmuntt-webfont.woff ├── index.css ├── index.js ├── redux ├── hooks.js └── store.js ├── serviceWorker.js └── setupTests.js /.coveragerc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RomanoLab/comptox_ai/HEAD/.coveragerc 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