Index

_

__call__() (tooluniverse.execute_function.ToolCallable method) __contains__() (tooluniverse.execute_function.ToolNamespace method) __del__() (tooluniverse.mcp_client_tool.MCPAutoLoaderTool method) (tooluniverse.MCPAutoLoaderTool method) __getattr__() (tooluniverse.execute_function.ToolNamespace method) __init__() (tooluniverse.admetai_tool.ADMETAITool method) (tooluniverse.ADMETAITool method) (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) (tooluniverse.alphafold_tool.AlphaFoldRESTTool method) (tooluniverse.AlphaFoldRESTTool method) (tooluniverse.arxiv_tool.ArXivTool method) (tooluniverse.ArXivTool method) (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseTool method) (tooluniverse.biogrid_tool.BioGRIDRESTTool method) (tooluniverse.biorxiv_tool.BioRxivTool method) (tooluniverse.BioRxivTool method) (tooluniverse.boltz_tool.Boltz2DockingTool method) (tooluniverse.cache.memory_cache.LRUCache method) (tooluniverse.cache.memory_cache.SingleFlight method) (tooluniverse.cache.result_cache_manager.CacheRecord method) (tooluniverse.cache.result_cache_manager.ResultCacheManager method) (tooluniverse.cache.sqlite_backend.CacheEntry method) (tooluniverse.cache.sqlite_backend.PersistentCache method) (tooluniverse.cellosaurus_tool.CellosaurusGetCellLineInfoTool method) (tooluniverse.cellosaurus_tool.CellosaurusQueryConverterTool method) (tooluniverse.cellosaurus_tool.CellosaurusSearchTool method) (tooluniverse.CellosaurusGetCellLineInfoTool method) (tooluniverse.CellosaurusQueryConverterTool method) (tooluniverse.CellosaurusSearchTool method) (tooluniverse.chem_tool.ChEMBLTool method) (tooluniverse.ChEMBLTool method) (tooluniverse.ClinicalTrialsDetailsTool method) (tooluniverse.ClinicalTrialsSearchTool method) (tooluniverse.clinvar_tool.ClinVarTool method) (tooluniverse.compose_tool.ComposeTool method) (tooluniverse.ComposeTool method) (tooluniverse.core_tool.CoreTool method) (tooluniverse.CoreTool method) (tooluniverse.crossref_tool.CrossrefTool method) (tooluniverse.CrossrefTool method) (tooluniverse.ctg_tool.ClinicalTrialsDetailsTool method) (tooluniverse.ctg_tool.ClinicalTrialsSearchTool method) (tooluniverse.ctg_tool.ClinicalTrialsTool method) (tooluniverse.custom_tool.CustomTool method) (tooluniverse.dailymed_tool.GetSPLBySetIDTool method) (tooluniverse.dailymed_tool.SearchSPLTool method) (tooluniverse.dataset_tool.DatasetTool method) (tooluniverse.DatasetTool method) (tooluniverse.dblp_tool.DBLPTool method) (tooluniverse.DBLPTool method) (tooluniverse.dbsnp_tool.DbSnpTool method) (tooluniverse.DiseaseTargetScoreTool method) (tooluniverse.doaj_tool.DOAJTool method) (tooluniverse.DOAJTool method) (tooluniverse.efo_tool.EFOTool method) (tooluniverse.EFOTool method) (tooluniverse.embedding_database.EmbeddingDatabase method) (tooluniverse.embedding_sync.EmbeddingSync method) (tooluniverse.EmbeddingDatabase method) (tooluniverse.EmbeddingSync method) (tooluniverse.enrichr_tool.EnrichrTool method) (tooluniverse.ensembl_tool.EnsemblTool method) (tooluniverse.europe_pmc_tool.EuropePMCTool method) (tooluniverse.EuropePMCTool method) (tooluniverse.exceptions.ToolAuthError method) (tooluniverse.exceptions.ToolConfigError method) (tooluniverse.exceptions.ToolDependencyError method) (tooluniverse.exceptions.ToolError method) (tooluniverse.exceptions.ToolRateLimitError method) (tooluniverse.exceptions.ToolServerError method) (tooluniverse.exceptions.ToolUnavailableError method) (tooluniverse.exceptions.ToolValidationError method) (tooluniverse.execute_function._BatchCacheInfo method) (tooluniverse.execute_function._BatchJob method) (tooluniverse.execute_function.ToolCallable method) (tooluniverse.execute_function.ToolNamespace method) (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.extended_hooks.FilteringHook method) (tooluniverse.extended_hooks.FormattingHook method) (tooluniverse.extended_hooks.LoggingHook method) (tooluniverse.extended_hooks.ValidationHook method) (tooluniverse.fatcat_tool.FatcatScholarTool method) (tooluniverse.FDACountAdditiveReactionsTool method) (tooluniverse.FDADrugAdverseEventTool method) (tooluniverse.FDADrugLabelGetDrugGenericNameTool method) (tooluniverse.FDADrugLabelSearchIDTool method) (tooluniverse.FDADrugLabelSearchTool method) (tooluniverse.FDADrugLabelTool method) (tooluniverse.gene_ontology_tool.GeneOntologyTool method) (tooluniverse.genomics_gene_search_tool.GWASGeneSearch method) (tooluniverse.geo_tool.GEORESTTool method) (tooluniverse.GetSPLBySetIDTool method) (tooluniverse.gnomad_tool.GnomadTool method) (tooluniverse.graphql_tool.DiseaseTargetScoreTool method) (tooluniverse.graphql_tool.GraphQLTool method) (tooluniverse.graphql_tool.OpentargetGeneticsTool method) (tooluniverse.graphql_tool.OpentargetTool method) (tooluniverse.graphql_tool.OpentargetToolDrugNameMatch method) (tooluniverse.gwas_tool.GWASAssociationByID method) (tooluniverse.gwas_tool.GWASAssociationSearch method) (tooluniverse.gwas_tool.GWASAssociationsForSNP method) (tooluniverse.gwas_tool.GWASAssociationsForStudy method) (tooluniverse.gwas_tool.GWASAssociationsForTrait method) (tooluniverse.gwas_tool.GWASRESTTool method) (tooluniverse.gwas_tool.GWASSNPByID method) (tooluniverse.gwas_tool.GWASSNPSearch method) (tooluniverse.gwas_tool.GWASSNPsForGene method) (tooluniverse.gwas_tool.GWASStudiesForTrait method) (tooluniverse.gwas_tool.GWASStudyByID method) (tooluniverse.gwas_tool.GWASStudySearch method) (tooluniverse.gwas_tool.GWASVariantsForTrait method) (tooluniverse.GWASAssociationByID method) (tooluniverse.GWASAssociationSearch method) (tooluniverse.GWASAssociationsForSNP method) (tooluniverse.GWASAssociationsForStudy method) (tooluniverse.GWASAssociationsForTrait method) (tooluniverse.GWASSNPByID method) (tooluniverse.GWASSNPSearch method) (tooluniverse.GWASSNPsForGene method) (tooluniverse.GWASStudiesForTrait method) (tooluniverse.GWASStudyByID method) (tooluniverse.GWASStudySearch method) (tooluniverse.GWASVariantsForTrait method) (tooluniverse.hal_tool.HALTool method) (tooluniverse.HALTool method) (tooluniverse.hpa_tool.HPAGetBiologicalProcessTool method) (tooluniverse.hpa_tool.HPAGetComparativeExpressionTool method) (tooluniverse.hpa_tool.HPAGetContextualBiologicalProcessTool method) (tooluniverse.hpa_tool.HPAGetDiseaseExpressionTool method) (tooluniverse.hpa_tool.HPAGetGenePageDetailsTool method) (tooluniverse.hpa_tool.HPAGetRnaExpressionBySourceTool method) (tooluniverse.hpa_tool.HPAJsonApiTool method) (tooluniverse.hpa_tool.HPASearchApiTool method) (tooluniverse.hpa_tool.HPAXmlApiTool method) (tooluniverse.humanbase_tool.HumanBaseTool method) (tooluniverse.llm_clients.AzureOpenAIClient method) (tooluniverse.llm_clients.GeminiClient method) (tooluniverse.llm_clients.OpenRouterClient method) (tooluniverse.llm_clients.VLLMClient method) (tooluniverse.logging_config.ToolUniverseLogger method) (tooluniverse.markitdown_tool.MarkItDownTool method) (tooluniverse.mcp_client_tool.BaseMCPClient method) (tooluniverse.mcp_client_tool.MCPAutoLoaderTool method) (tooluniverse.mcp_client_tool.MCPClientTool method) (tooluniverse.mcp_client_tool.MCPProxyTool method) (tooluniverse.MCPAutoLoaderTool method) (tooluniverse.MCPClientTool method) (tooluniverse.medlineplus_tool.MedlinePlusRESTTool method) (tooluniverse.MedlinePlusRESTTool method) (tooluniverse.medrxiv_tool.MedRxivTool method) (tooluniverse.MedRxivTool method) (tooluniverse.memory_manager.MemoryManager method) (tooluniverse.MonarchDiseasesForMultiplePhenoTool method) (tooluniverse.MonarchTool method) (tooluniverse.odphp_tool.ODPHPOutlinkFetch method) (tooluniverse.odphp_tool.ODPHPRESTTool method) (tooluniverse.ODPHPOutlinkFetch method) (tooluniverse.openaire_tool.OpenAIRETool method) (tooluniverse.openalex_tool.OpenAlexTool method) (tooluniverse.openfda_adv_tool.FDACountAdditiveReactionsTool method) (tooluniverse.openfda_adv_tool.FDADrugAdverseEventTool method) (tooluniverse.openfda_tool.FDADrugLabelGetDrugGenericNameTool method) (tooluniverse.openfda_tool.FDADrugLabelSearchIDTool method) (tooluniverse.openfda_tool.FDADrugLabelSearchTool method) (tooluniverse.openfda_tool.FDADrugLabelTool method) (tooluniverse.openfda_tool.FDATool method) (tooluniverse.OpentargetGeneticsTool method) (tooluniverse.OpentargetTool method) (tooluniverse.OpentargetToolDrugNameMatch method) (tooluniverse.osf_preprints_tool.OSFPreprintsTool method) (tooluniverse.output_hook.FileSaveHook method) (tooluniverse.output_hook.HookManager method) (tooluniverse.output_hook.HookRule method) (tooluniverse.output_hook.OutputHook method) (tooluniverse.output_hook.SummarizationHook method) (tooluniverse.output_hook.SummarizationHookConfig method) (tooluniverse.package_tool.PackageTool method) (tooluniverse.PackageTool method) (tooluniverse.pmc_tool.PMCTool method) (tooluniverse.PMCTool method) (tooluniverse.pubchem_tool.PubChemRESTTool method) (tooluniverse.PubChemRESTTool method) (tooluniverse.pubmed_tool.PubMedTool method) (tooluniverse.PubMedTool method) (tooluniverse.pubtator_tool.PubTatorTool method) (tooluniverse.PubTatorTool method) (tooluniverse.rcsb_pdb_tool.RCSBTool method) (tooluniverse.RCSBTool method) (tooluniverse.reactome_tool.ReactomeRESTTool method) (tooluniverse.ReactomeRESTTool method) (tooluniverse.remote_tool.RemoteTool method) (tooluniverse.restful_tool.MonarchDiseasesForMultiplePhenoTool method) (tooluniverse.restful_tool.MonarchTool method) (tooluniverse.restful_tool.RESTfulTool method) (tooluniverse.SearchSPLTool method) (tooluniverse.semantic_scholar_tool.SemanticScholarTool method) (tooluniverse.SemanticScholarTool method) (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) (tooluniverse.space.loader.SpaceLoader method) (tooluniverse.space.SpaceLoader method) (tooluniverse.string_tool.STRINGRESTTool method) (tooluniverse.tool_finder_embedding.ToolFinderEmbedding method) (tooluniverse.tool_finder_keyword.ToolFinderKeyword method) (tooluniverse.tool_finder_llm.ToolFinderLLM method) (tooluniverse.tool_graph_web_ui.ToolGraphWebUI method) (tooluniverse.ToolFinderEmbedding method) (tooluniverse.ToolFinderKeyword method) (tooluniverse.ToolFinderLLM method) (tooluniverse.ToolUniverse method) (tooluniverse.ucsc_tool.UCSCTool method) (tooluniverse.unified_guideline_tools.CMAGuidelinesTool method) (tooluniverse.unified_guideline_tools.EuropePMCGuidelinesTool method) (tooluniverse.unified_guideline_tools.GINGuidelinesTool method) (tooluniverse.unified_guideline_tools.NICEGuidelineFullTextTool method) (tooluniverse.unified_guideline_tools.NICEWebScrapingTool method) (tooluniverse.unified_guideline_tools.OpenAlexGuidelinesTool method) (tooluniverse.unified_guideline_tools.PubMedGuidelinesTool method) (tooluniverse.unified_guideline_tools.TRIPDatabaseTool method) (tooluniverse.unified_guideline_tools.WHOGuidelineFullTextTool method) (tooluniverse.unified_guideline_tools.WHOGuidelinesTool method) (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) (tooluniverse.unpaywall_tool.UnpaywallTool method) (tooluniverse.UnpaywallTool method) (tooluniverse.url_tool.URLHTMLTagTool method) (tooluniverse.url_tool.URLToPDFTextTool method) (tooluniverse.URLHTMLTagTool method) (tooluniverse.URLToPDFTextTool method) (tooluniverse.uspto_tool.USPTOOpenDataPortalTool method) (tooluniverse.USPTOOpenDataPortalTool method) (tooluniverse.visualization_tool.VisualizationTool method) (tooluniverse.wikidata_sparql_tool.WikidataSPARQLTool method) (tooluniverse.xml_tool.XMLDatasetTool method) (tooluniverse.XMLDatasetTool method) (tooluniverse.zenodo_tool.ZenodoTool method) (tooluniverse.ZenodoTool method) __iter__() (tooluniverse.execute_function.ToolNamespace method) __len__() (tooluniverse.execute_function.ToolNamespace method) __new__() (tooluniverse.logging_config.ToolUniverseLogger static method) _add_documents() (tooluniverse.EmbeddingDatabase method) _add_search_tools() (tooluniverse.SMCP method) _add_utility_tools() (tooluniverse.SMCP method) _api_type (tooluniverse.agentic_tool.AgenticTool attribute) _apply_boolean_operators() (tooluniverse.CellosaurusQueryConverterTool method) _apply_defaults() (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseTool method) _apply_hooks_config() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _apply_llm_config() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method)

_apply_range_queries() (tooluniverse.CellosaurusQueryConverterTool method) _apply_stemming() (tooluniverse.ToolFinderKeyword method) _apply_wildcards() (tooluniverse.CellosaurusQueryConverterTool method) _argument_defaults (tooluniverse.agentic_tool.AgenticTool attribute) _BatchCacheInfo (class in tooluniverse.execute_function) _BatchJob (class in tooluniverse.execute_function) _build_batch_jobs() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _build_tool_index() (tooluniverse.ToolFinderKeyword method) _build_url() (tooluniverse.AlphaFoldRESTTool method) (tooluniverse.MedlinePlusRESTTool method) (tooluniverse.PubChemRESTTool method) (tooluniverse.ReactomeRESTTool method) (tooluniverse.UniProtRESTTool method) _cache (tooluniverse.execute_function.ToolUniverse property) (tooluniverse.ToolUniverse property) _cached_version_hash (tooluniverse.agentic_tool.AgenticTool attribute) (tooluniverse.base_tool.BaseTool attribute) _calculate_exact_match_bonus() (tooluniverse.ToolFinderKeyword method) _calculate_similarity() (tooluniverse.CellosaurusQueryConverterTool method) _calculate_tfidf_score() (tooluniverse.ToolFinderKeyword method) _call_tool() (tooluniverse.ComposeTool method) _check_api_key_requirements() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _check_basic_type() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _classify_exception() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _close_session() (tooluniverse.mcp_client_tool.BaseMCPClient method) _compose_url() (tooluniverse.pubtator_tool.PubTatorTool method) (tooluniverse.PubTatorTool method) _construct_solr_query() (tooluniverse.CellosaurusQueryConverterTool method) _convert_query() (tooluniverse.CellosaurusQueryConverterTool method) _convert_to_string() (tooluniverse.humanbase_tool.HumanBaseTool method) _create_dual_format_error() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _create_event_emitter() (tooluniverse.ComposeTool method) _create_from_documents() (tooluniverse.EmbeddingDatabase method) _create_hook_config_from_type() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _create_mcp_tool_from_tooluniverse() (tooluniverse.SMCP method) _database_exists() (tooluniverse.EmbeddingDatabase method) _discover_tool_dependencies() (tooluniverse.ComposeTool method) _download_from_huggingface() (tooluniverse.EmbeddingSync method) _drugbank_filter() (tooluniverse.dataset_tool.DatasetTool method) (tooluniverse.DatasetTool method) _drugbank_search() (tooluniverse.dataset_tool.DatasetTool method) (tooluniverse.DatasetTool method) _emit_stream_chunk() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) (tooluniverse.ComposeTool method) _ensure_playwright_browsers() (tooluniverse.URLToPDFTextTool method) _ensure_tool_instance() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _execute_batch_jobs() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _execute_from_file() (tooluniverse.ComposeTool method) _execute_function_call_list() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _execute_inline_code() (tooluniverse.ComposeTool method) _execute_tool_with_stream() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _expose_tooluniverse_tools() (tooluniverse.SMCP method) _extract_authors() (tooluniverse.CoreTool method) (tooluniverse.PMCTool method) _extract_data() (tooluniverse.UniProtRESTTool method) _extract_field_terms() (tooluniverse.CellosaurusQueryConverterTool method) _extract_field_value() (tooluniverse.XMLDatasetTool method) _extract_outcomes_from_output() (tooluniverse.ClinicalTrialsDetailsTool method) (tooluniverse.ctg_tool.ClinicalTrialsDetailsTool method) _extract_paper_info() (tooluniverse.openalex_tool.OpenAlexTool method) _extract_parameter_text() (tooluniverse.ToolFinderKeyword method) _extract_phrases() (tooluniverse.ToolFinderKeyword method) _extract_record_data() (tooluniverse.XMLDatasetTool method) _extract_safety_from_output() (tooluniverse.ClinicalTrialsDetailsTool method) (tooluniverse.ctg_tool.ClinicalTrialsDetailsTool method) _extract_text() (tooluniverse.ODPHPOutlinkFetch method) _extract_text_content() (tooluniverse.MedlinePlusRESTTool method) _extract_year() (tooluniverse.CoreTool method) (tooluniverse.PMCTool method) _fallback_api_type (tooluniverse.agentic_tool.AgenticTool attribute) _fallback_model_id (tooluniverse.agentic_tool.AgenticTool attribute) _filter() (tooluniverse.XMLDatasetTool method) _filter_and_deduplicate_tools() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _filter_search_results() (tooluniverse.pubtator_tool.PubTatorTool method) (tooluniverse.PubTatorTool method) _find_matches() (tooluniverse.XMLDatasetTool method) _format_as_json() (tooluniverse.ToolFinderLLM method) _format_endpoint_url() (tooluniverse.ctg_tool.ClinicalTrialsTool method) _format_prompt() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) _format_response() (tooluniverse.MedlinePlusRESTTool method) _format_tools_for_prompt() (tooluniverse.ToolFinderLLM method) _gemini_model_id (tooluniverse.agentic_tool.AgenticTool attribute) _generate_embeddings() (tooluniverse.EmbeddingDatabase method) _generate_readme() (tooluniverse.EmbeddingSync method) _get_all_records_data() (tooluniverse.XMLDatasetTool method) _get_api_key() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _get_available_tools() (tooluniverse.ToolFinderLLM method) _get_cell_line_info() (tooluniverse.CellosaurusGetCellLineInfoTool method) _get_current_timestamp() (tooluniverse.humanbase_tool.HumanBaseTool method) _get_database_info() (tooluniverse.EmbeddingDatabase method) (tooluniverse.EmbeddingSync method) _get_dataset_path() (tooluniverse.XMLDatasetTool method) _get_filter_description() (tooluniverse.XMLDatasetTool method) _get_filter_function() (tooluniverse.XMLDatasetTool method) _get_global_fallback_chain() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) _get_installation_instructions() (tooluniverse.PackageTool method) _get_local_info() (tooluniverse.PackageTool method) _get_mcp_endpoint() (tooluniverse.mcp_client_tool.BaseMCPClient method) _get_pypi_info() (tooluniverse.PackageTool method) _get_quick_start_guide() (tooluniverse.PackageTool method) _get_searchable_value() (tooluniverse.XMLDatasetTool method) _get_tool_category_mapping() (tooluniverse.ComposeTool method) _get_tool_instance() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _get_tool_selection_prompt() (tooluniverse.ToolFinderLLM method) _get_tool_semaphore() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _get_usage_example() (tooluniverse.PackageTool method) _get_valid_categories() (tooluniverse.SMCP method) _global_fallback_chain (tooluniverse.agentic_tool.AgenticTool attribute) _handle_tools_find() (tooluniverse.SMCP method) _init_agentic_tool() (tooluniverse.ToolFinderLLM method) _init_azure_client() (tooluniverse.EmbeddingDatabase method) _init_database() (tooluniverse.EmbeddingDatabase method) _init_openai_client() (tooluniverse.EmbeddingDatabase method) _init_tool_finder() (tooluniverse.SMCP method) _input_arguments (tooluniverse.agentic_tool.AgenticTool attribute) _is_match() (tooluniverse.XMLDatasetTool method) _iter_chunks() (tooluniverse.agentic_tool.AgenticTool static method) (tooluniverse.AgenticTool static method) _load_auto_discovered_configs() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _load_code_from_file() (tooluniverse.ComposeTool method) _load_database() (tooluniverse.EmbeddingDatabase method) _load_dataset() (tooluniverse.dataset_tool.DatasetTool method) (tooluniverse.DatasetTool method) (tooluniverse.XMLDatasetTool method) _load_missing_dependencies() (tooluniverse.ComposeTool method) _load_space_configs() (tooluniverse.SMCP method) _load_tool_names_from_file() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _load_tools_from_mcp_server() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _local_database_exists() (tooluniverse.EmbeddingSync method) _lookup() (tooluniverse.UnpaywallTool method) _make_cache_key() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _make_mcp_request() (tooluniverse.mcp_client_tool.BaseMCPClient method) _make_request() (tooluniverse.AlphaFoldRESTTool method) _map_param_names() (tooluniverse.ctg_tool.ClinicalTrialsTool method) _map_term_to_field() (tooluniverse.CellosaurusQueryConverterTool method) _map_value() (tooluniverse.FDADrugAdverseEventTool method) (tooluniverse.openfda_adv_tool.FDADrugAdverseEventTool method) _matches_filters() (tooluniverse.EmbeddingDatabase method) _max_retries (tooluniverse.agentic_tool.AgenticTool attribute) _merge_databases() (tooluniverse.EmbeddingSync method) _model_id (tooluniverse.agentic_tool.AgenticTool attribute) _perform_tool_search() (tooluniverse.SMCP method) _post_process() (tooluniverse.FDADrugAdverseEventTool method) (tooluniverse.openfda_adv_tool.FDADrugAdverseEventTool method) _predict() (tooluniverse.ADMETAITool method) _prefilter_tools_by_keywords() (tooluniverse.ToolFinderLLM method) _prepare_api_params() (tooluniverse.ctg_tool.ClinicalTrialsTool method) _prime_batch_cache() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _print_tooluniverse_banner() (tooluniverse.SMCP method) _process_mcp_auto_loaders() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _prompt_template (tooluniverse.agentic_tool.AgenticTool attribute) _query_params() (tooluniverse.pubtator_tool.PubTatorTool method) (tooluniverse.PubTatorTool method) _read_tools_from_file() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _register_custom_mcp_methods() (tooluniverse.SMCP method) _remove_empty_values() (tooluniverse.ClinicalTrialsDetailsTool method) (tooluniverse.ctg_tool.ClinicalTrialsDetailsTool method) _rename_database_in_db() (tooluniverse.EmbeddingSync method) _required_arguments (tooluniverse.agentic_tool.AgenticTool attribute) _retry_delay (tooluniverse.agentic_tool.AgenticTool attribute) _return_json (tooluniverse.agentic_tool.AgenticTool attribute) _run_call_tool() (tooluniverse.mcp_client_tool.MCPClientTool method) (tooluniverse.MCPClientTool method) _run_get_prompt() (tooluniverse.mcp_client_tool.MCPClientTool method) (tooluniverse.MCPClientTool method) _run_json_search() (tooluniverse.ToolFinderKeyword method) _run_list_prompts() (tooluniverse.mcp_client_tool.MCPClientTool method) (tooluniverse.MCPClientTool method) _run_list_resources() (tooluniverse.mcp_client_tool.MCPClientTool method) (tooluniverse.MCPClientTool method) _run_list_tools() (tooluniverse.mcp_client_tool.MCPClientTool method) (tooluniverse.MCPClientTool method) _run_read_resource() (tooluniverse.mcp_client_tool.MCPClientTool method) (tooluniverse.MCPClientTool method) _run_with_cleanup() (tooluniverse.mcp_client_tool.BaseMCPClient method) _scan_all_json_files() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _scan_predefined_files() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _search() (tooluniverse.ArXivTool method) (tooluniverse.BioRxivTool method) (tooluniverse.CoreTool method) (tooluniverse.CrossrefTool method) (tooluniverse.DBLPTool method) (tooluniverse.efo_tool.EFOTool method) (tooluniverse.EFOTool method) (tooluniverse.EmbeddingDatabase method) (tooluniverse.europe_pmc_tool.EuropePMCTool method) (tooluniverse.EuropePMCTool method) (tooluniverse.FDADrugAdverseEventTool method) (tooluniverse.HALTool method) (tooluniverse.MedRxivTool method) (tooluniverse.openfda_adv_tool.FDADrugAdverseEventTool method) (tooluniverse.PMCTool method) (tooluniverse.PubMedTool method) (tooluniverse.semantic_scholar_tool.SemanticScholarTool method) (tooluniverse.SemanticScholarTool method) (tooluniverse.XMLDatasetTool method) _search_cell_lines() (tooluniverse.CellosaurusSearchTool method) _search_similar_molecules() (tooluniverse.chem_tool.ChEMBLTool method) (tooluniverse.ChEMBLTool method) _select_search_tool() (tooluniverse.SMCP method) _setup_smcp_tools() (tooluniverse.SMCP method) _simplify_output() (tooluniverse.ClinicalTrialsDetailsTool method) (tooluniverse.ClinicalTrialsSearchTool method) (tooluniverse.ctg_tool.ClinicalTrialsDetailsTool method) (tooluniverse.ctg_tool.ClinicalTrialsSearchTool method) _store_space_metadata() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _substitute_env_vars() (tooluniverse.EmbeddingDatabase method) _temperature (tooluniverse.agentic_tool.AgenticTool attribute) _tokenize_and_normalize() (tooluniverse.ToolFinderKeyword method) _tools_find_middleware() (tooluniverse.SMCP method) _try_api() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) _try_initialize_api() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) _upload_to_huggingface() (tooluniverse.EmbeddingSync method) _use_global_fallback (tooluniverse.agentic_tool.AgenticTool attribute) _validate_api_key (tooluniverse.agentic_tool.AgenticTool attribute) _validate_arguments() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) _validate_model_config() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) _validate_parameters() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _validate_solr_query() (tooluniverse.CellosaurusQueryConverterTool method)

A

acquire() (tooluniverse.cache.memory_cache.SingleFlight method) add_3d_controls_script() (tooluniverse.visualization_tool.VisualizationTool method) add_agent_result() (tooluniverse.memory_manager.MemoryManager method) add_custom_tool() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) ADMETAI_predict_BBB_penetrance() (in module tooluniverse.tools.ADMETAI_predict_BBB_penetrance) ADMETAI_predict_bioavailability() (in module tooluniverse.tools.ADMETAI_predict_bioavailability) ADMETAI_predict_clearance_distribution() (in module tooluniverse.tools.ADMETAI_predict_clearance_distribution) ADMETAI_predict_CYP_interactions() (in module tooluniverse.tools.ADMETAI_predict_CYP_interactions) ADMETAI_predict_nuclear_receptor_activity() (in module tooluniverse.tools.ADMETAI_predict_nuclear_receptor_activity) ADMETAI_predict_physicochemical_properties() (in module tooluniverse.tools.ADMETAI_predict_physicochemical_properties) ADMETAI_predict_solubility_lipophilicity_hydration() (in module tooluniverse.tools.ADMETAI_predict_solubility_lipophilicity_hydration) ADMETAI_predict_stress_response() (in module tooluniverse.tools.ADMETAI_predict_stress_response) ADMETAI_predict_toxicity() (in module tooluniverse.tools.ADMETAI_predict_toxicity) ADMETAITool (class in tooluniverse) (class in tooluniverse.admetai_tool) ADMETAnalyzerAgent() (in module tooluniverse.tools.ADMETAnalyzerAgent) AdvancedCodeQualityAnalyzer() (in module tooluniverse.tools.AdvancedCodeQualityAnalyzer) AdverseEventICDMapper() (in module tooluniverse.tools.AdverseEventICDMapper) AdverseEventPredictionQuestionGenerator() (in module tooluniverse.tools.AdverseEventPredictionQuestionGenerator) AdverseEventPredictionQuestionGeneratorWithContext() (in module tooluniverse.tools.AdverseEventPredictionQuestionGeneratorWithContext) AgenticTool (class in tooluniverse) (class in tooluniverse.agentic_tool)

all_tool_dict (tooluniverse.execute_function.ToolUniverse attribute) (tooluniverse.ToolUniverse attribute) all_tools (tooluniverse.execute_function.ToolUniverse attribute) (tooluniverse.ToolUniverse attribute) alphafold_get_annotations() (in module tooluniverse.tools.alphafold_get_annotations) alphafold_get_prediction() (in module tooluniverse.tools.alphafold_get_prediction) alphafold_get_summary() (in module tooluniverse.tools.alphafold_get_summary) AlphaFoldRESTTool (class in tooluniverse) (class in tooluniverse.alphafold_tool) apply_hooks() (tooluniverse.output_hook.HookManager method) ArgumentDescriptionOptimizer() (in module tooluniverse.tools.ArgumentDescriptionOptimizer) arguments (tooluniverse.execute_function._BatchJob attribute) ArXiv_search_papers() (in module tooluniverse.tools.ArXiv_search_papers) ArXivTool (class in tooluniverse) (class in tooluniverse.arxiv_tool) assign_by_path() (tooluniverse.uspto_tool.USPTOOpenDataPortalTool method) (tooluniverse.USPTOOpenDataPortalTool method) auto_discover_tools() (in module tooluniverse.tool_registry) auto_load_and_register() (tooluniverse.mcp_client_tool.MCPAutoLoaderTool method) (tooluniverse.MCPAutoLoaderTool method) AzureOpenAIClient (class in tooluniverse.llm_clients)

B

BaseLLMClient (class in tooluniverse.llm_clients) BaseMCPClient (class in tooluniverse.mcp_client_tool) BaseTool (class in tooluniverse) (class in tooluniverse.base_tool) BioGRIDRESTTool (class in tooluniverse.biogrid_tool) BiomarkerDiscoveryWorkflow() (in module tooluniverse.tools.BiomarkerDiscoveryWorkflow)

BioRxiv_search_preprints() (in module tooluniverse.tools.BioRxiv_search_preprints) BioRxivTool (class in tooluniverse) (class in tooluniverse.biorxiv_tool) Boltz2DockingTool (class in tooluniverse.boltz_tool) build_graph() (tooluniverse.enrichr_tool.EnrichrTool method) build_lazy_registry() (in module tooluniverse.tool_registry) bulk_get() (tooluniverse.cache.result_cache_manager.ResultCacheManager method)

C

cache_info (tooluniverse.execute_function._BatchJob attribute) cache_key (tooluniverse.execute_function._BatchCacheInfo attribute) cache_key_composed (tooluniverse.execute_function._BatchJob attribute) CacheEntry (class in tooluniverse.cache.sqlite_backend) CacheRecord (class in tooluniverse.cache.result_cache_manager) calculate_tool_hash() (in module tooluniverse.build_optimizer) call (tooluniverse.execute_function._BatchJob attribute) call_agentic_human() (in module tooluniverse.tools.call_agentic_human) call_id_gen() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) call_tool() (tooluniverse.mcp_client_tool.MCPAutoLoaderTool method) (tooluniverse.mcp_client_tool.MCPClientTool method) (tooluniverse.MCPAutoLoaderTool method) (tooluniverse.MCPClientTool method) callable_functions (tooluniverse.execute_function.ToolUniverse attribute) (tooluniverse.ToolUniverse attribute) CallAgent() (in module tooluniverse.tools.CallAgent) cancer_biomarkers_disease_target_score() (in module tooluniverse.tools.cancer_biomarkers_disease_target_score) cancer_gene_census_disease_target_score() (in module tooluniverse.tools.cancer_gene_census_disease_target_score) cellosaurus_get_cell_line_info() (in module tooluniverse.tools.cellosaurus_get_cell_line_info) cellosaurus_query_converter() (in module tooluniverse.tools.cellosaurus_query_converter) cellosaurus_search_cell_lines() (in module tooluniverse.tools.cellosaurus_search_cell_lines) CellosaurusGetCellLineInfoTool (class in tooluniverse) (class in tooluniverse.cellosaurus_tool) CellosaurusQueryConverterTool (class in tooluniverse) (class in tooluniverse.cellosaurus_tool) CellosaurusSearchTool (class in tooluniverse) (class in tooluniverse.cellosaurus_tool) check_function_call() (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseTool method) (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) check_keys_present() (in module tooluniverse.openfda_tool) chembl_disease_target_score() (in module tooluniverse.tools.chembl_disease_target_score) ChEMBL_search_similar_molecules() (in module tooluniverse.tools.ChEMBL_search_similar_molecules) ChEMBLTool (class in tooluniverse) (class in tooluniverse.chem_tool) chunk_size (tooluniverse.output_hook.SummarizationHook attribute) (tooluniverse.output_hook.SummarizationHookConfig attribute) cleanup_expired() (tooluniverse.cache.sqlite_backend.PersistentCache method) cleanup_orphaned_files() (in module tooluniverse.build_optimizer) clear() (tooluniverse.cache.memory_cache.LRUCache method) (tooluniverse.cache.result_cache_manager.ResultCacheManager method) (tooluniverse.cache.sqlite_backend.PersistentCache method) clear_cache() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.tool_finder_llm.ToolFinderLLM method) (tooluniverse.ToolFinderLLM method) (tooluniverse.ToolUniverse method) ClinicalTrialDesignAgent() (in module tooluniverse.tools.ClinicalTrialDesignAgent) ClinicalTrialsDetailsTool (class in tooluniverse) (class in tooluniverse.ctg_tool) ClinicalTrialsSearchTool (class in tooluniverse) (class in tooluniverse.ctg_tool) ClinicalTrialsTool (class in tooluniverse.ctg_tool) ClinVar_search_variants() (in module tooluniverse.tools.ClinVar_search_variants) ClinVarTool (class in tooluniverse.clinvar_tool) close() (tooluniverse.cache.result_cache_manager.ResultCacheManager method) (tooluniverse.cache.sqlite_backend.PersistentCache method) (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) (tooluniverse.ToolUniverse method)

close_session() (tooluniverse.memory_manager.MemoryManager method) CMA_Guidelines_Search() (in module tooluniverse.tools.CMA_Guidelines_Search) CMAGuidelinesTool (class in tooluniverse.unified_guideline_tools) CodeOptimizer() (in module tooluniverse.tools.CodeOptimizer) CodeQualityAnalyzer() (in module tooluniverse.tools.CodeQualityAnalyzer) COLORS (tooluniverse.logging_config.ToolUniverseFormatter attribute) compare_function_calls() (in module tooluniverse.utils) compose() (in module tooluniverse.compose_scripts.biomarker_discovery) (in module tooluniverse.compose_scripts.comprehensive_drug_discovery) (in module tooluniverse.compose_scripts.drug_safety_analyzer) (in module tooluniverse.compose_scripts.enhanced_multi_agent_literature_search) (in module tooluniverse.compose_scripts.literature_tool) (in module tooluniverse.compose_scripts.multi_agent_literature_search) (in module tooluniverse.compose_scripts.output_summarizer) (in module tooluniverse.compose_scripts.tool_description_optimizer) (in module tooluniverse.compose_scripts.tool_discover) (in module tooluniverse.compose_scripts.tool_graph_composer) (in module tooluniverse.compose_scripts.tool_graph_generation) (in module tooluniverse.compose_scripts.tool_metadata_generator) compose_key() (tooluniverse.cache.result_cache_manager.ResultCacheManager static method) composer_timeout_sec (tooluniverse.output_hook.SummarizationHookConfig attribute) composer_tool (tooluniverse.output_hook.SummarizationHook attribute) (tooluniverse.output_hook.SummarizationHookConfig attribute) ComposeTool (class in tooluniverse) (class in tooluniverse.compose_tool) CompoundDiscoveryAgent() (in module tooluniverse.tools.CompoundDiscoveryAgent) ComprehensiveDrugDiscoveryPipeline() (in module tooluniverse.tools.ComprehensiveDrugDiscoveryPipeline) conditions (tooluniverse.output_hook.HookRule attribute) config (tooluniverse.output_hook.HookManager attribute) (tooluniverse.output_hook.OutputHook attribute) config_path (tooluniverse.output_hook.HookManager attribute) connect_lookup_by_code() (tooluniverse.medlineplus_tool.MedlinePlusRESTTool method) (tooluniverse.MedlinePlusRESTTool method) convert_to_base64_image() (tooluniverse.visualization_tool.VisualizationTool method) convert_to_markdown() (in module tooluniverse.tools.convert_to_markdown) CORE_search_papers() (in module tooluniverse.tools.CORE_search_papers) CoreTool (class in tooluniverse) (class in tooluniverse.core_tool) create_error_response() (tooluniverse.visualization_tool.VisualizationTool method) create_mcp_tools_config() (tooluniverse.mcp_client_tool.MCPServerDiscovery static method) create_molecule_2d_html() (tooluniverse.visualization_tool.VisualizationTool method) create_plotly_html() (tooluniverse.visualization_tool.VisualizationTool method) create_py3dmol_html() (tooluniverse.visualization_tool.VisualizationTool method) create_session() (tooluniverse.memory_manager.MemoryManager method) create_smcp_server() (in module tooluniverse) (in module tooluniverse.smcp) create_visualization_response() (tooluniverse.visualization_tool.VisualizationTool method) create_web_ui_files() (in module tooluniverse.tool_graph_web_ui) created_at (tooluniverse.cache.sqlite_backend.CacheEntry attribute) critical() (in module tooluniverse.logging_config) Crossref_search_works() (in module tooluniverse.tools.Crossref_search_works) CrossrefTool (class in tooluniverse) (class in tooluniverse.crossref_tool) CustomTool (class in tooluniverse.custom_tool)

D

DailyMed_get_spl_by_setid() (in module tooluniverse.tools.DailyMed_get_spl_by_setid) DailyMed_search_spls() (in module tooluniverse.tools.DailyMed_search_spls) DataAnalysisValidityReviewer() (in module tooluniverse.tools.DataAnalysisValidityReviewer) DatasetTool (class in tooluniverse) (class in tooluniverse.dataset_tool) DBLP_search_publications() (in module tooluniverse.tools.DBLP_search_publications) DBLPTool (class in tooluniverse) (class in tooluniverse.dblp_tool) dbSNP_get_variant_by_rsid() (in module tooluniverse.tools.dbSNP_get_variant_by_rsid) DbSnpTool (class in tooluniverse.dbsnp_tool) debug() (in module tooluniverse.logging_config) DEFAULT_MODEL_LIMITS (tooluniverse.llm_clients.AzureOpenAIClient attribute) (tooluniverse.llm_clients.OpenRouterClient attribute) delete() (tooluniverse.cache.memory_cache.LRUCache method) (tooluniverse.cache.result_cache_manager.ResultCacheManager method) (tooluniverse.cache.sqlite_backend.PersistentCache method) DescriptionAnalyzer() (in module tooluniverse.tools.DescriptionAnalyzer) DescriptionQualityEvaluator() (in module tooluniverse.tools.DescriptionQualityEvaluator) details (tooluniverse.exceptions.ToolError attribute) dict_search() (in module tooluniverse.tools.dict_search) dili_search() (in module tooluniverse.tools.dili_search) diqt_search() (in module tooluniverse.tools.diqt_search) disable_hook() (tooluniverse.output_hook.HookManager method) disable_hooks() (tooluniverse.output_hook.HookManager method) discover_mcp_tools() (in module tooluniverse.mcp_integration) (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) discover_server_tools() (tooluniverse.mcp_client_tool.MCPServerDiscovery static method) discover_tools() (tooluniverse.mcp_client_tool.MCPAutoLoaderTool method) (tooluniverse.MCPAutoLoaderTool method) disease_target_score() (in module tooluniverse.tools.disease_target_score) DiseaseAnalyzerAgent() (in module tooluniverse.tools.DiseaseAnalyzerAgent)

DiseaseTargetScoreTool (class in tooluniverse) (class in tooluniverse.graphql_tool) DOAJ_search_articles() (in module tooluniverse.tools.DOAJ_search_articles) DOAJTool (class in tooluniverse) (class in tooluniverse.doaj_tool) DomainExpertValidator() (in module tooluniverse.tools.DomainExpertValidator) download_from_hf() (in module tooluniverse.utils) drugbank_filter_drugs_by_name() (in module tooluniverse.tools.drugbank_filter_drugs_by_name) drugbank_full_search() (in module tooluniverse.tools.drugbank_full_search) drugbank_get_drug_basic_info_by_drug_name_or_drugbank_id() (in module tooluniverse.tools.drugbank_get_drug_basic_info_by_drug_name_or_drugbank_id) drugbank_get_drug_chemistry_by_drug_name_or_drugbank_id() (in module tooluniverse.tools.drugbank_get_drug_chemistry_by_drug_name_or_drugbank_id) drugbank_get_drug_interactions_by_drug_name_or_drugbank_id() (in module tooluniverse.tools.drugbank_get_drug_interactions_by_drug_name_or_drugbank_id) drugbank_get_drug_name_and_description_by_indication() (in module tooluniverse.tools.drugbank_get_drug_name_and_description_by_indication) drugbank_get_drug_name_and_description_by_pathway_name() (in module tooluniverse.tools.drugbank_get_drug_name_and_description_by_pathway_name) drugbank_get_drug_name_and_description_by_target_name() (in module tooluniverse.tools.drugbank_get_drug_name_and_description_by_target_name) drugbank_get_drug_name_description_pharmacology_by_mechanism_of_action() (in module tooluniverse.tools.drugbank_get_drug_name_description_pharmacology_by_mechanism_of_action) drugbank_get_drug_pathways_and_reactions_by_drug_name_or_drugbank_id() (in module tooluniverse.tools.drugbank_get_drug_pathways_and_reactions_by_drug_name_or_drugbank_id) drugbank_get_drug_products_by_name_or_drugbank_id() (in module tooluniverse.tools.drugbank_get_drug_products_by_name_or_drugbank_id) drugbank_get_drug_references_by_drug_name_or_drugbank_id() (in module tooluniverse.tools.drugbank_get_drug_references_by_drug_name_or_drugbank_id) drugbank_get_indications_by_drug_name_or_drugbank_id() (in module tooluniverse.tools.drugbank_get_indications_by_drug_name_or_drugbank_id) drugbank_get_pharmacology_by_drug_name_or_drugbank_id() (in module tooluniverse.tools.drugbank_get_pharmacology_by_drug_name_or_drugbank_id) drugbank_get_safety_by_drug_name_or_drugbank_id() (in module tooluniverse.tools.drugbank_get_safety_by_drug_name_or_drugbank_id) drugbank_get_targets_by_drug_name_or_drugbank_id() (in module tooluniverse.tools.drugbank_get_targets_by_drug_name_or_drugbank_id) drugbank_links_search() (in module tooluniverse.tools.drugbank_links_search) drugbank_vocab_filter() (in module tooluniverse.tools.drugbank_vocab_filter) drugbank_vocab_search() (in module tooluniverse.tools.drugbank_vocab_search) DrugInteractionAnalyzerAgent() (in module tooluniverse.tools.DrugInteractionAnalyzerAgent) DrugOptimizationAgent() (in module tooluniverse.tools.DrugOptimizationAgent) DrugSafetyAnalyzer() (in module tooluniverse.tools.DrugSafetyAnalyzer) dump() (tooluniverse.cache.result_cache_manager.ResultCacheManager method) dump_cache() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method)

E

eager_load() (tooluniverse.execute_function.ToolNamespace method) eager_load_tools() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) EFOTool (class in tooluniverse) (class in tooluniverse.efo_tool) embedding_database_add() (in module tooluniverse.tools.embedding_database_add) embedding_database_create() (in module tooluniverse.tools.embedding_database_create) embedding_database_load() (in module tooluniverse.tools.embedding_database_load) embedding_database_search() (in module tooluniverse.tools.embedding_database_search) embedding_sync_download() (in module tooluniverse.tools.embedding_sync_download) embedding_sync_upload() (in module tooluniverse.tools.embedding_sync_upload) EmbeddingDatabase (class in tooluniverse) (class in tooluniverse.embedding_database) EmbeddingSync (class in tooluniverse) (class in tooluniverse.embedding_sync) EMOJI_PREFIX (tooluniverse.logging_config.ToolUniverseFormatter attribute) enable_hook() (tooluniverse.output_hook.HookManager method) enable_hooks() (tooluniverse.output_hook.HookManager method) enabled (tooluniverse.output_hook.HookManager attribute) (tooluniverse.output_hook.OutputHook attribute) enrichr_api() (tooluniverse.enrichr_tool.EnrichrTool method) enrichr_gene_enrichment_analysis() (in module tooluniverse.tools.enrichr_gene_enrichment_analysis) EnrichrTool (class in tooluniverse.enrichr_tool) Ensembl_lookup_gene_by_symbol() (in module tooluniverse.tools.Ensembl_lookup_gene_by_symbol) EnsemblTool (class in tooluniverse.ensembl_tool) error() (in module tooluniverse.logging_config) error_type (tooluniverse.exceptions.ToolError attribute)

estimate_token_usage() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) EthicalComplianceReviewer() (in module tooluniverse.tools.EthicalComplianceReviewer) europepmc_disease_target_score() (in module tooluniverse.tools.europepmc_disease_target_score) EuropePMC_Guidelines_Search() (in module tooluniverse.tools.EuropePMC_Guidelines_Search) EuropePMC_search_articles() (in module tooluniverse.tools.EuropePMC_search_articles) EuropePMCGuidelinesTool (class in tooluniverse.unified_guideline_tools) EuropePMCTool (class in tooluniverse) (class in tooluniverse.europe_pmc_tool) eva_disease_target_score() (in module tooluniverse.tools.eva_disease_target_score) eva_somatic_disease_target_score() (in module tooluniverse.tools.eva_somatic_disease_target_score) evaluate() (tooluniverse.output_hook.HookRule method) evaluate_function_call() (in module tooluniverse.utils) evaluate_function_call_from_toolbox() (in module tooluniverse.utils) execute_query() (in module tooluniverse.graphql_tool) execute_RESTful_query() (in module tooluniverse.restful_tool) ExperimentalDesignScorer() (in module tooluniverse.tools.ExperimentalDesignScorer) expires_at (tooluniverse.cache.result_cache_manager.CacheRecord attribute) export_tool_names() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) expression_atlas_disease_target_score() (in module tooluniverse.tools.expression_atlas_disease_target_score) extract_clinical_trial_adverse_events() (in module tooluniverse.tools.extract_clinical_trial_adverse_events) extract_clinical_trial_outcomes() (in module tooluniverse.tools.extract_clinical_trial_outcomes) extract_function_call_json() (in module tooluniverse.utils) (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) extract_nested_fields() (in module tooluniverse.openfda_tool) extract_sentences_with_keywords() (in module tooluniverse.openfda_tool)

F

FAERS_count_additive_administration_routes() (in module tooluniverse.tools.FAERS_count_additive_administration_routes) FAERS_count_additive_adverse_reactions() (in module tooluniverse.tools.FAERS_count_additive_adverse_reactions) FAERS_count_additive_event_reports_by_country() (in module tooluniverse.tools.FAERS_count_additive_event_reports_by_country) FAERS_count_additive_reaction_outcomes() (in module tooluniverse.tools.FAERS_count_additive_reaction_outcomes) FAERS_count_additive_reports_by_reporter_country() (in module tooluniverse.tools.FAERS_count_additive_reports_by_reporter_country) FAERS_count_additive_seriousness_classification() (in module tooluniverse.tools.FAERS_count_additive_seriousness_classification) FAERS_count_country_by_drug_event() (in module tooluniverse.tools.FAERS_count_country_by_drug_event) FAERS_count_death_related_by_drug() (in module tooluniverse.tools.FAERS_count_death_related_by_drug) FAERS_count_drug_routes_by_event() (in module tooluniverse.tools.FAERS_count_drug_routes_by_event) FAERS_count_drugs_by_drug_event() (in module tooluniverse.tools.FAERS_count_drugs_by_drug_event) FAERS_count_outcomes_by_drug_event() (in module tooluniverse.tools.FAERS_count_outcomes_by_drug_event) FAERS_count_patient_age_distribution() (in module tooluniverse.tools.FAERS_count_patient_age_distribution) FAERS_count_reactions_by_drug_event() (in module tooluniverse.tools.FAERS_count_reactions_by_drug_event) FAERS_count_reportercountry_by_drug_event() (in module tooluniverse.tools.FAERS_count_reportercountry_by_drug_event) FAERS_count_seriousness_by_drug_event() (in module tooluniverse.tools.FAERS_count_seriousness_by_drug_event) Fatcat_search_scholar() (in module tooluniverse.tools.Fatcat_search_scholar) FatcatScholarTool (class in tooluniverse.fatcat_tool) FDA_get_abuse_dependence_info_by_drug_name() (in module tooluniverse.tools.FDA_get_abuse_dependence_info_by_drug_name) FDA_get_abuse_info_by_drug_name() (in module tooluniverse.tools.FDA_get_abuse_info_by_drug_name) FDA_get_accessories_info_by_drug_name() (in module tooluniverse.tools.FDA_get_accessories_info_by_drug_name) FDA_get_active_ingredient_info_by_drug_name() (in module tooluniverse.tools.FDA_get_active_ingredient_info_by_drug_name) FDA_get_adverse_reactions_by_drug_name() (in module tooluniverse.tools.FDA_get_adverse_reactions_by_drug_name) FDA_get_alarms_by_drug_name() (in module tooluniverse.tools.FDA_get_alarms_by_drug_name) FDA_get_animal_pharmacology_info_by_drug_name() (in module tooluniverse.tools.FDA_get_animal_pharmacology_info_by_drug_name) FDA_get_assembly_installation_info_by_drug_name() (in module tooluniverse.tools.FDA_get_assembly_installation_info_by_drug_name) FDA_get_boxed_warning_info_by_drug_name() (in module tooluniverse.tools.FDA_get_boxed_warning_info_by_drug_name) FDA_get_brand_name_generic_name() (in module tooluniverse.tools.FDA_get_brand_name_generic_name) FDA_get_calibration_instructions_by_drug_name() (in module tooluniverse.tools.FDA_get_calibration_instructions_by_drug_name) FDA_get_carcinogenic_mutagenic_fertility_by_drug_name() (in module tooluniverse.tools.FDA_get_carcinogenic_mutagenic_fertility_by_drug_name) FDA_get_child_safety_info_by_drug_name() (in module tooluniverse.tools.FDA_get_child_safety_info_by_drug_name) FDA_get_clinical_pharmacology_by_drug_name() (in module tooluniverse.tools.FDA_get_clinical_pharmacology_by_drug_name) FDA_get_clinical_studies_info_by_drug_name() (in module tooluniverse.tools.FDA_get_clinical_studies_info_by_drug_name) FDA_get_contact_for_questions_info_by_drug_name() (in module tooluniverse.tools.FDA_get_contact_for_questions_info_by_drug_name) FDA_get_contraindications_by_drug_name() (in module tooluniverse.tools.FDA_get_contraindications_by_drug_name) FDA_get_controlled_substance_DEA_schedule_info_by_drug_name() (in module tooluniverse.tools.FDA_get_controlled_substance_DEA_schedule_info_by_drug_name) FDA_get_dear_health_care_provider_letter_info_by_drug_name() (in module tooluniverse.tools.FDA_get_dear_health_care_provider_letter_info_by_drug_name) FDA_get_dependence_info_by_drug_name() (in module tooluniverse.tools.FDA_get_dependence_info_by_drug_name) FDA_get_disposal_info_by_drug_name() (in module tooluniverse.tools.FDA_get_disposal_info_by_drug_name) FDA_get_do_not_use_info_by_drug_name() (in module tooluniverse.tools.FDA_get_do_not_use_info_by_drug_name) FDA_get_document_id_by_drug_name() (in module tooluniverse.tools.FDA_get_document_id_by_drug_name) FDA_get_dosage_and_storage_information_by_drug_name() (in module tooluniverse.tools.FDA_get_dosage_and_storage_information_by_drug_name) FDA_get_dosage_forms_and_strengths_by_drug_name() (in module tooluniverse.tools.FDA_get_dosage_forms_and_strengths_by_drug_name) FDA_get_drug_generic_name() (in module tooluniverse.tools.FDA_get_drug_generic_name) FDA_get_drug_interactions_by_drug_name() (in module tooluniverse.tools.FDA_get_drug_interactions_by_drug_name) FDA_get_drug_name_by_adverse_reaction() (in module tooluniverse.tools.FDA_get_drug_name_by_adverse_reaction) FDA_get_drug_name_by_calibration_instructions() (in module tooluniverse.tools.FDA_get_drug_name_by_calibration_instructions) FDA_get_drug_name_by_dependence_info() (in module tooluniverse.tools.FDA_get_drug_name_by_dependence_info) FDA_get_drug_name_by_document_id() (in module tooluniverse.tools.FDA_get_drug_name_by_document_id) FDA_get_drug_name_by_dosage_info() (in module tooluniverse.tools.FDA_get_drug_name_by_dosage_info) FDA_get_drug_name_by_environmental_warning() (in module tooluniverse.tools.FDA_get_drug_name_by_environmental_warning) FDA_get_drug_name_by_inactive_ingredient() (in module tooluniverse.tools.FDA_get_drug_name_by_inactive_ingredient) FDA_get_drug_name_by_info_on_conditions_for_doctor_consultation() (in module tooluniverse.tools.FDA_get_drug_name_by_info_on_conditions_for_doctor_consultation) FDA_get_drug_name_by_labor_and_delivery_info() (in module tooluniverse.tools.FDA_get_drug_name_by_labor_and_delivery_info) FDA_get_drug_name_by_microbiology() (in module tooluniverse.tools.FDA_get_drug_name_by_microbiology) FDA_get_drug_name_by_other_safety_info() (in module tooluniverse.tools.FDA_get_drug_name_by_other_safety_info) FDA_get_drug_name_by_pharmacodynamics() (in module tooluniverse.tools.FDA_get_drug_name_by_pharmacodynamics) FDA_get_drug_name_by_pharmacogenomics() (in module tooluniverse.tools.FDA_get_drug_name_by_pharmacogenomics) FDA_get_drug_name_by_precautions() (in module tooluniverse.tools.FDA_get_drug_name_by_precautions) FDA_get_drug_name_by_pregnancy_or_breastfeeding_info() (in module tooluniverse.tools.FDA_get_drug_name_by_pregnancy_or_breastfeeding_info) FDA_get_drug_name_by_principal_display_panel() (in module tooluniverse.tools.FDA_get_drug_name_by_principal_display_panel) FDA_get_drug_name_by_reference() (in module tooluniverse.tools.FDA_get_drug_name_by_reference) FDA_get_drug_name_by_set_id() (in module tooluniverse.tools.FDA_get_drug_name_by_set_id) FDA_get_drug_name_by_SPL_ID() (in module tooluniverse.tools.FDA_get_drug_name_by_SPL_ID) FDA_get_drug_name_by_stop_use_info() (in module tooluniverse.tools.FDA_get_drug_name_by_stop_use_info) FDA_get_drug_name_by_storage_and_handling_info() (in module tooluniverse.tools.FDA_get_drug_name_by_storage_and_handling_info) FDA_get_drug_name_by_warnings() (in module tooluniverse.tools.FDA_get_drug_name_by_warnings) FDA_get_drug_name_from_patient_package_insert() (in module tooluniverse.tools.FDA_get_drug_name_from_patient_package_insert) FDA_get_drug_names_by_abuse_dependence_info() (in module tooluniverse.tools.FDA_get_drug_names_by_abuse_dependence_info) FDA_get_drug_names_by_abuse_info() (in module tooluniverse.tools.FDA_get_drug_names_by_abuse_info) FDA_get_drug_names_by_accessories() (in module tooluniverse.tools.FDA_get_drug_names_by_accessories) FDA_get_drug_names_by_active_ingredient() (in module tooluniverse.tools.FDA_get_drug_names_by_active_ingredient) FDA_get_drug_names_by_alarm() (in module tooluniverse.tools.FDA_get_drug_names_by_alarm) FDA_get_drug_names_by_animal_pharmacology_info() (in module tooluniverse.tools.FDA_get_drug_names_by_animal_pharmacology_info) FDA_get_drug_names_by_application_number_NDC_number() (in module tooluniverse.tools.FDA_get_drug_names_by_application_number_NDC_number) FDA_get_drug_names_by_assembly_installation_info() (in module tooluniverse.tools.FDA_get_drug_names_by_assembly_installation_info) FDA_get_drug_names_by_boxed_warning() (in module tooluniverse.tools.FDA_get_drug_names_by_boxed_warning) FDA_get_drug_names_by_child_safety_info() (in module tooluniverse.tools.FDA_get_drug_names_by_child_safety_info) FDA_get_drug_names_by_clinical_pharmacology() (in module tooluniverse.tools.FDA_get_drug_names_by_clinical_pharmacology) FDA_get_drug_names_by_clinical_studies() (in module tooluniverse.tools.FDA_get_drug_names_by_clinical_studies) FDA_get_drug_names_by_consulting_doctor_pharmacist_info() (in module tooluniverse.tools.FDA_get_drug_names_by_consulting_doctor_pharmacist_info) FDA_get_drug_names_by_contraindications() (in module tooluniverse.tools.FDA_get_drug_names_by_contraindications) FDA_get_drug_names_by_controlled_substance_DEA_schedule() (in module tooluniverse.tools.FDA_get_drug_names_by_controlled_substance_DEA_schedule) FDA_get_drug_names_by_dear_health_care_provider_letter_info() (in module tooluniverse.tools.FDA_get_drug_names_by_dear_health_care_provider_letter_info) FDA_get_drug_names_by_disposal_info() (in module tooluniverse.tools.FDA_get_drug_names_by_disposal_info) FDA_get_drug_names_by_dosage_forms_and_strengths_info() (in module tooluniverse.tools.FDA_get_drug_names_by_dosage_forms_and_strengths_info) FDA_get_drug_names_by_drug_interactions() (in module tooluniverse.tools.FDA_get_drug_names_by_drug_interactions) FDA_get_drug_names_by_effective_time() (in module tooluniverse.tools.FDA_get_drug_names_by_effective_time) FDA_get_drug_names_by_food_safety_warnings() (in module tooluniverse.tools.FDA_get_drug_names_by_food_safety_warnings) FDA_get_drug_names_by_general_precautions() (in module tooluniverse.tools.FDA_get_drug_names_by_general_precautions) FDA_get_drug_names_by_geriatric_use() (in module tooluniverse.tools.FDA_get_drug_names_by_geriatric_use) FDA_get_drug_names_by_health_claim() (in module tooluniverse.tools.FDA_get_drug_names_by_health_claim) FDA_get_drug_names_by_indication() (in module tooluniverse.tools.FDA_get_drug_names_by_indication) FDA_get_drug_names_by_info_for_nursing_mothers() (in module tooluniverse.tools.FDA_get_drug_names_by_info_for_nursing_mothers) FDA_get_drug_names_by_information_for_owners_or_caregivers() (in module tooluniverse.tools.FDA_get_drug_names_by_information_for_owners_or_caregivers) FDA_get_drug_names_by_ingredient() (in module tooluniverse.tools.FDA_get_drug_names_by_ingredient) FDA_get_drug_names_by_instructions_for_use() (in module tooluniverse.tools.FDA_get_drug_names_by_instructions_for_use) FDA_get_drug_names_by_lab_test_interference() (in module tooluniverse.tools.FDA_get_drug_names_by_lab_test_interference) FDA_get_drug_names_by_lab_tests() (in module tooluniverse.tools.FDA_get_drug_names_by_lab_tests) FDA_get_drug_names_by_mechanism_of_action() (in module tooluniverse.tools.FDA_get_drug_names_by_mechanism_of_action) FDA_get_drug_names_by_medication_guide() (in module tooluniverse.tools.FDA_get_drug_names_by_medication_guide) FDA_get_drug_names_by_nonclinical_toxicology_info() (in module tooluniverse.tools.FDA_get_drug_names_by_nonclinical_toxicology_info) FDA_get_drug_names_by_nonteratogenic_effects() (in module tooluniverse.tools.FDA_get_drug_names_by_nonteratogenic_effects) FDA_get_drug_names_by_overdosage_info() (in module tooluniverse.tools.FDA_get_drug_names_by_overdosage_info) FDA_get_drug_names_by_pediatric_use() (in module tooluniverse.tools.FDA_get_drug_names_by_pediatric_use) FDA_get_drug_names_by_pharmacokinetics() (in module tooluniverse.tools.FDA_get_drug_names_by_pharmacokinetics) FDA_get_drug_names_by_population_use() (in module tooluniverse.tools.FDA_get_drug_names_by_population_use) FDA_get_drug_names_by_pregnancy_effects_info() (in module tooluniverse.tools.FDA_get_drug_names_by_pregnancy_effects_info) FDA_get_drug_names_by_residue_warning() (in module tooluniverse.tools.FDA_get_drug_names_by_residue_warning)

FDA_get_drug_names_by_risk() (in module tooluniverse.tools.FDA_get_drug_names_by_risk) FDA_get_drug_names_by_route() (in module tooluniverse.tools.FDA_get_drug_names_by_route) FDA_get_drug_names_by_safe_handling_warning() (in module tooluniverse.tools.FDA_get_drug_names_by_safe_handling_warning) FDA_get_drug_names_by_safety_summary() (in module tooluniverse.tools.FDA_get_drug_names_by_safety_summary) FDA_get_drug_names_by_spl_indexing_data_elements() (in module tooluniverse.tools.FDA_get_drug_names_by_spl_indexing_data_elements) FDA_get_drug_names_by_teratogenic_effects() (in module tooluniverse.tools.FDA_get_drug_names_by_teratogenic_effects) FDA_get_drug_names_by_user_safety_warning() (in module tooluniverse.tools.FDA_get_drug_names_by_user_safety_warning) FDA_get_drug_names_by_warnings_and_cautions() (in module tooluniverse.tools.FDA_get_drug_names_by_warnings_and_cautions) FDA_get_drugs_by_carcinogenic_mutagenic_fertility() (in module tooluniverse.tools.FDA_get_drugs_by_carcinogenic_mutagenic_fertility) FDA_get_effective_time_by_drug_name() (in module tooluniverse.tools.FDA_get_effective_time_by_drug_name) FDA_get_environmental_warning_by_drug_name() (in module tooluniverse.tools.FDA_get_environmental_warning_by_drug_name) FDA_get_general_precautions_by_drug_name() (in module tooluniverse.tools.FDA_get_general_precautions_by_drug_name) FDA_get_geriatric_use_info_by_drug_name() (in module tooluniverse.tools.FDA_get_geriatric_use_info_by_drug_name) FDA_get_health_claims_by_drug_name() (in module tooluniverse.tools.FDA_get_health_claims_by_drug_name) FDA_get_inactive_ingredient_info_by_drug_name() (in module tooluniverse.tools.FDA_get_inactive_ingredient_info_by_drug_name) FDA_get_indications_by_drug_name() (in module tooluniverse.tools.FDA_get_indications_by_drug_name) FDA_get_info_for_nursing_mothers_by_drug_name() (in module tooluniverse.tools.FDA_get_info_for_nursing_mothers_by_drug_name) FDA_get_info_for_patients_by_drug_name() (in module tooluniverse.tools.FDA_get_info_for_patients_by_drug_name) FDA_get_info_on_conditions_for_doctor_consultation_by_drug_name() (in module tooluniverse.tools.FDA_get_info_on_conditions_for_doctor_consultation_by_drug_name) FDA_get_info_on_consulting_doctor_pharmacist_by_drug_name() (in module tooluniverse.tools.FDA_get_info_on_consulting_doctor_pharmacist_by_drug_name) FDA_get_information_for_owners_or_caregivers_by_drug_name() (in module tooluniverse.tools.FDA_get_information_for_owners_or_caregivers_by_drug_name) FDA_get_ingredients_by_drug_name() (in module tooluniverse.tools.FDA_get_ingredients_by_drug_name) FDA_get_instructions_for_use_by_drug_name() (in module tooluniverse.tools.FDA_get_instructions_for_use_by_drug_name) FDA_get_lab_test_interference_info_by_drug_name() (in module tooluniverse.tools.FDA_get_lab_test_interference_info_by_drug_name) FDA_get_lab_tests_by_drug_name() (in module tooluniverse.tools.FDA_get_lab_tests_by_drug_name) FDA_get_labor_and_delivery_info_by_drug_name() (in module tooluniverse.tools.FDA_get_labor_and_delivery_info_by_drug_name) FDA_get_manufacturer_name_NDC_number_by_drug_name() (in module tooluniverse.tools.FDA_get_manufacturer_name_NDC_number_by_drug_name) FDA_get_mechanism_of_action_by_drug_name() (in module tooluniverse.tools.FDA_get_mechanism_of_action_by_drug_name) FDA_get_medication_guide_info_by_drug_name() (in module tooluniverse.tools.FDA_get_medication_guide_info_by_drug_name) FDA_get_microbiology_info_by_drug_name() (in module tooluniverse.tools.FDA_get_microbiology_info_by_drug_name) FDA_get_nonclinical_toxicology_info_by_drug_name() (in module tooluniverse.tools.FDA_get_nonclinical_toxicology_info_by_drug_name) FDA_get_nonteratogenic_effects_by_drug_name() (in module tooluniverse.tools.FDA_get_nonteratogenic_effects_by_drug_name) FDA_get_other_safety_info_by_drug_name() (in module tooluniverse.tools.FDA_get_other_safety_info_by_drug_name) FDA_get_overdosage_info_by_drug_name() (in module tooluniverse.tools.FDA_get_overdosage_info_by_drug_name) FDA_get_patient_package_insert_from_drug_name() (in module tooluniverse.tools.FDA_get_patient_package_insert_from_drug_name) FDA_get_pediatric_use_info_by_drug_name() (in module tooluniverse.tools.FDA_get_pediatric_use_info_by_drug_name) FDA_get_pharmacodynamics_by_drug_name() (in module tooluniverse.tools.FDA_get_pharmacodynamics_by_drug_name) FDA_get_pharmacogenomics_info_by_drug_name() (in module tooluniverse.tools.FDA_get_pharmacogenomics_info_by_drug_name) FDA_get_pharmacokinetics_by_drug_name() (in module tooluniverse.tools.FDA_get_pharmacokinetics_by_drug_name) FDA_get_population_use_info_by_drug_name() (in module tooluniverse.tools.FDA_get_population_use_info_by_drug_name) FDA_get_precautions_by_drug_name() (in module tooluniverse.tools.FDA_get_precautions_by_drug_name) FDA_get_pregnancy_effects_info_by_drug_name() (in module tooluniverse.tools.FDA_get_pregnancy_effects_info_by_drug_name) FDA_get_pregnancy_or_breastfeeding_info_by_drug_name() (in module tooluniverse.tools.FDA_get_pregnancy_or_breastfeeding_info_by_drug_name) FDA_get_principal_display_panel_by_drug_name() (in module tooluniverse.tools.FDA_get_principal_display_panel_by_drug_name) FDA_get_purpose_info_by_drug_name() (in module tooluniverse.tools.FDA_get_purpose_info_by_drug_name) FDA_get_recent_changes_by_drug_name() (in module tooluniverse.tools.FDA_get_recent_changes_by_drug_name) FDA_get_reference_info_by_drug_name() (in module tooluniverse.tools.FDA_get_reference_info_by_drug_name) FDA_get_residue_warning_by_drug_name() (in module tooluniverse.tools.FDA_get_residue_warning_by_drug_name) FDA_get_risk_info_by_drug_name() (in module tooluniverse.tools.FDA_get_risk_info_by_drug_name) FDA_get_route_info_by_drug_name() (in module tooluniverse.tools.FDA_get_route_info_by_drug_name) FDA_get_safe_handling_warnings_by_drug_name() (in module tooluniverse.tools.FDA_get_safe_handling_warnings_by_drug_name) FDA_get_safety_summary_by_drug_name() (in module tooluniverse.tools.FDA_get_safety_summary_by_drug_name) FDA_get_spl_indexing_data_elements_by_drug_name() (in module tooluniverse.tools.FDA_get_spl_indexing_data_elements_by_drug_name) FDA_get_spl_unclassified_section_by_drug_name() (in module tooluniverse.tools.FDA_get_spl_unclassified_section_by_drug_name) FDA_get_stop_use_info_by_drug_name() (in module tooluniverse.tools.FDA_get_stop_use_info_by_drug_name) FDA_get_storage_and_handling_info_by_drug_name() (in module tooluniverse.tools.FDA_get_storage_and_handling_info_by_drug_name) FDA_get_teratogenic_effects_by_drug_name() (in module tooluniverse.tools.FDA_get_teratogenic_effects_by_drug_name) FDA_get_user_safety_warning_by_drug_names() (in module tooluniverse.tools.FDA_get_user_safety_warning_by_drug_names) FDA_get_warnings_and_cautions_by_drug_name() (in module tooluniverse.tools.FDA_get_warnings_and_cautions_by_drug_name) FDA_get_warnings_by_drug_name() (in module tooluniverse.tools.FDA_get_warnings_by_drug_name) FDA_get_when_using_info() (in module tooluniverse.tools.FDA_get_when_using_info) FDA_retrieve_device_use_by_drug_name() (in module tooluniverse.tools.FDA_retrieve_device_use_by_drug_name) FDA_retrieve_drug_name_by_device_use() (in module tooluniverse.tools.FDA_retrieve_drug_name_by_device_use) FDA_retrieve_drug_names_by_patient_medication_info() (in module tooluniverse.tools.FDA_retrieve_drug_names_by_patient_medication_info) FDA_retrieve_patient_medication_info_by_drug_name() (in module tooluniverse.tools.FDA_retrieve_patient_medication_info_by_drug_name) FDACountAdditiveReactionsTool (class in tooluniverse) (class in tooluniverse.openfda_adv_tool) FDADrugAdverseEventTool (class in tooluniverse) (class in tooluniverse.openfda_adv_tool) FDADrugLabelGetDrugGenericNameTool (class in tooluniverse) (class in tooluniverse.openfda_tool) FDADrugLabelSearchIDTool (class in tooluniverse) (class in tooluniverse.openfda_tool) FDADrugLabelSearchTool (class in tooluniverse) (class in tooluniverse.openfda_tool) FDADrugLabelTool (class in tooluniverse) (class in tooluniverse.openfda_tool) FDATool (class in tooluniverse.openfda_tool) FileSaveHook (class in tooluniverse.output_hook) fill_defaults() (in module tooluniverse.space) (in module tooluniverse.space.validator) filter_tool_lists() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) filter_tools() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) FilteringHook (class in tooluniverse.extended_hooks) find_tools() (tooluniverse.tool_finder_embedding.ToolFinderEmbedding method) (tooluniverse.tool_finder_keyword.ToolFinderKeyword method) (tooluniverse.tool_finder_llm.ToolFinderLLM method) (tooluniverse.ToolFinderEmbedding method) (tooluniverse.ToolFinderKeyword method) (tooluniverse.ToolFinderLLM method) find_tools_by_pattern() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) find_tools_legacy() (tooluniverse.tool_finder_llm.ToolFinderLLM method) (tooluniverse.ToolFinderLLM method) find_tools_llm() (tooluniverse.tool_finder_llm.ToolFinderLLM method) (tooluniverse.ToolFinderLLM method) Finish() (in module tooluniverse.tools.Finish) flush() (tooluniverse.cache.result_cache_manager.ResultCacheManager method) focus_areas (tooluniverse.output_hook.SummarizationHook attribute) (tooluniverse.output_hook.SummarizationHookConfig attribute) force_full_discovery() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) format() (tooluniverse.logging_config.ToolUniverseFormatter method) format_api_response() (in module tooluniverse.utils) format_error_response() (in module tooluniverse.utils) FormattingHook (class in tooluniverse.extended_hooks) function_name (tooluniverse.execute_function._BatchJob attribute)

G

GeminiClient (class in tooluniverse.llm_clients) GeneOntologyTool (class in tooluniverse.gene_ontology_tool) generate_env_template() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) generate_init() (in module tooluniverse.generate_tools) generate_proxy_tool_configs() (tooluniverse.mcp_client_tool.MCPAutoLoaderTool method) (tooluniverse.MCPAutoLoaderTool method) generate_tool_file() (in module tooluniverse.generate_tools) genomics_england_disease_target_score() (in module tooluniverse.tools.genomics_england_disease_target_score) GEORESTTool (class in tooluniverse.geo_tool) get() (tooluniverse.cache.memory_cache.LRUCache method) (tooluniverse.cache.result_cache_manager.ResultCacheManager method) (tooluniverse.cache.sqlite_backend.PersistentCache method) get_albumentations_info() (in module tooluniverse.tools.get_albumentations_info) get_altair_info() (in module tooluniverse.tools.get_altair_info) get_anndata_info() (in module tooluniverse.tools.get_anndata_info) get_arboreto_info() (in module tooluniverse.tools.get_arboreto_info) get_arxiv_info() (in module tooluniverse.tools.get_arxiv_info) get_ase_info() (in module tooluniverse.tools.get_ase_info) get_assembly_info_by_pdb_id() (in module tooluniverse.tools.get_assembly_info_by_pdb_id) get_assembly_summary() (in module tooluniverse.tools.get_assembly_summary) get_astropy_info() (in module tooluniverse.tools.get_astropy_info) get_availability_status() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) get_available_tools() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) get_batch_concurrency_limit() (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseTool method) get_binding_affinity_by_pdb_id() (in module tooluniverse.tools.get_binding_affinity_by_pdb_id) get_biopandas_info() (in module tooluniverse.tools.get_biopandas_info) get_biopython_info() (in module tooluniverse.tools.get_biopython_info) get_bioservices_info() (in module tooluniverse.tools.get_bioservices_info) get_biotite_info() (in module tooluniverse.tools.get_biotite_info) get_bokeh_info() (in module tooluniverse.tools.get_bokeh_info) get_brian2_info() (in module tooluniverse.tools.get_brian2_info) get_by_path() (tooluniverse.uspto_tool.USPTOOpenDataPortalTool method) (tooluniverse.USPTOOpenDataPortalTool method) get_cache_key() (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseTool method) get_cache_namespace() (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseTool method) get_cache_stats() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) get_cache_ttl() (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseTool method) get_cache_version() (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseTool method) get_cartopy_info() (in module tooluniverse.tools.get_cartopy_info) get_catboost_info() (in module tooluniverse.tools.get_catboost_info) get_cellpose_info() (in module tooluniverse.tools.get_cellpose_info) get_cellrank_info() (in module tooluniverse.tools.get_cellrank_info) get_cellxgene_census_info() (in module tooluniverse.tools.get_cellxgene_census_info) get_cftime_info() (in module tooluniverse.tools.get_cftime_info) get_changed_tools() (in module tooluniverse.build_optimizer) get_chem_comp_audit_info() (in module tooluniverse.tools.get_chem_comp_audit_info) get_chem_comp_charge_and_ambiguity() (in module tooluniverse.tools.get_chem_comp_charge_and_ambiguity) get_chembl_id_by_name() (tooluniverse.chem_tool.ChEMBLTool method) (tooluniverse.ChEMBLTool method) get_chembl_smiles_pref_name_id_by_name() (tooluniverse.chem_tool.ChEMBLTool method) (tooluniverse.ChEMBLTool method) get_chembl_webresource_client_info() (in module tooluniverse.tools.get_chembl_webresource_client_info) get_citation_info_by_pdb_id() (in module tooluniverse.tools.get_citation_info_by_pdb_id) get_clair3_info() (in module tooluniverse.tools.get_clair3_info) get_clinical_trial_conditions_and_interventions() (in module tooluniverse.tools.get_clinical_trial_conditions_and_interventions) get_clinical_trial_descriptions() (in module tooluniverse.tools.get_clinical_trial_descriptions) get_clinical_trial_eligibility_criteria() (in module tooluniverse.tools.get_clinical_trial_eligibility_criteria) get_clinical_trial_locations() (in module tooluniverse.tools.get_clinical_trial_locations) get_clinical_trial_outcome_measures() (in module tooluniverse.tools.get_clinical_trial_outcome_measures) get_clinical_trial_references() (in module tooluniverse.tools.get_clinical_trial_references) get_clinical_trial_status_and_dates() (in module tooluniverse.tools.get_clinical_trial_status_and_dates) get_cobra_info() (in module tooluniverse.tools.get_cobra_info) get_cobrapy_info() (in module tooluniverse.tools.get_cobrapy_info) get_config_registry() (in module tooluniverse.tool_registry) get_context_for_agent() (tooluniverse.memory_manager.MemoryManager method) get_cooler_info() (in module tooluniverse.tools.get_cooler_info) get_core_refinement_statistics() (in module tooluniverse.tools.get_core_refinement_statistics) get_cryosparc_tools_info() (in module tooluniverse.tools.get_cryosparc_tools_info) get_crystal_growth_conditions_by_pdb_id() (in module tooluniverse.tools.get_crystal_growth_conditions_by_pdb_id) get_crystallization_ph_by_pdb_id() (in module tooluniverse.tools.get_crystallization_ph_by_pdb_id) get_crystallographic_properties_by_pdb_id() (in module tooluniverse.tools.get_crystallographic_properties_by_pdb_id) get_cupy_info() (in module tooluniverse.tools.get_cupy_info) get_cyvcf2_info() (in module tooluniverse.tools.get_cyvcf2_info) get_dask_info() (in module tooluniverse.tools.get_dask_info) get_datamol_info() (in module tooluniverse.tools.get_datamol_info) get_dataset_info() (tooluniverse.dataset_tool.DatasetTool method) (tooluniverse.DatasetTool method) (tooluniverse.xml_tool.XMLDatasetTool method) (tooluniverse.XMLDatasetTool method) get_datashader_info() (in module tooluniverse.tools.get_datashader_info) get_deepchem_info() (in module tooluniverse.tools.get_deepchem_info) get_deeppurpose_info() (in module tooluniverse.tools.get_deeppurpose_info) get_deeptools_info() (in module tooluniverse.tools.get_deeptools_info) get_deepxde_info() (in module tooluniverse.tools.get_deepxde_info) get_default_config_file() (tooluniverse.base_tool.BaseTool class method) (tooluniverse.BaseTool class method) get_default_hook_config() (in module tooluniverse.default_config) get_dendropy_info() (in module tooluniverse.tools.get_dendropy_info) get_descriptastorus_info() (in module tooluniverse.tools.get_descriptastorus_info) get_diffdock_info() (in module tooluniverse.tools.get_diffdock_info) get_disease_variants_by_accession() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) get_dscribe_info() (in module tooluniverse.tools.get_dscribe_info) get_ec_number_by_entity_id() (in module tooluniverse.tools.get_ec_number_by_entity_id) get_elephant_info() (in module tooluniverse.tools.get_elephant_info) get_em_3d_fitting_and_reconstruction_details() (in module tooluniverse.tools.get_em_3d_fitting_and_reconstruction_details) get_emdb_ids_by_pdb_id() (in module tooluniverse.tools.get_emdb_ids_by_pdb_id) get_enrichment_results() (tooluniverse.enrichr_tool.EnrichrTool method) get_entrez_ids() (tooluniverse.humanbase_tool.HumanBaseTool method) get_entry_by_accession() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) get_episcanpy_info() (in module tooluniverse.tools.get_episcanpy_info) get_ete3_info() (in module tooluniverse.tools.get_ete3_info) get_faiss_info() (in module tooluniverse.tools.get_faiss_info) get_fanc_info() (in module tooluniverse.tools.get_fanc_info) get_flask_info() (in module tooluniverse.tools.get_flask_info) get_flowio_info() (in module tooluniverse.tools.get_flowio_info) get_flowkit_info() (in module tooluniverse.tools.get_flowkit_info) get_flowutils_info() (in module tooluniverse.tools.get_flowutils_info) get_freesasa_info() (in module tooluniverse.tools.get_freesasa_info) get_function_by_accession() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) get_galpy_info() (in module tooluniverse.tools.get_galpy_info) get_gene_name_by_entity_id() (in module tooluniverse.tools.get_gene_name_by_entity_id) get_genes_for_term() (tooluniverse.gene_ontology_tool.GeneOntologyTool method) get_genetics_condition_by_name() (tooluniverse.medlineplus_tool.MedlinePlusRESTTool method) (tooluniverse.MedlinePlusRESTTool method) get_genetics_gene_by_name() (tooluniverse.medlineplus_tool.MedlinePlusRESTTool method) (tooluniverse.MedlinePlusRESTTool method) get_genetics_index() (tooluniverse.medlineplus_tool.MedlinePlusRESTTool method) (tooluniverse.MedlinePlusRESTTool method) get_geopandas_info() (in module tooluniverse.tools.get_geopandas_info) get_gget_info() (in module tooluniverse.tools.get_gget_info) get_googlesearch_python_info() (in module tooluniverse.tools.get_googlesearch_python_info) get_gseapy_info() (in module tooluniverse.tools.get_gseapy_info) get_h5py_info() (in module tooluniverse.tools.get_h5py_info) get_harmony_pytorch_info() (in module tooluniverse.tools.get_harmony_pytorch_info) get_hmmlearn_info() (in module tooluniverse.tools.get_hmmlearn_info) get_holoviews_info() (in module tooluniverse.tools.get_holoviews_info) get_hook() (tooluniverse.output_hook.HookManager method) get_hook_logger() (in module tooluniverse.logging_config) get_host_organism_by_pdb_id() (in module tooluniverse.tools.get_host_organism_by_pdb_id) get_HPO_ID_by_phenotype() (in module tooluniverse.tools.get_HPO_ID_by_phenotype) get_htmd_info() (in module tooluniverse.tools.get_htmd_info) get_hyperopt_info() (in module tooluniverse.tools.get_hyperopt_info) get_igraph_info() (in module tooluniverse.tools.get_igraph_info) get_imageio_info() (in module tooluniverse.tools.get_imageio_info) get_imbalanced_learn_info() (in module tooluniverse.tools.get_imbalanced_learn_info) get_input_arguments() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) get_jcvi_info() (in module tooluniverse.tools.get_jcvi_info) get_joblib_info() (in module tooluniverse.tools.get_joblib_info) get_joint_associated_diseases_by_HPO_ID_list() (in module tooluniverse.tools.get_joint_associated_diseases_by_HPO_ID_list) get_khmer_info() (in module tooluniverse.tools.get_khmer_info) get_kipoiseq_info() (in module tooluniverse.tools.get_kipoiseq_info) get_lazy_loading_status() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) get_lifelines_info() (in module tooluniverse.tools.get_lifelines_info) get_ligand_bond_count_by_pdb_id() (in module tooluniverse.tools.get_ligand_bond_count_by_pdb_id) get_ligand_smiles_by_chem_comp_id() (in module tooluniverse.tools.get_ligand_smiles_by_chem_comp_id) get_lightgbm_info() (in module tooluniverse.tools.get_lightgbm_info) get_llm_config() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) get_logger() (in module tooluniverse.logging_config) (tooluniverse.logging_config.ToolUniverseLogger method) get_loompy_info() (in module tooluniverse.tools.get_loompy_info) get_mageck_info() (in module tooluniverse.tools.get_mageck_info) get_matplotlib_info() (in module tooluniverse.tools.get_matplotlib_info) get_mcp_server_configs() (in module tooluniverse.mcp_tool_registry) get_mcp_tool_configs() (in module tooluniverse.mcp_tool_registry) get_mcp_tool_registry() (in module tooluniverse.mcp_tool_registry) get_mcp_tool_urls() (in module tooluniverse.mcp_tool_registry) get_md5() (in module tooluniverse.utils) get_mdanalysis_info() (in module tooluniverse.tools.get_mdanalysis_info) get_mdtraj_info() (in module tooluniverse.tools.get_mdtraj_info) get_mne_info() (in module tooluniverse.tools.get_mne_info) get_model_info() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) get_molfeat_info() (in module tooluniverse.tools.get_molfeat_info) get_molvs_info() (in module tooluniverse.tools.get_molvs_info) get_mordred_info() (in module tooluniverse.tools.get_mordred_info) get_msprime_info() (in module tooluniverse.tools.get_msprime_info) get_mudata_info() (in module tooluniverse.tools.get_mudata_info) get_mutation_annotations_by_pdb_id() (in module tooluniverse.tools.get_mutation_annotations_by_pdb_id) get_names_taxonomy_by_accession() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) get_neo_info() (in module tooluniverse.tools.get_neo_info) get_netcdf4_info() (in module tooluniverse.tools.get_netcdf4_info) get_networkx_info() (in module tooluniverse.tools.get_networkx_info) get_nglview_info() (in module tooluniverse.tools.get_nglview_info) get_nilearn_info() (in module tooluniverse.tools.get_nilearn_info) get_numba_info() (in module tooluniverse.tools.get_numba_info) get_numpy_info() (in module tooluniverse.tools.get_numpy_info) get_official_gene_name() (tooluniverse.enrichr_tool.EnrichrTool method) (tooluniverse.humanbase_tool.HumanBaseTool method) get_oligosaccharide_descriptors_by_entity_id() (in module tooluniverse.tools.get_oligosaccharide_descriptors_by_entity_id) get_one_tool_by_one_name() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) get_openbabel_info() (in module tooluniverse.tools.get_openbabel_info) get_openchem_info() (in module tooluniverse.tools.get_openchem_info) get_opencv_info() (in module tooluniverse.tools.get_opencv_info) get_openmm_info() (in module tooluniverse.tools.get_openmm_info)

get_optlang_info() (in module tooluniverse.tools.get_optlang_info) get_optuna_info() (in module tooluniverse.tools.get_optuna_info) get_palantir_info() (in module tooluniverse.tools.get_palantir_info) get_pandas_info() (in module tooluniverse.tools.get_pandas_info) get_paper_by_doi() (tooluniverse.openalex_tool.OpenAlexTool method) get_papers_by_author() (tooluniverse.openalex_tool.OpenAlexTool method) get_parameter_schema() (in module tooluniverse.utils) get_patsy_info() (in module tooluniverse.tools.get_patsy_info) get_pdbfixer_info() (in module tooluniverse.tools.get_pdbfixer_info) get_phenotype_by_HPO_ID() (in module tooluniverse.tools.get_phenotype_by_HPO_ID) get_pillow_info() (in module tooluniverse.tools.get_pillow_info) get_plantcv_info() (in module tooluniverse.tools.get_plantcv_info) get_plip_info() (in module tooluniverse.tools.get_plip_info) get_plotly_info() (in module tooluniverse.tools.get_plotly_info) get_poliastro_info() (in module tooluniverse.tools.get_poliastro_info) get_polymer_entity_annotations() (in module tooluniverse.tools.get_polymer_entity_annotations) get_polymer_entity_count_by_pdb_id() (in module tooluniverse.tools.get_polymer_entity_count_by_pdb_id) get_polymer_entity_ids_by_pdb_id() (in module tooluniverse.tools.get_polymer_entity_ids_by_pdb_id) get_polymer_entity_type_by_entity_id() (in module tooluniverse.tools.get_polymer_entity_type_by_entity_id) get_polymer_molecular_weight_by_entity_id() (in module tooluniverse.tools.get_polymer_molecular_weight_by_entity_id) get_poretools_info() (in module tooluniverse.tools.get_poretools_info) get_prody_info() (in module tooluniverse.tools.get_prody_info) get_prompt() (tooluniverse.mcp_client_tool.MCPClientTool method) (tooluniverse.MCPClientTool method) get_prompt_preview() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) get_prompt_template() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) get_protein_classification_by_pdb_id() (in module tooluniverse.tools.get_protein_classification_by_pdb_id) get_protein_metadata_by_pdb_id() (in module tooluniverse.tools.get_protein_metadata_by_pdb_id) get_ptm_processing_by_accession() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) get_pubchempy_info() (in module tooluniverse.tools.get_pubchempy_info) get_pybedtools_info() (in module tooluniverse.tools.get_pybedtools_info) get_pybigwig_info() (in module tooluniverse.tools.get_pybigwig_info) get_pydeseq2_info() (in module tooluniverse.tools.get_pydeseq2_info) get_pyensembl_info() (in module tooluniverse.tools.get_pyensembl_info) get_pyephem_info() (in module tooluniverse.tools.get_pyephem_info) get_pyfaidx_info() (in module tooluniverse.tools.get_pyfaidx_info) get_pyfasta_info() (in module tooluniverse.tools.get_pyfasta_info) get_pykalman_info() (in module tooluniverse.tools.get_pykalman_info) get_pyliftover_info() (in module tooluniverse.tools.get_pyliftover_info) get_pymassspec_info() (in module tooluniverse.tools.get_pymassspec_info) get_pymed_info() (in module tooluniverse.tools.get_pymed_info) get_pymzml_info() (in module tooluniverse.tools.get_pymzml_info) get_pypdf2_info() (in module tooluniverse.tools.get_pypdf2_info) get_pyranges_info() (in module tooluniverse.tools.get_pyranges_info) get_pyrosetta_info() (in module tooluniverse.tools.get_pyrosetta_info) get_pysam_info() (in module tooluniverse.tools.get_pysam_info) get_pyscenic_info() (in module tooluniverse.tools.get_pyscenic_info) get_pyscf_info() (in module tooluniverse.tools.get_pyscf_info) get_pyscreener_info() (in module tooluniverse.tools.get_pyscreener_info) get_pytdc_info() (in module tooluniverse.tools.get_pytdc_info) get_python_libsbml_info() (in module tooluniverse.tools.get_python_libsbml_info) get_pytorch_info() (in module tooluniverse.tools.get_pytorch_info) get_pyvcf_info() (in module tooluniverse.tools.get_pyvcf_info) get_pyvis_info() (in module tooluniverse.tools.get_pyvis_info) get_qutip_info() (in module tooluniverse.tools.get_qutip_info) get_rasterio_info() (in module tooluniverse.tools.get_rasterio_info) get_rdkit_info() (in module tooluniverse.tools.get_rdkit_info) get_refinement_resolution_by_pdb_id() (in module tooluniverse.tools.get_refinement_resolution_by_pdb_id) get_registered_tools() (in module tooluniverse.mcp_tool_registry) get_release_deposit_dates_by_pdb_id() (in module tooluniverse.tools.get_release_deposit_dates_by_pdb_id) get_remote_info() (tooluniverse.remote_tool.RemoteTool method) get_reportlab_info() (in module tooluniverse.tools.get_reportlab_info) get_requests_info() (in module tooluniverse.tools.get_requests_info) get_required_parameters() (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseTool method) (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) get_ruptures_info() (in module tooluniverse.tools.get_ruptures_info) get_scanorama_info() (in module tooluniverse.tools.get_scanorama_info) get_scanpy_info() (in module tooluniverse.tools.get_scanpy_info) get_schnetpack_info() (in module tooluniverse.tools.get_schnetpack_info) get_scholarly_info() (in module tooluniverse.tools.get_scholarly_info) get_scikit_bio_info() (in module tooluniverse.tools.get_scikit_bio_info) get_scikit_image_info() (in module tooluniverse.tools.get_scikit_image_info) get_scikit_learn_info() (in module tooluniverse.tools.get_scikit_learn_info) get_scipy_info() (in module tooluniverse.tools.get_scipy_info) get_scrublet_info() (in module tooluniverse.tools.get_scrublet_info) get_scvelo_info() (in module tooluniverse.tools.get_scvelo_info) get_scvi_tools_info() (in module tooluniverse.tools.get_scvi_tools_info) get_seaborn_info() (in module tooluniverse.tools.get_seaborn_info) get_sequence_by_pdb_id() (in module tooluniverse.tools.get_sequence_by_pdb_id) get_sequence_isoforms_by_accession() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) get_sequence_lengths_by_pdb_id() (in module tooluniverse.tools.get_sequence_lengths_by_pdb_id) get_sequence_positional_features_by_instance_id() (in module tooluniverse.tools.get_sequence_positional_features_by_instance_id) get_server_info() (tooluniverse.remote_tool.RemoteTool method) get_session() (tooluniverse.memory_manager.MemoryManager method) get_session_summary() (tooluniverse.memory_manager.MemoryManager method) get_skopt_info() (in module tooluniverse.tools.get_skopt_info) get_smiles_pref_name_by_chembl_id() (tooluniverse.chem_tool.ChEMBLTool method) (tooluniverse.ChEMBLTool method) get_souporcell_info() (in module tooluniverse.tools.get_souporcell_info) get_source_organism_by_pdb_id() (in module tooluniverse.tools.get_source_organism_by_pdb_id) get_space_group_by_pdb_id() (in module tooluniverse.tools.get_space_group_by_pdb_id) get_space_llm_config() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) get_space_metadata() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) get_statsmodels_info() (in module tooluniverse.tools.get_statsmodels_info) get_structure_determination_software_by_pdb_id() (in module tooluniverse.tools.get_structure_determination_software_by_pdb_id) get_structure_title_by_pdb_id() (in module tooluniverse.tools.get_structure_title_by_pdb_id) get_structure_validation_metrics_by_pdb_id() (in module tooluniverse.tools.get_structure_validation_metrics_by_pdb_id) get_subcellular_location_by_accession() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) get_sunpy_info() (in module tooluniverse.tools.get_sunpy_info) get_sympy_info() (in module tooluniverse.tools.get_sympy_info) get_target_cofactor_info() (in module tooluniverse.tools.get_target_cofactor_info) get_taxonomy_by_pdb_id() (in module tooluniverse.tools.get_taxonomy_by_pdb_id) get_term_details() (tooluniverse.gene_ontology_tool.GeneOntologyTool method) get_terms_for_gene() (tooluniverse.gene_ontology_tool.GeneOntologyTool method) get_tiledb_info() (in module tooluniverse.tools.get_tiledb_info) get_tiledbsoma_info() (in module tooluniverse.tools.get_tiledbsoma_info) get_tool_by_name() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) get_tool_class_lazy() (in module tooluniverse.tool_registry) get_tool_description() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) get_tool_errors() (in module tooluniverse.tool_registry) get_tool_health() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) get_tool_info() (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseTool method) get_tool_registry() (in module tooluniverse) (in module tooluniverse.tool_registry) get_tool_specification_by_names() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) get_tool_stats() (tooluniverse.tool_finder_llm.ToolFinderLLM method) (tooluniverse.ToolFinderLLM method) get_tool_type_by_name() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) get_tool_types() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) get_torch_geometric_info() (in module tooluniverse.tools.get_torch_geometric_info) get_tqdm_info() (in module tooluniverse.tools.get_tqdm_info) get_trackpy_info() (in module tooluniverse.tools.get_trackpy_info) get_tskit_info() (in module tooluniverse.tools.get_tskit_info) get_umap_learn_info() (in module tooluniverse.tools.get_umap_learn_info) get_uniprot_accession_by_entity_id() (in module tooluniverse.tools.get_uniprot_accession_by_entity_id) get_user_cache_dir() (in module tooluniverse.utils) get_velocyto_info() (in module tooluniverse.tools.get_velocyto_info) get_viennarna_info() (in module tooluniverse.tools.get_viennarna_info) get_webpage_text_from_url() (in module tooluniverse.tools.get_webpage_text_from_url) get_webpage_title() (in module tooluniverse.tools.get_webpage_title) get_xarray_info() (in module tooluniverse.tools.get_xarray_info) get_xesmf_info() (in module tooluniverse.tools.get_xesmf_info) get_xgboost_info() (in module tooluniverse.tools.get_xgboost_info) get_zarr_info() (in module tooluniverse.tools.get_zarr_info) GetSPLBySetIDTool (class in tooluniverse) (class in tooluniverse.dailymed_tool) GIN_Guidelines_Search() (in module tooluniverse.tools.GIN_Guidelines_Search) GINGuidelinesTool (class in tooluniverse.unified_guideline_tools) gnomAD_query_variant() (in module tooluniverse.tools.gnomAD_query_variant) GnomadTool (class in tooluniverse.gnomad_tool) GO_get_annotations_for_gene() (in module tooluniverse.tools.GO_get_annotations_for_gene) GO_get_genes_for_term() (in module tooluniverse.tools.GO_get_genes_for_term) GO_get_term_by_id() (in module tooluniverse.tools.GO_get_term_by_id) GO_get_term_details() (in module tooluniverse.tools.GO_get_term_details) GO_search_terms() (in module tooluniverse.tools.GO_search_terms) GraphQLTool (class in tooluniverse.graphql_tool) gwas_get_association_by_id() (in module tooluniverse.tools.gwas_get_association_by_id) gwas_get_associations_for_snp() (in module tooluniverse.tools.gwas_get_associations_for_snp) gwas_get_associations_for_study() (in module tooluniverse.tools.gwas_get_associations_for_study) gwas_get_associations_for_trait() (in module tooluniverse.tools.gwas_get_associations_for_trait) gwas_get_snp_by_id() (in module tooluniverse.tools.gwas_get_snp_by_id) gwas_get_snps_for_gene() (in module tooluniverse.tools.gwas_get_snps_for_gene) gwas_get_studies_for_trait() (in module tooluniverse.tools.gwas_get_studies_for_trait) gwas_get_study_by_id() (in module tooluniverse.tools.gwas_get_study_by_id) gwas_get_variants_for_trait() (in module tooluniverse.tools.gwas_get_variants_for_trait) gwas_search_associations() (in module tooluniverse.tools.gwas_search_associations) GWAS_search_associations_by_gene() (in module tooluniverse.tools.GWAS_search_associations_by_gene) gwas_search_snps() (in module tooluniverse.tools.gwas_search_snps) gwas_search_studies() (in module tooluniverse.tools.gwas_search_studies) GWASAssociationByID (class in tooluniverse) (class in tooluniverse.gwas_tool) GWASAssociationSearch (class in tooluniverse) (class in tooluniverse.gwas_tool) GWASAssociationsForSNP (class in tooluniverse) (class in tooluniverse.gwas_tool) GWASAssociationsForStudy (class in tooluniverse) (class in tooluniverse.gwas_tool) GWASAssociationsForTrait (class in tooluniverse) (class in tooluniverse.gwas_tool) GWASGeneSearch (class in tooluniverse.genomics_gene_search_tool) GWASRESTTool (class in tooluniverse.gwas_tool) GWASSNPByID (class in tooluniverse) (class in tooluniverse.gwas_tool) GWASSNPSearch (class in tooluniverse) (class in tooluniverse.gwas_tool) GWASSNPsForGene (class in tooluniverse) (class in tooluniverse.gwas_tool) GWASStudiesForTrait (class in tooluniverse) (class in tooluniverse.gwas_tool) GWASStudyByID (class in tooluniverse) (class in tooluniverse.gwas_tool) GWASStudySearch (class in tooluniverse) (class in tooluniverse.gwas_tool) GWASVariantsForTrait (class in tooluniverse) (class in tooluniverse.gwas_tool)

H

HAL_search_archive() (in module tooluniverse.tools.HAL_search_archive) HALTool (class in tooluniverse) (class in tooluniverse.hal_tool) handle_error() (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseTool method) has_any_api_keys() (tooluniverse.agentic_tool.AgenticTool static method) (tooluniverse.AgenticTool static method) hit_count (tooluniverse.cache.sqlite_backend.CacheEntry attribute) HookManager (class in tooluniverse.output_hook) HookRule (class in tooluniverse.output_hook) hooks (tooluniverse.output_hook.HookManager attribute) HPA_get_biological_processes_by_gene() (in module tooluniverse.tools.HPA_get_biological_processes_by_gene) HPA_get_cancer_prognostics_by_gene() (in module tooluniverse.tools.HPA_get_cancer_prognostics_by_gene) HPA_get_comparative_expression_by_gene_and_cellline() (in module tooluniverse.tools.HPA_get_comparative_expression_by_gene_and_cellline) HPA_get_comprehensive_gene_details_by_ensembl_id() (in module tooluniverse.tools.HPA_get_comprehensive_gene_details_by_ensembl_id) HPA_get_contextual_biological_process_analysis() (in module tooluniverse.tools.HPA_get_contextual_biological_process_analysis) HPA_get_disease_expression_by_gene_tissue_disease() (in module tooluniverse.tools.HPA_get_disease_expression_by_gene_tissue_disease) HPA_get_gene_basic_info_by_ensembl_id() (in module tooluniverse.tools.HPA_get_gene_basic_info_by_ensembl_id) HPA_get_gene_tsv_data_by_ensembl_id() (in module tooluniverse.tools.HPA_get_gene_tsv_data_by_ensembl_id) HPA_get_protein_interactions_by_gene() (in module tooluniverse.tools.HPA_get_protein_interactions_by_gene) HPA_get_rna_expression_by_source() (in module tooluniverse.tools.HPA_get_rna_expression_by_source) HPA_get_rna_expression_in_specific_tissues() (in module tooluniverse.tools.HPA_get_rna_expression_in_specific_tissues) HPA_get_subcellular_location() (in module tooluniverse.tools.HPA_get_subcellular_location)

HPA_search_genes_by_query() (in module tooluniverse.tools.HPA_search_genes_by_query) HPAGetBiologicalProcessTool (class in tooluniverse.hpa_tool) HPAGetCancerPrognosticsTool (class in tooluniverse.hpa_tool) HPAGetComparativeExpressionTool (class in tooluniverse.hpa_tool) HPAGetContextualBiologicalProcessTool (class in tooluniverse.hpa_tool) HPAGetDiseaseExpressionTool (class in tooluniverse.hpa_tool) HPAGetGeneJSONTool (class in tooluniverse) (class in tooluniverse.hpa_tool) HPAGetGenePageDetailsTool (class in tooluniverse.hpa_tool) HPAGetGeneXMLTool (class in tooluniverse) (class in tooluniverse.hpa_tool) HPAGetProteinInteractionsTool (class in tooluniverse.hpa_tool) HPAGetRnaExpressionBySourceTool (class in tooluniverse.hpa_tool) HPAGetRnaExpressionByTissueTool (class in tooluniverse.hpa_tool) HPAGetSubcellularLocationTool (class in tooluniverse.hpa_tool) HPAJsonApiTool (class in tooluniverse.hpa_tool) HPASearchApiTool (class in tooluniverse.hpa_tool) HPASearchGenesTool (class in tooluniverse.hpa_tool) HPAXmlApiTool (class in tooluniverse.hpa_tool) humanbase_ppi_analysis() (in module tooluniverse.tools.humanbase_ppi_analysis) humanbase_ppi_retrieve() (tooluniverse.humanbase_tool.HumanBaseTool method) HumanBaseTool (class in tooluniverse.humanbase_tool) HypothesisGenerator() (in module tooluniverse.tools.HypothesisGenerator)

I

indices (tooluniverse.execute_function._BatchJob attribute) infer() (tooluniverse.llm_clients.AzureOpenAIClient method) (tooluniverse.llm_clients.BaseLLMClient method) (tooluniverse.llm_clients.GeminiClient method) (tooluniverse.llm_clients.OpenRouterClient method) (tooluniverse.llm_clients.VLLMClient method) infer_stream() (tooluniverse.llm_clients.AzureOpenAIClient method) (tooluniverse.llm_clients.BaseLLMClient method) (tooluniverse.llm_clients.GeminiClient method)

info() (in module tooluniverse.logging_config) init_tool() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) is_available() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) is_available_locally() (tooluniverse.remote_tool.RemoteTool method) items() (tooluniverse.cache.memory_cache.LRUCache method) iter_entries() (tooluniverse.cache.sqlite_backend.PersistentCache method) iterative_code_improvement() (in module tooluniverse.compose_scripts.tool_discover)

J

json_type_to_python() (in module tooluniverse.generate_tools)

K

key (tooluniverse.cache.sqlite_backend.CacheEntry attribute)

L

LabelGenerator() (in module tooluniverse.tools.LabelGenerator) last_accessed (tooluniverse.cache.sqlite_backend.CacheEntry attribute) lazy_import_tool() (in module tooluniverse.tool_registry) list_built_in_tools() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) list_mcp_connections() (in module tooluniverse.mcp_integration) (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) list_mcp_tools() (in module tooluniverse.mcp_tool_registry) list_prompts() (tooluniverse.mcp_client_tool.MCPClientTool method) (tooluniverse.MCPClientTool method) list_resources() (tooluniverse.mcp_client_tool.MCPClientTool method) (tooluniverse.MCPClientTool method) list_tools() (tooluniverse.mcp_client_tool.MCPClientTool method) (tooluniverse.MCPClientTool method) list_user_sessions() (tooluniverse.memory_manager.MemoryManager method) LiteratureContextReviewer() (in module tooluniverse.tools.LiteratureContextReviewer) LiteratureSearchTool() (in module tooluniverse.tools.LiteratureSearchTool) LiteratureSynthesisAgent() (in module tooluniverse.tools.LiteratureSynthesisAgent) load() (tooluniverse.space.loader.SpaceLoader method) (tooluniverse.space.SpaceLoader method)

load_defaults_from_file() (tooluniverse.base_tool.BaseTool class method) (tooluniverse.BaseTool class method) load_mcp_tools() (in module tooluniverse.mcp_integration) (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) load_mcp_tools_to_tooluniverse() (in module tooluniverse.mcp_tool_registry) load_metadata() (in module tooluniverse.build_optimizer) load_rag_model() (tooluniverse.tool_finder_embedding.ToolFinderEmbedding method) (tooluniverse.ToolFinderEmbedding method) load_space() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) load_tool_desc_embedding() (tooluniverse.tool_finder_embedding.ToolFinderEmbedding method) (tooluniverse.ToolFinderEmbedding method) load_tools() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) load_tools_from_names_list() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) log_hook_execution() (in module tooluniverse.logging_config) LoggingHook (class in tooluniverse.extended_hooks) LRUCache (class in tooluniverse.cache.memory_cache)

M

main() (in module tooluniverse.doctor) (in module tooluniverse.generate_tools) map_properties_to_openfda_fields() (in module tooluniverse.openfda_tool) mark_tool_unavailable() (in module tooluniverse.tool_registry) MarkItDownTool (class in tooluniverse.markitdown_tool) max_summary_length (tooluniverse.output_hook.SummarizationHook attribute) (tooluniverse.output_hook.SummarizationHookConfig attribute) MCPAutoLoaderTool (class in tooluniverse) (class in tooluniverse.mcp_client_tool) MCPClientTool (class in tooluniverse) (class in tooluniverse.mcp_client_tool) MCPProxyTool (class in tooluniverse.mcp_client_tool) MCPServerDiscovery (class in tooluniverse.mcp_client_tool) MedicalLiteratureReviewer() (in module tooluniverse.tools.MedicalLiteratureReviewer) MedicalTermNormalizer() (in module tooluniverse.tools.MedicalTermNormalizer) MedlinePlus_connect_lookup_by_code() (in module tooluniverse.tools.MedlinePlus_connect_lookup_by_code) MedlinePlus_get_genetics_condition_by_name() (in module tooluniverse.tools.MedlinePlus_get_genetics_condition_by_name) MedlinePlus_get_genetics_gene_by_name() (in module tooluniverse.tools.MedlinePlus_get_genetics_gene_by_name) MedlinePlus_get_genetics_index() (in module tooluniverse.tools.MedlinePlus_get_genetics_index) MedlinePlus_search_topics_by_keyword() (in module tooluniverse.tools.MedlinePlus_search_topics_by_keyword) MedlinePlusRESTTool (class in tooluniverse) (class in tooluniverse.medlineplus_tool) MedRxiv_search_preprints() (in module tooluniverse.tools.MedRxiv_search_preprints) MedRxivTool (class in tooluniverse) (class in tooluniverse.medrxiv_tool) MemoryManager (class in tooluniverse.memory_manager) mesh_get_subjects_by_pharmacological_action() (in module tooluniverse.tools.mesh_get_subjects_by_pharmacological_action) mesh_get_subjects_by_subject_id() (in module tooluniverse.tools.mesh_get_subjects_by_subject_id) mesh_get_subjects_by_subject_name() (in module tooluniverse.tools.mesh_get_subjects_by_subject_name) mesh_get_subjects_by_subject_scope_or_definition() (in module tooluniverse.tools.mesh_get_subjects_by_subject_scope_or_definition) MethodologyRigorReviewer() (in module tooluniverse.tools.MethodologyRigorReviewer) minimal() (in module tooluniverse.logging_config) module tooluniverse tooluniverse.admetai_tool tooluniverse.agentic_tool tooluniverse.alphafold_tool tooluniverse.arxiv_tool tooluniverse.base_tool tooluniverse.biogrid_tool tooluniverse.biorxiv_tool tooluniverse.boltz_tool tooluniverse.build_optimizer tooluniverse.cache tooluniverse.cache.memory_cache tooluniverse.cache.result_cache_manager tooluniverse.cache.sqlite_backend tooluniverse.cellosaurus_tool tooluniverse.chem_tool tooluniverse.clinvar_tool tooluniverse.compose_scripts tooluniverse.compose_scripts.biomarker_discovery tooluniverse.compose_scripts.comprehensive_drug_discovery tooluniverse.compose_scripts.drug_safety_analyzer tooluniverse.compose_scripts.enhanced_multi_agent_literature_search tooluniverse.compose_scripts.literature_tool tooluniverse.compose_scripts.multi_agent_literature_search tooluniverse.compose_scripts.output_summarizer tooluniverse.compose_scripts.tool_description_optimizer tooluniverse.compose_scripts.tool_discover tooluniverse.compose_scripts.tool_graph_composer tooluniverse.compose_scripts.tool_graph_generation tooluniverse.compose_scripts.tool_metadata_generator tooluniverse.compose_tool tooluniverse.core_tool tooluniverse.crossref_tool tooluniverse.ctg_tool tooluniverse.custom_tool tooluniverse.dailymed_tool tooluniverse.data.fda_drugs_with_brand_generic_names_for_tool tooluniverse.dataset_tool tooluniverse.dblp_tool tooluniverse.dbsnp_tool tooluniverse.default_config tooluniverse.doaj_tool tooluniverse.doctor tooluniverse.efo_tool tooluniverse.embedding_database tooluniverse.embedding_sync tooluniverse.enrichr_tool tooluniverse.ensembl_tool tooluniverse.europe_pmc_tool tooluniverse.exceptions tooluniverse.execute_function tooluniverse.extended_hooks tooluniverse.fatcat_tool tooluniverse.gene_ontology_tool tooluniverse.generate_tools tooluniverse.genomics_gene_search_tool tooluniverse.geo_tool tooluniverse.gnomad_tool tooluniverse.graphql_tool tooluniverse.gwas_tool tooluniverse.hal_tool tooluniverse.hpa_tool tooluniverse.humanbase_tool tooluniverse.llm_clients tooluniverse.logging_config tooluniverse.markitdown_tool tooluniverse.mcp_client_tool tooluniverse.mcp_integration tooluniverse.mcp_tool_registry tooluniverse.medlineplus_tool tooluniverse.medrxiv_tool tooluniverse.memory_manager tooluniverse.molecule_2d_tool tooluniverse.molecule_3d_tool tooluniverse.odphp_tool tooluniverse.openaire_tool tooluniverse.openalex_tool tooluniverse.openfda_adv_tool tooluniverse.openfda_tool tooluniverse.osf_preprints_tool tooluniverse.output_hook tooluniverse.package_tool tooluniverse.pmc_tool tooluniverse.protein_structure_3d_tool tooluniverse.pubchem_tool tooluniverse.pubmed_tool tooluniverse.pubtator_tool tooluniverse.rcsb_pdb_tool tooluniverse.reactome_tool tooluniverse.remote_tool tooluniverse.restful_tool tooluniverse.semantic_scholar_tool tooluniverse.smcp tooluniverse.smcp_server tooluniverse.space tooluniverse.space.loader tooluniverse.space.validator tooluniverse.string_tool tooluniverse.tool_finder_embedding tooluniverse.tool_finder_keyword tooluniverse.tool_finder_llm tooluniverse.tool_graph_web_ui tooluniverse.tool_registry tooluniverse.tools.ADMETAI_predict_BBB_penetrance tooluniverse.tools.ADMETAI_predict_bioavailability tooluniverse.tools.ADMETAI_predict_clearance_distribution tooluniverse.tools.ADMETAI_predict_CYP_interactions tooluniverse.tools.ADMETAI_predict_nuclear_receptor_activity tooluniverse.tools.ADMETAI_predict_physicochemical_properties tooluniverse.tools.ADMETAI_predict_solubility_lipophilicity_hydration tooluniverse.tools.ADMETAI_predict_stress_response tooluniverse.tools.ADMETAI_predict_toxicity tooluniverse.tools.ADMETAnalyzerAgent tooluniverse.tools.AdvancedCodeQualityAnalyzer tooluniverse.tools.AdverseEventICDMapper tooluniverse.tools.AdverseEventPredictionQuestionGenerator tooluniverse.tools.AdverseEventPredictionQuestionGeneratorWithContext tooluniverse.tools.alphafold_get_annotations tooluniverse.tools.alphafold_get_prediction tooluniverse.tools.alphafold_get_summary tooluniverse.tools.ArgumentDescriptionOptimizer tooluniverse.tools.ArXiv_search_papers tooluniverse.tools.BiomarkerDiscoveryWorkflow tooluniverse.tools.BioRxiv_search_preprints tooluniverse.tools.call_agentic_human tooluniverse.tools.CallAgent tooluniverse.tools.cancer_biomarkers_disease_target_score tooluniverse.tools.cancer_gene_census_disease_target_score tooluniverse.tools.cellosaurus_get_cell_line_info tooluniverse.tools.cellosaurus_query_converter tooluniverse.tools.cellosaurus_search_cell_lines tooluniverse.tools.chembl_disease_target_score tooluniverse.tools.ChEMBL_search_similar_molecules tooluniverse.tools.ClinicalTrialDesignAgent tooluniverse.tools.ClinVar_search_variants tooluniverse.tools.CMA_Guidelines_Search tooluniverse.tools.CodeOptimizer tooluniverse.tools.CodeQualityAnalyzer tooluniverse.tools.CompoundDiscoveryAgent tooluniverse.tools.ComprehensiveDrugDiscoveryPipeline tooluniverse.tools.convert_to_markdown tooluniverse.tools.CORE_search_papers tooluniverse.tools.Crossref_search_works tooluniverse.tools.DailyMed_get_spl_by_setid tooluniverse.tools.DailyMed_search_spls tooluniverse.tools.DataAnalysisValidityReviewer tooluniverse.tools.DBLP_search_publications tooluniverse.tools.dbSNP_get_variant_by_rsid tooluniverse.tools.DescriptionAnalyzer tooluniverse.tools.DescriptionQualityEvaluator tooluniverse.tools.dict_search tooluniverse.tools.dili_search tooluniverse.tools.diqt_search tooluniverse.tools.disease_target_score tooluniverse.tools.DiseaseAnalyzerAgent tooluniverse.tools.DOAJ_search_articles tooluniverse.tools.DomainExpertValidator tooluniverse.tools.drugbank_filter_drugs_by_name tooluniverse.tools.drugbank_full_search tooluniverse.tools.drugbank_get_drug_basic_info_by_drug_name_or_drugbank_id tooluniverse.tools.drugbank_get_drug_chemistry_by_drug_name_or_drugbank_id tooluniverse.tools.drugbank_get_drug_interactions_by_drug_name_or_drugbank_id tooluniverse.tools.drugbank_get_drug_name_and_description_by_indication tooluniverse.tools.drugbank_get_drug_name_and_description_by_pathway_name tooluniverse.tools.drugbank_get_drug_name_and_description_by_target_name tooluniverse.tools.drugbank_get_drug_name_description_pharmacology_by_mechanism_of_action tooluniverse.tools.drugbank_get_drug_pathways_and_reactions_by_drug_name_or_drugbank_id tooluniverse.tools.drugbank_get_drug_products_by_name_or_drugbank_id tooluniverse.tools.drugbank_get_drug_references_by_drug_name_or_drugbank_id tooluniverse.tools.drugbank_get_indications_by_drug_name_or_drugbank_id tooluniverse.tools.drugbank_get_pharmacology_by_drug_name_or_drugbank_id tooluniverse.tools.drugbank_get_safety_by_drug_name_or_drugbank_id tooluniverse.tools.drugbank_get_targets_by_drug_name_or_drugbank_id tooluniverse.tools.drugbank_links_search tooluniverse.tools.drugbank_vocab_filter tooluniverse.tools.drugbank_vocab_search tooluniverse.tools.DrugInteractionAnalyzerAgent tooluniverse.tools.DrugOptimizationAgent tooluniverse.tools.DrugSafetyAnalyzer tooluniverse.tools.embedding_database_add tooluniverse.tools.embedding_database_create tooluniverse.tools.embedding_database_load tooluniverse.tools.embedding_database_search tooluniverse.tools.embedding_sync_download tooluniverse.tools.embedding_sync_upload tooluniverse.tools.enrichr_gene_enrichment_analysis tooluniverse.tools.Ensembl_lookup_gene_by_symbol tooluniverse.tools.EthicalComplianceReviewer tooluniverse.tools.europepmc_disease_target_score tooluniverse.tools.EuropePMC_Guidelines_Search tooluniverse.tools.EuropePMC_search_articles tooluniverse.tools.eva_disease_target_score tooluniverse.tools.eva_somatic_disease_target_score tooluniverse.tools.ExperimentalDesignScorer tooluniverse.tools.expression_atlas_disease_target_score tooluniverse.tools.extract_clinical_trial_adverse_events tooluniverse.tools.extract_clinical_trial_outcomes tooluniverse.tools.FAERS_count_additive_administration_routes tooluniverse.tools.FAERS_count_additive_adverse_reactions tooluniverse.tools.FAERS_count_additive_event_reports_by_country tooluniverse.tools.FAERS_count_additive_reaction_outcomes tooluniverse.tools.FAERS_count_additive_reports_by_reporter_country tooluniverse.tools.FAERS_count_additive_seriousness_classification tooluniverse.tools.FAERS_count_country_by_drug_event tooluniverse.tools.FAERS_count_death_related_by_drug tooluniverse.tools.FAERS_count_drug_routes_by_event tooluniverse.tools.FAERS_count_drugs_by_drug_event tooluniverse.tools.FAERS_count_outcomes_by_drug_event tooluniverse.tools.FAERS_count_patient_age_distribution tooluniverse.tools.FAERS_count_reactions_by_drug_event tooluniverse.tools.FAERS_count_reportercountry_by_drug_event tooluniverse.tools.FAERS_count_seriousness_by_drug_event tooluniverse.tools.Fatcat_search_scholar tooluniverse.tools.FDA_get_abuse_dependence_info_by_drug_name tooluniverse.tools.FDA_get_abuse_info_by_drug_name tooluniverse.tools.FDA_get_accessories_info_by_drug_name tooluniverse.tools.FDA_get_active_ingredient_info_by_drug_name tooluniverse.tools.FDA_get_adverse_reactions_by_drug_name tooluniverse.tools.FDA_get_alarms_by_drug_name tooluniverse.tools.FDA_get_animal_pharmacology_info_by_drug_name tooluniverse.tools.FDA_get_assembly_installation_info_by_drug_name tooluniverse.tools.FDA_get_boxed_warning_info_by_drug_name tooluniverse.tools.FDA_get_brand_name_generic_name tooluniverse.tools.FDA_get_calibration_instructions_by_drug_name tooluniverse.tools.FDA_get_carcinogenic_mutagenic_fertility_by_drug_name tooluniverse.tools.FDA_get_child_safety_info_by_drug_name tooluniverse.tools.FDA_get_clinical_pharmacology_by_drug_name tooluniverse.tools.FDA_get_clinical_studies_info_by_drug_name tooluniverse.tools.FDA_get_contact_for_questions_info_by_drug_name tooluniverse.tools.FDA_get_contraindications_by_drug_name tooluniverse.tools.FDA_get_controlled_substance_DEA_schedule_info_by_drug_name tooluniverse.tools.FDA_get_dear_health_care_provider_letter_info_by_drug_name tooluniverse.tools.FDA_get_dependence_info_by_drug_name tooluniverse.tools.FDA_get_disposal_info_by_drug_name tooluniverse.tools.FDA_get_do_not_use_info_by_drug_name tooluniverse.tools.FDA_get_document_id_by_drug_name tooluniverse.tools.FDA_get_dosage_and_storage_information_by_drug_name tooluniverse.tools.FDA_get_dosage_forms_and_strengths_by_drug_name tooluniverse.tools.FDA_get_drug_generic_name tooluniverse.tools.FDA_get_drug_interactions_by_drug_name tooluniverse.tools.FDA_get_drug_name_by_adverse_reaction tooluniverse.tools.FDA_get_drug_name_by_calibration_instructions 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tooluniverse.tools.MedlinePlus_search_topics_by_keyword tooluniverse.tools.MedRxiv_search_preprints tooluniverse.tools.mesh_get_subjects_by_pharmacological_action tooluniverse.tools.mesh_get_subjects_by_subject_id tooluniverse.tools.mesh_get_subjects_by_subject_name tooluniverse.tools.mesh_get_subjects_by_subject_scope_or_definition tooluniverse.tools.MethodologyRigorReviewer tooluniverse.tools.NICE_Clinical_Guidelines_Search tooluniverse.tools.NICE_Guideline_Full_Text tooluniverse.tools.NoveltySignificanceReviewer tooluniverse.tools.odphp_itemlist tooluniverse.tools.odphp_myhealthfinder tooluniverse.tools.odphp_outlink_fetch tooluniverse.tools.odphp_topicsearch tooluniverse.tools.OpenAIRE_search_publications tooluniverse.tools.OpenAlex_Guidelines_Search tooluniverse.tools.openalex_literature_search tooluniverse.tools.OpenTargets_drug_pharmacogenomics_data tooluniverse.tools.OpenTargets_get_approved_indications_by_drug_chemblId tooluniverse.tools.OpenTargets_get_associated_diseases_by_drug_chemblId tooluniverse.tools.OpenTargets_get_associated_drugs_by_disease_efoId tooluniverse.tools.OpenTargets_get_associated_drugs_by_target_ensemblID tooluniverse.tools.OpenTargets_get_associated_phenotypes_by_disease_efoId tooluniverse.tools.OpenTargets_get_associated_targets_by_disease_efoId tooluniverse.tools.OpenTargets_get_associated_targets_by_drug_chemblId tooluniverse.tools.OpenTargets_get_biological_mouse_models_by_ensemblID tooluniverse.tools.OpenTargets_get_chemical_probes_by_target_ensemblID tooluniverse.tools.OpenTargets_get_disease_ancestors_parents_by_efoId tooluniverse.tools.OpenTargets_get_disease_descendants_children_by_efoId tooluniverse.tools.OpenTargets_get_disease_description_by_efoId tooluniverse.tools.OpenTargets_get_disease_id_description_by_name tooluniverse.tools.OpenTargets_get_disease_ids_by_efoId tooluniverse.tools.OpenTargets_get_disease_ids_by_name tooluniverse.tools.OpenTargets_get_disease_locations_by_efoId tooluniverse.tools.OpenTargets_get_disease_synonyms_by_efoId tooluniverse.tools.OpenTargets_get_disease_therapeutic_areas_by_efoId tooluniverse.tools.OpenTargets_get_diseases_phenotypes_by_target_ensembl tooluniverse.tools.OpenTargets_get_drug_adverse_events_by_chemblId tooluniverse.tools.OpenTargets_get_drug_approval_status_by_chemblId tooluniverse.tools.OpenTargets_get_drug_chembId_by_generic_name tooluniverse.tools.OpenTargets_get_drug_description_by_chemblId tooluniverse.tools.OpenTargets_get_drug_id_description_by_name tooluniverse.tools.OpenTargets_get_drug_indications_by_chemblId tooluniverse.tools.OpenTargets_get_drug_mechanisms_of_action_by_chemblId tooluniverse.tools.OpenTargets_get_drug_synonyms_by_chemblId tooluniverse.tools.OpenTargets_get_drug_trade_names_by_chemblId tooluniverse.tools.OpenTargets_get_drug_warnings_by_chemblId tooluniverse.tools.OpenTargets_get_drug_withdrawn_blackbox_status_by_chemblId tooluniverse.tools.OpenTargets_get_gene_ontology_terms_by_goID tooluniverse.tools.OpenTargets_get_known_drugs_by_drug_chemblId tooluniverse.tools.OpenTargets_get_parent_child_molecules_by_drug_chembl_ID tooluniverse.tools.OpenTargets_get_publications_by_disease_efoId tooluniverse.tools.OpenTargets_get_publications_by_drug_chemblId tooluniverse.tools.OpenTargets_get_publications_by_target_ensemblID tooluniverse.tools.OpenTargets_get_similar_entities_by_disease_efoId tooluniverse.tools.OpenTargets_get_similar_entities_by_drug_chemblId tooluniverse.tools.OpenTargets_get_similar_entities_by_target_ensemblID tooluniverse.tools.OpenTargets_get_target_classes_by_ensemblID tooluniverse.tools.OpenTargets_get_target_constraint_info_by_ensemblID tooluniverse.tools.OpenTargets_get_target_enabling_packages_by_ensemblID tooluniverse.tools.OpenTargets_get_target_gene_ontology_by_ensemblID tooluniverse.tools.OpenTargets_get_target_genomic_location_by_ensemblID tooluniverse.tools.OpenTargets_get_target_homologues_by_ensemblID tooluniverse.tools.OpenTargets_get_target_id_description_by_name tooluniverse.tools.OpenTargets_get_target_interactions_by_ensemblID tooluniverse.tools.OpenTargets_get_target_safety_profile_by_ensemblID tooluniverse.tools.OpenTargets_get_target_subcellular_locations_by_ensemblID tooluniverse.tools.OpenTargets_get_target_synonyms_by_ensemblID tooluniverse.tools.OpenTargets_get_target_tractability_by_ensemblID tooluniverse.tools.OpenTargets_map_any_disease_id_to_all_other_ids tooluniverse.tools.OpenTargets_multi_entity_search_by_query_string tooluniverse.tools.OpenTargets_search_category_counts_by_query_string tooluniverse.tools.OpenTargets_target_disease_evidence tooluniverse.tools.OSF_search_preprints tooluniverse.tools.OSL_get_efo_id_by_disease_name tooluniverse.tools.OutputSummarizationComposer tooluniverse.tools.PMC_search_papers tooluniverse.tools.ProtocolOptimizer tooluniverse.tools.PubChem_get_associated_patents_by_CID tooluniverse.tools.PubChem_get_CID_by_compound_name tooluniverse.tools.PubChem_get_CID_by_SMILES tooluniverse.tools.PubChem_get_compound_2D_image_by_CID tooluniverse.tools.PubChem_get_compound_properties_by_CID tooluniverse.tools.PubChem_get_compound_synonyms_by_CID tooluniverse.tools.PubChem_get_compound_xrefs_by_CID tooluniverse.tools.PubChem_search_compounds_by_similarity tooluniverse.tools.PubChem_search_compounds_by_substructure tooluniverse.tools.PubMed_Guidelines_Search tooluniverse.tools.PubMed_search_articles tooluniverse.tools.PubTator3_EntityAutocomplete tooluniverse.tools.PubTator3_LiteratureSearch tooluniverse.tools.QuestionRephraser tooluniverse.tools.reactome_disease_target_score tooluniverse.tools.Reactome_get_pathway_reactions tooluniverse.tools.ReproducibilityTransparencyReviewer tooluniverse.tools.ResultsInterpretationReviewer tooluniverse.tools.ScientificTextSummarizer tooluniverse.tools.search_clinical_trials tooluniverse.tools.SemanticScholar_search_papers tooluniverse.tools.TestCaseGenerator tooluniverse.tools.Tool_Finder tooluniverse.tools.Tool_Finder_Keyword tooluniverse.tools.Tool_Finder_LLM tooluniverse.tools.Tool_RAG tooluniverse.tools.ToolCompatibilityAnalyzer tooluniverse.tools.ToolDescriptionOptimizer tooluniverse.tools.ToolDiscover tooluniverse.tools.ToolGraphComposer tooluniverse.tools.ToolGraphGenerationPipeline tooluniverse.tools.ToolImplementationGenerator tooluniverse.tools.ToolMetadataGenerationPipeline tooluniverse.tools.ToolMetadataGenerator tooluniverse.tools.ToolMetadataStandardizer tooluniverse.tools.ToolOptimizer tooluniverse.tools.ToolOutputSummarizer tooluniverse.tools.ToolQualityEvaluator tooluniverse.tools.ToolRelationshipDetector tooluniverse.tools.ToolSpecificationGenerator tooluniverse.tools.ToolSpecificationOptimizer tooluniverse.tools.TRIP_Database_Guidelines_Search tooluniverse.tools.UCSC_get_genes_by_region tooluniverse.tools.UniProt_get_alternative_names_by_accession tooluniverse.tools.UniProt_get_disease_variants_by_accession tooluniverse.tools.UniProt_get_entry_by_accession tooluniverse.tools.UniProt_get_function_by_accession tooluniverse.tools.UniProt_get_isoform_ids_by_accession tooluniverse.tools.UniProt_get_organism_by_accession tooluniverse.tools.UniProt_get_ptm_processing_by_accession tooluniverse.tools.UniProt_get_recommended_name_by_accession tooluniverse.tools.UniProt_get_sequence_by_accession tooluniverse.tools.UniProt_get_subcellular_location_by_accession tooluniverse.tools.Unpaywall_check_oa_status tooluniverse.tools.visualize_molecule_2d tooluniverse.tools.visualize_molecule_3d tooluniverse.tools.visualize_protein_structure_3d tooluniverse.tools.WHO_Guideline_Full_Text tooluniverse.tools.WHO_Guidelines_Search tooluniverse.tools.Wikidata_SPARQL_query tooluniverse.tools.WritingPresentationReviewer tooluniverse.tools.Zenodo_search_records tooluniverse.ucsc_tool tooluniverse.unified_guideline_tools tooluniverse.uniprot_tool tooluniverse.unpaywall_tool tooluniverse.url_tool tooluniverse.uspto_tool tooluniverse.utils tooluniverse.visualization_tool tooluniverse.wikidata_sparql_tool tooluniverse.xml_tool tooluniverse.zenodo_tool

Molecule2DTool (class in tooluniverse.molecule_2d_tool) Molecule3DTool (class in tooluniverse.molecule_3d_tool) MonarchDiseasesForMultiplePhenoTool (class in tooluniverse) (class in tooluniverse.restful_tool) MonarchTool (class in tooluniverse) (class in tooluniverse.restful_tool)

N

name (tooluniverse.agentic_tool.AgenticTool attribute) (tooluniverse.output_hook.OutputHook attribute) namespace (tooluniverse.cache.result_cache_manager.CacheRecord attribute) (tooluniverse.cache.sqlite_backend.CacheEntry attribute) (tooluniverse.execute_function._BatchCacheInfo attribute) next_steps (tooluniverse.exceptions.ToolError attribute)

NICE_Clinical_Guidelines_Search() (in module tooluniverse.tools.NICE_Clinical_Guidelines_Search) NICE_Guideline_Full_Text() (in module tooluniverse.tools.NICE_Guideline_Full_Text) NICEGuidelineFullTextTool (class in tooluniverse.unified_guideline_tools) NICEWebScrapingTool (class in tooluniverse.unified_guideline_tools) normalize_gene_symbol() (in module tooluniverse.utils) NoveltySignificanceReviewer() (in module tooluniverse.tools.NoveltySignificanceReviewer)

O

odphp_itemlist() (in module tooluniverse.tools.odphp_itemlist) odphp_myhealthfinder() (in module tooluniverse.tools.odphp_myhealthfinder) odphp_outlink_fetch() (in module tooluniverse.tools.odphp_outlink_fetch) odphp_topicsearch() (in module tooluniverse.tools.odphp_topicsearch) ODPHPItemList (class in tooluniverse) (class in tooluniverse.odphp_tool) ODPHPMyHealthfinder (class in tooluniverse) (class in tooluniverse.odphp_tool) ODPHPOutlinkFetch (class in tooluniverse) (class in tooluniverse.odphp_tool) ODPHPRESTTool (class in tooluniverse.odphp_tool) ODPHPTopicSearch (class in tooluniverse) (class in tooluniverse.odphp_tool) OpenAIRE_search_publications() (in module tooluniverse.tools.OpenAIRE_search_publications) OpenAIRETool (class in tooluniverse.openaire_tool) OpenAlex_Guidelines_Search() (in module tooluniverse.tools.OpenAlex_Guidelines_Search) openalex_literature_search() (in module tooluniverse.tools.openalex_literature_search) OpenAlexGuidelinesTool (class in tooluniverse.unified_guideline_tools) OpenAlexTool (class in tooluniverse.openalex_tool) OpenRouterClient (class in tooluniverse.llm_clients) OpentargetGeneticsTool (class in tooluniverse) (class in tooluniverse.graphql_tool) OpenTargets_drug_pharmacogenomics_data() (in module tooluniverse.tools.OpenTargets_drug_pharmacogenomics_data) OpenTargets_get_approved_indications_by_drug_chemblId() (in module tooluniverse.tools.OpenTargets_get_approved_indications_by_drug_chemblId) OpenTargets_get_associated_diseases_by_drug_chemblId() (in module tooluniverse.tools.OpenTargets_get_associated_diseases_by_drug_chemblId) OpenTargets_get_associated_drugs_by_disease_efoId() (in module tooluniverse.tools.OpenTargets_get_associated_drugs_by_disease_efoId) OpenTargets_get_associated_drugs_by_target_ensemblID() (in module tooluniverse.tools.OpenTargets_get_associated_drugs_by_target_ensemblID) OpenTargets_get_associated_phenotypes_by_disease_efoId() (in module tooluniverse.tools.OpenTargets_get_associated_phenotypes_by_disease_efoId) OpenTargets_get_associated_targets_by_disease_efoId() (in module tooluniverse.tools.OpenTargets_get_associated_targets_by_disease_efoId) OpenTargets_get_associated_targets_by_drug_chemblId() (in module tooluniverse.tools.OpenTargets_get_associated_targets_by_drug_chemblId) OpenTargets_get_biological_mouse_models_by_ensemblID() (in module tooluniverse.tools.OpenTargets_get_biological_mouse_models_by_ensemblID) OpenTargets_get_chemical_probes_by_target_ensemblID() (in module tooluniverse.tools.OpenTargets_get_chemical_probes_by_target_ensemblID) OpenTargets_get_disease_ancestors_parents_by_efoId() (in module tooluniverse.tools.OpenTargets_get_disease_ancestors_parents_by_efoId) OpenTargets_get_disease_descendants_children_by_efoId() (in module tooluniverse.tools.OpenTargets_get_disease_descendants_children_by_efoId) OpenTargets_get_disease_description_by_efoId() (in module tooluniverse.tools.OpenTargets_get_disease_description_by_efoId) OpenTargets_get_disease_id_description_by_name() (in module tooluniverse.tools.OpenTargets_get_disease_id_description_by_name) OpenTargets_get_disease_ids_by_efoId() (in module tooluniverse.tools.OpenTargets_get_disease_ids_by_efoId) OpenTargets_get_disease_ids_by_name() (in module tooluniverse.tools.OpenTargets_get_disease_ids_by_name) OpenTargets_get_disease_locations_by_efoId() (in module tooluniverse.tools.OpenTargets_get_disease_locations_by_efoId) OpenTargets_get_disease_synonyms_by_efoId() (in module tooluniverse.tools.OpenTargets_get_disease_synonyms_by_efoId) OpenTargets_get_disease_therapeutic_areas_by_efoId() (in module tooluniverse.tools.OpenTargets_get_disease_therapeutic_areas_by_efoId) OpenTargets_get_diseases_phenotypes_by_target_ensembl() (in module tooluniverse.tools.OpenTargets_get_diseases_phenotypes_by_target_ensembl) OpenTargets_get_drug_adverse_events_by_chemblId() (in module tooluniverse.tools.OpenTargets_get_drug_adverse_events_by_chemblId)

OpenTargets_get_drug_approval_status_by_chemblId() (in module tooluniverse.tools.OpenTargets_get_drug_approval_status_by_chemblId) OpenTargets_get_drug_chembId_by_generic_name() (in module tooluniverse.tools.OpenTargets_get_drug_chembId_by_generic_name) OpenTargets_get_drug_description_by_chemblId() (in module tooluniverse.tools.OpenTargets_get_drug_description_by_chemblId) OpenTargets_get_drug_id_description_by_name() (in module tooluniverse.tools.OpenTargets_get_drug_id_description_by_name) OpenTargets_get_drug_indications_by_chemblId() (in module tooluniverse.tools.OpenTargets_get_drug_indications_by_chemblId) OpenTargets_get_drug_mechanisms_of_action_by_chemblId() (in module tooluniverse.tools.OpenTargets_get_drug_mechanisms_of_action_by_chemblId) OpenTargets_get_drug_synonyms_by_chemblId() (in module tooluniverse.tools.OpenTargets_get_drug_synonyms_by_chemblId) OpenTargets_get_drug_trade_names_by_chemblId() (in module tooluniverse.tools.OpenTargets_get_drug_trade_names_by_chemblId) OpenTargets_get_drug_warnings_by_chemblId() (in module tooluniverse.tools.OpenTargets_get_drug_warnings_by_chemblId) OpenTargets_get_drug_withdrawn_blackbox_status_by_chemblId() (in module tooluniverse.tools.OpenTargets_get_drug_withdrawn_blackbox_status_by_chemblId) OpenTargets_get_gene_ontology_terms_by_goID() (in module tooluniverse.tools.OpenTargets_get_gene_ontology_terms_by_goID) OpenTargets_get_known_drugs_by_drug_chemblId() (in module tooluniverse.tools.OpenTargets_get_known_drugs_by_drug_chemblId) OpenTargets_get_parent_child_molecules_by_drug_chembl_ID() (in module tooluniverse.tools.OpenTargets_get_parent_child_molecules_by_drug_chembl_ID) OpenTargets_get_publications_by_disease_efoId() (in module tooluniverse.tools.OpenTargets_get_publications_by_disease_efoId) OpenTargets_get_publications_by_drug_chemblId() (in module tooluniverse.tools.OpenTargets_get_publications_by_drug_chemblId) OpenTargets_get_publications_by_target_ensemblID() (in module tooluniverse.tools.OpenTargets_get_publications_by_target_ensemblID) OpenTargets_get_similar_entities_by_disease_efoId() (in module tooluniverse.tools.OpenTargets_get_similar_entities_by_disease_efoId) OpenTargets_get_similar_entities_by_drug_chemblId() (in module tooluniverse.tools.OpenTargets_get_similar_entities_by_drug_chemblId) OpenTargets_get_similar_entities_by_target_ensemblID() (in module tooluniverse.tools.OpenTargets_get_similar_entities_by_target_ensemblID) OpenTargets_get_target_classes_by_ensemblID() (in module tooluniverse.tools.OpenTargets_get_target_classes_by_ensemblID) OpenTargets_get_target_constraint_info_by_ensemblID() (in module tooluniverse.tools.OpenTargets_get_target_constraint_info_by_ensemblID) OpenTargets_get_target_enabling_packages_by_ensemblID() (in module tooluniverse.tools.OpenTargets_get_target_enabling_packages_by_ensemblID) OpenTargets_get_target_gene_ontology_by_ensemblID() (in module tooluniverse.tools.OpenTargets_get_target_gene_ontology_by_ensemblID) OpenTargets_get_target_genomic_location_by_ensemblID() (in module tooluniverse.tools.OpenTargets_get_target_genomic_location_by_ensemblID) OpenTargets_get_target_homologues_by_ensemblID() (in module tooluniverse.tools.OpenTargets_get_target_homologues_by_ensemblID) OpenTargets_get_target_id_description_by_name() (in module tooluniverse.tools.OpenTargets_get_target_id_description_by_name) OpenTargets_get_target_interactions_by_ensemblID() (in module tooluniverse.tools.OpenTargets_get_target_interactions_by_ensemblID) OpenTargets_get_target_safety_profile_by_ensemblID() (in module tooluniverse.tools.OpenTargets_get_target_safety_profile_by_ensemblID) OpenTargets_get_target_subcellular_locations_by_ensemblID() (in module tooluniverse.tools.OpenTargets_get_target_subcellular_locations_by_ensemblID) OpenTargets_get_target_synonyms_by_ensemblID() (in module tooluniverse.tools.OpenTargets_get_target_synonyms_by_ensemblID) OpenTargets_get_target_tractability_by_ensemblID() (in module tooluniverse.tools.OpenTargets_get_target_tractability_by_ensemblID) OpenTargets_map_any_disease_id_to_all_other_ids() (in module tooluniverse.tools.OpenTargets_map_any_disease_id_to_all_other_ids) OpenTargets_multi_entity_search_by_query_string() (in module tooluniverse.tools.OpenTargets_multi_entity_search_by_query_string) OpenTargets_search_category_counts_by_query_string() (in module tooluniverse.tools.OpenTargets_search_category_counts_by_query_string) OpenTargets_target_disease_evidence() (in module tooluniverse.tools.OpenTargets_target_disease_evidence) OpentargetTool (class in tooluniverse) (class in tooluniverse.graphql_tool) OpentargetToolDrugNameMatch (class in tooluniverse) (class in tooluniverse.graphql_tool) OSF_search_preprints() (in module tooluniverse.tools.OSF_search_preprints) OSFPreprintsTool (class in tooluniverse.osf_preprints_tool) OSL_get_efo_id_by_disease_name() (in module tooluniverse.tools.OSL_get_efo_id_by_disease_name) OutputHook (class in tooluniverse.output_hook) OutputSummarizationComposer() (in module tooluniverse.tools.OutputSummarizationComposer)

P

PackageTool (class in tooluniverse) (class in tooluniverse.package_tool) PersistentCache (class in tooluniverse.cache.sqlite_backend) PMC_search_papers() (in module tooluniverse.tools.PMC_search_papers) PMCTool (class in tooluniverse) (class in tooluniverse.pmc_tool) prepare_input_ids() (tooluniverse.rcsb_pdb_tool.RCSBTool method) (tooluniverse.RCSBTool method) prepare_one_tool_prompt() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) prepare_tool_examples() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) prepare_tool_prompts() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) priority (tooluniverse.output_hook.OutputHook attribute) process() (tooluniverse.extended_hooks.FilteringHook method) (tooluniverse.extended_hooks.FormattingHook method) (tooluniverse.extended_hooks.LoggingHook method) (tooluniverse.extended_hooks.ValidationHook method) (tooluniverse.output_hook.FileSaveHook method) (tooluniverse.output_hook.OutputHook method) (tooluniverse.output_hook.SummarizationHook method) progress() (in module tooluniverse.logging_config) progress_log() (in module tooluniverse.logging_config)

ProteinStructure3DTool (class in tooluniverse.protein_structure_3d_tool) ProtocolOptimizer() (in module tooluniverse.tools.ProtocolOptimizer) prune_item() (tooluniverse.uspto_tool.USPTOOpenDataPortalTool method) (tooluniverse.USPTOOpenDataPortalTool method) PubChem_get_associated_patents_by_CID() (in module tooluniverse.tools.PubChem_get_associated_patents_by_CID) PubChem_get_CID_by_compound_name() (in module tooluniverse.tools.PubChem_get_CID_by_compound_name) PubChem_get_CID_by_SMILES() (in module tooluniverse.tools.PubChem_get_CID_by_SMILES) PubChem_get_compound_2D_image_by_CID() (in module tooluniverse.tools.PubChem_get_compound_2D_image_by_CID) PubChem_get_compound_properties_by_CID() (in module tooluniverse.tools.PubChem_get_compound_properties_by_CID) PubChem_get_compound_synonyms_by_CID() (in module tooluniverse.tools.PubChem_get_compound_synonyms_by_CID) PubChem_get_compound_xrefs_by_CID() (in module tooluniverse.tools.PubChem_get_compound_xrefs_by_CID) PubChem_search_compounds_by_similarity() (in module tooluniverse.tools.PubChem_search_compounds_by_similarity) PubChem_search_compounds_by_substructure() (in module tooluniverse.tools.PubChem_search_compounds_by_substructure) PubChemRESTTool (class in tooluniverse) (class in tooluniverse.pubchem_tool) PubMed_Guidelines_Search() (in module tooluniverse.tools.PubMed_Guidelines_Search) PubMed_search_articles() (in module tooluniverse.tools.PubMed_search_articles) PubMedGuidelinesTool (class in tooluniverse.unified_guideline_tools) PubMedTool (class in tooluniverse) (class in tooluniverse.pubmed_tool) PubTator3_EntityAutocomplete() (in module tooluniverse.tools.PubTator3_EntityAutocomplete) PubTator3_LiteratureSearch() (in module tooluniverse.tools.PubTator3_LiteratureSearch) PubTatorTool (class in tooluniverse) (class in tooluniverse.pubtator_tool)

Q

QuestionRephraser() (in module tooluniverse.tools.QuestionRephraser)

R

rag_infer() (tooluniverse.tool_finder_embedding.ToolFinderEmbedding method) (tooluniverse.ToolFinderEmbedding method) rag_model (tooluniverse.tool_finder_embedding.ToolFinderEmbedding attribute) (tooluniverse.ToolFinderEmbedding attribute) rag_model_name (tooluniverse.tool_finder_embedding.ToolFinderEmbedding attribute) (tooluniverse.ToolFinderEmbedding attribute) rank_paths_by_weight() (tooluniverse.enrichr_tool.EnrichrTool method) rank_paths_to_term() (tooluniverse.enrichr_tool.EnrichrTool method) RCSBTool (class in tooluniverse) (class in tooluniverse.rcsb_pdb_tool) reactome_disease_target_score() (in module tooluniverse.tools.reactome_disease_target_score) Reactome_get_pathway_reactions() (in module tooluniverse.tools.Reactome_get_pathway_reactions) ReactomeRESTTool (class in tooluniverse) (class in tooluniverse.reactome_tool) read_json_list() (in module tooluniverse.utils) read_resource() (tooluniverse.mcp_client_tool.MCPClientTool method) (tooluniverse.MCPClientTool method) reconfigure_for_stdio() (in module tooluniverse.logging_config) (tooluniverse.logging_config.ToolUniverseLogger method) refresh() (tooluniverse.execute_function.ToolNamespace method) refresh_tool_name_desc() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) refresh_tools() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) register_config() (in module tooluniverse.tool_registry) register_custom_tool() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) register_external_tool() (in module tooluniverse.tool_registry) register_mcp_tool() (in module tooluniverse.mcp_tool_registry) register_mcp_tool_from_config() (in module tooluniverse.mcp_tool_registry) register_tool() (in module tooluniverse) (in module tooluniverse.tool_registry) register_tools_in_engine() (tooluniverse.mcp_client_tool.MCPAutoLoaderTool method) (tooluniverse.MCPAutoLoaderTool method) reload_config() (tooluniverse.output_hook.HookManager method) remote_info (tooluniverse.remote_tool.RemoteTool attribute) RemoteTool (class in tooluniverse.remote_tool) remove_keys() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) remove_none_and_empty_values() (in module tooluniverse.graphql_tool) ReproducibilityTransparencyReviewer() (in module tooluniverse.tools.ReproducibilityTransparencyReviewer) RESTfulTool (class in tooluniverse.restful_tool) ResultCacheManager (class in tooluniverse.cache.result_cache_manager) ResultsInterpretationReviewer() (in module tooluniverse.tools.ResultsInterpretationReviewer) retriable (tooluniverse.exceptions.ToolError attribute) retry_initialization() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) return_all_loaded_tools() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) return_metadata (tooluniverse.agentic_tool.AgenticTool attribute) rule (tooluniverse.output_hook.OutputHook attribute) run() (tooluniverse.admetai_tool.ADMETAITool method) (tooluniverse.ADMETAITool method) (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) (tooluniverse.alphafold_tool.AlphaFoldRESTTool method) (tooluniverse.AlphaFoldRESTTool method) (tooluniverse.arxiv_tool.ArXivTool method) (tooluniverse.ArXivTool method) (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseTool method) (tooluniverse.biogrid_tool.BioGRIDRESTTool method) (tooluniverse.biorxiv_tool.BioRxivTool method) (tooluniverse.BioRxivTool method) (tooluniverse.boltz_tool.Boltz2DockingTool method) (tooluniverse.cellosaurus_tool.CellosaurusGetCellLineInfoTool method) (tooluniverse.cellosaurus_tool.CellosaurusQueryConverterTool method) (tooluniverse.cellosaurus_tool.CellosaurusSearchTool method) (tooluniverse.CellosaurusGetCellLineInfoTool method) (tooluniverse.CellosaurusQueryConverterTool method) (tooluniverse.CellosaurusSearchTool method) (tooluniverse.chem_tool.ChEMBLTool method) (tooluniverse.ChEMBLTool method) (tooluniverse.ClinicalTrialsDetailsTool method) (tooluniverse.ClinicalTrialsSearchTool method) (tooluniverse.clinvar_tool.ClinVarTool method) (tooluniverse.compose_tool.ComposeTool method) (tooluniverse.ComposeTool method) (tooluniverse.core_tool.CoreTool method) (tooluniverse.CoreTool method) (tooluniverse.crossref_tool.CrossrefTool method) (tooluniverse.CrossrefTool method) (tooluniverse.ctg_tool.ClinicalTrialsDetailsTool method) (tooluniverse.ctg_tool.ClinicalTrialsSearchTool method) (tooluniverse.ctg_tool.ClinicalTrialsTool method) (tooluniverse.custom_tool.CustomTool method) (tooluniverse.dailymed_tool.GetSPLBySetIDTool method) (tooluniverse.dailymed_tool.SearchSPLTool method) (tooluniverse.dataset_tool.DatasetTool method) (tooluniverse.DatasetTool method) (tooluniverse.dblp_tool.DBLPTool method) (tooluniverse.DBLPTool method) (tooluniverse.dbsnp_tool.DbSnpTool method) (tooluniverse.DiseaseTargetScoreTool method) (tooluniverse.doaj_tool.DOAJTool method) (tooluniverse.DOAJTool method) (tooluniverse.efo_tool.EFOTool method) (tooluniverse.EFOTool method) (tooluniverse.embedding_database.EmbeddingDatabase method) (tooluniverse.embedding_sync.EmbeddingSync method) (tooluniverse.EmbeddingDatabase method) (tooluniverse.EmbeddingSync method) (tooluniverse.enrichr_tool.EnrichrTool method) (tooluniverse.ensembl_tool.EnsemblTool method) (tooluniverse.europe_pmc_tool.EuropePMCTool method) (tooluniverse.EuropePMCTool method) (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.fatcat_tool.FatcatScholarTool method) (tooluniverse.FDACountAdditiveReactionsTool method) (tooluniverse.FDADrugAdverseEventTool method) (tooluniverse.FDADrugLabelGetDrugGenericNameTool method) (tooluniverse.FDADrugLabelSearchIDTool method) (tooluniverse.FDADrugLabelSearchTool method) (tooluniverse.gene_ontology_tool.GeneOntologyTool method) (tooluniverse.genomics_gene_search_tool.GWASGeneSearch method) (tooluniverse.geo_tool.GEORESTTool method) (tooluniverse.GetSPLBySetIDTool method) (tooluniverse.gnomad_tool.GnomadTool method) (tooluniverse.graphql_tool.DiseaseTargetScoreTool method) (tooluniverse.graphql_tool.GraphQLTool method) (tooluniverse.graphql_tool.OpentargetTool method) (tooluniverse.graphql_tool.OpentargetToolDrugNameMatch method) (tooluniverse.gwas_tool.GWASAssociationByID method) (tooluniverse.gwas_tool.GWASAssociationSearch method) (tooluniverse.gwas_tool.GWASAssociationsForSNP method) (tooluniverse.gwas_tool.GWASAssociationsForStudy method) (tooluniverse.gwas_tool.GWASAssociationsForTrait method) (tooluniverse.gwas_tool.GWASRESTTool method) (tooluniverse.gwas_tool.GWASSNPByID method) (tooluniverse.gwas_tool.GWASSNPSearch method) (tooluniverse.gwas_tool.GWASSNPsForGene method) (tooluniverse.gwas_tool.GWASStudiesForTrait method) (tooluniverse.gwas_tool.GWASStudyByID method) (tooluniverse.gwas_tool.GWASStudySearch method) (tooluniverse.gwas_tool.GWASVariantsForTrait method) (tooluniverse.GWASAssociationByID method) (tooluniverse.GWASAssociationSearch method) (tooluniverse.GWASAssociationsForSNP method) (tooluniverse.GWASAssociationsForStudy method) (tooluniverse.GWASAssociationsForTrait method) (tooluniverse.GWASSNPByID method) (tooluniverse.GWASSNPSearch method) (tooluniverse.GWASSNPsForGene method) (tooluniverse.GWASStudiesForTrait method) (tooluniverse.GWASStudyByID method) (tooluniverse.GWASStudySearch method) (tooluniverse.GWASVariantsForTrait method) (tooluniverse.hal_tool.HALTool method) (tooluniverse.HALTool method) (tooluniverse.hpa_tool.HPAGetBiologicalProcessTool method) (tooluniverse.hpa_tool.HPAGetCancerPrognosticsTool method) (tooluniverse.hpa_tool.HPAGetComparativeExpressionTool method) (tooluniverse.hpa_tool.HPAGetContextualBiologicalProcessTool method) (tooluniverse.hpa_tool.HPAGetDiseaseExpressionTool method) (tooluniverse.hpa_tool.HPAGetGeneJSONTool method) (tooluniverse.hpa_tool.HPAGetGenePageDetailsTool method) (tooluniverse.hpa_tool.HPAGetGeneXMLTool method) (tooluniverse.hpa_tool.HPAGetProteinInteractionsTool method) (tooluniverse.hpa_tool.HPAGetRnaExpressionBySourceTool method) (tooluniverse.hpa_tool.HPAGetRnaExpressionByTissueTool method) (tooluniverse.hpa_tool.HPAGetSubcellularLocationTool method) (tooluniverse.hpa_tool.HPASearchGenesTool method) (tooluniverse.HPAGetGeneJSONTool method) (tooluniverse.HPAGetGeneXMLTool method) (tooluniverse.humanbase_tool.HumanBaseTool method) (tooluniverse.markitdown_tool.MarkItDownTool method) (tooluniverse.mcp_client_tool.MCPAutoLoaderTool method) (tooluniverse.mcp_client_tool.MCPClientTool method) (tooluniverse.mcp_client_tool.MCPProxyTool method) (tooluniverse.MCPAutoLoaderTool method) (tooluniverse.MCPClientTool method) (tooluniverse.medlineplus_tool.MedlinePlusRESTTool method) (tooluniverse.MedlinePlusRESTTool method) (tooluniverse.medrxiv_tool.MedRxivTool method) (tooluniverse.MedRxivTool method) (tooluniverse.molecule_2d_tool.Molecule2DTool method) (tooluniverse.molecule_3d_tool.Molecule3DTool method) (tooluniverse.MonarchDiseasesForMultiplePhenoTool method) (tooluniverse.MonarchTool method) (tooluniverse.odphp_tool.ODPHPItemList method) (tooluniverse.odphp_tool.ODPHPMyHealthfinder method) (tooluniverse.odphp_tool.ODPHPOutlinkFetch method) (tooluniverse.odphp_tool.ODPHPTopicSearch method) (tooluniverse.ODPHPItemList method) (tooluniverse.ODPHPMyHealthfinder method) (tooluniverse.ODPHPOutlinkFetch method) (tooluniverse.ODPHPTopicSearch method) (tooluniverse.openaire_tool.OpenAIRETool method) (tooluniverse.openalex_tool.OpenAlexTool method) (tooluniverse.openfda_adv_tool.FDACountAdditiveReactionsTool method) (tooluniverse.openfda_adv_tool.FDADrugAdverseEventTool method) (tooluniverse.openfda_tool.FDADrugLabelGetDrugGenericNameTool method) (tooluniverse.openfda_tool.FDADrugLabelSearchIDTool method) (tooluniverse.openfda_tool.FDADrugLabelSearchTool method) (tooluniverse.openfda_tool.FDATool method) (tooluniverse.OpentargetTool method) (tooluniverse.OpentargetToolDrugNameMatch method) (tooluniverse.osf_preprints_tool.OSFPreprintsTool method) (tooluniverse.package_tool.PackageTool method) (tooluniverse.PackageTool method) (tooluniverse.pmc_tool.PMCTool method) (tooluniverse.PMCTool method) (tooluniverse.protein_structure_3d_tool.ProteinStructure3DTool method) (tooluniverse.pubchem_tool.PubChemRESTTool method) (tooluniverse.PubChemRESTTool method) (tooluniverse.pubmed_tool.PubMedTool method) (tooluniverse.PubMedTool method) (tooluniverse.pubtator_tool.PubTatorTool method) (tooluniverse.PubTatorTool method) (tooluniverse.rcsb_pdb_tool.RCSBTool method) (tooluniverse.RCSBTool method) (tooluniverse.reactome_tool.ReactomeRESTTool method) (tooluniverse.ReactomeRESTTool method) (tooluniverse.remote_tool.RemoteTool method) (tooluniverse.restful_tool.MonarchDiseasesForMultiplePhenoTool method) (tooluniverse.restful_tool.MonarchTool method) (tooluniverse.restful_tool.RESTfulTool method) (tooluniverse.SearchSPLTool method) (tooluniverse.semantic_scholar_tool.SemanticScholarTool method) (tooluniverse.SemanticScholarTool method) (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) (tooluniverse.string_tool.STRINGRESTTool method) (tooluniverse.tool_finder_embedding.ToolFinderEmbedding method) (tooluniverse.tool_finder_keyword.ToolFinderKeyword method) (tooluniverse.tool_finder_llm.ToolFinderLLM method) (tooluniverse.tool_graph_web_ui.ToolGraphWebUI method) (tooluniverse.ToolFinderEmbedding method) (tooluniverse.ToolFinderKeyword method) (tooluniverse.ToolFinderLLM method) (tooluniverse.ToolUniverse method) (tooluniverse.ucsc_tool.UCSCTool method) (tooluniverse.unified_guideline_tools.CMAGuidelinesTool method) (tooluniverse.unified_guideline_tools.EuropePMCGuidelinesTool method) (tooluniverse.unified_guideline_tools.GINGuidelinesTool method) (tooluniverse.unified_guideline_tools.NICEGuidelineFullTextTool method) (tooluniverse.unified_guideline_tools.NICEWebScrapingTool method) (tooluniverse.unified_guideline_tools.OpenAlexGuidelinesTool method) (tooluniverse.unified_guideline_tools.PubMedGuidelinesTool method) (tooluniverse.unified_guideline_tools.TRIPDatabaseTool method) (tooluniverse.unified_guideline_tools.WHOGuidelineFullTextTool method) (tooluniverse.unified_guideline_tools.WHOGuidelinesTool method) (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) (tooluniverse.unpaywall_tool.UnpaywallTool method) (tooluniverse.UnpaywallTool method) (tooluniverse.url_tool.URLHTMLTagTool method) (tooluniverse.url_tool.URLToPDFTextTool method) (tooluniverse.URLHTMLTagTool method) (tooluniverse.URLToPDFTextTool method) (tooluniverse.uspto_tool.USPTOOpenDataPortalTool method) (tooluniverse.USPTOOpenDataPortalTool method) (tooluniverse.wikidata_sparql_tool.WikidataSPARQLTool method) (tooluniverse.xml_tool.XMLDatasetTool method) (tooluniverse.XMLDatasetTool method) (tooluniverse.zenodo_tool.ZenodoTool method) (tooluniverse.ZenodoTool method)

run_http_server() (in module tooluniverse.smcp_server) run_one_function() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) run_simple() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) run_smcp_server() (in module tooluniverse.smcp_server) run_stdio_server() (in module tooluniverse.smcp_server)

S

save_metadata() (in module tooluniverse.build_optimizer) ScientificTextSummarizer() (in module tooluniverse.tools.ScientificTextSummarizer) search_clinical_trials() (in module tooluniverse.tools.search_clinical_trials) search_literature() (tooluniverse.openalex_tool.OpenAlexTool method) search_openfda() (in module tooluniverse.openfda_tool) search_terms() (tooluniverse.gene_ontology_tool.GeneOntologyTool method) search_topics_by_keyword() (tooluniverse.medlineplus_tool.MedlinePlusRESTTool method) (tooluniverse.MedlinePlusRESTTool method) SearchSPLTool (class in tooluniverse) (class in tooluniverse.dailymed_tool) select_tools() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) SemanticScholar_search_papers() (in module tooluniverse.tools.SemanticScholar_search_papers) SemanticScholarTool (class in tooluniverse) (class in tooluniverse.semantic_scholar_tool) set() (tooluniverse.cache.memory_cache.LRUCache method) (tooluniverse.cache.result_cache_manager.ResultCacheManager method) (tooluniverse.cache.sqlite_backend.PersistentCache method) set_current_phase() (tooluniverse.memory_manager.MemoryManager method) set_level() (tooluniverse.logging_config.ToolUniverseLogger method) set_log_level() (in module tooluniverse.logging_config) setup_logging() (in module tooluniverse.logging_config) should_trigger() (tooluniverse.output_hook.OutputHook method) signature (tooluniverse.execute_function._BatchJob attribute) SingleFlight (class in tooluniverse.cache.memory_cache) singleflight_guard() (tooluniverse.cache.result_cache_manager.ResultCacheManager method) skip_execution (tooluniverse.execute_function._BatchJob attribute)

SMCP (class in tooluniverse) (class in tooluniverse.smcp) SpaceLoader (class in tooluniverse.space) (class in tooluniverse.space.loader) special_tools_name (tooluniverse.tool_finder_embedding.ToolFinderEmbedding attribute) (tooluniverse.ToolFinderEmbedding attribute) start_mcp_server() (in module tooluniverse.mcp_tool_registry) start_mcp_server_for_tool() (in module tooluniverse.mcp_tool_registry) STATIC_CACHE_VERSION (tooluniverse.base_tool.BaseTool attribute) (tooluniverse.BaseTool attribute) stats() (tooluniverse.cache.memory_cache.LRUCache method) (tooluniverse.cache.result_cache_manager.ResultCacheManager method) (tooluniverse.cache.sqlite_backend.PersistentCache method) STEMMING_RULES (tooluniverse.tool_finder_keyword.ToolFinderKeyword attribute) (tooluniverse.ToolFinderKeyword attribute) stop_mcp_server() (in module tooluniverse.mcp_tool_registry) STOP_WORDS (tooluniverse.tool_finder_keyword.ToolFinderKeyword attribute) (tooluniverse.ToolFinderKeyword attribute) STREAM_FLAG_KEY (tooluniverse.agentic_tool.AgenticTool attribute) (tooluniverse.AgenticTool attribute) STRINGRESTTool (class in tooluniverse.string_tool) submit_gene_list() (tooluniverse.enrichr_tool.EnrichrTool method) SummarizationHook (class in tooluniverse.output_hook) SummarizationHookConfig (class in tooluniverse.output_hook) supports_caching() (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseTool method) supports_streaming() (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseTool method)

T

test_api() (tooluniverse.llm_clients.AzureOpenAIClient method) (tooluniverse.llm_clients.BaseLLMClient method) (tooluniverse.llm_clients.GeminiClient method) (tooluniverse.llm_clients.OpenRouterClient method) (tooluniverse.llm_clients.VLLMClient method) TestCaseGenerator() (in module tooluniverse.tools.TestCaseGenerator) to_dict() (tooluniverse.exceptions.ToolError method) toggle_hooks() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.output_hook.HookManager method) (tooluniverse.ToolUniverse method) tool_category_dicts (tooluniverse.execute_function.ToolUniverse attribute) (tooluniverse.ToolUniverse attribute) tool_config (tooluniverse.remote_tool.RemoteTool attribute) tool_desc_embedding (tooluniverse.tool_finder_embedding.ToolFinderEmbedding attribute) (tooluniverse.ToolFinderEmbedding attribute) tool_embedding_path (tooluniverse.tool_finder_embedding.ToolFinderEmbedding attribute) (tooluniverse.ToolFinderEmbedding attribute) tool_files (tooluniverse.execute_function.ToolUniverse attribute) (tooluniverse.ToolUniverse attribute) Tool_Finder() (in module tooluniverse.tools.Tool_Finder) Tool_Finder_Keyword() (in module tooluniverse.tools.Tool_Finder_Keyword) Tool_Finder_LLM() (in module tooluniverse.tools.Tool_Finder_LLM) tool_instance (tooluniverse.execute_function._BatchJob attribute) tool_name (tooluniverse.tool_finder_embedding.ToolFinderEmbedding attribute) (tooluniverse.ToolFinderEmbedding attribute) Tool_RAG() (in module tooluniverse.tools.Tool_RAG) tool_specification() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) tool_to_str() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) ToolAuthError ToolCallable (class in tooluniverse.execute_function) ToolCompatibilityAnalyzer() (in module tooluniverse.tools.ToolCompatibilityAnalyzer) ToolConfigError ToolDependencyError ToolDescriptionOptimizer() (in module tooluniverse.tools.ToolDescriptionOptimizer) ToolDiscover() (in module tooluniverse.tools.ToolDiscover) ToolError ToolFinderEmbedding (class in tooluniverse) (class in tooluniverse.tool_finder_embedding) ToolFinderKeyword (class in tooluniverse) (class in tooluniverse.tool_finder_keyword) ToolFinderLLM (class in tooluniverse) (class in tooluniverse.tool_finder_llm) ToolGraphComposer() (in module tooluniverse.tools.ToolGraphComposer) ToolGraphGenerationPipeline() (in module tooluniverse.tools.ToolGraphGenerationPipeline) ToolGraphWebUI (class in tooluniverse.tool_graph_web_ui) ToolImplementationGenerator() (in module tooluniverse.tools.ToolImplementationGenerator) ToolMetadataGenerationPipeline() (in module tooluniverse.tools.ToolMetadataGenerationPipeline) ToolMetadataGenerator() (in module tooluniverse.tools.ToolMetadataGenerator) ToolMetadataStandardizer() (in module tooluniverse.tools.ToolMetadataStandardizer) ToolNamespace (class in tooluniverse.execute_function) ToolOptimizer() (in module tooluniverse.tools.ToolOptimizer) ToolOutputSummarizer() (in module tooluniverse.tools.ToolOutputSummarizer) ToolQualityEvaluator() (in module tooluniverse.tools.ToolQualityEvaluator) ToolRateLimitError ToolRelationshipDetector() (in module tooluniverse.tools.ToolRelationshipDetector) ToolServerError ToolSpecificationGenerator() (in module tooluniverse.tools.ToolSpecificationGenerator) ToolSpecificationOptimizer() (in module tooluniverse.tools.ToolSpecificationOptimizer) ToolUnavailableError tooluniverse module ToolUniverse (class in tooluniverse) (class in tooluniverse.execute_function) tooluniverse (tooluniverse.output_hook.HookManager attribute) (tooluniverse.output_hook.SummarizationHook attribute) (tooluniverse.tool_finder_embedding.ToolFinderEmbedding attribute) (tooluniverse.ToolFinderEmbedding attribute) tooluniverse.admetai_tool module tooluniverse.agentic_tool module tooluniverse.alphafold_tool module tooluniverse.arxiv_tool module tooluniverse.base_tool module tooluniverse.biogrid_tool module tooluniverse.biorxiv_tool module tooluniverse.boltz_tool module tooluniverse.build_optimizer module tooluniverse.cache module tooluniverse.cache.memory_cache module tooluniverse.cache.result_cache_manager module tooluniverse.cache.sqlite_backend module tooluniverse.cellosaurus_tool module tooluniverse.chem_tool module tooluniverse.clinvar_tool module tooluniverse.compose_scripts module tooluniverse.compose_scripts.biomarker_discovery module tooluniverse.compose_scripts.comprehensive_drug_discovery module tooluniverse.compose_scripts.drug_safety_analyzer module tooluniverse.compose_scripts.enhanced_multi_agent_literature_search module tooluniverse.compose_scripts.literature_tool module tooluniverse.compose_scripts.multi_agent_literature_search module tooluniverse.compose_scripts.output_summarizer module tooluniverse.compose_scripts.tool_description_optimizer module tooluniverse.compose_scripts.tool_discover module tooluniverse.compose_scripts.tool_graph_composer module tooluniverse.compose_scripts.tool_graph_generation module tooluniverse.compose_scripts.tool_metadata_generator module tooluniverse.compose_tool module tooluniverse.core_tool module tooluniverse.crossref_tool module tooluniverse.ctg_tool module tooluniverse.custom_tool module tooluniverse.dailymed_tool module tooluniverse.data.fda_drugs_with_brand_generic_names_for_tool module tooluniverse.dataset_tool module tooluniverse.dblp_tool module tooluniverse.dbsnp_tool module tooluniverse.default_config module tooluniverse.doaj_tool module tooluniverse.doctor module tooluniverse.efo_tool module tooluniverse.embedding_database module tooluniverse.embedding_sync module tooluniverse.enrichr_tool module tooluniverse.ensembl_tool module tooluniverse.europe_pmc_tool module tooluniverse.exceptions module tooluniverse.execute_function module tooluniverse.extended_hooks module tooluniverse.fatcat_tool module tooluniverse.gene_ontology_tool module tooluniverse.generate_tools module tooluniverse.genomics_gene_search_tool module tooluniverse.geo_tool module tooluniverse.gnomad_tool module tooluniverse.graphql_tool module tooluniverse.gwas_tool module tooluniverse.hal_tool module tooluniverse.hpa_tool module tooluniverse.humanbase_tool module tooluniverse.llm_clients module tooluniverse.logging_config module tooluniverse.markitdown_tool module tooluniverse.mcp_client_tool module tooluniverse.mcp_integration module tooluniverse.mcp_tool_registry module tooluniverse.medlineplus_tool module tooluniverse.medrxiv_tool module tooluniverse.memory_manager module tooluniverse.molecule_2d_tool module tooluniverse.molecule_3d_tool module tooluniverse.odphp_tool module tooluniverse.openaire_tool module tooluniverse.openalex_tool module tooluniverse.openfda_adv_tool module tooluniverse.openfda_tool module tooluniverse.osf_preprints_tool module tooluniverse.output_hook module tooluniverse.package_tool module tooluniverse.pmc_tool module tooluniverse.protein_structure_3d_tool module tooluniverse.pubchem_tool module tooluniverse.pubmed_tool module tooluniverse.pubtator_tool module tooluniverse.rcsb_pdb_tool module tooluniverse.reactome_tool module tooluniverse.remote_tool module tooluniverse.restful_tool module tooluniverse.semantic_scholar_tool module tooluniverse.smcp module tooluniverse.smcp_server module tooluniverse.space module tooluniverse.space.loader module tooluniverse.space.validator module tooluniverse.string_tool module tooluniverse.tool_finder_embedding module tooluniverse.tool_finder_keyword module tooluniverse.tool_finder_llm module tooluniverse.tool_graph_web_ui module tooluniverse.tool_registry module tooluniverse.tools.ADMETAI_predict_BBB_penetrance module tooluniverse.tools.ADMETAI_predict_bioavailability module tooluniverse.tools.ADMETAI_predict_clearance_distribution module tooluniverse.tools.ADMETAI_predict_CYP_interactions module tooluniverse.tools.ADMETAI_predict_nuclear_receptor_activity module tooluniverse.tools.ADMETAI_predict_physicochemical_properties module tooluniverse.tools.ADMETAI_predict_solubility_lipophilicity_hydration module tooluniverse.tools.ADMETAI_predict_stress_response module tooluniverse.tools.ADMETAI_predict_toxicity module tooluniverse.tools.ADMETAnalyzerAgent module tooluniverse.tools.AdvancedCodeQualityAnalyzer module tooluniverse.tools.AdverseEventICDMapper module tooluniverse.tools.AdverseEventPredictionQuestionGenerator module tooluniverse.tools.AdverseEventPredictionQuestionGeneratorWithContext module tooluniverse.tools.alphafold_get_annotations module tooluniverse.tools.alphafold_get_prediction module tooluniverse.tools.alphafold_get_summary module tooluniverse.tools.ArgumentDescriptionOptimizer module tooluniverse.tools.ArXiv_search_papers module tooluniverse.tools.BiomarkerDiscoveryWorkflow module tooluniverse.tools.BioRxiv_search_preprints module tooluniverse.tools.call_agentic_human module tooluniverse.tools.CallAgent module tooluniverse.tools.cancer_biomarkers_disease_target_score module tooluniverse.tools.cancer_gene_census_disease_target_score module tooluniverse.tools.cellosaurus_get_cell_line_info module tooluniverse.tools.cellosaurus_query_converter module tooluniverse.tools.cellosaurus_search_cell_lines module tooluniverse.tools.chembl_disease_target_score module tooluniverse.tools.ChEMBL_search_similar_molecules module tooluniverse.tools.ClinicalTrialDesignAgent module tooluniverse.tools.ClinVar_search_variants module tooluniverse.tools.CMA_Guidelines_Search module tooluniverse.tools.CodeOptimizer module tooluniverse.tools.CodeQualityAnalyzer module tooluniverse.tools.CompoundDiscoveryAgent module tooluniverse.tools.ComprehensiveDrugDiscoveryPipeline module tooluniverse.tools.convert_to_markdown module tooluniverse.tools.CORE_search_papers module tooluniverse.tools.Crossref_search_works module tooluniverse.tools.DailyMed_get_spl_by_setid module tooluniverse.tools.DailyMed_search_spls module tooluniverse.tools.DataAnalysisValidityReviewer module tooluniverse.tools.DBLP_search_publications module tooluniverse.tools.dbSNP_get_variant_by_rsid module tooluniverse.tools.DescriptionAnalyzer module tooluniverse.tools.DescriptionQualityEvaluator module tooluniverse.tools.dict_search module tooluniverse.tools.dili_search module tooluniverse.tools.diqt_search module tooluniverse.tools.disease_target_score module tooluniverse.tools.DiseaseAnalyzerAgent module tooluniverse.tools.DOAJ_search_articles module tooluniverse.tools.DomainExpertValidator module tooluniverse.tools.drugbank_filter_drugs_by_name module tooluniverse.tools.drugbank_full_search module tooluniverse.tools.drugbank_get_drug_basic_info_by_drug_name_or_drugbank_id module tooluniverse.tools.drugbank_get_drug_chemistry_by_drug_name_or_drugbank_id module tooluniverse.tools.drugbank_get_drug_interactions_by_drug_name_or_drugbank_id module tooluniverse.tools.drugbank_get_drug_name_and_description_by_indication module tooluniverse.tools.drugbank_get_drug_name_and_description_by_pathway_name module tooluniverse.tools.drugbank_get_drug_name_and_description_by_target_name module tooluniverse.tools.drugbank_get_drug_name_description_pharmacology_by_mechanism_of_action module tooluniverse.tools.drugbank_get_drug_pathways_and_reactions_by_drug_name_or_drugbank_id module tooluniverse.tools.drugbank_get_drug_products_by_name_or_drugbank_id module tooluniverse.tools.drugbank_get_drug_references_by_drug_name_or_drugbank_id module tooluniverse.tools.drugbank_get_indications_by_drug_name_or_drugbank_id module tooluniverse.tools.drugbank_get_pharmacology_by_drug_name_or_drugbank_id module tooluniverse.tools.drugbank_get_safety_by_drug_name_or_drugbank_id module tooluniverse.tools.drugbank_get_targets_by_drug_name_or_drugbank_id module tooluniverse.tools.drugbank_links_search module tooluniverse.tools.drugbank_vocab_filter module tooluniverse.tools.drugbank_vocab_search module tooluniverse.tools.DrugInteractionAnalyzerAgent module tooluniverse.tools.DrugOptimizationAgent module tooluniverse.tools.DrugSafetyAnalyzer module tooluniverse.tools.embedding_database_add module tooluniverse.tools.embedding_database_create module tooluniverse.tools.embedding_database_load module tooluniverse.tools.embedding_database_search module tooluniverse.tools.embedding_sync_download module tooluniverse.tools.embedding_sync_upload module tooluniverse.tools.enrichr_gene_enrichment_analysis module tooluniverse.tools.Ensembl_lookup_gene_by_symbol module tooluniverse.tools.EthicalComplianceReviewer module tooluniverse.tools.europepmc_disease_target_score module tooluniverse.tools.EuropePMC_Guidelines_Search module tooluniverse.tools.EuropePMC_search_articles module tooluniverse.tools.eva_disease_target_score module tooluniverse.tools.eva_somatic_disease_target_score module tooluniverse.tools.ExperimentalDesignScorer module tooluniverse.tools.expression_atlas_disease_target_score module tooluniverse.tools.extract_clinical_trial_adverse_events module tooluniverse.tools.extract_clinical_trial_outcomes module tooluniverse.tools.FAERS_count_additive_administration_routes module tooluniverse.tools.FAERS_count_additive_adverse_reactions module tooluniverse.tools.FAERS_count_additive_event_reports_by_country module tooluniverse.tools.FAERS_count_additive_reaction_outcomes module tooluniverse.tools.FAERS_count_additive_reports_by_reporter_country module tooluniverse.tools.FAERS_count_additive_seriousness_classification module tooluniverse.tools.FAERS_count_country_by_drug_event module tooluniverse.tools.FAERS_count_death_related_by_drug module tooluniverse.tools.FAERS_count_drug_routes_by_event module tooluniverse.tools.FAERS_count_drugs_by_drug_event module tooluniverse.tools.FAERS_count_outcomes_by_drug_event module tooluniverse.tools.FAERS_count_patient_age_distribution module tooluniverse.tools.FAERS_count_reactions_by_drug_event module tooluniverse.tools.FAERS_count_reportercountry_by_drug_event module tooluniverse.tools.FAERS_count_seriousness_by_drug_event module tooluniverse.tools.Fatcat_search_scholar module tooluniverse.tools.FDA_get_abuse_dependence_info_by_drug_name module tooluniverse.tools.FDA_get_abuse_info_by_drug_name module tooluniverse.tools.FDA_get_accessories_info_by_drug_name module tooluniverse.tools.FDA_get_active_ingredient_info_by_drug_name module tooluniverse.tools.FDA_get_adverse_reactions_by_drug_name module tooluniverse.tools.FDA_get_alarms_by_drug_name module tooluniverse.tools.FDA_get_animal_pharmacology_info_by_drug_name module tooluniverse.tools.FDA_get_assembly_installation_info_by_drug_name module tooluniverse.tools.FDA_get_boxed_warning_info_by_drug_name module tooluniverse.tools.FDA_get_brand_name_generic_name module tooluniverse.tools.FDA_get_calibration_instructions_by_drug_name module tooluniverse.tools.FDA_get_carcinogenic_mutagenic_fertility_by_drug_name module tooluniverse.tools.FDA_get_child_safety_info_by_drug_name module tooluniverse.tools.FDA_get_clinical_pharmacology_by_drug_name module tooluniverse.tools.FDA_get_clinical_studies_info_by_drug_name module tooluniverse.tools.FDA_get_contact_for_questions_info_by_drug_name module tooluniverse.tools.FDA_get_contraindications_by_drug_name module tooluniverse.tools.FDA_get_controlled_substance_DEA_schedule_info_by_drug_name module tooluniverse.tools.FDA_get_dear_health_care_provider_letter_info_by_drug_name module tooluniverse.tools.FDA_get_dependence_info_by_drug_name module tooluniverse.tools.FDA_get_disposal_info_by_drug_name module tooluniverse.tools.FDA_get_do_not_use_info_by_drug_name module tooluniverse.tools.FDA_get_document_id_by_drug_name module tooluniverse.tools.FDA_get_dosage_and_storage_information_by_drug_name module tooluniverse.tools.FDA_get_dosage_forms_and_strengths_by_drug_name module tooluniverse.tools.FDA_get_drug_generic_name module tooluniverse.tools.FDA_get_drug_interactions_by_drug_name module tooluniverse.tools.FDA_get_drug_name_by_adverse_reaction module tooluniverse.tools.FDA_get_drug_name_by_calibration_instructions module tooluniverse.tools.FDA_get_drug_name_by_dependence_info module tooluniverse.tools.FDA_get_drug_name_by_document_id module tooluniverse.tools.FDA_get_drug_name_by_dosage_info module tooluniverse.tools.FDA_get_drug_name_by_environmental_warning module tooluniverse.tools.FDA_get_drug_name_by_inactive_ingredient module tooluniverse.tools.FDA_get_drug_name_by_info_on_conditions_for_doctor_consultation module tooluniverse.tools.FDA_get_drug_name_by_labor_and_delivery_info module tooluniverse.tools.FDA_get_drug_name_by_microbiology module tooluniverse.tools.FDA_get_drug_name_by_other_safety_info module tooluniverse.tools.FDA_get_drug_name_by_pharmacodynamics module tooluniverse.tools.FDA_get_drug_name_by_pharmacogenomics module tooluniverse.tools.FDA_get_drug_name_by_precautions module tooluniverse.tools.FDA_get_drug_name_by_pregnancy_or_breastfeeding_info module tooluniverse.tools.FDA_get_drug_name_by_principal_display_panel module tooluniverse.tools.FDA_get_drug_name_by_reference module tooluniverse.tools.FDA_get_drug_name_by_set_id module tooluniverse.tools.FDA_get_drug_name_by_SPL_ID module tooluniverse.tools.FDA_get_drug_name_by_stop_use_info module tooluniverse.tools.FDA_get_drug_name_by_storage_and_handling_info module tooluniverse.tools.FDA_get_drug_name_by_warnings module tooluniverse.tools.FDA_get_drug_name_from_patient_package_insert module tooluniverse.tools.FDA_get_drug_names_by_abuse_dependence_info module tooluniverse.tools.FDA_get_drug_names_by_abuse_info module tooluniverse.tools.FDA_get_drug_names_by_accessories module tooluniverse.tools.FDA_get_drug_names_by_active_ingredient module tooluniverse.tools.FDA_get_drug_names_by_alarm module tooluniverse.tools.FDA_get_drug_names_by_animal_pharmacology_info module tooluniverse.tools.FDA_get_drug_names_by_application_number_NDC_number module tooluniverse.tools.FDA_get_drug_names_by_assembly_installation_info module tooluniverse.tools.FDA_get_drug_names_by_boxed_warning module tooluniverse.tools.FDA_get_drug_names_by_child_safety_info module tooluniverse.tools.FDA_get_drug_names_by_clinical_pharmacology module tooluniverse.tools.FDA_get_drug_names_by_clinical_studies module tooluniverse.tools.FDA_get_drug_names_by_consulting_doctor_pharmacist_info module tooluniverse.tools.FDA_get_drug_names_by_contraindications module tooluniverse.tools.FDA_get_drug_names_by_controlled_substance_DEA_schedule module tooluniverse.tools.FDA_get_drug_names_by_dear_health_care_provider_letter_info module tooluniverse.tools.FDA_get_drug_names_by_disposal_info module tooluniverse.tools.FDA_get_drug_names_by_dosage_forms_and_strengths_info module tooluniverse.tools.FDA_get_drug_names_by_drug_interactions module tooluniverse.tools.FDA_get_drug_names_by_effective_time module tooluniverse.tools.FDA_get_drug_names_by_food_safety_warnings module tooluniverse.tools.FDA_get_drug_names_by_general_precautions module tooluniverse.tools.FDA_get_drug_names_by_geriatric_use module tooluniverse.tools.FDA_get_drug_names_by_health_claim module tooluniverse.tools.FDA_get_drug_names_by_indication module tooluniverse.tools.FDA_get_drug_names_by_info_for_nursing_mothers module tooluniverse.tools.FDA_get_drug_names_by_information_for_owners_or_caregivers module tooluniverse.tools.FDA_get_drug_names_by_ingredient module tooluniverse.tools.FDA_get_drug_names_by_instructions_for_use module tooluniverse.tools.FDA_get_drug_names_by_lab_test_interference module tooluniverse.tools.FDA_get_drug_names_by_lab_tests module tooluniverse.tools.FDA_get_drug_names_by_mechanism_of_action module tooluniverse.tools.FDA_get_drug_names_by_medication_guide module tooluniverse.tools.FDA_get_drug_names_by_nonclinical_toxicology_info module tooluniverse.tools.FDA_get_drug_names_by_nonteratogenic_effects module tooluniverse.tools.FDA_get_drug_names_by_overdosage_info module tooluniverse.tools.FDA_get_drug_names_by_pediatric_use module tooluniverse.tools.FDA_get_drug_names_by_pharmacokinetics module tooluniverse.tools.FDA_get_drug_names_by_population_use module tooluniverse.tools.FDA_get_drug_names_by_pregnancy_effects_info module tooluniverse.tools.FDA_get_drug_names_by_residue_warning module tooluniverse.tools.FDA_get_drug_names_by_risk module tooluniverse.tools.FDA_get_drug_names_by_route module tooluniverse.tools.FDA_get_drug_names_by_safe_handling_warning module tooluniverse.tools.FDA_get_drug_names_by_safety_summary module tooluniverse.tools.FDA_get_drug_names_by_spl_indexing_data_elements module tooluniverse.tools.FDA_get_drug_names_by_teratogenic_effects module tooluniverse.tools.FDA_get_drug_names_by_user_safety_warning module tooluniverse.tools.FDA_get_drug_names_by_warnings_and_cautions module tooluniverse.tools.FDA_get_drugs_by_carcinogenic_mutagenic_fertility module tooluniverse.tools.FDA_get_effective_time_by_drug_name module tooluniverse.tools.FDA_get_environmental_warning_by_drug_name module tooluniverse.tools.FDA_get_general_precautions_by_drug_name module tooluniverse.tools.FDA_get_geriatric_use_info_by_drug_name module tooluniverse.tools.FDA_get_health_claims_by_drug_name module tooluniverse.tools.FDA_get_inactive_ingredient_info_by_drug_name module tooluniverse.tools.FDA_get_indications_by_drug_name module tooluniverse.tools.FDA_get_info_for_nursing_mothers_by_drug_name module tooluniverse.tools.FDA_get_info_for_patients_by_drug_name module tooluniverse.tools.FDA_get_info_on_conditions_for_doctor_consultation_by_drug_name module tooluniverse.tools.FDA_get_info_on_consulting_doctor_pharmacist_by_drug_name module tooluniverse.tools.FDA_get_information_for_owners_or_caregivers_by_drug_name module tooluniverse.tools.FDA_get_ingredients_by_drug_name module tooluniverse.tools.FDA_get_instructions_for_use_by_drug_name module tooluniverse.tools.FDA_get_lab_test_interference_info_by_drug_name module tooluniverse.tools.FDA_get_lab_tests_by_drug_name module tooluniverse.tools.FDA_get_labor_and_delivery_info_by_drug_name module tooluniverse.tools.FDA_get_manufacturer_name_NDC_number_by_drug_name module tooluniverse.tools.FDA_get_mechanism_of_action_by_drug_name module tooluniverse.tools.FDA_get_medication_guide_info_by_drug_name module tooluniverse.tools.FDA_get_microbiology_info_by_drug_name module tooluniverse.tools.FDA_get_nonclinical_toxicology_info_by_drug_name module tooluniverse.tools.FDA_get_nonteratogenic_effects_by_drug_name module tooluniverse.tools.FDA_get_other_safety_info_by_drug_name module tooluniverse.tools.FDA_get_overdosage_info_by_drug_name module tooluniverse.tools.FDA_get_patient_package_insert_from_drug_name module tooluniverse.tools.FDA_get_pediatric_use_info_by_drug_name module tooluniverse.tools.FDA_get_pharmacodynamics_by_drug_name module tooluniverse.tools.FDA_get_pharmacogenomics_info_by_drug_name module tooluniverse.tools.FDA_get_pharmacokinetics_by_drug_name module tooluniverse.tools.FDA_get_population_use_info_by_drug_name module tooluniverse.tools.FDA_get_precautions_by_drug_name module tooluniverse.tools.FDA_get_pregnancy_effects_info_by_drug_name module tooluniverse.tools.FDA_get_pregnancy_or_breastfeeding_info_by_drug_name module tooluniverse.tools.FDA_get_principal_display_panel_by_drug_name module tooluniverse.tools.FDA_get_purpose_info_by_drug_name module tooluniverse.tools.FDA_get_recent_changes_by_drug_name module tooluniverse.tools.FDA_get_reference_info_by_drug_name module tooluniverse.tools.FDA_get_residue_warning_by_drug_name module tooluniverse.tools.FDA_get_risk_info_by_drug_name module tooluniverse.tools.FDA_get_route_info_by_drug_name module tooluniverse.tools.FDA_get_safe_handling_warnings_by_drug_name module tooluniverse.tools.FDA_get_safety_summary_by_drug_name module tooluniverse.tools.FDA_get_spl_indexing_data_elements_by_drug_name module tooluniverse.tools.FDA_get_spl_unclassified_section_by_drug_name module tooluniverse.tools.FDA_get_stop_use_info_by_drug_name module tooluniverse.tools.FDA_get_storage_and_handling_info_by_drug_name module tooluniverse.tools.FDA_get_teratogenic_effects_by_drug_name module tooluniverse.tools.FDA_get_user_safety_warning_by_drug_names module tooluniverse.tools.FDA_get_warnings_and_cautions_by_drug_name module tooluniverse.tools.FDA_get_warnings_by_drug_name module tooluniverse.tools.FDA_get_when_using_info module tooluniverse.tools.FDA_retrieve_device_use_by_drug_name module tooluniverse.tools.FDA_retrieve_drug_name_by_device_use module tooluniverse.tools.FDA_retrieve_drug_names_by_patient_medication_info module tooluniverse.tools.FDA_retrieve_patient_medication_info_by_drug_name module tooluniverse.tools.Finish module tooluniverse.tools.genomics_england_disease_target_score module tooluniverse.tools.get_albumentations_info module tooluniverse.tools.get_altair_info module tooluniverse.tools.get_anndata_info module tooluniverse.tools.get_arboreto_info module tooluniverse.tools.get_arxiv_info module

tooluniverse.tools.get_ase_info module tooluniverse.tools.get_assembly_info_by_pdb_id module tooluniverse.tools.get_assembly_summary module tooluniverse.tools.get_astropy_info module tooluniverse.tools.get_binding_affinity_by_pdb_id module tooluniverse.tools.get_biopandas_info module tooluniverse.tools.get_biopython_info module tooluniverse.tools.get_bioservices_info module tooluniverse.tools.get_biotite_info module tooluniverse.tools.get_bokeh_info module tooluniverse.tools.get_brian2_info module tooluniverse.tools.get_cartopy_info module tooluniverse.tools.get_catboost_info module tooluniverse.tools.get_cellpose_info module tooluniverse.tools.get_cellrank_info module tooluniverse.tools.get_cellxgene_census_info module tooluniverse.tools.get_cftime_info module tooluniverse.tools.get_chem_comp_audit_info module tooluniverse.tools.get_chem_comp_charge_and_ambiguity module tooluniverse.tools.get_chembl_webresource_client_info module tooluniverse.tools.get_citation_info_by_pdb_id module tooluniverse.tools.get_clair3_info module tooluniverse.tools.get_clinical_trial_conditions_and_interventions module tooluniverse.tools.get_clinical_trial_descriptions module tooluniverse.tools.get_clinical_trial_eligibility_criteria module tooluniverse.tools.get_clinical_trial_locations module tooluniverse.tools.get_clinical_trial_outcome_measures module tooluniverse.tools.get_clinical_trial_references module tooluniverse.tools.get_clinical_trial_status_and_dates module tooluniverse.tools.get_cobra_info module tooluniverse.tools.get_cobrapy_info module tooluniverse.tools.get_cooler_info module tooluniverse.tools.get_core_refinement_statistics module tooluniverse.tools.get_cryosparc_tools_info module tooluniverse.tools.get_crystal_growth_conditions_by_pdb_id module tooluniverse.tools.get_crystallization_ph_by_pdb_id module tooluniverse.tools.get_crystallographic_properties_by_pdb_id module tooluniverse.tools.get_cupy_info module tooluniverse.tools.get_cyvcf2_info module tooluniverse.tools.get_dask_info module tooluniverse.tools.get_datamol_info module tooluniverse.tools.get_datashader_info module tooluniverse.tools.get_deepchem_info module tooluniverse.tools.get_deeppurpose_info module tooluniverse.tools.get_deeptools_info module tooluniverse.tools.get_deepxde_info module tooluniverse.tools.get_dendropy_info module tooluniverse.tools.get_descriptastorus_info module tooluniverse.tools.get_diffdock_info module tooluniverse.tools.get_dscribe_info module tooluniverse.tools.get_ec_number_by_entity_id module tooluniverse.tools.get_elephant_info module tooluniverse.tools.get_em_3d_fitting_and_reconstruction_details module tooluniverse.tools.get_emdb_ids_by_pdb_id module tooluniverse.tools.get_episcanpy_info module tooluniverse.tools.get_ete3_info module tooluniverse.tools.get_faiss_info module tooluniverse.tools.get_fanc_info module tooluniverse.tools.get_flask_info module tooluniverse.tools.get_flowio_info module tooluniverse.tools.get_flowkit_info module tooluniverse.tools.get_flowutils_info module tooluniverse.tools.get_freesasa_info module tooluniverse.tools.get_galpy_info module tooluniverse.tools.get_gene_name_by_entity_id module tooluniverse.tools.get_geopandas_info module tooluniverse.tools.get_gget_info module tooluniverse.tools.get_googlesearch_python_info module tooluniverse.tools.get_gseapy_info module tooluniverse.tools.get_h5py_info module tooluniverse.tools.get_harmony_pytorch_info module tooluniverse.tools.get_hmmlearn_info module tooluniverse.tools.get_holoviews_info module tooluniverse.tools.get_host_organism_by_pdb_id module tooluniverse.tools.get_HPO_ID_by_phenotype module tooluniverse.tools.get_htmd_info module tooluniverse.tools.get_hyperopt_info module tooluniverse.tools.get_igraph_info module tooluniverse.tools.get_imageio_info module tooluniverse.tools.get_imbalanced_learn_info module tooluniverse.tools.get_jcvi_info module tooluniverse.tools.get_joblib_info module tooluniverse.tools.get_joint_associated_diseases_by_HPO_ID_list module tooluniverse.tools.get_khmer_info module tooluniverse.tools.get_kipoiseq_info module tooluniverse.tools.get_lifelines_info module tooluniverse.tools.get_ligand_bond_count_by_pdb_id module tooluniverse.tools.get_ligand_smiles_by_chem_comp_id module tooluniverse.tools.get_lightgbm_info module tooluniverse.tools.get_loompy_info module tooluniverse.tools.get_mageck_info module tooluniverse.tools.get_matplotlib_info module tooluniverse.tools.get_mdanalysis_info module tooluniverse.tools.get_mdtraj_info module tooluniverse.tools.get_mne_info module tooluniverse.tools.get_molfeat_info module tooluniverse.tools.get_molvs_info module tooluniverse.tools.get_mordred_info module tooluniverse.tools.get_msprime_info module tooluniverse.tools.get_mudata_info module tooluniverse.tools.get_mutation_annotations_by_pdb_id module tooluniverse.tools.get_neo_info module tooluniverse.tools.get_netcdf4_info module tooluniverse.tools.get_networkx_info module tooluniverse.tools.get_nglview_info module tooluniverse.tools.get_nilearn_info module tooluniverse.tools.get_numba_info module tooluniverse.tools.get_numpy_info module tooluniverse.tools.get_oligosaccharide_descriptors_by_entity_id module tooluniverse.tools.get_openbabel_info module tooluniverse.tools.get_openchem_info module tooluniverse.tools.get_opencv_info module tooluniverse.tools.get_openmm_info module tooluniverse.tools.get_optlang_info module tooluniverse.tools.get_optuna_info module tooluniverse.tools.get_palantir_info module tooluniverse.tools.get_pandas_info module tooluniverse.tools.get_patsy_info module tooluniverse.tools.get_pdbfixer_info module tooluniverse.tools.get_phenotype_by_HPO_ID module tooluniverse.tools.get_pillow_info module tooluniverse.tools.get_plantcv_info module tooluniverse.tools.get_plip_info module tooluniverse.tools.get_plotly_info module tooluniverse.tools.get_poliastro_info module tooluniverse.tools.get_polymer_entity_annotations module tooluniverse.tools.get_polymer_entity_count_by_pdb_id module tooluniverse.tools.get_polymer_entity_ids_by_pdb_id module tooluniverse.tools.get_polymer_entity_type_by_entity_id module tooluniverse.tools.get_polymer_molecular_weight_by_entity_id module tooluniverse.tools.get_poretools_info module tooluniverse.tools.get_prody_info module tooluniverse.tools.get_protein_classification_by_pdb_id module tooluniverse.tools.get_protein_metadata_by_pdb_id module tooluniverse.tools.get_pubchempy_info module tooluniverse.tools.get_pybedtools_info module tooluniverse.tools.get_pybigwig_info module tooluniverse.tools.get_pydeseq2_info module tooluniverse.tools.get_pyensembl_info module tooluniverse.tools.get_pyephem_info module tooluniverse.tools.get_pyfaidx_info module tooluniverse.tools.get_pyfasta_info module tooluniverse.tools.get_pykalman_info module tooluniverse.tools.get_pyliftover_info module tooluniverse.tools.get_pymassspec_info module tooluniverse.tools.get_pymed_info module tooluniverse.tools.get_pymzml_info module tooluniverse.tools.get_pypdf2_info module tooluniverse.tools.get_pyranges_info module tooluniverse.tools.get_pyrosetta_info module tooluniverse.tools.get_pysam_info module tooluniverse.tools.get_pyscenic_info module tooluniverse.tools.get_pyscf_info module tooluniverse.tools.get_pyscreener_info module tooluniverse.tools.get_pytdc_info module tooluniverse.tools.get_python_libsbml_info module tooluniverse.tools.get_pytorch_info module tooluniverse.tools.get_pyvcf_info module tooluniverse.tools.get_pyvis_info module tooluniverse.tools.get_qutip_info module tooluniverse.tools.get_rasterio_info module tooluniverse.tools.get_rdkit_info module tooluniverse.tools.get_refinement_resolution_by_pdb_id module tooluniverse.tools.get_release_deposit_dates_by_pdb_id module tooluniverse.tools.get_reportlab_info module tooluniverse.tools.get_requests_info module tooluniverse.tools.get_ruptures_info module tooluniverse.tools.get_scanorama_info module tooluniverse.tools.get_scanpy_info module tooluniverse.tools.get_schnetpack_info module tooluniverse.tools.get_scholarly_info module tooluniverse.tools.get_scikit_bio_info module tooluniverse.tools.get_scikit_image_info module tooluniverse.tools.get_scikit_learn_info module tooluniverse.tools.get_scipy_info module tooluniverse.tools.get_scrublet_info module tooluniverse.tools.get_scvelo_info module tooluniverse.tools.get_scvi_tools_info module tooluniverse.tools.get_seaborn_info module tooluniverse.tools.get_sequence_by_pdb_id module tooluniverse.tools.get_sequence_lengths_by_pdb_id module tooluniverse.tools.get_sequence_positional_features_by_instance_id module tooluniverse.tools.get_skopt_info module tooluniverse.tools.get_souporcell_info module tooluniverse.tools.get_source_organism_by_pdb_id module tooluniverse.tools.get_space_group_by_pdb_id module tooluniverse.tools.get_statsmodels_info module tooluniverse.tools.get_structure_determination_software_by_pdb_id module tooluniverse.tools.get_structure_title_by_pdb_id module tooluniverse.tools.get_structure_validation_metrics_by_pdb_id module tooluniverse.tools.get_sunpy_info module tooluniverse.tools.get_sympy_info module tooluniverse.tools.get_target_cofactor_info module tooluniverse.tools.get_taxonomy_by_pdb_id module tooluniverse.tools.get_tiledb_info module tooluniverse.tools.get_tiledbsoma_info module tooluniverse.tools.get_torch_geometric_info module tooluniverse.tools.get_tqdm_info module tooluniverse.tools.get_trackpy_info module tooluniverse.tools.get_tskit_info module tooluniverse.tools.get_umap_learn_info module tooluniverse.tools.get_uniprot_accession_by_entity_id module tooluniverse.tools.get_velocyto_info module tooluniverse.tools.get_viennarna_info module tooluniverse.tools.get_webpage_text_from_url module tooluniverse.tools.get_webpage_title module tooluniverse.tools.get_xarray_info module tooluniverse.tools.get_xesmf_info module tooluniverse.tools.get_xgboost_info module tooluniverse.tools.get_zarr_info module tooluniverse.tools.GIN_Guidelines_Search module tooluniverse.tools.gnomAD_query_variant module tooluniverse.tools.GO_get_annotations_for_gene module tooluniverse.tools.GO_get_genes_for_term module tooluniverse.tools.GO_get_term_by_id module tooluniverse.tools.GO_get_term_details module tooluniverse.tools.GO_search_terms module tooluniverse.tools.gwas_get_association_by_id module tooluniverse.tools.gwas_get_associations_for_snp module tooluniverse.tools.gwas_get_associations_for_study module tooluniverse.tools.gwas_get_associations_for_trait module tooluniverse.tools.gwas_get_snp_by_id module tooluniverse.tools.gwas_get_snps_for_gene module tooluniverse.tools.gwas_get_studies_for_trait module tooluniverse.tools.gwas_get_study_by_id module tooluniverse.tools.gwas_get_variants_for_trait module tooluniverse.tools.gwas_search_associations module tooluniverse.tools.GWAS_search_associations_by_gene module tooluniverse.tools.gwas_search_snps module tooluniverse.tools.gwas_search_studies module tooluniverse.tools.HAL_search_archive module tooluniverse.tools.HPA_get_biological_processes_by_gene module tooluniverse.tools.HPA_get_cancer_prognostics_by_gene module tooluniverse.tools.HPA_get_comparative_expression_by_gene_and_cellline module tooluniverse.tools.HPA_get_comprehensive_gene_details_by_ensembl_id module tooluniverse.tools.HPA_get_contextual_biological_process_analysis module tooluniverse.tools.HPA_get_disease_expression_by_gene_tissue_disease module tooluniverse.tools.HPA_get_gene_basic_info_by_ensembl_id module tooluniverse.tools.HPA_get_gene_tsv_data_by_ensembl_id module tooluniverse.tools.HPA_get_protein_interactions_by_gene module tooluniverse.tools.HPA_get_rna_expression_by_source module tooluniverse.tools.HPA_get_rna_expression_in_specific_tissues module tooluniverse.tools.HPA_get_subcellular_location module tooluniverse.tools.HPA_search_genes_by_query module tooluniverse.tools.humanbase_ppi_analysis module tooluniverse.tools.HypothesisGenerator module tooluniverse.tools.LabelGenerator module tooluniverse.tools.LiteratureContextReviewer module tooluniverse.tools.LiteratureSearchTool module tooluniverse.tools.LiteratureSynthesisAgent module tooluniverse.tools.MedicalLiteratureReviewer module tooluniverse.tools.MedicalTermNormalizer module tooluniverse.tools.MedlinePlus_connect_lookup_by_code module tooluniverse.tools.MedlinePlus_get_genetics_condition_by_name module tooluniverse.tools.MedlinePlus_get_genetics_gene_by_name module tooluniverse.tools.MedlinePlus_get_genetics_index module tooluniverse.tools.MedlinePlus_search_topics_by_keyword module tooluniverse.tools.MedRxiv_search_preprints module tooluniverse.tools.mesh_get_subjects_by_pharmacological_action module tooluniverse.tools.mesh_get_subjects_by_subject_id module tooluniverse.tools.mesh_get_subjects_by_subject_name module tooluniverse.tools.mesh_get_subjects_by_subject_scope_or_definition module tooluniverse.tools.MethodologyRigorReviewer module tooluniverse.tools.NICE_Clinical_Guidelines_Search module tooluniverse.tools.NICE_Guideline_Full_Text module tooluniverse.tools.NoveltySignificanceReviewer module tooluniverse.tools.odphp_itemlist module tooluniverse.tools.odphp_myhealthfinder module tooluniverse.tools.odphp_outlink_fetch module tooluniverse.tools.odphp_topicsearch module tooluniverse.tools.OpenAIRE_search_publications module tooluniverse.tools.OpenAlex_Guidelines_Search module tooluniverse.tools.openalex_literature_search module tooluniverse.tools.OpenTargets_drug_pharmacogenomics_data module tooluniverse.tools.OpenTargets_get_approved_indications_by_drug_chemblId module tooluniverse.tools.OpenTargets_get_associated_diseases_by_drug_chemblId module tooluniverse.tools.OpenTargets_get_associated_drugs_by_disease_efoId module tooluniverse.tools.OpenTargets_get_associated_drugs_by_target_ensemblID module tooluniverse.tools.OpenTargets_get_associated_phenotypes_by_disease_efoId module tooluniverse.tools.OpenTargets_get_associated_targets_by_disease_efoId module tooluniverse.tools.OpenTargets_get_associated_targets_by_drug_chemblId module tooluniverse.tools.OpenTargets_get_biological_mouse_models_by_ensemblID module tooluniverse.tools.OpenTargets_get_chemical_probes_by_target_ensemblID module tooluniverse.tools.OpenTargets_get_disease_ancestors_parents_by_efoId module tooluniverse.tools.OpenTargets_get_disease_descendants_children_by_efoId module tooluniverse.tools.OpenTargets_get_disease_description_by_efoId module tooluniverse.tools.OpenTargets_get_disease_id_description_by_name module tooluniverse.tools.OpenTargets_get_disease_ids_by_efoId module tooluniverse.tools.OpenTargets_get_disease_ids_by_name module tooluniverse.tools.OpenTargets_get_disease_locations_by_efoId module tooluniverse.tools.OpenTargets_get_disease_synonyms_by_efoId module tooluniverse.tools.OpenTargets_get_disease_therapeutic_areas_by_efoId module tooluniverse.tools.OpenTargets_get_diseases_phenotypes_by_target_ensembl module tooluniverse.tools.OpenTargets_get_drug_adverse_events_by_chemblId module tooluniverse.tools.OpenTargets_get_drug_approval_status_by_chemblId module tooluniverse.tools.OpenTargets_get_drug_chembId_by_generic_name module tooluniverse.tools.OpenTargets_get_drug_description_by_chemblId module tooluniverse.tools.OpenTargets_get_drug_id_description_by_name module tooluniverse.tools.OpenTargets_get_drug_indications_by_chemblId module tooluniverse.tools.OpenTargets_get_drug_mechanisms_of_action_by_chemblId module tooluniverse.tools.OpenTargets_get_drug_synonyms_by_chemblId module tooluniverse.tools.OpenTargets_get_drug_trade_names_by_chemblId module tooluniverse.tools.OpenTargets_get_drug_warnings_by_chemblId module tooluniverse.tools.OpenTargets_get_drug_withdrawn_blackbox_status_by_chemblId module tooluniverse.tools.OpenTargets_get_gene_ontology_terms_by_goID module tooluniverse.tools.OpenTargets_get_known_drugs_by_drug_chemblId module tooluniverse.tools.OpenTargets_get_parent_child_molecules_by_drug_chembl_ID module tooluniverse.tools.OpenTargets_get_publications_by_disease_efoId module tooluniverse.tools.OpenTargets_get_publications_by_drug_chemblId module tooluniverse.tools.OpenTargets_get_publications_by_target_ensemblID module tooluniverse.tools.OpenTargets_get_similar_entities_by_disease_efoId module tooluniverse.tools.OpenTargets_get_similar_entities_by_drug_chemblId module tooluniverse.tools.OpenTargets_get_similar_entities_by_target_ensemblID module tooluniverse.tools.OpenTargets_get_target_classes_by_ensemblID module tooluniverse.tools.OpenTargets_get_target_constraint_info_by_ensemblID module tooluniverse.tools.OpenTargets_get_target_enabling_packages_by_ensemblID module tooluniverse.tools.OpenTargets_get_target_gene_ontology_by_ensemblID module tooluniverse.tools.OpenTargets_get_target_genomic_location_by_ensemblID module tooluniverse.tools.OpenTargets_get_target_homologues_by_ensemblID module tooluniverse.tools.OpenTargets_get_target_id_description_by_name module tooluniverse.tools.OpenTargets_get_target_interactions_by_ensemblID module tooluniverse.tools.OpenTargets_get_target_safety_profile_by_ensemblID module tooluniverse.tools.OpenTargets_get_target_subcellular_locations_by_ensemblID module tooluniverse.tools.OpenTargets_get_target_synonyms_by_ensemblID module tooluniverse.tools.OpenTargets_get_target_tractability_by_ensemblID module tooluniverse.tools.OpenTargets_map_any_disease_id_to_all_other_ids module tooluniverse.tools.OpenTargets_multi_entity_search_by_query_string module tooluniverse.tools.OpenTargets_search_category_counts_by_query_string module tooluniverse.tools.OpenTargets_target_disease_evidence module tooluniverse.tools.OSF_search_preprints module tooluniverse.tools.OSL_get_efo_id_by_disease_name module tooluniverse.tools.OutputSummarizationComposer module tooluniverse.tools.PMC_search_papers module tooluniverse.tools.ProtocolOptimizer module tooluniverse.tools.PubChem_get_associated_patents_by_CID module tooluniverse.tools.PubChem_get_CID_by_compound_name module tooluniverse.tools.PubChem_get_CID_by_SMILES module tooluniverse.tools.PubChem_get_compound_2D_image_by_CID module tooluniverse.tools.PubChem_get_compound_properties_by_CID module tooluniverse.tools.PubChem_get_compound_synonyms_by_CID module tooluniverse.tools.PubChem_get_compound_xrefs_by_CID module tooluniverse.tools.PubChem_search_compounds_by_similarity module tooluniverse.tools.PubChem_search_compounds_by_substructure module tooluniverse.tools.PubMed_Guidelines_Search module tooluniverse.tools.PubMed_search_articles module tooluniverse.tools.PubTator3_EntityAutocomplete module tooluniverse.tools.PubTator3_LiteratureSearch module tooluniverse.tools.QuestionRephraser module tooluniverse.tools.reactome_disease_target_score module tooluniverse.tools.Reactome_get_pathway_reactions module tooluniverse.tools.ReproducibilityTransparencyReviewer module tooluniverse.tools.ResultsInterpretationReviewer module tooluniverse.tools.ScientificTextSummarizer module tooluniverse.tools.search_clinical_trials module tooluniverse.tools.SemanticScholar_search_papers module tooluniverse.tools.TestCaseGenerator module tooluniverse.tools.Tool_Finder module tooluniverse.tools.Tool_Finder_Keyword module tooluniverse.tools.Tool_Finder_LLM module tooluniverse.tools.Tool_RAG module tooluniverse.tools.ToolCompatibilityAnalyzer module tooluniverse.tools.ToolDescriptionOptimizer module tooluniverse.tools.ToolDiscover module tooluniverse.tools.ToolGraphComposer module tooluniverse.tools.ToolGraphGenerationPipeline module tooluniverse.tools.ToolImplementationGenerator module tooluniverse.tools.ToolMetadataGenerationPipeline module tooluniverse.tools.ToolMetadataGenerator module tooluniverse.tools.ToolMetadataStandardizer module tooluniverse.tools.ToolOptimizer module tooluniverse.tools.ToolOutputSummarizer module tooluniverse.tools.ToolQualityEvaluator module tooluniverse.tools.ToolRelationshipDetector module tooluniverse.tools.ToolSpecificationGenerator module tooluniverse.tools.ToolSpecificationOptimizer module tooluniverse.tools.TRIP_Database_Guidelines_Search module tooluniverse.tools.UCSC_get_genes_by_region module tooluniverse.tools.UniProt_get_alternative_names_by_accession module tooluniverse.tools.UniProt_get_disease_variants_by_accession module tooluniverse.tools.UniProt_get_entry_by_accession module tooluniverse.tools.UniProt_get_function_by_accession module tooluniverse.tools.UniProt_get_isoform_ids_by_accession module tooluniverse.tools.UniProt_get_organism_by_accession module tooluniverse.tools.UniProt_get_ptm_processing_by_accession module tooluniverse.tools.UniProt_get_recommended_name_by_accession module tooluniverse.tools.UniProt_get_sequence_by_accession module tooluniverse.tools.UniProt_get_subcellular_location_by_accession module tooluniverse.tools.Unpaywall_check_oa_status module tooluniverse.tools.visualize_molecule_2d module tooluniverse.tools.visualize_molecule_3d module tooluniverse.tools.visualize_protein_structure_3d module tooluniverse.tools.WHO_Guideline_Full_Text module tooluniverse.tools.WHO_Guidelines_Search module tooluniverse.tools.Wikidata_SPARQL_query module tooluniverse.tools.WritingPresentationReviewer module tooluniverse.tools.Zenodo_search_records module tooluniverse.ucsc_tool module tooluniverse.unified_guideline_tools module tooluniverse.uniprot_tool module tooluniverse.unpaywall_tool module tooluniverse.url_tool module tooluniverse.uspto_tool module tooluniverse.utils module tooluniverse.visualization_tool module tooluniverse.wikidata_sparql_tool module tooluniverse.xml_tool module tooluniverse.zenodo_tool module ToolUniverseFormatter (class in tooluniverse.logging_config) ToolUniverseLogger (class in tooluniverse.logging_config) ToolValidationError TRIP_Database_Guidelines_Search() (in module tooluniverse.tools.TRIP_Database_Guidelines_Search) TRIPDatabaseTool (class in tooluniverse.unified_guideline_tools) ttl (tooluniverse.cache.sqlite_backend.CacheEntry attribute)

U

UCSC_get_genes_by_region() (in module tooluniverse.tools.UCSC_get_genes_by_region) UCSCTool (class in tooluniverse.ucsc_tool) UniProt_get_alternative_names_by_accession() (in module tooluniverse.tools.UniProt_get_alternative_names_by_accession) UniProt_get_disease_variants_by_accession() (in module tooluniverse.tools.UniProt_get_disease_variants_by_accession) UniProt_get_entry_by_accession() (in module tooluniverse.tools.UniProt_get_entry_by_accession) UniProt_get_function_by_accession() (in module tooluniverse.tools.UniProt_get_function_by_accession) UniProt_get_isoform_ids_by_accession() (in module tooluniverse.tools.UniProt_get_isoform_ids_by_accession) UniProt_get_organism_by_accession() (in module tooluniverse.tools.UniProt_get_organism_by_accession) UniProt_get_ptm_processing_by_accession() (in module tooluniverse.tools.UniProt_get_ptm_processing_by_accession) UniProt_get_recommended_name_by_accession() (in module tooluniverse.tools.UniProt_get_recommended_name_by_accession) UniProt_get_sequence_by_accession() (in module tooluniverse.tools.UniProt_get_sequence_by_accession) UniProt_get_subcellular_location_by_accession() (in module tooluniverse.tools.UniProt_get_subcellular_location_by_accession)

UniProtRESTTool (class in tooluniverse) (class in tooluniverse.uniprot_tool) Unpaywall_check_oa_status() (in module tooluniverse.tools.Unpaywall_check_oa_status) UnpaywallTool (class in tooluniverse) (class in tooluniverse.unpaywall_tool) update_session_context() (tooluniverse.memory_manager.MemoryManager method) URLHTMLTagTool (class in tooluniverse) (class in tooluniverse.url_tool) URLToPDFTextTool (class in tooluniverse) (class in tooluniverse.url_tool) USPTOOpenDataPortalTool (class in tooluniverse) (class in tooluniverse.uspto_tool)

V

validate() (tooluniverse.output_hook.SummarizationHookConfig method) validate_configuration() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) validate_enum_arguments() (tooluniverse.FDADrugAdverseEventTool method) (tooluniverse.openfda_adv_tool.FDADrugAdverseEventTool method) validate_hook_conditions() (in module tooluniverse.utils) validate_hook_config() (in module tooluniverse.utils) validate_parameters() (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseTool method) validate_params() (tooluniverse.rcsb_pdb_tool.RCSBTool method) (tooluniverse.RCSBTool method) validate_query() (in module tooluniverse.graphql_tool) (in module tooluniverse.utils) validate_space_config() (in module tooluniverse.space) (in module tooluniverse.space.validator) validate_with_schema() (in module tooluniverse.space) (in module tooluniverse.space.validator) validate_yaml_file() (in module tooluniverse.space) (in module tooluniverse.space.validator)

validate_yaml_file_with_schema() (in module tooluniverse.space) (in module tooluniverse.space.validator) validate_yaml_format_by_template() (in module tooluniverse.space) (in module tooluniverse.space.validator) ValidationError, [1] ValidationHook (class in tooluniverse.extended_hooks) value (tooluniverse.cache.result_cache_manager.CacheRecord attribute) (tooluniverse.cache.sqlite_backend.CacheEntry attribute) verbose() (in module tooluniverse.logging_config) version (tooluniverse.cache.result_cache_manager.CacheRecord attribute) (tooluniverse.cache.sqlite_backend.CacheEntry attribute) (tooluniverse.execute_function._BatchCacheInfo attribute) VisualizationTool (class in tooluniverse.visualization_tool) visualize_molecule_2d() (in module tooluniverse.tools.visualize_molecule_2d) visualize_molecule_3d() (in module tooluniverse.tools.visualize_molecule_3d) visualize_protein_structure_3d() (in module tooluniverse.tools.visualize_protein_structure_3d) VLLMClient (class in tooluniverse.llm_clients)

W

warning() (in module tooluniverse.logging_config) WHO_Guideline_Full_Text() (in module tooluniverse.tools.WHO_Guideline_Full_Text) WHO_Guidelines_Search() (in module tooluniverse.tools.WHO_Guidelines_Search) WHOGuidelineFullTextTool (class in tooluniverse.unified_guideline_tools)

WHOGuidelinesTool (class in tooluniverse.unified_guideline_tools) Wikidata_SPARQL_query() (in module tooluniverse.tools.Wikidata_SPARQL_query) WikidataSPARQLTool (class in tooluniverse.wikidata_sparql_tool) WritingPresentationReviewer() (in module tooluniverse.tools.WritingPresentationReviewer)

X

XMLDatasetTool (class in tooluniverse) (class in tooluniverse.xml_tool)

Y

yaml_to_dict() (in module tooluniverse.utils)

Z

Zenodo_search_records() (in module tooluniverse.tools.Zenodo_search_records)

ZenodoTool (class in tooluniverse) (class in tooluniverse.zenodo_tool)