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.ClinVarGetClinicalSignificance method) (tooluniverse.clinvar_tool.ClinVarGetVariantDetails method) (tooluniverse.clinvar_tool.ClinVarRESTTool method) (tooluniverse.clinvar_tool.ClinVarSearchVariants method) (tooluniverse.ClinVarGetClinicalSignificance method) (tooluniverse.ClinVarGetVariantDetails method) (tooluniverse.ClinVarSearchVariants 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.database_setup.Embedder method) (tooluniverse.database_setup.embedder.Embedder method) (tooluniverse.database_setup.embedding_database.EmbeddingDatabase method) (tooluniverse.database_setup.embedding_sync.EmbeddingSync method) (tooluniverse.database_setup.search.SearchEngine method) (tooluniverse.database_setup.SearchEngine method) (tooluniverse.database_setup.sqlite_store.SQLiteStore method) (tooluniverse.database_setup.SQLiteStore method) (tooluniverse.database_setup.vector_store.VectorStore method) (tooluniverse.database_setup.VectorStore method) (tooluniverse.dataset_tool.DatasetTool method) (tooluniverse.DatasetTool method) (tooluniverse.dblp_tool.DBLPTool method) (tooluniverse.DBLPTool method) (tooluniverse.dbsnp_tool.dbSNPGetFrequencies method) (tooluniverse.dbsnp_tool.dbSNPGetVariantByRsID method) (tooluniverse.dbsnp_tool.dbSNPSearchByGene method) (tooluniverse.DiseaseTargetScoreTool method) (tooluniverse.doaj_tool.DOAJTool method) (tooluniverse.DOAJTool method) (tooluniverse.DynamicPackageDiscovery method) (tooluniverse.efo_tool.EFOTool method) (tooluniverse.EFOTool method) (tooluniverse.EmbeddingDatabase method) (tooluniverse.EmbeddingSync method) (tooluniverse.enrichr_tool.EnrichrTool method) (tooluniverse.ensembl_tool.EnsemblGetSequence method) (tooluniverse.ensembl_tool.EnsemblGetVariants method) (tooluniverse.ensembl_tool.EnsemblLookupGene method) (tooluniverse.ensembl_tool.EnsemblRESTTool 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.GEOGetDatasetInfo method) (tooluniverse.geo_tool.GEOGetSampleInfo method) (tooluniverse.geo_tool.GEORESTTool method) (tooluniverse.geo_tool.GEOSearchDatasets method) (tooluniverse.GetSPLBySetIDTool method) (tooluniverse.gnomad_tool.gnomADGetGeneConstraints method) (tooluniverse.gnomad_tool.gnomADGraphQLTool 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.OLSTool method) (tooluniverse.openaire_tool.OpenAIRETool method) (tooluniverse.openalex_tool.OpenAlexTool method) (tooluniverse.openfda_adv_tool.FDACountAdditiveReactionsTool method) (tooluniverse.openfda_adv_tool.FDADrugAdverseEventDetailTool method) (tooluniverse.openfda_adv_tool.FDADrugAdverseEventTool method) (tooluniverse.openfda_adv_tool.FDADrugInteractionDetailTool method) (tooluniverse.openfda_tool.FDADrugLabelGetDrugGenericNameTool method) (tooluniverse.openfda_tool.FDADrugLabelGetDrugNamesByIndicationAggregated method) (tooluniverse.openfda_tool.FDADrugLabelGetDrugNamesByIndicationStats 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.PyPIPackageInspector method) (tooluniverse.rcsb_pdb_tool.RCSBTool method) (tooluniverse.RCSBSearchTool 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.RxNormTool 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.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.WebSearchTool 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) _auto_load_tools_if_empty() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method)

_BatchCacheInfo (class in tooluniverse.execute_function) _BatchJob (class in tooluniverse.execute_function) _build_batch_jobs() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _build_sequence_query() (tooluniverse.RCSBSearchTool method) _build_structure_query() (tooluniverse.RCSBSearchTool method) _build_term_model() (tooluniverse.OLSTool static method) _build_text_query() (tooluniverse.RCSBSearchTool 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_quality_scores() (tooluniverse.PyPIPackageInspector 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) _coerce_arguments_to_schema() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _coerce_value_to_type() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _compose_url() (tooluniverse.pubtator_tool.PubTatorTool method) (tooluniverse.PubTatorTool method) _construct_solr_query() (tooluniverse.CellosaurusQueryConverterTool method) _convert_id_to_drug_name() (tooluniverse.FDADrugLabelTool method) (tooluniverse.openfda_tool.FDADrugLabelTool 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) _discover_tool_dependencies() (tooluniverse.ComposeTool method) _download() (tooluniverse.EmbeddingSync method) _drugbank_filter() (tooluniverse.dataset_tool.DatasetTool method) (tooluniverse.DatasetTool method) _drugbank_search() (tooluniverse.dataset_tool.DatasetTool method) (tooluniverse.DatasetTool method) _embedder() (tooluniverse.EmbeddingDatabase 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) _evaluate_package() (tooluniverse.DynamicPackageDiscovery 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_opentargets_query() (in module tooluniverse.openfda_tool) _execute_tool_with_stream() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _existing_vector_doc_ids() (tooluniverse.EmbeddingDatabase method) _expose_core_discovery_tools() (tooluniverse.SMCP method) _expose_tooluniverse_tools() (tooluniverse.SMCP method) _extract_authors() (tooluniverse.CoreTool method) (tooluniverse.PMCTool method) _extract_custom_fields() (tooluniverse.openfda_adv_tool.FDADrugAdverseEventDetailTool method) (tooluniverse.openfda_adv_tool.FDADrugInteractionDetailTool method) _extract_data() (tooluniverse.UniProtRESTTool method) _extract_essential_fields() (tooluniverse.openfda_adv_tool.FDADrugAdverseEventDetailTool method) (tooluniverse.openfda_adv_tool.FDADrugInteractionDetailTool 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_term_collection() (tooluniverse.OLSTool method) _format_tools_for_prompt() (tooluniverse.ToolFinderLLM method) _gemini_model_id (tooluniverse.agentic_tool.AgenticTool attribute) _generate_recommendation() (tooluniverse.PyPIPackageInspector method) _get_all_names_by_rxcui() (tooluniverse.RxNormTool 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_collection_meta() (tooluniverse.EmbeddingDatabase method) _get_current_timestamp() (tooluniverse.humanbase_tool.HumanBaseTool method) _get_dataset_path() (tooluniverse.XMLDatasetTool method) _get_download_stats() (tooluniverse.PyPIPackageInspector method) _get_drug_names_query() (in module tooluniverse.openfda_tool) _get_filter_description() (tooluniverse.XMLDatasetTool method) _get_filter_function() (tooluniverse.XMLDatasetTool method) _get_github_stats() (tooluniverse.PyPIPackageInspector method) _get_global_fallback_chain() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) _get_installation_instructions() (tooluniverse.PackageTool method) _get_json() (tooluniverse.OLSTool method) _get_local_info() (tooluniverse.PackageTool method) _get_mcp_endpoint() (tooluniverse.mcp_client_tool.BaseMCPClient method) _get_nested_value() (tooluniverse.openfda_adv_tool.FDADrugAdverseEventDetailTool method) (tooluniverse.openfda_adv_tool.FDADrugInteractionDetailTool method) _get_pypi_info() (tooluniverse.PackageTool method) _get_pypi_metadata() (tooluniverse.PyPIPackageInspector method) _get_quick_start_guide() (tooluniverse.PackageTool method) _get_rxcui_by_name() (tooluniverse.RxNormTool 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_find_similar_terms() (tooluniverse.OLSTool method) _handle_get_ontology_info() (tooluniverse.OLSTool method) _handle_get_term_ancestors() (tooluniverse.OLSTool method) _handle_get_term_children() (tooluniverse.OLSTool method) _handle_get_term_info() (tooluniverse.OLSTool method) _handle_id_mapping() (tooluniverse.UniProtRESTTool method) _handle_search() (tooluniverse.UniProtRESTTool method) _handle_search_ontologies() (tooluniverse.OLSTool method) _handle_search_terms() (tooluniverse.OLSTool method) _handle_tools_find() (tooluniverse.SMCP method) _init_agentic_tool() (tooluniverse.ToolFinderLLM method) _init_tool_finder() (tooluniverse.SMCP method) _input_arguments (tooluniverse.agentic_tool.AgenticTool attribute) _is_chembl_id() (tooluniverse.FDADrugLabelTool method) (tooluniverse.openfda_tool.FDADrugLabelTool method) _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_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) _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.FDADrugAdverseEventDetailTool method) (tooluniverse.openfda_adv_tool.FDADrugAdverseEventTool method) (tooluniverse.openfda_adv_tool.FDADrugInteractionDetailTool method) _max_retries (tooluniverse.agentic_tool.AgenticTool attribute) _model_id (tooluniverse.agentic_tool.AgenticTool attribute) _OPERATIONS (tooluniverse.OLSTool attribute) _parse_search_results() (tooluniverse.RCSBSearchTool method) _paths() (tooluniverse.EmbeddingDatabase method) _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) _preprocess_drug_name() (tooluniverse.RxNormTool 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) _rank_packages() (tooluniverse.DynamicPackageDiscovery 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) _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.FDADrugAdverseEventDetailTool method) (tooluniverse.openfda_adv_tool.FDADrugAdverseEventTool method) (tooluniverse.openfda_adv_tool.FDADrugInteractionDetailTool 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_pypi_via_web() (tooluniverse.DynamicPackageDiscovery method) _search_similar_molecules() (tooluniverse.chem_tool.ChEMBLTool method) (tooluniverse.ChEMBLTool method) _search_with_ddgs() (tooluniverse.WebSearchTool method) _select_search_tool() (tooluniverse.SMCP method) _set_nested_value() (tooluniverse.openfda_adv_tool.FDADrugAdverseEventDetailTool method) (tooluniverse.openfda_adv_tool.FDADrugInteractionDetailTool 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) _stores() (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() (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_pdb_id() (tooluniverse.RCSBSearchTool method) _validate_sequence() (tooluniverse.RCSBSearchTool 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) add_embeddings() (tooluniverse.database_setup.vector_store.VectorStore method) (tooluniverse.database_setup.VectorStore 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_collection() (in module tooluniverse.database_setup) (in module tooluniverse.database_setup.pipeline) 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) ClinVarGetClinicalSignificance (class in tooluniverse) (class in tooluniverse.clinvar_tool) ClinVarGetVariantDetails (class in tooluniverse) (class in tooluniverse.clinvar_tool) ClinVarRESTTool (class in tooluniverse.clinvar_tool) ClinVarSearchVariants (class in tooluniverse) (class in tooluniverse.clinvar_tool)

close() (tooluniverse.cache.result_cache_manager.ResultCacheManager method) (tooluniverse.cache.sqlite_backend.PersistentCache method) (tooluniverse.database_setup.sqlite_store.SQLiteStore method) (tooluniverse.database_setup.SQLiteStore 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) 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) 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) dbSNPGetFrequencies (class in tooluniverse.dbsnp_tool) dbSNPGetVariantByRsID (class in tooluniverse.dbsnp_tool) dbSNPRESTTool (class in tooluniverse.dbsnp_tool) dbSNPSearchByGene (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) 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) 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() (in module tooluniverse.database_setup) download_from_hf() (in module tooluniverse.utils) 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) DynamicPackageDiscovery (class in tooluniverse)

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) embed() (tooluniverse.database_setup.Embedder method) (tooluniverse.database_setup.embedder.Embedder method) embed_texts() (in module tooluniverse.database_setup.embed_utils) Embedder (class in tooluniverse.database_setup) (class in tooluniverse.database_setup.embedder) embedding_search() (tooluniverse.database_setup.search.SearchEngine method) (tooluniverse.database_setup.SearchEngine method) EmbeddingCollectionSearchTool (class in tooluniverse.database_setup.generic_embedding_search_tool) EmbeddingDatabase (class in tooluniverse) (class in tooluniverse.database_setup.embedding_database) EmbeddingSync (class in tooluniverse) (class in tooluniverse.database_setup.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) EnrichrTool (class in tooluniverse.enrichr_tool) EnsemblGetSequence (class in tooluniverse.ensembl_tool) EnsemblGetVariants (class in tooluniverse.ensembl_tool) EnsemblLookupGene (class in tooluniverse.ensembl_tool)

EnsemblRESTTool (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) EuHealthDeepDiveTool (class in tooluniverse) EuHealthTopicSearchTool (class in tooluniverse) 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) 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) 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) FDADrugAdverseEventDetailTool (class in tooluniverse.openfda_adv_tool) FDADrugAdverseEventTool (class in tooluniverse) (class in tooluniverse.openfda_adv_tool) FDADrugInteractionDetailTool (class in tooluniverse.openfda_adv_tool) FDADrugLabelGetDrugGenericNameTool (class in tooluniverse) (class in tooluniverse.openfda_tool) FDADrugLabelGetDrugNamesByIndicationAggregated (class in tooluniverse.openfda_tool) FDADrugLabelGetDrugNamesByIndicationStats (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) fetch_docs() (tooluniverse.database_setup.search.SearchEngine method) (tooluniverse.database_setup.SearchEngine method) (tooluniverse.database_setup.sqlite_store.SQLiteStore method) (tooluniverse.database_setup.SQLiteStore method) fetch_docs_by_ids() (tooluniverse.database_setup.sqlite_store.SQLiteStore method) (tooluniverse.database_setup.SQLiteStore method) fetch_random_docs() (tooluniverse.database_setup.search.SearchEngine method) (tooluniverse.database_setup.SearchEngine method) (tooluniverse.database_setup.sqlite_store.SQLiteStore method) (tooluniverse.database_setup.SQLiteStore method) 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) GEOGetDatasetInfo (class in tooluniverse.geo_tool) GEOGetSampleInfo (class in tooluniverse.geo_tool) GEORESTTool (class in tooluniverse.geo_tool) GEOSearchDatasets (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_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_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_changed_tools() (in module tooluniverse.build_optimizer) 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_config_registry() (in module tooluniverse.tool_registry) get_context_for_agent() (tooluniverse.memory_manager.MemoryManager method) get_dataset_info() (tooluniverse.dataset_tool.DatasetTool method) (tooluniverse.DatasetTool method) (tooluniverse.xml_tool.XMLDatasetTool method) (tooluniverse.XMLDatasetTool method) get_default_config_file() (tooluniverse.base_tool.BaseTool class method) (tooluniverse.BaseTool class method) get_default_hook_config() (in module tooluniverse.default_config) get_disease_variants_by_accession() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) 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_function_by_accession() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) 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_hook() (tooluniverse.output_hook.HookManager method) get_hook_logger() (in module tooluniverse.logging_config) get_input_arguments() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) get_lazy_loading_status() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) get_llm_config() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) get_logger() (in module tooluniverse.logging_config) (tooluniverse.logging_config.ToolUniverseLogger method) 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_model_dim() (in module tooluniverse.database_setup.embed_utils) get_model_info() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) get_names_taxonomy_by_accession() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) get_official_gene_name() (tooluniverse.enrichr_tool.EnrichrTool method) (tooluniverse.humanbase_tool.HumanBaseTool method) get_one_tool_by_one_name() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) 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_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_ptm_processing_by_accession() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) get_registered_tools() (in module tooluniverse.mcp_tool_registry) get_remote_info() (tooluniverse.remote_tool.RemoteTool method) get_required_parameters() (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseTool method) (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) get_sequence_isoforms_by_accession() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) get_server_info() (tooluniverse.remote_tool.RemoteTool method) get_session() (tooluniverse.memory_manager.MemoryManager method) get_session_summary() (tooluniverse.memory_manager.MemoryManager method) get_smiles_pref_name_by_chembl_id() (tooluniverse.chem_tool.ChEMBLTool method) (tooluniverse.ChEMBLTool method) get_space_llm_config() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) get_space_metadata() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) get_subcellular_location_by_accession() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) get_term_details() (tooluniverse.gene_ontology_tool.GeneOntologyTool method) get_terms_for_gene() (tooluniverse.gene_ontology_tool.GeneOntologyTool method) 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_user_cache_dir() (in module tooluniverse.utils) 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) gnomADGetGeneConstraints (class in tooluniverse.gnomad_tool) gnomADGraphQLTool (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_search_associations_by_gene() (in module tooluniverse.tools.GWAS_search_associations_by_gene) 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_retrieve() (tooluniverse.humanbase_tool.HumanBaseTool method) HumanBaseTool (class in tooluniverse.humanbase_tool) hybrid_search() (tooluniverse.database_setup.search.SearchEngine method) (tooluniverse.database_setup.SearchEngine method) 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) insert_docs() (tooluniverse.database_setup.sqlite_store.SQLiteStore method) (tooluniverse.database_setup.SQLiteStore 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_comprehensive_optimization() (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)

keyword_search() (tooluniverse.database_setup.search.SearchEngine method) (tooluniverse.database_setup.SearchEngine method)

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_collections() (tooluniverse.database_setup.search.SearchEngine method) (tooluniverse.database_setup.SearchEngine 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_index() (tooluniverse.database_setup.vector_store.VectorStore method) (tooluniverse.database_setup.VectorStore 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.database_setup.cli) (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) 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.database_setup tooluniverse.database_setup.cli tooluniverse.database_setup.embed_utils tooluniverse.database_setup.embedder tooluniverse.database_setup.embedding_database tooluniverse.database_setup.embedding_sync tooluniverse.database_setup.generic_embedding_search_tool tooluniverse.database_setup.packager tooluniverse.database_setup.pipeline tooluniverse.database_setup.provider_resolver tooluniverse.database_setup.search tooluniverse.database_setup.sqlite_store tooluniverse.database_setup.vector_store tooluniverse.dataset_tool tooluniverse.dblp_tool tooluniverse.dbsnp_tool tooluniverse.default_config tooluniverse.doaj_tool tooluniverse.doctor tooluniverse.efo_tool 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 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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) multi_collection_search() (tooluniverse.database_setup.search.SearchEngine method) (tooluniverse.database_setup.SearchEngine method)

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) normalize_text() (in module tooluniverse.database_setup.sqlite_store) NoveltySignificanceReviewer() (in module tooluniverse.tools.NoveltySignificanceReviewer)

O

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) OLSTool (class in tooluniverse) 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) 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) optimize_code() (in module tooluniverse.compose_scripts.tool_discover) 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

pack_folder() (in module tooluniverse.database_setup.packager) 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) PyPIPackageInspector (class in tooluniverse)

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) RCSBSearchTool (class in tooluniverse) RCSBTool (class in tooluniverse) (class in tooluniverse.rcsb_pdb_tool) 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) resolve_db_path() (in module tooluniverse.database_setup.cli) resolve_model() (in module tooluniverse.database_setup.provider_resolver) resolve_provider() (in module tooluniverse.database_setup.provider_resolver) resolve_provider_model() (in module tooluniverse.database_setup.cli) 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.ClinVarGetClinicalSignificance method) (tooluniverse.clinvar_tool.ClinVarGetVariantDetails method) (tooluniverse.clinvar_tool.ClinVarRESTTool method) (tooluniverse.clinvar_tool.ClinVarSearchVariants method) (tooluniverse.ClinVarGetClinicalSignificance method) (tooluniverse.ClinVarGetVariantDetails method) (tooluniverse.ClinVarSearchVariants 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.database_setup.embedding_database.EmbeddingDatabase method) (tooluniverse.database_setup.embedding_sync.EmbeddingSync method) (tooluniverse.database_setup.generic_embedding_search_tool.EmbeddingCollectionSearchTool method) (tooluniverse.dataset_tool.DatasetTool method) (tooluniverse.DatasetTool method) (tooluniverse.dblp_tool.DBLPTool method) (tooluniverse.DBLPTool method) (tooluniverse.dbsnp_tool.dbSNPGetFrequencies method) (tooluniverse.dbsnp_tool.dbSNPGetVariantByRsID method) (tooluniverse.dbsnp_tool.dbSNPSearchByGene method) (tooluniverse.DiseaseTargetScoreTool method) (tooluniverse.doaj_tool.DOAJTool method) (tooluniverse.DOAJTool method) (tooluniverse.DynamicPackageDiscovery method) (tooluniverse.efo_tool.EFOTool method) (tooluniverse.EFOTool method) (tooluniverse.EmbeddingDatabase method) (tooluniverse.EmbeddingSync method) (tooluniverse.enrichr_tool.EnrichrTool method) (tooluniverse.ensembl_tool.EnsemblGetSequence method) (tooluniverse.ensembl_tool.EnsemblGetVariants method) (tooluniverse.ensembl_tool.EnsemblLookupGene method) (tooluniverse.ensembl_tool.EnsemblRESTTool method) (tooluniverse.EuHealthDeepDiveTool method) (tooluniverse.EuHealthTopicSearchTool 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.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.gnomADGetGeneConstraints method) (tooluniverse.gnomad_tool.gnomADGraphQLTool 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.OLSTool method) (tooluniverse.openaire_tool.OpenAIRETool method) (tooluniverse.openalex_tool.OpenAlexTool method) (tooluniverse.openfda_adv_tool.FDACountAdditiveReactionsTool method) (tooluniverse.openfda_adv_tool.FDADrugAdverseEventDetailTool method) (tooluniverse.openfda_adv_tool.FDADrugAdverseEventTool method) (tooluniverse.openfda_adv_tool.FDADrugInteractionDetailTool method) (tooluniverse.openfda_tool.FDADrugLabelGetDrugGenericNameTool method) (tooluniverse.openfda_tool.FDADrugLabelGetDrugNamesByIndicationAggregated method) (tooluniverse.openfda_tool.FDADrugLabelGetDrugNamesByIndicationStats method) (tooluniverse.openfda_tool.FDADrugLabelSearchIDTool method) (tooluniverse.openfda_tool.FDADrugLabelSearchTool method) (tooluniverse.openfda_tool.FDADrugLabelTool 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.PyPIPackageInspector method) (tooluniverse.rcsb_pdb_tool.RCSBTool method) (tooluniverse.RCSBSearchTool 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.RxNormTool 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.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.WebAPIDocumentationSearchTool method) (tooluniverse.WebSearchTool 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) RxNormTool (class in tooluniverse)

S

safe_for_fts() (in module tooluniverse.database_setup.sqlite_store) save_index() (tooluniverse.database_setup.vector_store.VectorStore method) (tooluniverse.database_setup.VectorStore method) save_metadata() (in module tooluniverse.build_optimizer) ScientificTextSummarizer() (in module tooluniverse.tools.ScientificTextSummarizer) search() (in module tooluniverse.database_setup.pipeline) search_collection() (tooluniverse.database_setup.search.SearchEngine method) (tooluniverse.database_setup.SearchEngine method) search_embeddings() (tooluniverse.database_setup.vector_store.VectorStore method) (tooluniverse.database_setup.VectorStore method) search_keyword() (tooluniverse.database_setup.sqlite_store.SQLiteStore method) (tooluniverse.database_setup.SQLiteStore method) 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) SearchEngine (class in tooluniverse.database_setup) (class in tooluniverse.database_setup.search) 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) SQLiteStore (class in tooluniverse.database_setup) (class in tooluniverse.database_setup.sqlite_store) 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) ToolMetadataGenerationPipeline() (in module tooluniverse.tools.ToolMetadataGenerationPipeline) ToolMetadataGenerator() (in module tooluniverse.tools.ToolMetadataGenerator) ToolMetadataStandardizer() (in module tooluniverse.tools.ToolMetadataStandardizer) ToolNamespace (class in tooluniverse.execute_function) ToolOutputSummarizer() (in module tooluniverse.tools.ToolOutputSummarizer) ToolQualityEvaluator() (in module tooluniverse.tools.ToolQualityEvaluator) ToolRateLimitError ToolRelationshipDetector() (in module tooluniverse.tools.ToolRelationshipDetector) ToolServerError 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.database_setup module tooluniverse.database_setup.cli module tooluniverse.database_setup.embed_utils module tooluniverse.database_setup.embedder module tooluniverse.database_setup.embedding_database module tooluniverse.database_setup.embedding_sync module tooluniverse.database_setup.generic_embedding_search_tool module tooluniverse.database_setup.packager module tooluniverse.database_setup.pipeline module tooluniverse.database_setup.provider_resolver module tooluniverse.database_setup.search module tooluniverse.database_setup.sqlite_store module tooluniverse.database_setup.vector_store 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.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.CMA_Guidelines_Search module tooluniverse.tools.CodeQualityAnalyzer module tooluniverse.tools.CompoundDiscoveryAgent module tooluniverse.tools.ComprehensiveDrugDiscoveryPipeline 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.DescriptionAnalyzer module tooluniverse.tools.DescriptionQualityEvaluator module tooluniverse.tools.DiseaseAnalyzerAgent module tooluniverse.tools.DOAJ_search_articles module tooluniverse.tools.DomainExpertValidator module tooluniverse.tools.DrugInteractionAnalyzerAgent module tooluniverse.tools.DrugOptimizationAgent module tooluniverse.tools.DrugSafetyAnalyzer module tooluniverse.tools.EthicalComplianceReviewer module tooluniverse.tools.EuropePMC_Guidelines_Search module tooluniverse.tools.EuropePMC_search_articles module tooluniverse.tools.ExperimentalDesignScorer 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.GIN_Guidelines_Search 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_search_associations_by_gene 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.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.MethodologyRigorReviewer module tooluniverse.tools.NICE_Clinical_Guidelines_Search module tooluniverse.tools.NICE_Guideline_Full_Text module tooluniverse.tools.NoveltySignificanceReviewer module tooluniverse.tools.OpenAIRE_search_publications module tooluniverse.tools.OpenAlex_Guidelines_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_get_pathway_reactions module tooluniverse.tools.ReproducibilityTransparencyReviewer module tooluniverse.tools.ResultsInterpretationReviewer module tooluniverse.tools.ScientificTextSummarizer 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.ToolMetadataGenerationPipeline module tooluniverse.tools.ToolMetadataGenerator module tooluniverse.tools.ToolMetadataStandardizer module tooluniverse.tools.ToolOutputSummarizer module tooluniverse.tools.ToolQualityEvaluator module tooluniverse.tools.ToolRelationshipDetector module tooluniverse.tools.TRIP_Database_Guidelines_Search 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.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.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

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) upload() (in module tooluniverse.database_setup) upsert_collection() (tooluniverse.database_setup.sqlite_store.SQLiteStore method) (tooluniverse.database_setup.SQLiteStore 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.FDADrugAdverseEventDetailTool method) (tooluniverse.openfda_adv_tool.FDADrugAdverseEventTool method) (tooluniverse.openfda_adv_tool.FDADrugInteractionDetailTool method) validate_generated_code() (in module tooluniverse.generate_tools) validate_hook_conditions() (in module tooluniverse.utils) validate_hook_config() (in module tooluniverse.utils) validate_parameters() (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseTool method) (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool 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) VectorStore (class in tooluniverse.database_setup) (class in tooluniverse.database_setup.vector_store) 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) VLLMClient (class in tooluniverse.llm_clients)

W

warning() (in module tooluniverse.logging_config) WebAPIDocumentationSearchTool (class in tooluniverse) WebSearchTool (class in tooluniverse) 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)