├── .github ├── ISSUE_TEMPLATE │ └── build-kg2.md └── workflows │ └── main.yml ├── .gitignore ├── .travis.yml ├── LICENSE ├── README.md ├── RTXConfiguration-config-EXAMPLE.json ├── convert ├── archive │ ├── build-multi-ont-kg.sh │ ├── multi_ont_to_kg_jsonl.py │ ├── pubmed_xml_to_kg_json.py │ ├── repodb_csv_to_kg_jsonl.py │ └── save_owl_datatypeproperties.py ├── chembl_mysql_to_kg_jsonl.py ├── clinicaltrialskg_tsv_to_kg_jsonl.py ├── dgidb_tsv_to_kg_jsonl.py ├── disgenet_tsv_to_kg_jsonl.py ├── drugapprovalskg_tsv_to_kg_jsonl.py ├── drugbank_xml_to_kg_jsonl.py ├── drugcentral_json_to_kg_jsonl.py ├── ensembl_json_to_kg_jsonl.py ├── go_gpa_to_kg_jsonl.py ├── hmdb_xml_to_kg_jsonl.py ├── intact_tsv_to_kg_jsonl.py ├── jensenlab_tsv_to_kg_jsonl.py ├── kegg_jsonl_to_kg_jsonl.py ├── kg2_util.py ├── master-config.shinc ├── mirbase_dat_to_kg_jsonl.py ├── ncbigene_tsv_to_kg_jsonl.py ├── ontologies_jsonl_to_kg_jsonl.py ├── reactome_mysql_to_kg_jsonl.py ├── semmeddb_tuplelist_json_to_kg_jsonl.py ├── smpdb_csv_to_kg_jsonl.py ├── umls_list_jsonl_to_kg_jsonl.py ├── umls_util.py ├── unichem_tsv_to_kg_jsonl.py ├── unii_tsv_to_kg_jsonl.py └── uniprotkb_dat_to_kg_jsonl.py ├── docs ├── Adding-properties.md ├── JSONLines_Time_Comparison.md ├── KG2.10.3report.md ├── Snakefile-maintenance.md ├── archive │ ├── macos-docker-notes.md │ ├── s3-index.html │ └── understanding_umls.md ├── biolink-kg-schema.md └── kg2-versions.md ├── extract ├── archive │ ├── cache_control_helper.py │ ├── extract-pubmed.sh │ ├── extract-repodb.sh │ ├── extract_kg2_pmids.py │ └── umls2rdf-umls.conf ├── drugcentral_psql_to_drugcentral_json.py ├── extract-chembl.sh ├── extract-clinicaltrialskg.sh ├── extract-dgidb.sh ├── extract-disgenet.sh ├── extract-drugapprovalskg.sh ├── extract-drugbank.sh ├── extract-drugcentral.sh ├── extract-ensembl.sh ├── extract-go-annotations.sh ├── extract-hmdb.sh ├── extract-intact.sh ├── extract-jensenlab.sh ├── extract-kegg.sh ├── extract-mirbase.sh ├── extract-ncbigene.sh ├── extract-ontologies.sh ├── extract-reactome.sh ├── extract-semmeddb.sh ├── extract-smpdb.sh ├── extract-umls.sh ├── extract-unichem.sh ├── extract-unii.sh ├── extract-uniprotkb.sh ├── kg2_util.py ├── master-config.shinc ├── owlparser.py ├── query_kegg.py ├── semmeddb_mysql_to_tuplelist_jsonl.py ├── umls-config.prop └── umls_mysql_to_list_jsonl.py ├── instance_management ├── clear-instance.sh ├── get-system-memory-gb.sh ├── kg2_util.py ├── master-config.shinc └── primative-instance-data-tracker.sh ├── kg2_util.py ├── kgx └── archive │ ├── kg2_json_to_kgx_tsv.py │ ├── kgx-validation-and-metagraph.sh │ ├── make-kgx-export.sh │ └── split_kgx_tsv.py ├── maps ├── curies-to-categories.yaml ├── curies-to-urls-map.yaml ├── edge-blocklist.yaml ├── kg2-provided-by-curie-to-infores-curie.yaml ├── knowledge-level-agent-type-map.yaml ├── ont-load-inventory.yaml ├── predicate-remap.yaml ├── tui_combo_mappings.json └── umls-name-heirarchy.yaml ├── master-config.shinc ├── mediKanren ├── Dockerfile ├── README.md ├── config.scm ├── config.yml ├── create-index.sh ├── download-graph.sh ├── kg2_tsv_to_medikanren_csv.py ├── kg2_tsv_to_medikanren_tsv.py └── setup.sh ├── misc-tools ├── biolink-yaml-to-schema-documentation-run.sh ├── biolink_yaml_to_schema_documentation.py ├── count_orphan_curie_prefix_pairs.py ├── covid19 │ ├── README.md │ ├── approved_ids.csv │ ├── covid_drugs.py │ └── results │ │ ├── ace2_direct_connections.csv │ │ ├── antimalarials.csv │ │ ├── antiviral_agents.csv │ │ ├── hepC_remdesivir.csv │ │ └── pneumonia.csv ├── decorate_organism_taxon_nodes.py ├── drugbank_get_approved_drugs_and_ids.py ├── drugbank_sentence_parsing.py ├── dump_list_of_predicates.py ├── find_check_ro_prefixes.py ├── find_none_synonym.py ├── fix-predicates.py ├── generate_owl_conf.py ├── generate_umls2rdf_conf.py ├── json_tsv_stats_generators │ ├── README.md │ ├── get_stats_json.py │ ├── get_stats_tsv.py │ ├── requirements.txt │ ├── sample_plots │ │ ├── log_log_degree_distr_json.png │ │ └── log_log_degree_distr_tsv.png │ └── sample_reports │ │ ├── stats_report_json_1141_nodes.json │ │ ├── stats_report_json_40_nodes.json │ │ ├── stats_report_tsv_1141_nodes.json │ │ └── stats_report_tsv_140_nodes.json ├── map_predicates_to_biolink.py ├── modify_edges_tsv.py ├── mysql_table_to_md_table.sh ├── predicate_remapper_tsv_to_json.py ├── predicate_sources_kg2.py ├── report_problem_cuis_in_kg_edges.py ├── sample_subgraph.py ├── tui_combo_mappings.py └── validate_predicate_remapping_file.R ├── neo4j ├── archive │ └── report_stats_on_neo4j_kg.py ├── create_indexes_constraints.py ├── install-neo4j.sh ├── kg2_util.py ├── master-config.shinc ├── read_kg2_password_from_rtxconfig.py ├── requirements-kg2-neo4j.txt ├── setup-kg2-neo4j.sh └── tsv-to-neo4j.sh ├── process ├── archive │ └── get_nodes_json_from_kg_json.py ├── compare_edge_reports.py ├── download-babel.sh ├── filter_kg_and_remap_predicates.py ├── jsonl_to_tsv.py ├── kg2_util.py ├── kg2pre_to_kg2c_edges.py ├── kg2pre_to_kg2c_nodes.py ├── kg_json_to_tsv.py ├── local_babel.py ├── master-config.shinc ├── merge_graphs.py ├── report_stats_on_kg_jsonl.py ├── run-simplify.sh ├── slim_kg2.py └── update_version.py ├── setup ├── archive │ ├── Dockerfile │ ├── ec2-setup-remote-instance.sh │ └── install-docker-ubuntu18.sh ├── delete-mysql-ubuntu.sh ├── delete-postgresql-ubuntu.sh ├── kg2_util.py ├── master-config.shinc ├── requirements-kg2-build.txt ├── setup-kg2-build.sh ├── setup-python313-with-pip3-in-ubuntu.shinc └── setup-python37-with-pip3-in-ubuntu.shinc ├── source-licenses ├── README.md ├── drugbank-license.pdf └── umls-license.pdf └── validate ├── archive ├── validate_ont_load_inventory.py └── validate_rtx_kg1_curie_mappings.py ├── kg2_util.py ├── master-config.shinc ├── run-validation-tests.sh ├── validate_curies_to_categories_yaml.py ├── validate_curies_to_urls_map_yaml.py ├── validate_kg2_util_curies_urls_categories.py ├── validate_predicate_remap_yaml.py └── 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