├── .gitignore ├── README.md ├── README_CN.md ├── assets ├── evaluation.png ├── infomosaic.png ├── infomosaic_flow.png └── overview.png ├── data ├── info_mosaic_gt_answer.jsonl └── prepare_data.py ├── docs ├── css │ ├── bulma.min.css │ └── style.css ├── images │ ├── bio.png │ ├── data-sources.png │ ├── evaluation.png │ ├── exp.png │ ├── exp_2.png │ ├── exp_3.png │ ├── finance.png │ ├── gt-demo.png │ ├── heapmaps.png │ ├── icon.png │ ├── infomosaic.png │ ├── infomosaic_flow.png │ ├── map.png │ ├── overview.png │ ├── table_1.png │ ├── web.png │ └── y2b.png ├── index.html └── js │ └── main.js ├── eval ├── evaluate_all.py ├── judge_config.yaml └── run_eval.sh ├── inference ├── configs │ ├── r1_tool.jinja │ └── tool_metata.json ├── model_forwards │ ├── __init__.py │ ├── agent_w_multi_tool.py │ ├── agent_w_web_tool.py │ ├── agent_wo_tool.py │ └── multitool_utils.py ├── run_infer.py ├── run_infer.sh └── tool_manager.py ├── pyproject.toml ├── tool_backends ├── MCP │ ├── README_API_KEYS_EN.md │ ├── README_API_KEYS_ZH.md │ ├── README_SANDBOX_EN.md │ ├── README_SANDBOX_ZH.md │ ├── __init__.py │ ├── cleanup.sh │ ├── config │ │ ├── agent_tools.json │ │ ├── api_keys.template.json │ │ └── server_list.json │ ├── config_manager.py │ ├── deploy_server.sh │ ├── deploy_sse_servers.sh │ ├── io_manage.py │ ├── logs │ │ ├── biomcp.log │ │ ├── fmp.log │ │ ├── serper.log │ │ └── youtube.log │ ├── mcp_client.py │ ├── mcp_manager.py │ ├── proxy_service.py │ ├── server │ │ ├── AMap-Server │ │ │ └── amap_server.py │ │ ├── BASE-TOOL-Server │ │ │ ├── base_tool_server.py │ │ │ ├── configs │ │ │ │ └── common_config.py │ │ │ ├── mcp_tool_tester.py │ │ │ ├── utils │ │ │ │ ├── __init__.py │ │ │ │ └── llm_caller.py │ │ │ └── web_agent │ │ │ │ ├── get_html.py │ │ │ │ ├── tool_api.py │ │ │ │ ├── web_parse.py │ │ │ │ └── web_search.py │ │ └── Google_Map_server │ │ │ ├── googlemap_server.py │ │ │ └── server.py │ ├── sse_server │ │ ├── Google_Map_server │ │ │ ├── index.html │ │ │ ├── index.html.1 │ │ │ └── server.py │ │ ├── Youtube-Server │ │ │ ├── =2.169.0 │ │ │ ├── Dockerfile │ │ │ ├── README.md │ │ │ ├── client.py │ │ │ ├── env.example │ │ │ ├── logs │ │ │ │ └── youtube_toolbox.log │ │ │ ├── main.py │ │ │ ├── new_new_server.py │ │ │ ├── new_server.py │ │ │ ├── pyproject.toml │ │ │ ├── requirements.txt │ │ │ ├── run_server.py │ │ │ ├── server.py │ │ │ ├── server_old.py │ │ │ └── smithery.yaml │ │ ├── biomcp-main │ │ │ ├── .github │ │ │ │ ├── actions │ │ │ │ │ └── setup-python-env │ │ │ │ │ │ └── action.yml │ │ │ │ ├── dependabot.yml │ │ │ │ └── workflows │ │ │ │ │ ├── ci.yml │ │ │ │ │ ├── deploy-docs.yml │ │ │ │ │ ├── main.yml.disabled │ │ │ │ │ ├── on-release-main.yml │ │ │ │ │ └── validate-codecov-config.yml │ │ │ ├── .gitignore │ │ │ ├── .pre-commit-config.yaml │ │ │ ├── BIOMCP_DATA_FLOW.md │ │ │ ├── CHANGELOG.md │ │ │ ├── CNAME │ │ │ ├── Dockerfile │ │ │ ├── LICENSE │ │ │ ├── Makefile │ │ │ ├── README.md │ │ │ ├── THIRD_PARTY_ENDPOINTS.md │ │ │ ├── codecov.yaml │ │ │ ├── docker-compose.yml │ │ │ ├── docs │ │ │ │ ├── CNAME │ │ │ │ ├── FDA_SECURITY.md │ │ │ │ ├── apis │ │ │ │ │ ├── error-codes.md │ │ │ │ │ ├── overview.md │ │ │ │ │ └── python-sdk.md │ │ │ │ ├── assets │ │ │ │ │ ├── biomcp-cursor-locations.png │ │ │ │ │ ├── favicon.ico │ │ │ │ │ ├── icon.png │ │ │ │ │ ├── logo.png │ │ │ │ │ ├── mcp_architecture.txt │ │ │ │ │ └── remote-connection │ │ │ │ │ │ ├── 00_connectors.png │ │ │ │ │ │ ├── 01_add_custom_connector.png │ │ │ │ │ │ ├── 02_connector_enabled.png │ │ │ │ │ │ ├── 03_connect_to_biomcp.png │ │ │ │ │ │ ├── 04_select_google_oauth.png │ │ │ │ │ │ └── 05_success_connect.png │ │ │ │ ├── backend-services-reference │ │ │ │ │ ├── 01-overview.md │ │ │ │ │ ├── 02-biothings-suite.md │ │ │ │ │ ├── 03-cbioportal.md │ │ │ │ │ ├── 04-clinicaltrials-gov.md │ │ │ │ │ ├── 05-nci-cts-api.md │ │ │ │ │ ├── 06-pubtator3.md │ │ │ │ │ └── 07-alphagenome.md │ │ │ │ ├── blog │ │ │ │ │ ├── ai-assisted-clinical-trial-search-analysis.md │ │ │ │ │ ├── images │ │ │ │ │ │ ├── deep-researcher-video.png │ │ │ │ │ │ ├── researcher-announce.png │ │ │ │ │ │ ├── researcher-drop-down.png │ │ │ │ │ │ ├── researcher-prompt.png │ │ │ │ │ │ ├── trial-search-assistant.png │ │ │ │ │ │ └── what_is_biomcp_thumbnail.png │ │ │ │ │ └── researcher-persona-resource.md │ │ │ │ ├── changelog.md │ │ │ │ ├── concepts │ │ │ │ │ ├── 01-what-is-biomcp.md │ │ │ │ │ ├── 02-the-deep-researcher-persona.md │ │ │ │ │ └── 03-sequential-thinking-with-the-think-tool.md │ │ │ │ ├── developer-guides │ │ │ │ │ ├── 01-server-deployment.md │ │ │ │ │ ├── 02-contributing-and-testing.md │ │ │ │ │ ├── 03-third-party-endpoints.md │ │ │ │ │ ├── 04-transport-protocol.md │ │ │ │ │ ├── 05-error-handling.md │ │ │ │ │ ├── 06-http-client-and-caching.md │ │ │ │ │ ├── 07-performance-optimizations.md │ │ │ │ │ └── generate_endpoints.py │ │ │ │ ├── faq-condensed.md │ │ │ │ ├── genomoncology.md │ │ │ │ ├── getting-started │ │ │ │ │ ├── 01-quickstart-cli.md │ │ │ │ │ ├── 02-claude-desktop-integration.md │ │ │ │ │ └── 03-authentication-and-api-keys.md │ │ │ │ ├── how-to-guides │ │ │ │ │ ├── 01-find-articles-and-cbioportal-data.md │ │ │ │ │ ├── 02-find-trials-with-nci-and-biothings.md │ │ │ │ │ ├── 03-get-comprehensive-variant-annotations.md │ │ │ │ │ ├── 04-predict-variant-effects-with-alphagenome.md │ │ │ │ │ ├── 05-logging-and-monitoring-with-bigquery.md │ │ │ │ │ └── 06-search-nci-organizations-and-interventions.md │ │ │ │ ├── index.md │ │ │ │ ├── policies.md │ │ │ │ ├── reference │ │ │ │ │ ├── architecture-diagrams.md │ │ │ │ │ ├── quick-architecture.md │ │ │ │ │ ├── quick-reference.md │ │ │ │ │ └── visual-architecture.md │ │ │ │ ├── robots.txt │ │ │ │ ├── stylesheets │ │ │ │ │ ├── announcement.css │ │ │ │ │ └── extra.css │ │ │ │ ├── troubleshooting.md │ │ │ │ ├── tutorials │ │ │ │ │ ├── biothings-prompts.md │ │ │ │ │ ├── claude-code-biomcp-alphagenome.md │ │ │ │ │ ├── nci-prompts.md │ │ │ │ │ ├── openfda-integration.md │ │ │ │ │ ├── openfda-prompts.md │ │ │ │ │ └── remote-connection.md │ │ │ │ ├── user-guides │ │ │ │ │ ├── 01-command-line-interface.md │ │ │ │ │ ├── 02-mcp-tools-reference.md │ │ │ │ │ └── 03-integrating-with-ides-and-clients.md │ │ │ │ └── workflows │ │ │ │ │ └── all-workflows.md │ │ │ ├── example_scripts │ │ │ │ ├── mcp_integration.py │ │ │ │ └── python_sdk.py │ │ │ ├── glama.json │ │ │ ├── mkdocs.yml │ │ │ ├── package-lock.json │ │ │ ├── package.json │ │ │ ├── pyproject.toml │ │ │ ├── scripts │ │ │ │ ├── check_docs_in_mkdocs.py │ │ │ │ ├── check_http_imports.py │ │ │ │ └── generate_endpoints_doc.py │ │ │ ├── smithery.yaml │ │ │ ├── src │ │ │ │ └── biomcp │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── __main__.py │ │ │ │ │ ├── articles │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── autocomplete.py │ │ │ │ │ ├── fetch.py │ │ │ │ │ ├── preprints.py │ │ │ │ │ ├── search.py │ │ │ │ │ ├── search_optimized.py │ │ │ │ │ └── unified.py │ │ │ │ │ ├── biomarkers │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── search.py │ │ │ │ │ ├── cbioportal_helper.py │ │ │ │ │ ├── circuit_breaker.py │ │ │ │ │ ├── cli │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── articles.py │ │ │ │ │ ├── biomarkers.py │ │ │ │ │ ├── diseases.py │ │ │ │ │ ├── health.py │ │ │ │ │ ├── interventions.py │ │ │ │ │ ├── main.py │ │ │ │ │ ├── openfda.py │ │ │ │ │ ├── organizations.py │ │ │ │ │ ├── server.py │ │ │ │ │ ├── trials.py │ │ │ │ │ └── variants.py │ │ │ │ │ ├── connection_pool.py │ │ │ │ │ ├── constants.py │ │ │ │ │ ├── core.py │ │ │ │ │ ├── diseases │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── getter.py │ │ │ │ │ └── search.py │ │ │ │ │ ├── domain_handlers.py │ │ │ │ │ ├── drugs │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── getter.py │ │ │ │ │ ├── exceptions.py │ │ │ │ │ ├── genes │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── getter.py │ │ │ │ │ ├── http_client.py │ │ │ │ │ ├── http_client_simple.py │ │ │ │ │ ├── individual_tools.py │ │ │ │ │ ├── integrations │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── biothings_client.py │ │ │ │ │ └── cts_api.py │ │ │ │ │ ├── interventions │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── getter.py │ │ │ │ │ └── search.py │ │ │ │ │ ├── logging_filter.py │ │ │ │ │ ├── metrics.py │ │ │ │ │ ├── metrics_handler.py │ │ │ │ │ ├── openfda │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── adverse_events.py │ │ │ │ │ ├── adverse_events_helpers.py │ │ │ │ │ ├── cache.py │ │ │ │ │ ├── constants.py │ │ │ │ │ ├── device_events.py │ │ │ │ │ ├── device_events_helpers.py │ │ │ │ │ ├── drug_approvals.py │ │ │ │ │ ├── drug_labels.py │ │ │ │ │ ├── drug_labels_helpers.py │ │ │ │ │ ├── drug_recalls.py │ │ │ │ │ ├── drug_recalls_helpers.py │ │ │ │ │ ├── drug_shortages.py │ │ │ │ │ ├── drug_shortages_detail_helpers.py │ │ │ │ │ ├── drug_shortages_helpers.py │ │ │ │ │ ├── exceptions.py │ │ │ │ │ ├── input_validation.py │ │ │ │ │ ├── rate_limiter.py │ │ │ │ │ ├── utils.py │ │ │ │ │ └── validation.py │ │ │ │ │ ├── organizations │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── getter.py │ │ │ │ │ └── search.py │ │ │ │ │ ├── parameter_parser.py │ │ │ │ │ ├── prefetch.py │ │ │ │ │ ├── query_parser.py │ │ │ │ │ ├── query_router.py │ │ │ │ │ ├── rate_limiter.py │ │ │ │ │ ├── render.py │ │ │ │ │ ├── request_batcher.py │ │ │ │ │ ├── resources │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── getter.py │ │ │ │ │ ├── instructions.md │ │ │ │ │ └── researcher.md │ │ │ │ │ ├── retry.py │ │ │ │ │ ├── router.py │ │ │ │ │ ├── router_handlers.py │ │ │ │ │ ├── shared_context.py │ │ │ │ │ ├── thinking │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── sequential.py │ │ │ │ │ └── session.py │ │ │ │ │ ├── thinking_tool.py │ │ │ │ │ ├── thinking_tracker.py │ │ │ │ │ ├── trials │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── getter.py │ │ │ │ │ ├── nci_getter.py │ │ │ │ │ ├── nci_search.py │ │ │ │ │ └── search.py │ │ │ │ │ ├── utils │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── cancer_types_api.py │ │ │ │ │ ├── cbio_http_adapter.py │ │ │ │ │ ├── endpoint_registry.py │ │ │ │ │ ├── gene_validator.py │ │ │ │ │ ├── metrics.py │ │ │ │ │ ├── mutation_filter.py │ │ │ │ │ ├── query_utils.py │ │ │ │ │ ├── rate_limiter.py │ │ │ │ │ └── request_cache.py │ │ │ │ │ ├── variants │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── alphagenome.py │ │ │ │ │ ├── cancer_types.py │ │ │ │ │ ├── cbio_external_client.py │ │ │ │ │ ├── cbioportal_mutations.py │ │ │ │ │ ├── cbioportal_search.py │ │ │ │ │ ├── cbioportal_search_helpers.py │ │ │ │ │ ├── constants.py │ │ │ │ │ ├── external.py │ │ │ │ │ ├── filters.py │ │ │ │ │ ├── getter.py │ │ │ │ │ ├── links.py │ │ │ │ │ └── search.py │ │ │ │ │ └── workers │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── worker.py │ │ │ │ │ ├── worker_entry.js │ │ │ │ │ └── worker_entry_stytch.js │ │ │ ├── tests │ │ │ │ ├── bdd │ │ │ │ │ ├── cli_help │ │ │ │ │ │ ├── help.feature │ │ │ │ │ │ └── test_help.py │ │ │ │ │ ├── conftest.py │ │ │ │ │ ├── features │ │ │ │ │ │ └── alphagenome_integration.feature │ │ │ │ │ ├── fetch_articles │ │ │ │ │ │ ├── fetch.feature │ │ │ │ │ │ └── test_fetch.py │ │ │ │ │ ├── get_trials │ │ │ │ │ │ ├── get.feature │ │ │ │ │ │ └── test_get.py │ │ │ │ │ ├── get_variants │ │ │ │ │ │ ├── get.feature │ │ │ │ │ │ └── test_get.py │ │ │ │ │ ├── search_articles │ │ │ │ │ │ ├── autocomplete.feature │ │ │ │ │ │ ├── search.feature │ │ │ │ │ │ ├── test_autocomplete.py │ │ │ │ │ │ └── test_search.py │ │ │ │ │ ├── search_trials │ │ │ │ │ │ ├── search.feature │ │ │ │ │ │ └── test_search.py │ │ │ │ │ ├── search_variants │ │ │ │ │ │ ├── search.feature │ │ │ │ │ │ └── test_search.py │ │ │ │ │ └── steps │ │ │ │ │ │ └── test_alphagenome_steps.py │ │ │ │ ├── config │ │ │ │ │ └── test_smithery_config.py │ │ │ │ ├── conftest.py │ │ │ │ ├── data │ │ │ │ │ ├── ct_gov │ │ │ │ │ │ ├── clinical_trials_api_v2.yaml │ │ │ │ │ │ ├── trials_NCT04280705.json │ │ │ │ │ │ └── trials_NCT04280705.txt │ │ │ │ │ ├── myvariant │ │ │ │ │ │ ├── myvariant_api.yaml │ │ │ │ │ │ ├── myvariant_field_descriptions.csv │ │ │ │ │ │ ├── variants_full_braf_v600e.json │ │ │ │ │ │ ├── variants_full_braf_v600e.txt │ │ │ │ │ │ └── variants_part_braf_v600_multiple.json │ │ │ │ │ ├── openfda │ │ │ │ │ │ ├── drugsfda_detail.json │ │ │ │ │ │ ├── drugsfda_search.json │ │ │ │ │ │ ├── enforcement_detail.json │ │ │ │ │ │ └── enforcement_search.json │ │ │ │ │ └── pubtator │ │ │ │ │ │ ├── pubtator3_paper.txt │ │ │ │ │ │ └── pubtator_autocomplete.json │ │ │ │ ├── integration │ │ │ │ │ ├── test_openfda_integration.py │ │ │ │ │ ├── test_preprints_integration.py │ │ │ │ │ ├── test_simple.py │ │ │ │ │ └── test_variants_integration.py │ │ │ │ └── tdd │ │ │ │ │ ├── articles │ │ │ │ │ ├── test_autocomplete.py │ │ │ │ │ ├── test_cbioportal_integration.py │ │ │ │ │ ├── test_fetch.py │ │ │ │ │ ├── test_preprints.py │ │ │ │ │ ├── test_search.py │ │ │ │ │ └── test_unified.py │ │ │ │ │ ├── conftest.py │ │ │ │ │ ├── drugs │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── test_drug_getter.py │ │ │ │ │ ├── openfda │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── test_adverse_events.py │ │ │ │ │ ├── test_device_events.py │ │ │ │ │ ├── test_drug_approvals.py │ │ │ │ │ ├── test_drug_labels.py │ │ │ │ │ ├── test_drug_recalls.py │ │ │ │ │ ├── test_drug_shortages.py │ │ │ │ │ └── test_security.py │ │ │ │ │ ├── test_biothings_integration.py │ │ │ │ │ ├── test_biothings_integration_real.py │ │ │ │ │ ├── test_circuit_breaker.py │ │ │ │ │ ├── test_concurrent_requests.py │ │ │ │ │ ├── test_connection_pool.py │ │ │ │ │ ├── test_domain_handlers.py │ │ │ │ │ ├── test_drug_approvals.py │ │ │ │ │ ├── test_drug_recalls.py │ │ │ │ │ ├── test_drug_shortages.py │ │ │ │ │ ├── test_endpoint_documentation.py │ │ │ │ │ ├── test_error_scenarios.py │ │ │ │ │ ├── test_europe_pmc_fetch.py │ │ │ │ │ ├── test_mcp_integration.py │ │ │ │ │ ├── test_mcp_tools.py │ │ │ │ │ ├── test_metrics.py │ │ │ │ │ ├── test_nci_integration.py │ │ │ │ │ ├── test_nci_mcp_tools.py │ │ │ │ │ ├── test_network_policies.py │ │ │ │ │ ├── test_offline_mode.py │ │ │ │ │ ├── test_openfda_unified.py │ │ │ │ │ ├── test_pten_r173_search.py │ │ │ │ │ ├── test_render.py │ │ │ │ │ ├── test_request_batcher.py.disabled │ │ │ │ │ ├── test_retry.py │ │ │ │ │ ├── test_router.py │ │ │ │ │ ├── test_shared_context.py.disabled │ │ │ │ │ ├── test_unified_biothings.py │ │ │ │ │ ├── thinking │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── test_sequential.py │ │ │ │ │ ├── trials │ │ │ │ │ ├── test_backward_compatibility.py │ │ │ │ │ ├── test_getter.py │ │ │ │ │ └── test_search.py │ │ │ │ │ ├── utils │ │ │ │ │ ├── test_gene_validator.py │ │ │ │ │ ├── test_mutation_filter.py │ │ │ │ │ ├── test_rate_limiter.py │ │ │ │ │ └── test_request_cache.py │ │ │ │ │ ├── variants │ │ │ │ │ ├── constants.py │ │ │ │ │ ├── test_alphagenome.py │ │ │ │ │ ├── test_alphagenome_api_key.py │ │ │ │ │ ├── test_alphagenome_comprehensive.py │ │ │ │ │ ├── test_cbioportal_mutations.py │ │ │ │ │ ├── test_cbioportal_search.py │ │ │ │ │ ├── test_external.py │ │ │ │ │ ├── test_external_integration.py │ │ │ │ │ ├── test_extract_gene_aa_change.py │ │ │ │ │ ├── test_filters.py │ │ │ │ │ ├── test_links.py │ │ │ │ │ └── test_search.py │ │ │ │ │ └── workers │ │ │ │ │ └── test_worker_sanitization.js │ │ │ ├── tox.ini │ │ │ ├── uv.lock │ │ │ └── wrangler.toml │ │ └── serper-mcp-server-main │ │ │ ├── .env.example │ │ │ ├── .github │ │ │ └── workflows │ │ │ │ └── push-to-pypi.yaml │ │ │ ├── .gitignore │ │ │ ├── .python-version │ │ │ ├── Dockerfile │ │ │ ├── README.md │ │ │ ├── pyproject.toml │ │ │ ├── run_server.py │ │ │ ├── smithery.yaml │ │ │ ├── src │ │ │ └── serper_mcp_server │ │ │ │ ├── __init__.py │ │ │ │ ├── core.py │ │ │ │ ├── enums.py │ │ │ │ ├── schemas.py │ │ │ │ └── server.py │ │ │ └── uv.lock │ ├── tool_caller.py │ ├── tool_server.py │ └── utils.py ├── README.md ├── README_ZH.md ├── api_proxy │ ├── __init__.py │ ├── api_server.py │ ├── api_utils │ │ ├── fetch_web_page_api.py │ │ ├── pdf_read_api.py │ │ └── web_search_api.py │ ├── models.py │ └── tool_api.py ├── configs │ ├── llm_call.json │ ├── mcp_config.json │ └── web_agent.json ├── quick_deploy.sh ├── run_docker.sh └── test │ ├── biomcp_test.py │ ├── fmp_test.py │ ├── googlemap_test.py │ ├── serper_test.py │ ├── test_all.py │ ├── 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