Index

_

__call__() (tooluniverse.execute_function.ToolCallable method) __contains__() (tooluniverse.execute_function.ToolNamespace method) __del__() (tooluniverse.cache.result_cache_manager.ResultCacheManager method) (tooluniverse.mcp_client_tool.MCPAutoLoaderTool method) (tooluniverse.MCPAutoLoaderTool method) __dir__() (in module tooluniverse) __enter__() (tooluniverse.ToolUniverseClient method) __exit__() (tooluniverse.ToolUniverseClient method) __getattr__() (in module tooluniverse) (tooluniverse.execute_function.ToolNamespace method) (tooluniverse.ToolUniverseClient method) __init__() (tooluniverse.ADAStandardsTool method) (tooluniverse.AddgeneTool method) (tooluniverse.admetai_tool.ADMETAITool method) (tooluniverse.ADMETAITool method) (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) (tooluniverse.AHAACCGuidelineTool method) (tooluniverse.AllenBrainTool method) (tooluniverse.AllianceGenomeTool method) (tooluniverse.alphafold_tool.AlphaFoldRESTTool method) (tooluniverse.AlphaFoldRESTTool method) (tooluniverse.AlphaMissenseTool method) (tooluniverse.AOPWikiDetailTool method) (tooluniverse.AOPWikiListTool method) (tooluniverse.ARCHS4Tool method) (tooluniverse.ArrayExpressRESTTool method) (tooluniverse.arxiv_tool.ArXivPDFSnippetsTool method) (tooluniverse.arxiv_tool.ArXivTool method) (tooluniverse.ArXivPDFSnippetsTool method) (tooluniverse.ArXivTool method) (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseMCPClient method) (tooluniverse.BasePythonExecutor method) (tooluniverse.BaseRESTTool method) (tooluniverse.BaseTool method) (tooluniverse.BgeeTool method) (tooluniverse.BiGGModelsTool method) (tooluniverse.BinaryDownloadTool method) (tooluniverse.BindingDBTool method) (tooluniverse.biogrid_tool.BioGRIDRESTTool method) (tooluniverse.BioGRIDRESTTool method) (tooluniverse.BioImageArchiveTool method) (tooluniverse.BioPortalTool method) (tooluniverse.BioregistryTool method) (tooluniverse.biorxiv_tool.BioRxivTool method) (tooluniverse.BioRxivTool method) (tooluniverse.BioSamplesTool method) (tooluniverse.BioStudiesRESTTool method) (tooluniverse.blast_tool.NCBIBlastTool method) (tooluniverse.Boltz2DockingTool method) (tooluniverse.boltz_tool.Boltz2DockingTool method) (tooluniverse.BRENDATool method) (tooluniverse.BridgeDbTool method) (tooluniverse.BVBRCTool 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.CADDTool method) (tooluniverse.CancerPrognosisTool method) (tooluniverse.CancerVarTool method) (tooluniverse.CATHTool method) (tooluniverse.cbioportal_tool.CBioPortalRESTTool method) (tooluniverse.CBioPortalRESTTool method) (tooluniverse.cdc_tool.CDCRESTTool method) (tooluniverse.CDCRESTTool method) (tooluniverse.CellMarkerTool 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.CellPaintingTool method) (tooluniverse.CellxGeneDiscoveryTool method) (tooluniverse.ChEBITool method) (tooluniverse.chem_tool.ChEMBLRESTTool method) (tooluniverse.chem_tool.ChEMBLTool method) (tooluniverse.ChEMBLRESTTool method) (tooluniverse.ChEMBLTool method) (tooluniverse.ChemComputeTool method) (tooluniverse.CIViCTool method) (tooluniverse.ClinGenAlleleTool method) (tooluniverse.ClinGenARTool method) (tooluniverse.ClinGenDosageTool method) (tooluniverse.ClinGenTool method) (tooluniverse.ClinicalTrialsDetailsTool method) (tooluniverse.ClinicalTrialsSearchTool method) (tooluniverse.ClinicalTrialsTool 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.ClinVarRESTTool method) (tooluniverse.ClinVarSearchVariants method) (tooluniverse.ClueTool method) (tooluniverse.CMAGuidelinesTool method) (tooluniverse.ComplexPortalTool method) (tooluniverse.compose_tool.ComposeTool method) (tooluniverse.ComposeTool method) (tooluniverse.core_tool.CorePDFSnippetsTool method) (tooluniverse.core_tool.CoreTool method) (tooluniverse.CorePDFSnippetsTool method) (tooluniverse.CoreTool method) (tooluniverse.COSMICTool method) (tooluniverse.CrystalStructureTool method) (tooluniverse.CTDTool method) (tooluniverse.ctg_tool.ClinicalTrialsDetailsTool method) (tooluniverse.ctg_tool.ClinicalTrialsSearchTool method) (tooluniverse.ctg_tool.ClinicalTrialsTool method) (tooluniverse.CTGovAPITool method) (tooluniverse.custom_tool.CustomTool method) (tooluniverse.CustomTool method) (tooluniverse.dailymed_tool.DailyMedSPLParserTool method) (tooluniverse.dailymed_tool.GetSPLBySetIDTool method) (tooluniverse.dailymed_tool.SearchSPLTool method) (tooluniverse.DailyMedSPLParserTool 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.DataQualityTool method) (tooluniverse.dataset_tool.DatasetTool method) (tooluniverse.DatasetTool method) (tooluniverse.DbfetchRESTTool method) (tooluniverse.dblp_tool.DBLPTool method) (tooluniverse.DBLPTool method) (tooluniverse.dbpedia_tool.DBpediaSPARQLTool method) (tooluniverse.DBpediaSPARQLTool method) (tooluniverse.dbsnp_tool.dbSNPGetFrequencies method) (tooluniverse.dbsnp_tool.dbSNPGetVariantByRsID method) (tooluniverse.dbsnp_tool.dbSNPSearchByGene method) (tooluniverse.dbSNPGetFrequencies method) (tooluniverse.dbSNPGetVariantByRsID method) (tooluniverse.dbSNPSearchByGene method) (tooluniverse.DeepGOTool method) (tooluniverse.DegreesOfUnsaturationTool method) (tooluniverse.DepMapTool method) (tooluniverse.DfamTool method) (tooluniverse.DGIdbTool method) (tooluniverse.DiseaseOntologyTool method) (tooluniverse.DiseaseTargetScoreTool method) (tooluniverse.DisGeNETTool method) (tooluniverse.DisProtTool method) (tooluniverse.DNATool method) (tooluniverse.doaj_tool.DOAJTool method) (tooluniverse.DOAJTool method) (tooluniverse.DoseResponseTool method) (tooluniverse.DrugCentralTool method) (tooluniverse.DrugPropertiesTool method) (tooluniverse.DrugSynergyTool method) (tooluniverse.DynamicPackageDiscovery method) (tooluniverse.DynaMut2Tool method) (tooluniverse.EBIProteinsCoordinatesTool method) (tooluniverse.EBIProteinsEpitopeTool method) (tooluniverse.EBIProteinsExtTool method) (tooluniverse.EBIProteinsFeaturesTool method) (tooluniverse.EBIProteinsInteractionsTool method) (tooluniverse.EBISearchRESTTool method) (tooluniverse.EBITaxonomyTool method) (tooluniverse.efo_tool.EFOTool method) (tooluniverse.EFOTool method) (tooluniverse.ELMTool method) (tooluniverse.EmbeddingDatabase method) (tooluniverse.EmbeddingSync method) (tooluniverse.emdb_tool.EMDBRESTTool method) (tooluniverse.EMDBRESTTool method) (tooluniverse.EMoleculesTool method) (tooluniverse.EMPIARTool method) (tooluniverse.ENABrowserRESTTool method) (tooluniverse.EnamineTool method) (tooluniverse.ENAPortalTool method) (tooluniverse.encode_tool.ENCODESearchTool method) (tooluniverse.ENCODESearchTool method) (tooluniverse.enrichr_tool.EnrichrTool method) (tooluniverse.EnrichrExtTool method) (tooluniverse.EnrichrTool method) (tooluniverse.ensembl_tool.EnsemblGetSequence method) (tooluniverse.ensembl_tool.EnsemblGetVariants method) (tooluniverse.ensembl_tool.EnsemblLookupGene method) (tooluniverse.ensembl_tool.EnsemblRESTTool method) (tooluniverse.EnsemblArchiveTool method) (tooluniverse.EnsemblComparaTool method) (tooluniverse.EnsemblGetSequence method) (tooluniverse.EnsemblGetVariants method) (tooluniverse.EnsemblInfoTool method) (tooluniverse.EnsemblLDTool method) (tooluniverse.EnsemblLookupGene method) (tooluniverse.EnsemblMapTool method) (tooluniverse.EnsemblOverlapTool method) (tooluniverse.EnsemblPhenotypeTool method) (tooluniverse.EnsemblRegulationTool method) (tooluniverse.EnsemblRESTTool method) (tooluniverse.EnsemblSequenceTool method) (tooluniverse.EnsemblVariationExtTool method) (tooluniverse.EnsemblVEPTool method) (tooluniverse.EnsemblXrefsTool method) (tooluniverse.EOLTool method) (tooluniverse.EpidemiologyTool method) (tooluniverse.EpigenomicsTool method) (tooluniverse.EpiGraphDBTool method) (tooluniverse.EPMCAnnotationsTool method) (tooluniverse.ESMFoldTool method) (tooluniverse.europe_pmc_tool.EuropePMCFullTextFetchTool method) (tooluniverse.europe_pmc_tool.EuropePMCFullTextSnippetsTool method) (tooluniverse.europe_pmc_tool.EuropePMCRESTTool method) (tooluniverse.europe_pmc_tool.EuropePMCStructuredFullTextTool method) (tooluniverse.europe_pmc_tool.EuropePMCTool method) (tooluniverse.EuropePMCFullTextFetchTool method) (tooluniverse.EuropePMCFullTextSnippetsTool method) (tooluniverse.EuropePMCGuidelinesTool method) (tooluniverse.EuropePMCRESTTool method) (tooluniverse.EuropePMCStructuredFullTextTool method) (tooluniverse.EuropePMCTool method) (tooluniverse.EuroPMCAnnotationsTool method) (tooluniverse.EVETool 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.ExecuteToolTool method) (tooluniverse.ExpressionAtlasTool method) (tooluniverse.extended_hooks.FilteringHook method) (tooluniverse.extended_hooks.FormattingHook method) (tooluniverse.extended_hooks.LoggingHook method) (tooluniverse.extended_hooks.ValidationHook method) (tooluniverse.FAERSAnalyticsTool method) (tooluniverse.fatcat_tool.FatcatMetadataParser method) (tooluniverse.fatcat_tool.FatcatResultParser method) (tooluniverse.fatcat_tool.FatcatScholarTool method) (tooluniverse.FatcatMetadataParser method) (tooluniverse.FatcatResultParser method) (tooluniverse.FatcatScholarTool method) (tooluniverse.FDACountAdditiveReactionsTool method) (tooluniverse.FDADrugAdverseEventDetailTool method) (tooluniverse.FDADrugAdverseEventTool method) (tooluniverse.FDADrugInteractionDetailTool method) (tooluniverse.FDADrugLabelFieldValueTool method) (tooluniverse.FDADrugLabelGetDrugGenericNameTool method) (tooluniverse.FDADrugLabelGetDrugNamesByIndicationAggregated method) (tooluniverse.FDADrugLabelGetDrugNamesByIndicationStats method) (tooluniverse.FDADrugLabelSearchIDTool method) (tooluniverse.FDADrugLabelSearchTool method) (tooluniverse.FDADrugLabelTool method) (tooluniverse.FDAGSRSTool method) (tooluniverse.FDALabelTool method) (tooluniverse.FDAOrangeBookTool method) (tooluniverse.FDATool method) (tooluniverse.file_download_tool.BinaryDownloadTool method) (tooluniverse.file_download_tool.FileDownloadTool method) (tooluniverse.file_download_tool.TextDownloadTool method) (tooluniverse.FileDownloadTool method) (tooluniverse.FinnGenTool method) (tooluniverse.FoldseekTool method) (tooluniverse.FoodDataCentralTool method) (tooluniverse.gbif_tool.GBIFOccurrenceTool method) (tooluniverse.gbif_tool.GBIFTool method) (tooluniverse.GBIFOccurrenceTool method) (tooluniverse.GBIFTool method) (tooluniverse.gdc_tool.GDCCasesTool method) (tooluniverse.gdc_tool.GDCClinicalDataTool method) (tooluniverse.gdc_tool.GDCCNVTool method) (tooluniverse.gdc_tool.GDCFilesTool method) (tooluniverse.gdc_tool.GDCGeneExpressionTool method) (tooluniverse.gdc_tool.GDCMutationFrequencyTool method) (tooluniverse.gdc_tool.GDCProjectsTool method) (tooluniverse.gdc_tool.GDCSSMTool method) (tooluniverse.gdc_tool.GDCSurvivalTool method) (tooluniverse.GDCCasesTool method) (tooluniverse.GDCClinicalDataTool method) (tooluniverse.GDCCNVTool method) (tooluniverse.GDCFilesTool method) (tooluniverse.GDCGeneExpressionTool method) (tooluniverse.GDCMutationFrequencyTool method) (tooluniverse.GDCProjectsTool method) (tooluniverse.GDCSSMTool method) (tooluniverse.GDCSurvivalTool method) (tooluniverse.GenCCTool method) (tooluniverse.gene_ontology_tool.GeneOntologyTool method) (tooluniverse.GeneOntologyTool method) (tooluniverse.GenomeNexusTool 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.GEOGetDatasetInfo method) (tooluniverse.GEOGetSampleInfo method) (tooluniverse.GEORESTTool method) (tooluniverse.GEOSearchDatasets method) (tooluniverse.GetSPLBySetIDTool method) (tooluniverse.GetToolInfoTool method) (tooluniverse.GINGuidelinesTool method) (tooluniverse.GlyGenTool method) (tooluniverse.GmrepoTool method) (tooluniverse.gnomad_tool.gnomADGetGeneConstraints method) (tooluniverse.gnomad_tool.gnomADGraphQLQueryTool method) (tooluniverse.gnomad_tool.gnomADGraphQLTool method) (tooluniverse.gnomADGetGeneConstraints method) (tooluniverse.gnomADGraphQLQueryTool method) (tooluniverse.gnomADGraphQLTool method) (tooluniverse.GNPSTool method) (tooluniverse.GOAPITool method) (tooluniverse.GPCRdbTool method) (tooluniverse.GProfilerTool 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.GraphQLTool method) (tooluniverse.GrepToolsTool method) (tooluniverse.GTDBTool method) (tooluniverse.gtex_tool.GTExEQTLTool method) (tooluniverse.gtex_tool.GTExExpressionTool method) (tooluniverse.GTExEQTLTool method) (tooluniverse.GTExExpressionTool method) (tooluniverse.GTExV2Tool method) (tooluniverse.gtopdb_tool.GtoPdbRESTTool method) (tooluniverse.GtoPdbRESTTool 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.GWASGeneSearch method) (tooluniverse.GWASRESTTool method) (tooluniverse.GWASSNPByID method) (tooluniverse.GWASSNPSearch method) (tooluniverse.GWASSNPsForGene method) (tooluniverse.GWASStudiesForTrait method) (tooluniverse.GWASStudyByID method) (tooluniverse.GWASStudySearch method) (tooluniverse.GWASSumStatsTool method) (tooluniverse.GWASVariantsForTrait method) (tooluniverse.GxATool method) (tooluniverse.hal_tool.HALTool method) (tooluniverse.HALTool method) (tooluniverse.HarmonizomeTool method) (tooluniverse.health_disparities_tool.HealthDisparitiesTool method) (tooluniverse.HealthDisparitiesTool method) (tooluniverse.HGNCTool method) (tooluniverse.HocomocoTool 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.HPAGetBiologicalProcessTool method) (tooluniverse.HPAGetComparativeExpressionTool method) (tooluniverse.HPAGetContextualBiologicalProcessTool method) (tooluniverse.HPAGetDiseaseExpressionTool method) (tooluniverse.HPAGetGenePageDetailsTool method) (tooluniverse.HPAGetRnaExpressionBySourceTool method) (tooluniverse.HPAJsonApiTool method) (tooluniverse.HPASearchApiTool method) (tooluniverse.HPAXmlApiTool method) (tooluniverse.HPOTool method) (tooluniverse.HuBMAPTool method) (tooluniverse.humanbase_tool.HumanBaseTool method) (tooluniverse.HumanBaseTool method) (tooluniverse.ICD10Tool method) (tooluniverse.ICDTool method) (tooluniverse.IdentifiersOrgTool method) (tooluniverse.IDTTool method) (tooluniverse.IEDBPredictionTool method) (tooluniverse.IGSRTool method) (tooluniverse.IMGTTool method) (tooluniverse.ImmPortTool method) (tooluniverse.IMPCTool method) (tooluniverse.INaturalistTool method) (tooluniverse.INDRADBTool method) (tooluniverse.IntActRESTTool method) (tooluniverse.interpro_tool.InterProRESTTool method) (tooluniverse.InterProDomainArchTool method) (tooluniverse.InterProEntryTool method) (tooluniverse.InterProExtTool method) (tooluniverse.InterProRESTTool method) (tooluniverse.InterProScanTool method) (tooluniverse.InterVarTool method) (tooluniverse.IntOGenTool method) (tooluniverse.iPTMnetTool method) (tooluniverse.ITISTool method) (tooluniverse.jaspar_tool.JASPARRESTTool method) (tooluniverse.JASPARRESTTool method) (tooluniverse.kegg_tool.KEGGFindGenes method) (tooluniverse.kegg_tool.KEGGGetGeneInfo method) (tooluniverse.kegg_tool.KEGGGetPathwayInfo method) (tooluniverse.kegg_tool.KEGGListOrganisms method) (tooluniverse.kegg_tool.KEGGRESTTool method) (tooluniverse.kegg_tool.KEGGSearchPathway method) (tooluniverse.KEGGExtTool method) (tooluniverse.KEGGFindGenes method) (tooluniverse.KEGGGetGeneInfo method) (tooluniverse.KEGGGetPathwayInfo method) (tooluniverse.KEGGListOrganisms method) (tooluniverse.KEGGRESTTool method) (tooluniverse.KEGGSearchPathway method) (tooluniverse.L1000FWDTool method) (tooluniverse.LINCSSignatureTool method) (tooluniverse.LipidMapsTool method) (tooluniverse.ListToolsTool method) (tooluniverse.llm_clients.AzureOpenAIClient method) (tooluniverse.llm_clients.GeminiClient method) (tooluniverse.llm_clients.OpenRouterClient method) (tooluniverse.llm_clients.VLLMClient method) (tooluniverse.logging_config.ToolUniverseFormatter method) (tooluniverse.logging_config.ToolUniverseLogger method) (tooluniverse.LOINCTool method) (tooluniverse.LOVDTool method) (tooluniverse.markitdown_tool.MarkItDownTool method) (tooluniverse.MarkItDownTool method) (tooluniverse.MassIVETool method) (tooluniverse.MaveDBTool 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.MCPProxyTool method) (tooluniverse.MculeTool method) (tooluniverse.MedGenTool method) (tooluniverse.medlineplus_tool.MedlinePlusRESTTool method) (tooluniverse.MedlinePlusRESTTool method) (tooluniverse.MEMETool method) (tooluniverse.memory_manager.MemoryManager method) (tooluniverse.MeSHTool method) (tooluniverse.MetaAnalysisTool method) (tooluniverse.MetaboAnalystTool method) (tooluniverse.MetaboLightsRESTTool method) (tooluniverse.MetaboliteTool method) (tooluniverse.MetabolomicsWorkbenchTool method) (tooluniverse.MetaCycTool method) (tooluniverse.mgnify_tool.MGnifyAnalysesTool method) (tooluniverse.mgnify_tool.MGnifyStudiesTool method) (tooluniverse.MGnifyAnalysesTool method) (tooluniverse.MGnifyExpandedTool method) (tooluniverse.MGnifyStudiesTool method) (tooluniverse.miRNAGetTool method) (tooluniverse.miRNASearchTool method) (tooluniverse.MobiDBTool method) (tooluniverse.MODOMICSTool method) (tooluniverse.MonarchDiseasesForMultiplePhenoTool method) (tooluniverse.MonarchTool method) (tooluniverse.MonarchV3Tool method) (tooluniverse.mpd_tool.MPDRESTTool method) (tooluniverse.MPDRESTTool method) (tooluniverse.MutalyzerTool method) (tooluniverse.MyChemTool method) (tooluniverse.MyDiseaseTool method) (tooluniverse.MyGeneTool method) (tooluniverse.MyVariantTool method) (tooluniverse.NCATool method) (tooluniverse.ncbi_eutils_tool.NCBIEUtilsTool method) (tooluniverse.NCBIBlastTool method) (tooluniverse.NCBIDatasetsTool method) (tooluniverse.NCBIEUtilsTool method) (tooluniverse.NCBINucleotideSearchTool method) (tooluniverse.NCBISRATool method) (tooluniverse.NCBIVariationTool method) (tooluniverse.NCCNGuidelineTool method) (tooluniverse.NCICACTUSTool method) (tooluniverse.NCIThesaurusTool method) (tooluniverse.NDExTool method) (tooluniverse.NEBTmTool method) (tooluniverse.NeuroMorphoTool method) (tooluniverse.NextstrainTool method) (tooluniverse.nhanes_tool.NHANESTool method) (tooluniverse.NHANESTool method) (tooluniverse.NICEGuidelineFullTextTool method) (tooluniverse.NICEWebScrapingTool method) (tooluniverse.NvidiaNIMTool method) (tooluniverse.obis_tool.OBISOccurrenceTool method) (tooluniverse.obis_tool.OBISTaxaTool method) (tooluniverse.OBISOccurrenceTool method) (tooluniverse.OBISTaxaTool method) (tooluniverse.odphp_tool.ODPHPOutlinkFetch method) (tooluniverse.odphp_tool.ODPHPRESTTool method) (tooluniverse.ODPHPOutlinkFetch method) (tooluniverse.ODPHPRESTTool method) (tooluniverse.ols_tool.OLSTool method) (tooluniverse.OLSTool method) (tooluniverse.OMATool method) (tooluniverse.OMIMTool method) (tooluniverse.OmniPathTool method) (tooluniverse.OncoKBTool method) (tooluniverse.OncoTreeBaseTool method) (tooluniverse.openaire_tool.OpenAIRETool method) (tooluniverse.OpenAIRETool method) (tooluniverse.openalex_tool.OpenAlexRESTTool method) (tooluniverse.openalex_tool.OpenAlexTool method) (tooluniverse.OpenAlexGuidelinesTool method) (tooluniverse.OpenAlexRESTTool method) (tooluniverse.OpenAlexTool method) (tooluniverse.OpenCRAVATTool 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.FDADrugLabelFieldValueTool 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.OpenFDAApprovalTool method) (tooluniverse.OpenNeuroTool method) (tooluniverse.OpentargetGeneticsTool method) (tooluniverse.OpentargetTool method) (tooluniverse.OpentargetToolDrugNameMatch method) (tooluniverse.OpenTreeTool method) (tooluniverse.ORCIDTool method) (tooluniverse.OrphanetTool method) (tooluniverse.OrthoDBTool method) (tooluniverse.osf_preprints_tool.OSFPreprintsTool method) (tooluniverse.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.OxOTool method) (tooluniverse.package_discovery_tool.DynamicPackageDiscovery method) (tooluniverse.package_tool.PackageTool method) (tooluniverse.PackageTool method) (tooluniverse.paleobiology_tool.PaleobiologyRESTTool method) (tooluniverse.PaleobiologyRESTTool method) (tooluniverse.PANTHERTool method) (tooluniverse.PathwayCommonsTool method) (tooluniverse.PDBe_KB_Tool method) (tooluniverse.PDBeAPIRESTTool method) (tooluniverse.PDBECompoundTool method) (tooluniverse.PDBeLigandsTool method) (tooluniverse.PDBePISATool method) (tooluniverse.PDBeSearchTool method) (tooluniverse.PDBeSIFTSTool method) (tooluniverse.PDBeValidationTool method) (tooluniverse.PDCTool method) (tooluniverse.PfamTool method) (tooluniverse.PharmacoDBTool method) (tooluniverse.PharmGKBTool method) (tooluniverse.PharosTool method) (tooluniverse.PlantReactomeTool method) (tooluniverse.pmc_tool.PMCTool method) (tooluniverse.PMCTool method) (tooluniverse.PomBaseTool method) (tooluniverse.PopGenTool method) (tooluniverse.pride_tool.PRIDERESTTool method) (tooluniverse.PRIDERESTTool method) (tooluniverse.profile.loader.ProfileLoader method) (tooluniverse.profile.ProfileLoader method) (tooluniverse.ProfileLoader method) (tooluniverse.ProgenetixTool method) (tooluniverse.PROSITETool method) (tooluniverse.ProtacDBTool method) (tooluniverse.ProteinsAPIRESTTool method) (tooluniverse.ProteinsPlusRESTTool method) (tooluniverse.ProteomeXchangeTool method) (tooluniverse.ProteomicsDBTool method) (tooluniverse.ProtParamTool method) (tooluniverse.ProtVarFunctionTool method) (tooluniverse.ProtVarMapTool method) (tooluniverse.ProtVarPopulationTool method) (tooluniverse.pubchem_tool.PubChemRESTTool method) (tooluniverse.PubChemBioAssayTool method) (tooluniverse.PubChemRESTTool method) (tooluniverse.PubChemToxTool method) (tooluniverse.pubmed_tool.PubMedRESTTool method) (tooluniverse.PubMedGuidelinesTool method) (tooluniverse.PubMedRESTTool method) (tooluniverse.pubtator_tool.PubTatorTool method) (tooluniverse.PubTatorTool method) (tooluniverse.pypi_package_inspector_tool.PyPIPackageInspector method) (tooluniverse.PyPIPackageInspector method) (tooluniverse.python_executor_tool.BasePythonExecutor method) (tooluniverse.python_executor_tool.PythonCodeExecutor method) (tooluniverse.python_executor_tool.PythonScriptRunner method) (tooluniverse.PythonCodeExecutor method) (tooluniverse.PythonScriptRunner method) (tooluniverse.QuickGOTool method) (tooluniverse.rcsb_pdb_tool.RCSBTool method) (tooluniverse.rcsb_search_tool.RCSBSearchTool method) (tooluniverse.RCSBAdvancedSearchTool method) (tooluniverse.RCSBDataTool method) (tooluniverse.RCSBGraphQLTool method) (tooluniverse.RCSBSearchTool method) (tooluniverse.RCSBTool method) (tooluniverse.RDKitCheminfoTool method) (tooluniverse.Re3DataTool method) (tooluniverse.reactome_tool.ReactomeRESTTool method) (tooluniverse.ReactomeAnalysisTool method) (tooluniverse.ReactomeContentTool method) (tooluniverse.ReactomeInteractorsTool method) (tooluniverse.ReactomeRESTTool method) (tooluniverse.regulomedb_tool.RegulomeDBRESTTool method) (tooluniverse.RegulomeDBRESTTool method) (tooluniverse.remap_tool.ReMapRESTTool method) (tooluniverse.ReMapRESTTool method) (tooluniverse.remote_tool.RemoteTool method) (tooluniverse.RemoteTool method) (tooluniverse.restful_tool.MonarchDiseasesForMultiplePhenoTool method) (tooluniverse.restful_tool.MonarchTool method) (tooluniverse.restful_tool.RESTfulTool method) (tooluniverse.RESTfulTool method) (tooluniverse.RfamTool method) (tooluniverse.RGDTool method) (tooluniverse.RheaTool method) (tooluniverse.rnacentral_tool.RNAcentralGetTool method) (tooluniverse.rnacentral_tool.RNAcentralSearchTool method) (tooluniverse.RNAcentralGetTool method) (tooluniverse.RNAcentralSearchTool method) (tooluniverse.RxClassTool method) (tooluniverse.rxnorm_tool.RxNormTool method) (tooluniverse.RxNormExtendedTool method) (tooluniverse.RxNormTool method) (tooluniverse.SAbDabTool method) (tooluniverse.SABIORKTool method) (tooluniverse.SASBDBRESTTool method) (tooluniverse.SASBDBSearchTool method) (tooluniverse.SASBDBTextSearchTool method) (tooluniverse.SCExpressionAtlasTool method) (tooluniverse.ScientificCalculatorTool method) (tooluniverse.screen_tool.SCREENRESTTool method) (tooluniverse.SCREENRESTTool method) (tooluniverse.SearchSPLTool method) (tooluniverse.semantic_scholar_tool.SemanticScholarPDFSnippetsTool method) (tooluniverse.semantic_scholar_tool.SemanticScholarTool method) (tooluniverse.SemanticScholarPDFSnippetsTool method) (tooluniverse.SemanticScholarTool method) (tooluniverse.SequenceAnalyzeTool method) (tooluniverse.SGDTool method) (tooluniverse.SiderTool method) (tooluniverse.SIGNORTool method) (tooluniverse.SIMBADAdvancedTool method) (tooluniverse.SIMBADTool method) (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) (tooluniverse.SMILESVerifyTool method) (tooluniverse.smolagent_tool.SmolAgentTool method) (tooluniverse.SmolAgentTool method) (tooluniverse.SpliceAITool method) (tooluniverse.SRATool method) (tooluniverse.STITCHTool method) (tooluniverse.string_tool.STRINGRESTTool method) (tooluniverse.STRINGExtTool method) (tooluniverse.STRINGRESTTool method) (tooluniverse.SurvivalTool method) (tooluniverse.SwissADMETool method) (tooluniverse.SwissDockTool method) (tooluniverse.SwissModelTool method) (tooluniverse.SwissTargetTool method) (tooluniverse.SynBioHubTool method) (tooluniverse.SYNERGxDBTool method) (tooluniverse.T3DBTool method) (tooluniverse.TCDBTool method) (tooluniverse.TextDownloadTool method) (tooluniverse.TheraSAbDabTool method) (tooluniverse.ThreeDBeaconsTool method) (tooluniverse.TIMERTool method) (tooluniverse.tool_defaults.ToolAnnotations method) (tooluniverse.tool_defaults.ToolDefaultsConfig method) (tooluniverse.tool_discovery_tools.ExecuteToolTool method) (tooluniverse.tool_discovery_tools.GetToolInfoTool method) (tooluniverse.tool_discovery_tools.GrepToolsTool method) (tooluniverse.tool_discovery_tools.ListToolsTool method) (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) (tooluniverse.ToolUniverse method) (tooluniverse.ToolUniverseClient method) (tooluniverse.TRIPDatabaseTool method) (tooluniverse.UCSCEpigenomicsTool method) (tooluniverse.UCSCGenomeTool method) (tooluniverse.umls_tool.UMLSRESTTool method) (tooluniverse.UMLSRESTTool method) (tooluniverse.UniChemTool 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.UniParcTool method) (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtIDMappingTool method) (tooluniverse.UniProtLocationsTool method) (tooluniverse.UniProtRefTool method) (tooluniverse.UniProtRESTTool method) (tooluniverse.UniProtTaxonomyTool method) (tooluniverse.UniRefTool 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.VDJDBTool method) (tooluniverse.visualization_tool.VisualizationTool method) (tooluniverse.VisualizationTool method) (tooluniverse.web_search_tool.WebSearchTool method) (tooluniverse.WebSearchTool method) (tooluniverse.WFGYPromptBundleTool method) (tooluniverse.who_gho_tool.WHOGHOQueryTool method) (tooluniverse.who_gho_tool.WHOGHORESTTool method) (tooluniverse.who_gho_tool.WHOGHOStatisticTool method) (tooluniverse.who_gho_tool.WHOGHOTopicTool method) (tooluniverse.WHOGHOQueryTool method) (tooluniverse.WHOGHORESTTool method) (tooluniverse.WHOGHOStatisticTool method) (tooluniverse.WHOGHOTopicTool method) (tooluniverse.WHOGuidelineFullTextTool method) (tooluniverse.WHOGuidelinesTool method) (tooluniverse.wikidata_sparql_tool.WikidataSPARQLTool method) (tooluniverse.WikidataSPARQLTool method) (tooluniverse.wikipathways_tool.WikiPathwaysGetTool method) (tooluniverse.wikipathways_tool.WikiPathwaysSearchTool method) (tooluniverse.WikiPathwaysExtTool method) (tooluniverse.WikiPathwaysGetTool method) (tooluniverse.WikiPathwaysSearchTool method) (tooluniverse.wikipedia_tool.WikipediaContentTool method) (tooluniverse.wikipedia_tool.WikipediaSearchTool method) (tooluniverse.wikipedia_tool.WikipediaSummaryTool method) (tooluniverse.WikipediaContentTool method) (tooluniverse.WikipediaSearchTool method) (tooluniverse.WikipediaSummaryTool method) (tooluniverse.WormBaseTool method) (tooluniverse.worms_tool.WoRMSRESTTool method) (tooluniverse.WoRMSRESTTool method) (tooluniverse.XenbaseTool method) (tooluniverse.xml_tool.XMLDatasetTool method) (tooluniverse.XMLDatasetTool method) (tooluniverse.ZincTool method) __iter__() (tooluniverse.execute_function.ToolNamespace method) __len__() (tooluniverse.execute_function.ToolNamespace method) __new__() (tooluniverse.logging_config.ToolUniverseLogger static method) (tooluniverse.smolagent_tool.ToolUniverseTool static method) (tooluniverse.ToolUniverseTool static method) _abc_impl (tooluniverse.DetailedTermInfo attribute) (tooluniverse.ols_tool.DetailedTermInfo attribute) (tooluniverse.ols_tool.OntologyInfo attribute) (tooluniverse.ols_tool.OntologySearchResponse attribute) (tooluniverse.ols_tool.TermInfo attribute) (tooluniverse.ols_tool.TermSearchResponse attribute) (tooluniverse.OntologyInfo attribute) (tooluniverse.OntologySearchResponse attribute) (tooluniverse.PagedResponse attribute) (tooluniverse.ProteinsPlusRESTTool attribute) (tooluniverse.SwissDockTool attribute) (tooluniverse.TermInfo attribute) (tooluniverse.TermSearchResponse attribute) _accession_to_uid() (tooluniverse.geo_tool.GEORESTTool method) (tooluniverse.GEORESTTool method) _add_documents() (tooluniverse.EmbeddingDatabase method) _add_empty_result_note() (tooluniverse.gwas_tool.GWASRESTTool method) (tooluniverse.GWASRESTTool method) _add_profile_args() (in module tooluniverse.smcp_server) _add_search_tools() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) _add_utility_tools() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) _additional_http_routes (tooluniverse.smcp.SMCP attribute) _advanced_search() (tooluniverse.RCSBAdvancedSearchTool method) _analysis_go_terms() (tooluniverse.MGnifyExpandedTool method) _analysis_interpro() (tooluniverse.MGnifyExpandedTool method) _analysis_taxonomy() (tooluniverse.MGnifyExpandedTool method) _analyze_data() (tooluniverse.output_hook.FileSaveHook method) _analyze_formula() (tooluniverse.ScientificCalculatorTool method) _analyze_oligo() (tooluniverse.IDTTool method) _analyze_temporal_trends() (tooluniverse.FAERSAnalyticsTool method) _annotate_copy_number() (tooluniverse.OncoKBTool method) _annotate_mutation() (tooluniverse.GenomeNexusTool method) _annotate_text() (tooluniverse.BioPortalTool method) _annotate_variant() (tooluniverse.GenomeNexusTool method) (tooluniverse.OncoKBTool method) (tooluniverse.OpenCRAVATTool method) _annotation_by_gene() (tooluniverse.QuickGOTool method) _annotation_by_goterm() (tooluniverse.QuickGOTool method) _api_get() (tooluniverse.CancerPrognosisTool method) (tooluniverse.FDAGSRSTool method) _api_mode (tooluniverse.OncoKBTool property) _api_post() (tooluniverse.CancerPrognosisTool method) _api_type (tooluniverse.agentic_tool.AgenticTool attribute) _apply_boolean_operators() (tooluniverse.cellosaurus_tool.CellosaurusQueryConverterTool method) (tooluniverse.CellosaurusQueryConverterTool method) _apply_cache_config() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _apply_defaults() (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseTool method) _apply_demo_gene_warning() (tooluniverse.OncoKBTool method) _apply_hook_type_defaults() (tooluniverse.output_hook.HookManager method) _apply_hooks_config() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _apply_llm_config() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _apply_log_level_config() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _apply_range_queries() (tooluniverse.cellosaurus_tool.CellosaurusQueryConverterTool method) (tooluniverse.CellosaurusQueryConverterTool method) _apply_stemming() (tooluniverse.tool_finder_keyword.ToolFinderKeyword method) (tooluniverse.ToolFinderKeyword method) _apply_wildcards() (tooluniverse.cellosaurus_tool.CellosaurusQueryConverterTool method) (tooluniverse.CellosaurusQueryConverterTool method) _argument_defaults (tooluniverse.agentic_tool.AgenticTool attribute) _assembly_map() (tooluniverse.EnsemblMapTool method) _assess() (tooluniverse.DataQualityTool method) _auc_trapezoid() (tooluniverse.NCATool method) _aumc_trapezoid() (tooluniverse.NCATool method) _auth_error() (tooluniverse.BRENDATool method) _auto_import_subpackages() (in module tooluniverse.tool_registry) _auto_load_hook_tools() (tooluniverse.output_hook.HookManager method) _auto_load_tools_if_empty() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _back_translate() (tooluniverse.MutalyzerTool method) _BASE_URL (tooluniverse.ClinicalTrialsTool attribute) (tooluniverse.ctg_tool.ClinicalTrialsTool attribute) _batch_by_type() (tooluniverse.EuroPMCAnnotationsTool method) _batch_lookup() (tooluniverse.EnsemblArchiveTool method) _BatchCacheInfo (class in tooluniverse.execute_function) _BatchJob (class in tooluniverse.execute_function) _bayesian() (tooluniverse.EpidemiologyTool method) _binding_matrix() (tooluniverse.EnsemblRegulationTool method) _biomarker_enrichment() (tooluniverse.MetaboAnalystTool method) _biome_list() (tooluniverse.MGnifyExpandedTool method) _BOOL_PARAMS (tooluniverse.ICDTool attribute) _BROKEN_MSG (tooluniverse.BindingDBTool attribute) _build_api_url() (tooluniverse.ProteinsPlusRESTTool method) _build_batch_jobs() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _build_doc_rows() (tooluniverse.EmbeddingDatabase static method) _build_files() (tooluniverse.ProtacDBTool method) _build_fulltext_xml_url() (tooluniverse.europe_pmc_tool.EuropePMCFullTextFetchTool method) (tooluniverse.europe_pmc_tool.EuropePMCFullTextSnippetsTool method) (tooluniverse.europe_pmc_tool.EuropePMCTool method) (tooluniverse.EuropePMCFullTextFetchTool method) (tooluniverse.EuropePMCFullTextSnippetsTool method) (tooluniverse.EuropePMCTool method) _build_graphql_query() (tooluniverse.CIViCTool method) _build_model() (tooluniverse.llm_clients.GeminiClient method) _build_ncbi_pmc_efetch_url() (in module tooluniverse.europe_pmc_tool) _build_ncbi_pmc_html_url() (in module tooluniverse.europe_pmc_tool) _build_ncbi_pmc_oai_url() (in module tooluniverse.europe_pmc_tool) _build_paper_from_summary() (tooluniverse.pmc_tool.PMCTool method) (tooluniverse.PMCTool method) _build_params() (tooluniverse.ArrayExpressRESTTool method) (tooluniverse.BaseRESTTool method) (tooluniverse.biogrid_tool.BioGRIDRESTTool method) (tooluniverse.BioGRIDRESTTool method) (tooluniverse.BioStudiesRESTTool method) (tooluniverse.chem_tool.ChEMBLRESTTool method) (tooluniverse.ChEMBLRESTTool method) (tooluniverse.CPICSearchPairsTool method) (tooluniverse.DbfetchRESTTool method) (tooluniverse.EBISearchRESTTool method) (tooluniverse.ENABrowserRESTTool method) (tooluniverse.geo_tool.GEOGetDatasetInfo method) (tooluniverse.geo_tool.GEOGetSampleInfo method) (tooluniverse.geo_tool.GEORESTTool method) (tooluniverse.geo_tool.GEOSearchDatasets method) (tooluniverse.GEOGetDatasetInfo method) (tooluniverse.GEOGetSampleInfo method) (tooluniverse.GEORESTTool method) (tooluniverse.GEOSearchDatasets method) (tooluniverse.IntActRESTTool method) (tooluniverse.MetaboLightsRESTTool method) (tooluniverse.PDBeAPIRESTTool method) (tooluniverse.ProteinsAPIRESTTool method) (tooluniverse.pubmed_tool.PubMedRESTTool method) (tooluniverse.PubMedRESTTool method) (tooluniverse.string_tool.STRINGRESTTool method) (tooluniverse.STRINGRESTTool method) _build_pmc_html_url() (tooluniverse.europe_pmc_tool.EuropePMCFullTextSnippetsTool method) (tooluniverse.EuropePMCFullTextSnippetsTool method) _build_pmc_oai_url() (tooluniverse.europe_pmc_tool.EuropePMCFullTextSnippetsTool method) (tooluniverse.europe_pmc_tool.EuropePMCTool method) (tooluniverse.EuropePMCFullTextSnippetsTool method) (tooluniverse.EuropePMCTool method) _build_query() (tooluniverse.SABIORKTool method) _build_query_params() (tooluniverse.SASBDBRESTTool method) _build_query_string() (tooluniverse.BVBRCTool method) _build_search_query() (tooluniverse.arxiv_tool.ArXivTool method) (tooluniverse.ArXivTool method) _build_search_term() (tooluniverse.NCBINucleotideSearchTool method) (tooluniverse.NCBISRATool method) _build_sequence_query() (tooluniverse.rcsb_search_tool.RCSBSearchTool method) (tooluniverse.RCSBSearchTool method) _build_structure_query() (tooluniverse.rcsb_search_tool.RCSBSearchTool method) (tooluniverse.RCSBSearchTool method) _build_system_prompt() (tooluniverse.WFGYPromptBundleTool static method) _build_term_model() (tooluniverse.ols_tool.OLSTool static method) (tooluniverse.OLSTool static method) _build_text_query() (tooluniverse.rcsb_search_tool.RCSBSearchTool method) (tooluniverse.RCSBSearchTool method) _build_tool_index() (tooluniverse.tool_finder_keyword.ToolFinderKeyword method) (tooluniverse.ToolFinderKeyword method) _build_url() (tooluniverse.alphafold_tool.AlphaFoldRESTTool method) (tooluniverse.AlphaFoldRESTTool method) (tooluniverse.APPRISTool method) (tooluniverse.ArrayExpressRESTTool method) (tooluniverse.BaseRESTTool method) (tooluniverse.biogrid_tool.BioGRIDRESTTool method) (tooluniverse.BioGRIDRESTTool method) (tooluniverse.BioStudiesRESTTool method) (tooluniverse.cbioportal_tool.CBioPortalRESTTool method) (tooluniverse.CBioPortalRESTTool method) (tooluniverse.cdc_tool.CDCRESTTool method) (tooluniverse.CDCRESTTool method) (tooluniverse.chem_tool.ChEMBLRESTTool method) (tooluniverse.ChEMBLRESTTool method) (tooluniverse.CPICSearchPairsTool method) (tooluniverse.EBISearchRESTTool method) (tooluniverse.emdb_tool.EMDBRESTTool method) (tooluniverse.EMDBRESTTool method) (tooluniverse.ENABrowserRESTTool method) (tooluniverse.ensembl_tool.EnsemblRESTTool method) (tooluniverse.EnsemblRESTTool method) (tooluniverse.europe_pmc_tool.EuropePMCRESTTool method) (tooluniverse.EuropePMCRESTTool method) (tooluniverse.gene_ontology_tool.GeneOntologyTool method) (tooluniverse.GeneOntologyTool method) (tooluniverse.geo_tool.GEORESTTool method) (tooluniverse.GEORESTTool method) (tooluniverse.gtopdb_tool.GtoPdbRESTTool method) (tooluniverse.GtoPdbRESTTool method) (tooluniverse.ICD10Tool method) (tooluniverse.ICDTool method) (tooluniverse.IntActRESTTool method) (tooluniverse.interpro_tool.InterProRESTTool method) (tooluniverse.InterProRESTTool method) (tooluniverse.jaspar_tool.JASPARRESTTool method) (tooluniverse.JASPARRESTTool method) (tooluniverse.medlineplus_tool.MedlinePlusRESTTool method) (tooluniverse.MedlinePlusRESTTool method) (tooluniverse.MetaboLightsRESTTool method) (tooluniverse.NvidiaNIMTool method) (tooluniverse.paleobiology_tool.PaleobiologyRESTTool method) (tooluniverse.PaleobiologyRESTTool method) (tooluniverse.PDBeAPIRESTTool method) (tooluniverse.pride_tool.PRIDERESTTool method) (tooluniverse.PRIDERESTTool method) (tooluniverse.ProteinsAPIRESTTool method) (tooluniverse.pubchem_tool.PubChemRESTTool method) (tooluniverse.PubChemRESTTool method) (tooluniverse.reactome_tool.ReactomeRESTTool method) (tooluniverse.ReactomeRESTTool method) (tooluniverse.regulomedb_tool.RegulomeDBRESTTool method) (tooluniverse.RegulomeDBRESTTool method) (tooluniverse.SASBDBRESTTool method) (tooluniverse.string_tool.STRINGRESTTool method) (tooluniverse.STRINGRESTTool method) (tooluniverse.umls_tool.UMLSRESTTool method) (tooluniverse.UMLSRESTTool method) (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) (tooluniverse.worms_tool.WoRMSRESTTool method) (tooluniverse.WoRMSRESTTool method) _build_url_and_params() (tooluniverse.openalex_tool.OpenAlexRESTTool method) (tooluniverse.OpenAlexRESTTool method) _build_user_prompt() (tooluniverse.WFGYPromptBundleTool static method) _build_xpt_url() (tooluniverse.nhanes_tool.NHANESTool method) (tooluniverse.NHANESTool method) _build_yaml_input() (tooluniverse.Boltz2DockingTool method) (tooluniverse.boltz_tool.Boltz2DockingTool method) _by_article() (tooluniverse.EuroPMCAnnotationsTool method) _cache (tooluniverse.execute_function.ToolUniverse property) (tooluniverse.TCDBTool attribute) (tooluniverse.ToolUniverse property) _cached_version_hash (tooluniverse.agentic_tool.AgenticTool attribute) (tooluniverse.arxiv_tool.ArXivTool attribute) (tooluniverse.base_tool.BaseTool attribute) (tooluniverse.biogrid_tool.BioGRIDRESTTool attribute) (tooluniverse.clinical_trials_tool.ClinicalTrialsGovTool attribute) (tooluniverse.ctg_tool.ClinicalTrialsTool attribute) (tooluniverse.efo_tool.OLSRESTTool attribute) (tooluniverse.europe_pmc_tool.EuropePMCStructuredFullTextTool attribute) (tooluniverse.hca_tool.HCATool attribute) (tooluniverse.iedb_tool.IEDBTool attribute) (tooluniverse.nhanes_tool.NHANESTool attribute) (tooluniverse.ols_tool.OLSTool attribute) (tooluniverse.openfda_tool.OpenFDADrugEventsTool attribute) (tooluniverse.pubmed_tool.PubMedRESTTool attribute) (tooluniverse.semantic_scholar_tool.SemanticScholarTool attribute) (tooluniverse.tool_finder_keyword.ToolFinderKeyword attribute) _calc_tm_nn() (tooluniverse.DNATool method) _calculate() (tooluniverse.DegreesOfUnsaturationTool method) _calculate_adme() (tooluniverse.SwissADMETool method) _calculate_bioavailability() (tooluniverse.NCATool method) _calculate_bliss() (tooluniverse.DrugSynergyTool method) _calculate_ci() (tooluniverse.DrugSynergyTool method) _calculate_disproportionality() (tooluniverse.FAERSAnalyticsTool method) _calculate_eqtl() (tooluniverse.GTExV2Tool method) _calculate_exact_match_bonus() (tooluniverse.tool_finder_keyword.ToolFinderKeyword method) (tooluniverse.ToolFinderKeyword method) _calculate_gc_content() (tooluniverse.DNATool method) _calculate_hsa() (tooluniverse.DrugSynergyTool method) _calculate_ic() (tooluniverse.FAERSAnalyticsTool method) _calculate_ic50() (tooluniverse.DoseResponseTool method) _calculate_ic_ci() (tooluniverse.FAERSAnalyticsTool method) _calculate_loewe() (tooluniverse.DrugSynergyTool method) _calculate_molecular_properties() (tooluniverse.Molecule2DTool method) (tooluniverse.Molecule3DTool method) (tooluniverse.molecule_2d_tool.Molecule2DTool method) (tooluniverse.molecule_3d_tool.Molecule3DTool method) _calculate_prr_ci() (tooluniverse.FAERSAnalyticsTool method) _calculate_qed() (tooluniverse.DrugPropertiesTool method) _calculate_quality_scores() (tooluniverse.pypi_package_inspector_tool.PyPIPackageInspector method) (tooluniverse.PyPIPackageInspector method) _calculate_ror_ci() (tooluniverse.FAERSAnalyticsTool method) _calculate_similarity() (tooluniverse.cellosaurus_tool.CellosaurusQueryConverterTool method) (tooluniverse.CellosaurusQueryConverterTool method) _calculate_tfidf_score() (tooluniverse.tool_finder_keyword.ToolFinderKeyword method) (tooluniverse.ToolFinderKeyword method) _calculate_tm() (tooluniverse.NEBTmTool method) _calculate_zip() (tooluniverse.DrugSynergyTool method) _call_api() (tooluniverse.unpaywall_tool.UnpaywallTool method) (tooluniverse.UnpaywallTool method) _call_async() (tooluniverse.execute_function.ToolCallable method) _call_sync() (tooluniverse.execute_function.ToolCallable method) _call_tool() (tooluniverse.compose_tool.ComposeTool method) (tooluniverse.ComposeTool method) _capture_output() (tooluniverse.BasePythonExecutor method) (tooluniverse.python_executor_tool.BasePythonExecutor method) _categorize_expression() (tooluniverse.hpa_tool.HPAGetRnaExpressionByTissueTool method) (tooluniverse.HPAGetRnaExpressionByTissueTool method) _check_and_install_dependencies() (tooluniverse.BasePythonExecutor method) (tooluniverse.python_executor_tool.BasePythonExecutor method) _check_api_key_requirements() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _check_ast_safety() (tooluniverse.BasePythonExecutor method) (tooluniverse.python_executor_tool.BasePythonExecutor method) _check_basic_type() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _check_druglikeness() (tooluniverse.SwissADMETool method) _check_generic_availability() (tooluniverse.FDAOrangeBookTool method) _check_job_status_operation() (tooluniverse.SwissDockTool method) _check_oa_status() (tooluniverse.unpaywall_tool.UnpaywallTool method) (tooluniverse.UnpaywallTool method) _check_self_dimer() (tooluniverse.IDTTool method) _check_server_status() (tooluniverse.SwissDockTool method) _check_status_api() (tooluniverse.SwissDockTool method) _chemicals_shortcut() (tooluniverse.EuroPMCAnnotationsTool method) _chi_square() (tooluniverse.ScientificCalculatorTool method) _chunked() (in module tooluniverse.generate_tools) _classify_exception() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _classify_score() (tooluniverse.AlphaMissenseTool method) (tooluniverse.EVETool method) _classify_section() (tooluniverse.europe_pmc_tool.EuropePMCStructuredFullTextTool method) (tooluniverse.EuropePMCStructuredFullTextTool method) _classify_variant() (tooluniverse.CancerVarTool method) (tooluniverse.InterVarTool method) _clean_generic_content() (tooluniverse.TRIPDatabaseTool method) (tooluniverse.unified_guideline_tools.TRIPDatabaseTool method) _clean_substance() (tooluniverse.FDAGSRSTool method) _cleanup_expired_sessions() (tooluniverse.memory_manager.MemoryManager method) _cleanup_old_files() (tooluniverse.output_hook.FileSaveHook method) _CLINICAL_FIELDS (tooluniverse.gdc_tool.GDCClinicalDataTool attribute) (tooluniverse.GDCClinicalDataTool attribute) _close_session() (tooluniverse.BaseMCPClient method) (tooluniverse.mcp_client_tool.BaseMCPClient method) _cnv_search() (tooluniverse.ProgenetixTool method) _codon_optimize() (tooluniverse.DNATool method) _coerce_arguments_to_schema() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _coerce_int() (tooluniverse.gwas_tool.GWASRESTTool method) (tooluniverse.GWASRESTTool method) _coerce_str() (tooluniverse.gwas_tool.GWASRESTTool method) (tooluniverse.GWASRESTTool method) _coerce_value_to_type() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _collect_members() (tooluniverse.EnsemblComparaTool method) _combustion_analysis() (tooluniverse.ScientificCalculatorTool method) _common_ion() (tooluniverse.ScientificCalculatorTool method) _compact_entry() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) _compare_configs() (in module tooluniverse.build_optimizer) _compare_disease_healthy() (tooluniverse.hpa_tool.HPAGetDiseaseExpressionTool method) (tooluniverse.HPAGetDiseaseExpressionTool method) _compare_drugs() (tooluniverse.FAERSAnalyticsTool method) _compare_potency() (tooluniverse.DoseResponseTool method) _compare_spectra() (tooluniverse.GNPSTool method) _COMPONENT_PREFIX (tooluniverse.nhanes_tool.NHANESTool attribute) (tooluniverse.NHANESTool attribute) _compose_url() (tooluniverse.pubtator_tool.PubTatorTool method) (tooluniverse.PubTatorTool method) _compute_parameters() (tooluniverse.NCATool method) _compute_summary_stats() (tooluniverse.nhanes_tool.NHANESTool method) (tooluniverse.NHANESTool method) _constrained_elements() (tooluniverse.EnsemblRegulationTool method) _construct_solr_query() (tooluniverse.cellosaurus_tool.CellosaurusQueryConverterTool method) (tooluniverse.CellosaurusQueryConverterTool method) _conv_ids() (tooluniverse.KEGGExtTool method) _convert() (tooluniverse.UniProtIDMappingTool method) _convert_html_to_markdown() (tooluniverse.BioStudiesRESTTool method) _convert_id_to_drug_name() (tooluniverse.FDADrugLabelTool method) (tooluniverse.openfda_tool.FDADrugLabelTool method) _convert_ids() (tooluniverse.GProfilerTool method) _convert_query() (tooluniverse.cellosaurus_tool.CellosaurusQueryConverterTool method) (tooluniverse.CellosaurusQueryConverterTool method) _convert_to_markdown() (tooluniverse.markitdown_tool.MarkItDownTool method) (tooluniverse.MarkItDownTool method) _convert_to_string() (tooluniverse.humanbase_tool.HumanBaseTool method) (tooluniverse.HumanBaseTool method) _convert_tools() (tooluniverse.smolagent_tool.SmolAgentTool method) (tooluniverse.SmolAgentTool method) _count() (tooluniverse.ENAPortalTool method) _count_residues() (tooluniverse.SequenceAnalyzeTool method) _cox_regression() (tooluniverse.SurvivalTool method) _create_control_panel() (tooluniverse.protein_structure_3d_tool.ProteinStructure3DTool method) (tooluniverse.ProteinStructure3DTool method) _create_dual_format_error() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _create_event_emitter() (tooluniverse.compose_tool.ComposeTool method) (tooluniverse.ComposeTool method) _create_from_documents() (tooluniverse.EmbeddingDatabase method) _create_hook_config_from_type() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _create_hook_instance() (tooluniverse.output_hook.HookManager method) _create_log_entry() (tooluniverse.extended_hooks.LoggingHook method) _create_mcp_tool_from_tooluniverse() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) _create_molecule_control_panel() (tooluniverse.Molecule3DTool method) (tooluniverse.molecule_3d_tool.Molecule3DTool method) _create_molecule_html() (tooluniverse.Molecule2DTool method) (tooluniverse.Molecule3DTool method) (tooluniverse.molecule_2d_tool.Molecule2DTool method) (tooluniverse.molecule_3d_tool.Molecule3DTool method) _create_molecule_info_cards() (tooluniverse.Molecule3DTool method) (tooluniverse.molecule_3d_tool.Molecule3DTool method) _create_protein_info_cards() (tooluniverse.protein_structure_3d_tool.ProteinStructure3DTool method) (tooluniverse.ProteinStructure3DTool method) _create_safe_globals() (tooluniverse.BasePythonExecutor method) (tooluniverse.python_executor_tool.BasePythonExecutor method) _create_shared_client() (in module tooluniverse.generate_tools) _create_sub_agents() (tooluniverse.smolagent_tool.SmolAgentTool method) (tooluniverse.SmolAgentTool method) _create_toolbar() (tooluniverse.Molecule3DTool method) (tooluniverse.molecule_3d_tool.Molecule3DTool method) (tooluniverse.protein_structure_3d_tool.ProteinStructure3DTool method) (tooluniverse.ProteinStructure3DTool method) _credentials() (tooluniverse.BRENDATool method) _ctd_diseases() (tooluniverse.MetaboliteTool method) _CYCLE_SUFFIX (tooluniverse.nhanes_tool.NHANESTool attribute) (tooluniverse.NHANESTool attribute) _DATASET_NAME_TO_ID (tooluniverse.SYNERGxDBTool attribute) _deduplicate_types() (in module tooluniverse.generate_tools) _deep_merge() (tooluniverse.ProfileLoader static method) _demo_gene_note() (tooluniverse.OncoKBTool method) _derive_category_from_config() (in module tooluniverse.tool_defaults) _description_to_model() (tooluniverse.MutalyzerTool method) _detect_database() (tooluniverse.geo_tool.GEORESTTool method) (tooluniverse.GEORESTTool method) _detect_ncbi_oai_error() (in module tooluniverse.europe_pmc_tool) _diagnostic() (tooluniverse.EpidemiologyTool method) _discover_entry_point_plugins() (in module tooluniverse.tool_registry) _discover_from_ast() (in module tooluniverse.tool_registry) _discover_motifs() (tooluniverse.MEMETool method) _discover_tool_dependencies() (tooluniverse.compose_tool.ComposeTool method) (tooluniverse.ComposeTool method) _dispatch() (tooluniverse.BioSamplesTool method) (tooluniverse.ChEBITool method) (tooluniverse.ENAPortalTool method) (tooluniverse.EnsemblLDTool method) (tooluniverse.EnsemblPhenotypeTool method) (tooluniverse.EnsemblRegulationTool method) (tooluniverse.EpigenomicsTool method) (tooluniverse.EuroPMCAnnotationsTool method) (tooluniverse.FinnGenTool method) (tooluniverse.GlyGenTool method) (tooluniverse.GNPSTool method) (tooluniverse.GWASSumStatsTool method) (tooluniverse.MetaboAnalystTool method) (tooluniverse.MGnifyExpandedTool method) (tooluniverse.NextstrainTool method) (tooluniverse.PANTHERTool method) (tooluniverse.PDBeSearchTool method) (tooluniverse.PomBaseTool method) (tooluniverse.ProteomeXchangeTool method) (tooluniverse.SGDTool method) (tooluniverse.SwissModelTool method) (tooluniverse.UCSCEpigenomicsTool method) (tooluniverse.UCSCGenomeTool method) (tooluniverse.UniChemTool method) (tooluniverse.UniProtIDMappingTool method) (tooluniverse.WormBaseTool method) _dosage_by_gene() (tooluniverse.ClinGenDosageTool method) _dosage_region_search() (tooluniverse.ClinGenDosageTool method) _double_urlencode() (tooluniverse.efo_tool.OLSRESTTool static method) (tooluniverse.OLSRESTTool static method) _download() (tooluniverse.EmbeddingSync method) _download_and_parse() (tooluniverse.nhanes_tool.NHANESTool method) (tooluniverse.NHANESTool method) _download_file_url() (tooluniverse.FourDNTool method) _download_from_url() (tooluniverse.markitdown_tool.MarkItDownTool method) (tooluniverse.MarkItDownTool method) _download_h5ad() (tooluniverse.CELLxGENECensusTool method) _download_xpt() (tooluniverse.nhanes_tool.NHANESTool method) (tooluniverse.NHANESTool method) _DRUG_SYNONYMS (tooluniverse.SYNERGxDBTool attribute) _drugbank_filter() (tooluniverse.dataset_tool.DatasetTool method) (tooluniverse.DatasetTool method) _drugbank_search() (tooluniverse.dataset_tool.DatasetTool method) (tooluniverse.DatasetTool method) _efo_id_from_uri_or_id() (tooluniverse.gwas_tool.GWASRESTTool method) (tooluniverse.GWASRESTTool method) _embedder() (tooluniverse.EmbeddingDatabase method) _emit_stream_chunk() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) (tooluniverse.compose_tool.ComposeTool method) (tooluniverse.ComposeTool method) _empty_result_note() (tooluniverse.gwas_tool.GWASRESTTool static method) (tooluniverse.GWASRESTTool static method) _encode_annotations_search() (tooluniverse.EpigenomicsTool method) _encode_chromatin_accessibility_search() (tooluniverse.EpigenomicsTool method) _encode_chromatin_state_search() (tooluniverse.EpigenomicsTool method) _encode_hic_search() (tooluniverse.EpigenomicsTool method) _encode_histone_search() (tooluniverse.EpigenomicsTool method) _encode_methylation_search() (tooluniverse.EpigenomicsTool method) _encode_microrna_search() (tooluniverse.EpigenomicsTool method) _encode_rnaseq_search() (tooluniverse.EpigenomicsTool method) _encode_search() (tooluniverse.EpigenomicsTool method) _endpoint_for_type() (tooluniverse.openaire_tool.OpenAIRETool method) (tooluniverse.OpenAIRETool method) _enforce_rate_limit() (tooluniverse.ICiteSearchPublicationsTool method) (tooluniverse.pubmed_tool.PubMedRESTTool method) (tooluniverse.PubMedRESTTool method) (tooluniverse.semantic_scholar_tool.SemanticScholarTool method) (tooluniverse.SemanticScholarTool method) _enrich() (tooluniverse.EnrichrExtTool method) _enrich_text_results() (tooluniverse.rcsb_search_tool.RCSBSearchTool method) (tooluniverse.RCSBSearchTool method) _enrich_with_properties() (tooluniverse.ZincTool method) _enrichment() (tooluniverse.GProfilerTool method) (tooluniverse.PANTHERTool method) _enrichment_analysis() (tooluniverse.ChIPAtlasTool method) _ensembl_regulatory_features() (tooluniverse.EpigenomicsTool method) _ensure_compact_mode_categories() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) _ensure_hook_tools_loaded() (tooluniverse.output_hook.HookManager method) _ensure_playwright_browsers() (tooluniverse.url_tool.URLToPDFTextTool method) (tooluniverse.URLToPDFTextTool method) _ensure_task_manager() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) _ensure_tool_instance() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _error() (tooluniverse.PharmGKBTool method) _ERROR_CLASSIFICATION (tooluniverse.base_tool.BaseTool attribute) (tooluniverse.BaseTool attribute) _es_search() (tooluniverse.IGSRTool method) _estimate_terminal_slope() (tooluniverse.NCATool method) _evaluate_package() (tooluniverse.DynamicPackageDiscovery method) (tooluniverse.package_discovery_tool.DynamicPackageDiscovery method) _excluded_api_key_tools (tooluniverse.execute_function.ToolUniverse attribute) _execute_batch_jobs() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _execute_from_file() (tooluniverse.compose_tool.ComposeTool method) (tooluniverse.ComposeTool method) _execute_function_call_list() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _execute_function_call_list_async() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _execute_graphql() (tooluniverse.PharosTool method) (tooluniverse.RCSBGraphQLTool method) _execute_inline_code() (tooluniverse.compose_tool.ComposeTool method) (tooluniverse.ComposeTool method) _execute_opentargets_query() (in module tooluniverse.openfda_tool) _execute_query() (tooluniverse.SIMBADTool method) _execute_tool_with_stream() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _execute_tool_with_stream_async() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _execute_with_timeout() (tooluniverse.BasePythonExecutor method) (tooluniverse.python_executor_tool.BasePythonExecutor method) _existing_vector_doc_ids() (tooluniverse.EmbeddingDatabase method) _expose_core_discovery_tools() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) _expose_tooluniverse_tools() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) _extract_abstract_from_fulltext_xml() (tooluniverse.europe_pmc_tool.EuropePMCTool method) (tooluniverse.EuropePMCTool method) _extract_abstract_from_pmc_html() (in module tooluniverse.europe_pmc_tool) _extract_all_cv_values() (tooluniverse.MassIVETool method) _extract_antibodies() (tooluniverse.hpa_tool.HPAGetGenePageDetailsTool method) (tooluniverse.HPAGetGenePageDetailsTool method) _extract_approval_summary() (tooluniverse.OpenFDAApprovalTool method) _extract_assemblies_from_summary() (tooluniverse.PDBeAPIRESTTool method) _extract_authors() (tooluniverse.core_tool.CoreTool method) (tooluniverse.CoreTool method) (tooluniverse.pmc_tool.PMCTool method) (tooluniverse.PMCTool method) _extract_bmj_guideline_content() (tooluniverse.TRIPDatabaseTool method) (tooluniverse.unified_guideline_tools.TRIPDatabaseTool method) _extract_cell_line_expression() (tooluniverse.hpa_tool.HPAGetGenePageDetailsTool method) (tooluniverse.HPAGetGenePageDetailsTool method) _extract_clinical_features_from_meta() (tooluniverse.MedGenTool method) _extract_custom_fields() (tooluniverse.FDADrugAdverseEventDetailTool method) (tooluniverse.FDADrugInteractionDetailTool method) (tooluniverse.openfda_adv_tool.FDADrugAdverseEventDetailTool method) (tooluniverse.openfda_adv_tool.FDADrugInteractionDetailTool method) _extract_cv_value() (tooluniverse.ProteomeXchangeTool method) _extract_data() (tooluniverse.EBISearchRESTTool method) (tooluniverse.gene_ontology_tool.GeneOntologyTool method) (tooluniverse.GeneOntologyTool method) (tooluniverse.interpro_tool.InterProRESTTool method) (tooluniverse.InterProRESTTool method) (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) _extract_data_list() (in module tooluniverse.gtex_tool) _extract_dmj_guideline_content() (tooluniverse.TRIPDatabaseTool method) (tooluniverse.unified_guideline_tools.TRIPDatabaseTool method) _extract_doi() (tooluniverse.OpenAIREDatasetTool static method) _extract_embedded_data() (tooluniverse.gwas_tool.GWASRESTTool method) (tooluniverse.GWASRESTTool method) _extract_essential_fields() (tooluniverse.FDADrugAdverseEventDetailTool method) (tooluniverse.FDADrugInteractionDetailTool method) (tooluniverse.openfda_adv_tool.FDADrugAdverseEventDetailTool method) (tooluniverse.openfda_adv_tool.FDADrugInteractionDetailTool method) _extract_expression_summary() (tooluniverse.hpa_tool.HPAGetGenePageDetailsTool method) (tooluniverse.HPAGetGenePageDetailsTool method) _extract_field_terms() (tooluniverse.cellosaurus_tool.CellosaurusQueryConverterTool method) (tooluniverse.CellosaurusQueryConverterTool method) _extract_field_value() (tooluniverse.xml_tool.XMLDatasetTool method) (tooluniverse.XMLDatasetTool method) _extract_files() (tooluniverse.BioStudiesRESTTool method) _extract_files_from_section() (tooluniverse.ArrayExpressRESTTool method) (tooluniverse.BioStudiesRESTTool method) _extract_files_from_study() (tooluniverse.MetaboLightsRESTTool method) _extract_form_error() (tooluniverse.MEMETool method) _extract_from_protein_endpoint() (tooluniverse.ProteinsAPIRESTTool method) _extract_genes() (tooluniverse.MedGenTool method) _extract_genes_from_associations() (tooluniverse.OrphanetTool method) _extract_guideline_content() (tooluniverse.CMAGuidelinesTool method) (tooluniverse.unified_guideline_tools.CMAGuidelinesTool method) _extract_identifier() (tooluniverse.MetaboliteTool method) _extract_if_images() (tooluniverse.hpa_tool.HPAGetGenePageDetailsTool method) (tooluniverse.HPAGetGenePageDetailsTool method) _extract_ihc_images() (tooluniverse.hpa_tool.HPAGetGenePageDetailsTool method) (tooluniverse.HPAGetGenePageDetailsTool method) _extract_info_from_sections() (tooluniverse.PubChemToxTool method) _extract_inheritance() (tooluniverse.MedGenTool method) _extract_job_id() (tooluniverse.MEMETool method) _extract_job_url() (tooluniverse.SwissTargetTool method) _extract_locations() (tooluniverse.NCBIDatasetsTool method) _extract_meaningful_terms() (in module tooluniverse.unified_guideline_tools) _extract_missing_package() (in module tooluniverse.tool_registry) _extract_oa_location() (tooluniverse.unpaywall_tool.UnpaywallTool static method) (tooluniverse.UnpaywallTool static method) _extract_omim() (tooluniverse.MedGenTool method) _extract_outcomes_from_output() (tooluniverse.ClinicalTrialsDetailsTool method) (tooluniverse.ctg_tool.ClinicalTrialsDetailsTool method) _extract_paper_info() (tooluniverse.openalex_tool.OpenAlexTool method) (tooluniverse.OpenAlexTool method) _extract_parameter_text() (tooluniverse.tool_finder_keyword.ToolFinderKeyword method) (tooluniverse.ToolFinderKeyword method) _extract_parent_chembl_id() (tooluniverse.chem_tool.ChEMBLRESTTool method) (tooluniverse.ChEMBLRESTTool method) _extract_phrases() (tooluniverse.tool_finder_keyword.ToolFinderKeyword method) (tooluniverse.ToolFinderKeyword method) _extract_query_context() (tooluniverse.output_hook.SummarizationHook method) _extract_record_data() (tooluniverse.xml_tool.XMLDatasetTool method) (tooluniverse.XMLDatasetTool method) _extract_safety_from_output() (tooluniverse.ClinicalTrialsDetailsTool method) (tooluniverse.ctg_tool.ClinicalTrialsDetailsTool method) _extract_samples_from_section() (tooluniverse.ArrayExpressRESTTool method) _extract_samples_from_study() (tooluniverse.MetaboLightsRESTTool method) _extract_synonyms() (tooluniverse.MedGenTool method) _extract_table_data() (tooluniverse.dailymed_tool.DailyMedSPLParserTool method) (tooluniverse.DailyMedSPLParserTool method) _extract_text() (tooluniverse.europe_pmc_tool.EuropePMCFullTextSnippetsTool method) (tooluniverse.EuropePMCFullTextSnippetsTool method) (tooluniverse.odphp_tool.ODPHPOutlinkFetch method) (tooluniverse.ODPHPOutlinkFetch method) (tooluniverse.OpenAIREDatasetTool static method) _extract_text_content() (tooluniverse.medlineplus_tool.MedlinePlusRESTTool method) (tooluniverse.MedlinePlusRESTTool method) _extract_text_from_html() (in module tooluniverse.europe_pmc_tool) (tooluniverse.europe_pmc_tool.EuropePMCFullTextSnippetsTool method) (tooluniverse.EuropePMCFullTextSnippetsTool method) _extract_text_from_stream_chunk() (tooluniverse.llm_clients.GeminiClient static method) _extract_text_list() (tooluniverse.OpenAIREDatasetTool static method) _extract_tissue_expression() (tooluniverse.hpa_tool.HPAGetGenePageDetailsTool method) (tooluniverse.HPAGetGenePageDetailsTool method) _extract_year() (tooluniverse.core_tool.CoreTool method) (tooluniverse.CoreTool method) (tooluniverse.pmc_tool.PMCTool method) (tooluniverse.PMCTool method) _extract_year_from_date() (tooluniverse.pmc_tool.PMCTool method) (tooluniverse.PMCTool method) _fallback_api_type (tooluniverse.agentic_tool.AgenticTool attribute) _fallback_model_id (tooluniverse.agentic_tool.AgenticTool attribute) _family_for_tc() (tooluniverse.TCDBTool method) _FAMILY_NAME_TO_SLUG (tooluniverse.GPCRdbTool attribute) _fetch() (tooluniverse.APPRISTool method) (tooluniverse.HGNCTool method) _fetch_abstracts() (tooluniverse.pubmed_tool.PubMedRESTTool method) (tooluniverse.PubMedRESTTool method) _fetch_accession() (tooluniverse.NCBINucleotideSearchTool method) _fetch_analysis_annotations() (tooluniverse.MGnifyExpandedTool method) _fetch_and_cache() (tooluniverse.TCDBTool method) _fetch_annotations() (tooluniverse.EuroPMCAnnotationsTool method) _fetch_biocyc_xml() (tooluniverse.MetaCycTool method) _fetch_ctfphc_links() (in module tooluniverse.unified_guideline_tools) _fetch_expasy_enzyme() (tooluniverse.BRENDATool method) _fetch_full_guideline() (tooluniverse.NICEGuidelineFullTextTool method) (tooluniverse.unified_guideline_tools.NICEGuidelineFullTextTool method) _fetch_fulltext_with_trace() (in module tooluniverse.europe_pmc_tool) (tooluniverse.europe_pmc_tool.EuropePMCTool method) (tooluniverse.EuropePMCTool method) _fetch_genes_for_code() (tooluniverse.OrphanetTool method) _fetch_guideline_content() (tooluniverse.TRIPDatabaseTool method) (tooluniverse.unified_guideline_tools.TRIPDatabaseTool method) _fetch_guideline_summary() (tooluniverse.NICEWebScrapingTool method) (tooluniverse.unified_guideline_tools.NICEWebScrapingTool method) _fetch_icite() (tooluniverse.ICiteSearchPublicationsTool method) _fetch_missing_abstract() (tooluniverse.semantic_scholar_tool.SemanticScholarTool method) (tooluniverse.SemanticScholarTool method) _fetch_motif_summary() (tooluniverse.HocomocoTool method) _fetch_page() (tooluniverse.SiderTool method) _fetch_pdb_content() (tooluniverse.protein_structure_3d_tool.ProteinStructure3DTool method) (tooluniverse.ProteinStructure3DTool method) _fetch_protein_data() (tooluniverse.iPTMnetTool method) _fetch_pubmed_abstracts() (tooluniverse.pmc_tool.PMCTool method) (tooluniverse.PMCTool method) _fetch_results() (tooluniverse.InterProScanTool method) _fetch_sabiork_kinetics() (tooluniverse.BRENDATool method) _fetch_sequence() (tooluniverse.NCBINucleotideSearchTool method) _fetch_sign_table() (in module tooluniverse.unified_guideline_tools) _fetch_spl_xml() (tooluniverse.dailymed_tool.DailyMedSPLParserTool method) (tooluniverse.DailyMedSPLParserTool method) _fetch_summaries() (tooluniverse.pubmed_tool.PubMedRESTTool method) (tooluniverse.PubMedRESTTool method) _fetch_term() (tooluniverse.DiseaseOntologyTool method) _fetch_variant() (tooluniverse.clinvar_tool.ClinVarRESTTool method) (tooluniverse.ClinVarRESTTool method) _fetch_who_guideline() (tooluniverse.unified_guideline_tools.WHOGuidelineFullTextTool method) (tooluniverse.WHOGuidelineFullTextTool method) _fetch_xml() (tooluniverse.PDBePISATool method) _filter() (tooluniverse.xml_tool.XMLDatasetTool method) (tooluniverse.XMLDatasetTool method) _filter_and_deduplicate_tools() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _filter_by_age() (tooluniverse.nhanes_tool.NHANESTool static method) (tooluniverse.NHANESTool static method) _FILTER_MAP (tooluniverse.gdc_tool.GDCClinicalDataTool attribute) (tooluniverse.GDCClinicalDataTool attribute) _FILTER_PARAMS (tooluniverse.CPICSearchPairsTool attribute) _filter_principal_isoforms() (tooluniverse.APPRISTool static method) _filter_search_results() (tooluniverse.pubtator_tool.PubTatorTool method) (tooluniverse.PubTatorTool method) _filter_serious_events() (tooluniverse.FAERSAnalyticsTool method) _fimo_scan() (tooluniverse.MEMETool method) _find_classes() (tooluniverse.RxClassTool method) _find_entry_id_via_search() (tooluniverse.EBISearchRESTTool method) _find_matches() (tooluniverse.xml_tool.XMLDatasetTool method) (tooluniverse.XMLDatasetTool method) _find_orfs() (tooluniverse.DNATool method) _find_orthologs() (tooluniverse.GProfilerTool method) _find_pathways_by_gene() (tooluniverse.WikiPathwaysExtTool method) _find_restriction_sites() (tooluniverse.DNATool method) _find_rxcui() (tooluniverse.RxNormExtendedTool method) _find_sections_recursive() (tooluniverse.PubChemToxTool method) _find_subtype_codes() (tooluniverse.OrphanetTool method) _find_text() (tooluniverse.SynBioHubTool static method) _fisher_exact() (tooluniverse.ScientificCalculatorTool method) _fit_4pl() (tooluniverse.DoseResponseTool method) _fit_curve() (tooluniverse.DoseResponseTool method) _fit_hill_for_loewe() (tooluniverse.DrugSynergyTool method) _fit_one_compartment() (tooluniverse.NCATool method) _fix_output() (tooluniverse.extended_hooks.ValidationHook method) _fold_protein() (tooluniverse.ESMTool method) _force_load_hook_tools_from_json() (tooluniverse.output_hook.HookManager method) _format_age_bounds() (tooluniverse.nhanes_tool.NHANESTool static method) (tooluniverse.NHANESTool static method) _format_allele() (tooluniverse.ClinGenAlleleTool method) _format_analysis_result() (tooluniverse.ReactomeAnalysisTool method) _format_annotation() (tooluniverse.GenomeNexusTool method) _format_as_json() (tooluniverse.tool_finder_llm.ToolFinderLLM method) (tooluniverse.ToolFinderLLM method) _format_batch_as_messages() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _format_date() (tooluniverse.OpenFDAApprovalTool method) _format_endpoint_url() (tooluniverse.ClinicalTrialsTool method) (tooluniverse.ctg_tool.ClinicalTrialsTool method) _format_error_response() (tooluniverse.BasePythonExecutor method) (tooluniverse.python_executor_tool.BasePythonExecutor method) _format_files() (in module tooluniverse.generate_tools) _format_json() (tooluniverse.extended_hooks.FormattingHook method) _format_list() (tooluniverse.extended_hooks.FormattingHook method) _format_prompt() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) _format_response() (tooluniverse.medlineplus_tool.MedlinePlusRESTTool method) (tooluniverse.MedlinePlusRESTTool method) _format_success_response() (tooluniverse.BasePythonExecutor method) (tooluniverse.python_executor_tool.BasePythonExecutor method) _format_term_collection() (tooluniverse.ols_tool.OLSTool method) (tooluniverse.OLSTool method) _format_text() (tooluniverse.extended_hooks.FormattingHook method) _format_tools_for_prompt() (tooluniverse.tool_finder_llm.ToolFinderLLM method) (tooluniverse.ToolFinderLLM method) _format_vep_result() (tooluniverse.EnsemblVEPTool method) _fst() (tooluniverse.PopGenTool method) _gc_content() (tooluniverse.SequenceAnalyzeTool method) _gemini_model_id (tooluniverse.agentic_tool.AgenticTool attribute) _gene_correlation() (tooluniverse.TIMERTool method) _gene_detail() (tooluniverse.PomBaseTool method) _gene_expression() (tooluniverse.BgeeTool method) (tooluniverse.WormBaseTool method) _gene_id_matches() (tooluniverse.GxATool static method) _gene_info() (tooluniverse.PANTHERTool method) _gene_overview() (tooluniverse.WormBaseTool method) _gene_phenotypes() (tooluniverse.PomBaseTool method) (tooluniverse.WormBaseTool method) _gene_search() (tooluniverse.BgeeTool method) _gene_summary_search() (tooluniverse.PomBaseTool method) _gene_to_uniprot() (tooluniverse.UniProtIDMappingTool method) _generate_comparison_summary() (tooluniverse.hpa_tool.HPAGetComparativeExpressionTool method) (tooluniverse.HPAGetComparativeExpressionTool method) _generate_location_summary() (tooluniverse.hpa_tool.HPAGetSubcellularLocationTool method) (tooluniverse.HPAGetSubcellularLocationTool method) _generate_protein_sequence() (tooluniverse.ESMTool method) _generate_recommendation() (tooluniverse.pypi_package_inspector_tool.PyPIPackageInspector method) (tooluniverse.PyPIPackageInspector method) _generate_session_id() (tooluniverse.SwissDockTool method) _genome_detail() (tooluniverse.MGnifyExpandedTool method) _genome_search() (tooluniverse.MGnifyExpandedTool method) _geo_atacseq_search() (tooluniverse.EpigenomicsTool method) _geo_chipseq_search() (tooluniverse.EpigenomicsTool method) _geo_dataset_details() (tooluniverse.EpigenomicsTool method) _geo_esearch() (tooluniverse.EpigenomicsTool method) _geo_esummary() (tooluniverse.EpigenomicsTool method) _geo_methylation_search() (tooluniverse.EpigenomicsTool method) _geo_rnaseq_search() (tooluniverse.EpigenomicsTool method) _get() (tooluniverse.OncoTreeBaseTool method) _get_acc2tcid() (tooluniverse.TCDBTool method) _get_access_token() (tooluniverse.ICDTool method) _get_actionability() (tooluniverse.ClinGenTool method) _get_actionability_adult() (tooluniverse.ClinGenTool method) _get_actionability_pediatric() (tooluniverse.ClinGenTool method) _get_acute_effects() (tooluniverse.PubChemToxTool method) _get_alignment() (tooluniverse.RfamTool method) _get_all_names_by_rxcui() (tooluniverse.rxnorm_tool.RxNormTool method) (tooluniverse.RxNormTool method) _get_all_records_data() (tooluniverse.xml_tool.XMLDatasetTool method) (tooluniverse.XMLDatasetTool method) _get_all_therapeutics() (tooluniverse.TheraSAbDabTool method) _get_allele() (tooluniverse.ClinGenAlleleTool method) _get_allele_detail() (tooluniverse.AllianceGenomeTool method) _get_anndata() (tooluniverse.CELLxGENECensusTool method) _get_annotations() (tooluniverse.DfamTool method) (tooluniverse.EPMCAnnotationsTool method) (tooluniverse.OmniPathTool method) (tooluniverse.RGDTool method) _get_answer_list() (tooluniverse.LOINCTool method) _get_antigen() (tooluniverse.EBIProteinsExtTool method) _get_antigen_specificity() (tooluniverse.VDJDBTool method) _get_api_key() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smolagent_tool.SmolAgentTool method) (tooluniverse.SmolAgentTool method) (tooluniverse.ToolUniverse method) (tooluniverse.umls_tool.UMLSRESTTool method) (tooluniverse.UMLSRESTTool method)

_get_approval_history() (tooluniverse.FDAOrangeBookTool method) (tooluniverse.OpenFDAApprovalTool method) _get_approved_products() (tooluniverse.OpenFDAApprovalTool method) _get_assay() (tooluniverse.PubChemBioAssayTool method) _get_assay_summary() (tooluniverse.PubChemBioAssayTool method) _get_assemblies() (tooluniverse.PDBePISATool method) _get_assembly() (tooluniverse.RCSBDataTool method) _get_assembly_info() (tooluniverse.EnsemblInfoTool method) _get_associations() (tooluniverse.MonarchV3Tool method) _get_attributes() (tooluniverse.BridgeDbTool method) _get_available_methods() (tooluniverse.ToolUniverseClient method) _get_available_tools() (tooluniverse.tool_finder_llm.ToolFinderLLM method) (tooluniverse.ToolFinderLLM method) _get_baseline_expression() (tooluniverse.ExpressionAtlasTool method) _get_best_structures() (tooluniverse.PDBeSIFTSTool method) _get_biomarker_associations() (tooluniverse.PharmacoDBTool method) _get_biosamples() (tooluniverse.ProgenetixTool method) _get_brite_hierarchy() (tooluniverse.KEGGExtTool method) _get_by_any_name() (tooluniverse.EBITaxonomyTool method) _get_by_scientific_name() (tooluniverse.EBITaxonomyTool method) _get_by_tax_id() (tooluniverse.EBITaxonomyTool method) _get_cancer_genes() (tooluniverse.OncoKBTool method) _get_cancer_hotspots() (tooluniverse.GenomeNexusTool method) _get_canonical_transcript() (tooluniverse.GenomeNexusTool method) _get_carcinogen_classification() (tooluniverse.PubChemToxTool method) _get_cell_line() (tooluniverse.DepMapTool method) (tooluniverse.PharmacoDBTool method) _get_cell_line_info() (tooluniverse.cellosaurus_tool.CellosaurusGetCellLineInfoTool method) (tooluniverse.CellosaurusGetCellLineInfoTool method) _get_cell_lines() (tooluniverse.ClueTool method) (tooluniverse.DepMapTool method) _get_census_versions() (tooluniverse.CELLxGENECensusTool method) _get_chemical() (tooluniverse.MyChemTool method) _get_children() (tooluniverse.NCIThesaurusTool method) _get_clan_members() (tooluniverse.InterProDomainArchTool method) _get_class_members() (tooluniverse.RxClassTool method) _get_classification() (tooluniverse.OrphanetTool method) _get_classifications() (tooluniverse.GenCCTool method) _get_clinical_annotations() (tooluniverse.PharmGKBTool method) _get_clinical_data() (tooluniverse.PDCTool method) _get_clinical_features() (tooluniverse.MedGenTool method) _get_clinical_synopsis() (tooluniverse.OMIMTool method) _get_cluster() (tooluniverse.UniRefTool method) _get_code_details() (tooluniverse.LOINCTool method) _get_cohorts() (tooluniverse.ProgenetixTool method) _get_collection() (tooluniverse.CellxGeneDiscoveryTool method) (tooluniverse.EOLTool method) _get_collection_meta() (tooluniverse.EmbeddingDatabase method) _get_collections() (tooluniverse.SynBioHubTool method) _get_combo_matrix() (tooluniverse.SYNERGxDBTool method) _get_combo_stats() (tooluniverse.SYNERGxDBTool method) _get_complex() (tooluniverse.ComplexPortalTool method) _get_complex_details() (tooluniverse.IntActRESTTool method) _get_complexes() (tooluniverse.OmniPathTool method) _get_compound() (tooluniverse.ChEBITool method) (tooluniverse.EMoleculesTool method) (tooluniverse.EnamineTool method) (tooluniverse.KEGGExtTool method) (tooluniverse.MculeTool method) (tooluniverse.MetaCycTool method) (tooluniverse.PDBeSearchTool method) (tooluniverse.PharmacoDBTool method) (tooluniverse.ZincTool method) _get_concept() (tooluniverse.BioPortalTool method) (tooluniverse.NCIThesaurusTool method) _get_condition() (tooluniverse.MedGenTool method) _get_config_file_path() (tooluniverse.output_hook.HookManager method) _get_consensus() (tooluniverse.MobiDBTool method) _get_contained_events() (tooluniverse.ReactomeContentTool method) _get_coordinates() (tooluniverse.EBIProteinsCoordinatesTool method) (tooluniverse.EBIProteinsExtTool method) _get_county_rankings_info() (tooluniverse.health_disparities_tool.HealthDisparitiesTool method) (tooluniverse.HealthDisparitiesTool method) _get_covariance_model() (tooluniverse.RfamTool method) _get_cpg_islands() (tooluniverse.UCSCEpigenomicsTool method) _get_current_timestamp() (tooluniverse.humanbase_tool.HumanBaseTool method) (tooluniverse.HumanBaseTool method) _get_database() (tooluniverse.MculeTool method) _get_database_summary() (tooluniverse.VDJDBTool method) _get_database_version() (tooluniverse.BiGGModelsTool method) _get_dataset() (tooluniverse.CryoETTool method) (tooluniverse.HarmonizomeTool method) (tooluniverse.HuBMAPTool method) (tooluniverse.MassIVETool method) (tooluniverse.NextstrainTool method) (tooluniverse.ProteomeXchangeTool method) _get_dataset_info() (tooluniverse.GTExV2Tool method) (tooluniverse.nhanes_tool.NHANESTool method) (tooluniverse.NHANESTool method) _get_dataset_path() (tooluniverse.xml_tool.XMLDatasetTool method) (tooluniverse.XMLDatasetTool method) _get_descriptor() (tooluniverse.MeSHTool method) _get_descriptors() (tooluniverse.RDKitCheminfoTool method) _get_disease() (tooluniverse.KEGGExtTool method) (tooluniverse.MyDiseaseTool method) (tooluniverse.OrphanetTool method) (tooluniverse.UniProtRefTool method) _get_disease_detail() (tooluniverse.AllianceGenomeTool method) _get_disease_efo() (tooluniverse.EpiGraphDBTool method) _get_disease_genes() (tooluniverse.AllianceGenomeTool method) (tooluniverse.DisGeNETTool method) (tooluniverse.KEGGExtTool method) _get_disease_targets() (tooluniverse.PharosTool method) _get_diseases() (tooluniverse.MetaboliteTool method) _get_domain_summary() (tooluniverse.CATHTool method) _get_dorothea_regulon() (tooluniverse.OmniPathTool method) _get_dosage_sensitivity() (tooluniverse.ClinGenTool method) _get_dosing_guidelines() (tooluniverse.PharmGKBTool method) _get_download_stats() (tooluniverse.pypi_package_inspector_tool.PyPIPackageInspector method) (tooluniverse.PyPIPackageInspector method) _get_download_urls() (tooluniverse.NCBISRATool method) _get_drivers() (tooluniverse.IntOGenTool method) _get_drug() (tooluniverse.DrugCentralTool method) (tooluniverse.KEGGExtTool method) (tooluniverse.SYNERGxDBTool method) _get_drug_classes() (tooluniverse.RxClassTool method) _get_drug_info() (tooluniverse.RxNormExtendedTool method) _get_drug_names_query() (in module tooluniverse.openfda_tool) _get_drug_response() (tooluniverse.DepMapTool method) _get_drug_targets() (tooluniverse.KEGGExtTool method) _get_drugs() (tooluniverse.DGIdbTool method) _get_drugs_for_side_effect() (tooluniverse.SiderTool method) _get_drugs_risk_factors() (tooluniverse.EpiGraphDBTool method) _get_embeddings() (tooluniverse.CELLxGENECensusTool method) _get_employments() (tooluniverse.ORCIDTool method) _get_encode_ccres() (tooluniverse.UCSCEpigenomicsTool method) _get_enhanced_pathway() (tooluniverse.ReactomeContentTool method) _get_enrichment() (tooluniverse.STRINGExtTool method) _get_entity() (tooluniverse.MonarchV3Tool method) _get_entity_details() (tooluniverse.PharmGKBTool method) _get_entity_pathways() (tooluniverse.ReactomeInteractorsTool method) _get_entity_type() (tooluniverse.EPMCAnnotationsTool method) _get_entries_for_protein() (tooluniverse.InterProEntryTool method) _get_entry() (tooluniverse.DisProtTool method) (tooluniverse.EMPIARTool method) (tooluniverse.OMIMTool method) (tooluniverse.PROSITETool method) (tooluniverse.RCSBDataTool method) (tooluniverse.UniParcTool method) _get_enzyme_info() (tooluniverse.BRENDATool method) _get_enzyme_kinetics() (tooluniverse.BRENDATool method) _get_enzyme_substrate() (tooluniverse.OmniPathTool method) _get_epidemiology() (tooluniverse.OrphanetTool method) _get_epitopes() (tooluniverse.EBIProteinsEpitopeTool method) _get_eqtl_genes() (tooluniverse.GTExV2Tool method) _get_europepmc_abstract() (tooluniverse.EuropePMCGuidelinesTool method) (tooluniverse.unified_guideline_tools.EuropePMCGuidelinesTool method) _get_europepmc_full_content() (tooluniverse.EuropePMCGuidelinesTool method) (tooluniverse.unified_guideline_tools.EuropePMCGuidelinesTool method) _get_evidence_count() (tooluniverse.INDRADBTool method) _get_exclusivity() (tooluniverse.FDAOrangeBookTool method) _get_experiment() (tooluniverse.ExpressionAtlasTool method) (tooluniverse.SRATool method) _get_experiment_expression() (tooluniverse.GxATool method) _get_experiment_info() (tooluniverse.GxATool method) _get_experiment_list() (tooluniverse.ChIPAtlasTool method) _get_experiment_metadata() (tooluniverse.FourDNTool method) _get_experiments() (tooluniverse.PharmacoDBTool method) _get_expression() (tooluniverse.TIMERTool method) _get_expression_data() (tooluniverse.AllenBrainTool method) _get_expression_summary() (tooluniverse.ProteomicsDBTool method) _get_expression_units() (tooluniverse.CancerPrognosisTool method) _get_external_records() (tooluniverse.ClinGenARTool method) _get_faers_count() (tooluniverse.FAERSAnalyticsTool method) _get_faers_total_count() (tooluniverse.FAERSAnalyticsTool method) _get_families() (tooluniverse.TCDBTool method) _get_family() (tooluniverse.DfamTool method) (tooluniverse.RfamTool method) _get_family_accession() (tooluniverse.RfamTool method) _get_family_detail() (tooluniverse.PfamTool method) _get_family_id() (tooluniverse.RfamTool method) _get_family_proteins() (tooluniverse.PfamTool method) _get_family_proteomes() (tooluniverse.PfamTool method) _get_features() (tooluniverse.EBIProteinsExtTool method) (tooluniverse.EBIProteinsFeaturesTool method) _get_field_values() (tooluniverse.CTGovAPITool method) (tooluniverse.NeuroMorphoTool method) _get_file_metadata() (tooluniverse.FourDNTool method) _get_filter_description() (tooluniverse.xml_tool.XMLDatasetTool method) (tooluniverse.XMLDatasetTool method) _get_filter_function() (tooluniverse.xml_tool.XMLDatasetTool method) (tooluniverse.XMLDatasetTool method) _get_filtering_terms() (tooluniverse.ProgenetixTool method) _get_food_detail() (tooluniverse.FoodDataCentralTool method) _get_food_nutrients() (tooluniverse.FoodDataCentralTool method) _get_format_string() (tooluniverse.SIMBADTool method) _get_full_record() (tooluniverse.ITISTool method) _get_full_text_url() (tooluniverse.unpaywall_tool.UnpaywallTool method) (tooluniverse.UnpaywallTool method) _get_functional_annotations() (tooluniverse.APPRISTool method) (tooluniverse.STRINGExtTool method) _get_funfam() (tooluniverse.CATHTool method) _get_gene() (tooluniverse.BiGGModelsTool method) (tooluniverse.HarmonizomeTool method) (tooluniverse.LOVDTool method) (tooluniverse.MyGeneTool method) (tooluniverse.RGDTool method) (tooluniverse.XenbaseTool method) _get_gene_alleles() (tooluniverse.AllianceGenomeTool method) _get_gene_by_id() (tooluniverse.NCBIDatasetsTool method) _get_gene_by_symbol() (tooluniverse.NCBIDatasetsTool method) _get_gene_categories() (tooluniverse.DGIdbTool method) _get_gene_correlations() (tooluniverse.ARCHS4Tool method) _get_gene_dependencies() (tooluniverse.DepMapTool method) _get_gene_detail() (tooluniverse.AllianceGenomeTool method) _get_gene_disease_associations() (tooluniverse.DisGeNETTool method) _get_gene_disease_models() (tooluniverse.AllianceGenomeTool method) _get_gene_diseases() (tooluniverse.OrphanetTool method) _get_gene_drugs() (tooluniverse.EpiGraphDBTool method) _get_gene_entrez_id() (tooluniverse.CancerPrognosisTool method) _get_gene_entrez_ids() (tooluniverse.cbioportal_tool.CBioPortalRESTTool method) (tooluniverse.CBioPortalRESTTool method) _get_gene_expression() (tooluniverse.ARCHS4Tool method) (tooluniverse.CancerPrognosisTool method) (tooluniverse.ClueTool method) (tooluniverse.GTExV2Tool method) _get_gene_expression_summary() (tooluniverse.AllianceGenomeTool method) _get_gene_functions() (tooluniverse.GOAPITool method) _get_gene_id() (tooluniverse.TIMERTool method) _get_gene_info() (tooluniverse.EVETool method) (tooluniverse.IMGTTool method) (tooluniverse.IntOGenTool method) (tooluniverse.OncoKBTool method) _get_gene_interactions() (tooluniverse.AllianceGenomeTool method) _get_gene_map() (tooluniverse.OMIMTool method) _get_gene_orthologs() (tooluniverse.AllianceGenomeTool method) (tooluniverse.NCBIDatasetsTool method) _get_gene_pathways() (tooluniverse.KEGGExtTool method) _get_gene_phenotype_hits() (tooluniverse.IMPCTool method) _get_gene_phenotypes() (tooluniverse.AllianceGenomeTool method) _get_gene_protein() (tooluniverse.PDCTool method) _get_gene_summary() (tooluniverse.IMPCTool method) _get_gene_tree() (tooluniverse.EnsemblComparaTool method) _get_gene_validity() (tooluniverse.ClinGenTool method) _get_genes() (tooluniverse.DGIdbTool method) (tooluniverse.OrphanetTool method) _get_genetic_cor() (tooluniverse.EpiGraphDBTool method) _get_genome() (tooluniverse.BVBRCTool method) (tooluniverse.GTDBTool method) _get_ghs_classification() (tooluniverse.PubChemToxTool method) _get_github_stats() (tooluniverse.pypi_package_inspector_tool.PyPIPackageInspector method) (tooluniverse.PyPIPackageInspector method) _get_global_fallback_chain() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) _get_group() (tooluniverse.OMATool method) (tooluniverse.OrthoDBTool method) _get_guideline() (tooluniverse.AHAACCGuidelineTool method) _get_gwas_efo() (tooluniverse.EpiGraphDBTool method) _get_headers() (tooluniverse.AddgeneTool method) (tooluniverse.ClueTool method) (tooluniverse.DisGeNETTool method) (tooluniverse.NvidiaNIMTool method) (tooluniverse.OncoKBTool method) _get_hierarchy() (tooluniverse.BioPortalTool method) (tooluniverse.ITISTool method) _get_hierarchy_entry() (tooluniverse.EOLTool method) _get_hog() (tooluniverse.OMATool method) _get_hook_config_file_path() (in module tooluniverse.default_config) _get_human_transporters() (tooluniverse.TCDBTool method) _get_icd_mapping() (tooluniverse.OrphanetTool method) _get_id_history() (tooluniverse.EnsemblArchiveTool method) _get_id_sequence() (tooluniverse.EnsemblSequenceTool method) _get_indications() (tooluniverse.SiderTool method) _get_individuals() (tooluniverse.ProgenetixTool method) _get_induced_subtree() (tooluniverse.OpenTreeTool method) _get_info() (tooluniverse.MetaboliteTool method) _get_inhibitors() (tooluniverse.BRENDATool method) _get_installation_instructions() (tooluniverse.package_tool.PackageTool method) (tooluniverse.PackageTool method) _get_instances() (tooluniverse.ELMTool method) _get_interaction_details() (tooluniverse.EBIProteinsInteractionsTool method) _get_interactions() (tooluniverse.DGIdbTool method) (tooluniverse.EBIProteinsInteractionsTool method) (tooluniverse.SIGNORTool method) (tooluniverse.STITCHTool method) _get_interactors() (tooluniverse.ReactomeInteractorsTool method) (tooluniverse.STITCHTool method) _get_intercell() (tooluniverse.OmniPathTool method) _get_interface_residues() (tooluniverse.PDBe_KB_Tool method) _get_interfaces() (tooluniverse.PDBePISATool method) _get_isoforms() (tooluniverse.APPRISTool method) _get_job() (tooluniverse.DynaMut2Tool method) _get_job_error() (tooluniverse.MEMETool method) _get_job_results() (tooluniverse.InterProScanTool method) _get_job_status() (tooluniverse.InterProScanTool method) _get_json() (tooluniverse.ols_tool.OLSTool method) (tooluniverse.OLSTool method) _get_kcat() (tooluniverse.BRENDATool method) _get_keyword() (tooluniverse.UniProtRefTool method) _get_km() (tooluniverse.BRENDATool method) _get_label() (tooluniverse.FDALabelTool method) _get_levels() (tooluniverse.OncoKBTool method) _get_libraries() (tooluniverse.EnamineTool method) _get_ligand_info() (tooluniverse.RCSBGraphQLTool method) _get_ligand_monomers() (tooluniverse.PDBeLigandsTool method) _get_ligand_receptor() (tooluniverse.OmniPathTool method) _get_ligand_sites() (tooluniverse.PDBe_KB_Tool method) _get_ligands() (tooluniverse.GPCRdbTool method) _get_local_info() (tooluniverse.package_tool.PackageTool method) (tooluniverse.PackageTool method) _get_location() (tooluniverse.UniProtLocationsTool method) _get_mappings() (tooluniverse.MonarchV3Tool method) (tooluniverse.OxOTool method) _get_max_delta() (tooluniverse.SpliceAITool method) _get_mcp_endpoint() (tooluniverse.BaseMCPClient method) (tooluniverse.mcp_client_tool.BaseMCPClient method) _get_median_gene_expression() (tooluniverse.GTExV2Tool method) _get_metabolite() (tooluniverse.BiGGModelsTool method) _get_model() (tooluniverse.BiGGModelsTool method) _get_model_genes() (tooluniverse.BiGGModelsTool method) _get_model_metabolites() (tooluniverse.BiGGModelsTool method) _get_model_reactions() (tooluniverse.BiGGModelsTool method) _get_model_summary() (tooluniverse.SwissModelTool method) _get_models() (tooluniverse.SwissModelTool method) _get_modification() (tooluniverse.MODOMICSTool method) _get_monomer_analysis() (tooluniverse.PDBePISATool method) _get_morphometry() (tooluniverse.NeuroMorphoTool method) _get_motif() (tooluniverse.HocomocoTool method) _get_mr() (tooluniverse.EpiGraphDBTool method) _get_mrca() (tooluniverse.OpenTreeTool method) _get_mrna_profile() (tooluniverse.CancerPrognosisTool method) (tooluniverse.TIMERTool method) _get_multi_tissue_eqtls() (tooluniverse.GTExV2Tool method) _get_mutagenesis() (tooluniverse.EBIProteinsExtTool method) _get_mutation_profile_id() (tooluniverse.cbioportal_tool.CBioPortalRESTTool method) (tooluniverse.CBioPortalRESTTool method) _get_mutations() (tooluniverse.GPCRdbTool method) _get_mutations_by_gene() (tooluniverse.COSMICTool method) _get_namespace() (tooluniverse.IdentifiersOrgTool method) _get_natural_history() (tooluniverse.OrphanetTool method) _get_neighborhood() (tooluniverse.PathwayCommonsTool method) _get_nested_value() (tooluniverse.FDADrugAdverseEventDetailTool method) (tooluniverse.FDADrugInteractionDetailTool method) (tooluniverse.openfda_adv_tool.FDADrugAdverseEventDetailTool method) (tooluniverse.openfda_adv_tool.FDADrugInteractionDetailTool method) _get_network() (tooluniverse.KEGGExtTool method) (tooluniverse.NDExTool method) _get_network_summary() (tooluniverse.NDExTool method) _get_neuron_by_id() (tooluniverse.NeuroMorphoTool method) _get_nonpolymer_entity() (tooluniverse.RCSBDataTool method) _get_obs_metadata() (tooluniverse.CELLxGENECensusTool method) _get_organisms() (tooluniverse.SwissTargetTool method) _get_orthologs() (tooluniverse.OMATool method) (tooluniverse.OrthoDBTool method) (tooluniverse.RGDTool method) _get_orthologues() (tooluniverse.EnsemblComparaTool method) _get_os_data() (tooluniverse.TIMERTool method) _get_outlier_residues() (tooluniverse.PDBeValidationTool method) _get_package_to_install() (tooluniverse.BasePythonExecutor method) (tooluniverse.python_executor_tool.BasePythonExecutor method) _get_page() (tooluniverse.EOLTool method) _get_paralogues() (tooluniverse.EnsemblComparaTool method) _get_param_mapping() (tooluniverse.BaseRESTTool method) (tooluniverse.biomodels_tool.BioModelsRESTTool method) (tooluniverse.BioModelsRESTTool method) (tooluniverse.crossref_tool.CrossrefRESTTool method) (tooluniverse.CrossrefRESTTool method) (tooluniverse.DataCiteRESTTool method) (tooluniverse.FederalRegisterTool method) (tooluniverse.pubmed_tool.PubMedRESTTool method) (tooluniverse.PubMedRESTTool method) (tooluniverse.zenodo_tool.ZenodoRESTTool method) (tooluniverse.ZenodoRESTTool method) _get_params() (tooluniverse.OMIMTool method) _get_parents() (tooluniverse.DiseaseOntologyTool method) _get_part() (tooluniverse.SynBioHubTool method) _get_patent_info() (tooluniverse.FDAOrangeBookTool method) _get_pathway() (tooluniverse.MetaCycTool method) (tooluniverse.PathwayCommonsTool method) (tooluniverse.PlantReactomeTool method) (tooluniverse.SIGNORTool method) _get_pathway_genes() (tooluniverse.KEGGExtTool method) (tooluniverse.WikiPathwaysExtTool method) _get_pathway_library() (tooluniverse.MetaboAnalystTool method) _get_patient_guideline() (tooluniverse.NCCNGuidelineTool method) _get_pdb_mapping() (tooluniverse.TCDBTool method) _get_pdb_to_uniprot() (tooluniverse.PDBeSIFTSTool method) _get_peak_data() (tooluniverse.ChIPAtlasTool method) _get_perturbation() (tooluniverse.ClueTool method) _get_phenotype() (tooluniverse.FinnGenTool method) _get_phenotypes() (tooluniverse.GmrepoTool method) (tooluniverse.OrphanetTool method) _get_phenotypes_by_gene() (tooluniverse.IMPCTool method) _get_plasmid() (tooluniverse.AddgeneTool method) _get_polymer_entity() (tooluniverse.RCSBGraphQLTool method) _get_population_frequencies() (tooluniverse.EnsemblVariationExtTool method) _get_position_scores() (tooluniverse.CADDTool method) _get_presence_matrix() (tooluniverse.CELLxGENECensusTool method) _get_principal() (tooluniverse.APPRISTool method) _get_profile() (tooluniverse.ORCIDTool method) _get_properties() (tooluniverse.MetaboliteTool method) _get_protac() (tooluniverse.ProtacDBTool method) _get_protein() (tooluniverse.GPCRdbTool method) (tooluniverse.MobiDBTool method) (tooluniverse.OMATool method) _get_protein_domain_architecture() (tooluniverse.InterProDomainArchTool method) _get_protein_embedding() (tooluniverse.ESMTool method) _get_protein_expression() (tooluniverse.ProteomicsDBTool method) _get_protein_pfam() (tooluniverse.PfamTool method) _get_protein_scores() (tooluniverse.AlphaMissenseTool method) _get_protein_structure() (tooluniverse.BVBRCTool method) _get_proteins_by_domain() (tooluniverse.InterProExtTool method) _get_proteoforms() (tooluniverse.iPTMnetTool method) _get_proteome() (tooluniverse.UniProtRefTool method) _get_proteomics() (tooluniverse.EBIProteinsExtTool method) _get_proteomics_ptm() (tooluniverse.EBIProteinsExtTool method) _get_ptm_ppi() (tooluniverse.iPTMnetTool method) _get_ptm_sites() (tooluniverse.iPTMnetTool method) _get_publications() (tooluniverse.miRNAGetTool method) _get_pugview_data() (tooluniverse.PubChemToxTool method) _get_purchasable() (tooluniverse.ZincTool method) _get_pypi_info() (tooluniverse.package_tool.PackageTool method) (tooluniverse.PackageTool method) _get_pypi_metadata() (tooluniverse.pypi_package_inspector_tool.PyPIPackageInspector method) (tooluniverse.PyPIPackageInspector method) _get_quality_scores() (tooluniverse.PDBeValidationTool method) _get_quick_start_guide() (tooluniverse.package_tool.PackageTool method) (tooluniverse.PackageTool method) _get_range_scores() (tooluniverse.CADDTool method) _get_reaction() (tooluniverse.BiGGModelsTool method) (tooluniverse.MetaCycTool method) _get_region_associations() (tooluniverse.FinnGenTool method) (tooluniverse.GWASSumStatsTool method) _get_region_sequence() (tooluniverse.EnsemblSequenceTool method) _get_registry() (tooluniverse.BioregistryTool method) _get_related_drugs() (tooluniverse.RxNormExtendedTool method) _get_repository() (tooluniverse.Re3DataTool method) _get_residue_listing() (tooluniverse.PDBeLigandsTool method) _get_residue_scores() (tooluniverse.AlphaMissenseTool method) _get_result() (tooluniverse.FoldseekTool method) _get_rna() (tooluniverse.miRNAGetTool method) _get_run_info() (tooluniverse.NCBISRATool method) _get_rxcui_by_name() (tooluniverse.rxnorm_tool.RxNormTool method) (tooluniverse.RxNormTool method) _get_sample() (tooluniverse.BioSamplesTool method) _get_sample_info() (tooluniverse.GTExV2Tool method) _get_samples() (tooluniverse.TIMERTool method) _get_score_set() (tooluniverse.MaveDBTool method) _get_screen_plates() (tooluniverse.CellPaintingTool method) _get_searchable_value() (tooluniverse.xml_tool.XMLDatasetTool method) (tooluniverse.XMLDatasetTool method) _get_section() (tooluniverse.ADAStandardsTool method) _get_sequence() (tooluniverse.IMGTTool method) (tooluniverse.UCSCGenomeTool method) _get_sequence_regions() (tooluniverse.RfamTool method) _get_session_with_xsrf() (tooluniverse.ProtacDBTool method) _get_side_effects() (tooluniverse.SiderTool method) _get_signaling() (tooluniverse.OmniPathTool method) _get_single_tissue_eqtls() (tooluniverse.GTExV2Tool method) _get_smcp() (in module tooluniverse.mcp_tool_registry) _get_species() (tooluniverse.GTDBTool method) _get_species_counts() (tooluniverse.INaturalistTool method) _get_species_info() (tooluniverse.EnsemblInfoTool method) _get_spectrum() (tooluniverse.GNPSTool method) _get_statement_by_hash() (tooluniverse.INDRADBTool method) _get_statements() (tooluniverse.INDRADBTool method) _get_stats_size() (tooluniverse.CTGovAPITool method) _get_structure() (tooluniverse.FDAGSRSTool method) (tooluniverse.SAbDabTool method) _get_structure_by_id() (tooluniverse.AllenBrainTool method) _get_structure_mapping() (tooluniverse.RfamTool method) _get_structure_summary() (tooluniverse.RCSBGraphQLTool method) (tooluniverse.ThreeDBeaconsTool method) _get_structures() (tooluniverse.GPCRdbTool method) (tooluniverse.PDBECompoundTool method) (tooluniverse.ThreeDBeaconsTool method) _get_structures_for_domain() (tooluniverse.InterProDomainArchTool method) _get_study() (tooluniverse.BioImageArchiveTool method) (tooluniverse.CTGovAPITool method) _get_study_summary() (tooluniverse.CancerPrognosisTool method) (tooluniverse.PDCTool method) _get_substance() (tooluniverse.FDAGSRSTool method) _get_substrates() (tooluniverse.TCDBTool method) _get_suggestions() (tooluniverse.EBITaxonomyTool method) _get_summary() (tooluniverse.PDBECompoundTool method) (tooluniverse.SAbDabTool method) _get_summary_stats() (tooluniverse.PDBe_KB_Tool method) _get_superfamily() (tooluniverse.CATHTool method) _get_superposition() (tooluniverse.PDBe_KB_Tool method) _get_survival_data() (tooluniverse.CancerPrognosisTool method) _get_svi_info() (tooluniverse.health_disparities_tool.HealthDisparitiesTool method) (tooluniverse.HealthDisparitiesTool method) _get_synonyms() (tooluniverse.MetaboliteTool method) _get_target() (tooluniverse.PharosTool method) _get_target_organs() (tooluniverse.PubChemToxTool method) _get_targets() (tooluniverse.DrugCentralTool method) _get_taxon() (tooluniverse.INaturalistTool method) (tooluniverse.UniProtTaxonomyTool method) _get_taxon_info() (tooluniverse.GTDBTool method) (tooluniverse.OpenTreeTool method) _get_taxonomy() (tooluniverse.BVBRCTool method) (tooluniverse.NCBIDatasetsTool method) _get_taxonomy_suggest() (tooluniverse.NCBIDatasetsTool method) _get_tdl_summary() (tooluniverse.PharosTool method) _get_te_code() (tooluniverse.FDAOrangeBookTool method) _get_term() (tooluniverse.DiseaseOntologyTool method) (tooluniverse.GOAPITool method) (tooluniverse.HPOTool method) _get_term_hierarchy() (tooluniverse.HPOTool method) _get_tf_binding_clusters() (tooluniverse.UCSCEpigenomicsTool method) _get_tf_target_interactions() (tooluniverse.OmniPathTool method) _get_tissue_sites() (tooluniverse.GTExV2Tool method) _get_tool_annotations() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) _get_tool_category() (in module tooluniverse.tool_discovery_tools) _get_tool_category_mapping() (tooluniverse.compose_tool.ComposeTool method) (tooluniverse.ComposeTool method) _get_tool_instance() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _get_tool_selection_prompt() (tooluniverse.tool_finder_llm.ToolFinderLLM method) (tooluniverse.ToolFinderLLM method) _get_tool_semaphore() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _get_tooluniverse() (in module tooluniverse.mcp_tool_registry) _get_top_enriched() (tooluniverse.EnrichrExtTool method) _get_top_expressed_genes() (tooluniverse.GTExV2Tool method) _get_toxicity_summary() (tooluniverse.PubChemToxTool method) _get_toxicity_values() (tooluniverse.PubChemToxTool method) _get_toxin() (tooluniverse.T3DBTool method) _get_track() (tooluniverse.UCSCGenomeTool method) _get_trait_studies() (tooluniverse.GWASSumStatsTool method) _get_transporter() (tooluniverse.TCDBTool method) _get_tree_data() (tooluniverse.RfamTool method) _get_uniprot_to_pdb() (tooluniverse.PDBeSIFTSTool method) _get_usage_example() (tooluniverse.package_tool.PackageTool method) (tooluniverse.PackageTool method) _get_user_tool_files() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _get_valid_categories() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) _get_var_metadata() (tooluniverse.CELLxGENECensusTool method) _get_variant() (tooluniverse.KEGGExtTool method) (tooluniverse.MyVariantTool method) _get_variant_classifications() (tooluniverse.ClinGenTool method) _get_variant_detail() (tooluniverse.EnsemblVariationExtTool method) _get_variant_disease_associations() (tooluniverse.DisGeNETTool method) _get_variant_finemapping() (tooluniverse.FinnGenTool method) _get_variant_score() (tooluniverse.AlphaMissenseTool method) (tooluniverse.CADDTool method) (tooluniverse.EVETool method) _get_variant_scores() (tooluniverse.MaveDBTool method) _get_variants() (tooluniverse.LOVDTool method) _get_variants_for_gene_id() (tooluniverse.CIViCTool method) _get_variation() (tooluniverse.EBIProteinsExtTool method) _get_vendors() (tooluniverse.EMoleculesTool method) _get_well_data() (tooluniverse.CellPaintingTool method) _get_with_retry() (tooluniverse.SRATool method) _get_works() (tooluniverse.ORCIDTool method) _get_xrefs() (tooluniverse.BridgeDbTool method) (tooluniverse.EnsemblXrefsTool method) (tooluniverse.miRNAGetTool method) _get_xrefs_by_symbol() (tooluniverse.EnsemblXrefsTool method) _gibson_design() (tooluniverse.DNATool method) _global_fallback_chain (tooluniverse.agentic_tool.AgenticTool attribute) _glycan_detail() (tooluniverse.GlyGenTool method) _glycan_search() (tooluniverse.GlyGenTool method) _golden_gate_design() (tooluniverse.DNATool method) _handle_batch_request() (tooluniverse.ProteinsAPIRESTTool method) _handle_data_uri() (tooluniverse.markitdown_tool.MarkItDownTool method) (tooluniverse.MarkItDownTool method) _handle_diffdock_staged() (tooluniverse.NvidiaNIMTool method) _handle_encode_error() (in module tooluniverse.encode_tool) _handle_find_similar_terms() (tooluniverse.ols_tool.OLSTool method) (tooluniverse.OLSTool method) _handle_get_ontology_info() (tooluniverse.ols_tool.OLSTool method) (tooluniverse.OLSTool method) _handle_get_term_ancestors() (tooluniverse.ols_tool.OLSTool method) (tooluniverse.OLSTool method) _handle_get_term_children() (tooluniverse.ols_tool.OLSTool method) (tooluniverse.OLSTool method) _handle_get_term_info() (tooluniverse.ols_tool.OLSTool method) (tooluniverse.OLSTool method) _handle_id_mapping() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) _handle_request() (tooluniverse.OncoTreeBaseTool method) _handle_search() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) _handle_search_ontologies() (tooluniverse.ols_tool.OLSTool method) (tooluniverse.OLSTool method) _handle_search_terms() (tooluniverse.ols_tool.OLSTool method) (tooluniverse.OLSTool method) _handle_special_endpoint() (tooluniverse.BaseRESTTool method) (tooluniverse.biomodels_tool.BioModelsRESTTool method) (tooluniverse.BioModelsRESTTool method) _handle_timeout() (tooluniverse.BasePythonExecutor method) (tooluniverse.python_executor_tool.BasePythonExecutor method) _handle_tools_find() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) _handle_uniparc_search() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) _handle_uniref_search() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) _haplotype_count() (tooluniverse.PopGenTool method) _hgvs_to_spdi() (tooluniverse.NCBIVariationTool method) _hill() (tooluniverse.ScientificCalculatorTool method) _histopheno() (tooluniverse.MonarchV3Tool method) _http_get() (in module tooluniverse.encode_tool) (in module tooluniverse.gbif_tool) (in module tooluniverse.gdc_tool) (in module tooluniverse.gtex_tool) (in module tooluniverse.mgnify_tool) (in module tooluniverse.obis_tool) (in module tooluniverse.rnacentral_tool) (in module tooluniverse.wikipathways_tool) _http_post() (in module tooluniverse.gdc_tool) _hwe_test() (tooluniverse.PopGenTool method) _immune_estimation() (tooluniverse.TIMERTool method) _import_admet_model() (in module tooluniverse.admetai_tool) _import_smolagents_tool() (tooluniverse.smolagent_tool.SmolAgentTool method) (tooluniverse.SmolAgentTool method) _import_user_python_tools() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _inbreeding() (tooluniverse.PopGenTool method) _infer_operation() (tooluniverse.BridgeDbTool method) (tooluniverse.iPTMnetTool method) _inhibition() (tooluniverse.ScientificCalculatorTool method) _init_agent() (tooluniverse.smolagent_tool.SmolAgentTool method) (tooluniverse.SmolAgentTool method) _init_agentic_tool() (tooluniverse.tool_finder_llm.ToolFinderLLM method) (tooluniverse.ToolFinderLLM method) _init_model() (tooluniverse.smolagent_tool.SmolAgentTool method) (tooluniverse.SmolAgentTool method) _init_tool_finder() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) _initialized (tooluniverse.logging_config.ToolUniverseLogger attribute) _input_arguments (tooluniverse.agentic_tool.AgenticTool attribute) _instance (tooluniverse.logging_config.ToolUniverseLogger attribute) _interpret_phred() (tooluniverse.CADDTool method) _interpret_potency() (tooluniverse.DoseResponseTool static method) _interpret_score() (tooluniverse.SpliceAITool method) _interpret_synergy_score() (tooluniverse.DrugSynergyTool method) _interpret_te_code() (tooluniverse.FDAOrangeBookTool method) _invoke_tool_async() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _is_api_error() (tooluniverse.LOINCTool static method) _is_chembl_id() (tooluniverse.FDADrugLabelTool method) (tooluniverse.openfda_tool.FDADrugLabelTool method) _is_histone_mark() (tooluniverse.EpigenomicsTool static method) _is_hook_applicable() (tooluniverse.output_hook.HookManager method) _is_hook_tool() (tooluniverse.output_hook.HookManager method) _is_match() (tooluniverse.xml_tool.XMLDatasetTool method) (tooluniverse.XMLDatasetTool method) _iter_chunks() (tooluniverse.agentic_tool.AgenticTool static method) (tooluniverse.AgenticTool static method) _itertext() (tooluniverse.europe_pmc_tool.EuropePMCStructuredFullTextTool static method) (tooluniverse.EuropePMCStructuredFullTextTool static method) _join_pipe_delimited() (in module tooluniverse.biogrid_tool) _kaplan_meier() (tooluniverse.SurvivalTool method) _kegg_find_compound() (tooluniverse.MetaboAnalystTool method) _kegg_get_compound_info() (tooluniverse.MetaboAnalystTool method) _kegg_get_pathway_compounds() (tooluniverse.MetaboAnalystTool method) _kegg_list_pathways() (tooluniverse.MetaboAnalystTool method) _km_estimator() (tooluniverse.SurvivalTool method) _ksp_complex() (tooluniverse.ScientificCalculatorTool method) _ksp_simple() (tooluniverse.ScientificCalculatorTool method) _last_request_time (tooluniverse.ICiteSearchPublicationsTool attribute) (tooluniverse.pubmed_tool.PubMedRESTTool attribute) (tooluniverse.PubMedRESTTool attribute) (tooluniverse.semantic_scholar_tool.SemanticScholarTool attribute) (tooluniverse.SemanticScholarTool attribute) _ld_pairwise() (tooluniverse.EnsemblLDTool method) _ld_variants() (tooluniverse.EnsemblLDTool method) _lifespan (tooluniverse.smcp.SMCP attribute) _lifespan_lock (tooluniverse.smcp.SMCP attribute) _lifespan_ref_count (tooluniverse.smcp.SMCP attribute) _lifespan_result (tooluniverse.smcp.SMCP attribute) _lifespan_result_set (tooluniverse.smcp.SMCP attribute) _linear_regression() (tooluniverse.ScientificCalculatorTool method) _link_entries() (tooluniverse.KEGGExtTool method) _link_to_biosample() (tooluniverse.NCBISRATool method) _lipinski_filter() (tooluniverse.DrugPropertiesTool method) _list_annotations() (tooluniverse.CryoETTool method) _list_annotators() (tooluniverse.OpenCRAVATTool method) _list_brite() (tooluniverse.KEGGExtTool method) _list_cancer_types() (tooluniverse.IntOGenTool method) _list_cell_lines() (tooluniverse.SYNERGxDBTool method) _list_cell_types() (tooluniverse.CellMarkerTool method) _list_classes() (tooluniverse.ELMTool method) (tooluniverse.FDALabelTool method) _list_cohorts() (tooluniverse.IntOGenTool method) _list_collections() (tooluniverse.CellxGeneDiscoveryTool method) _list_data_collections() (tooluniverse.IGSRTool method) _list_databases() (tooluniverse.MculeTool method) (tooluniverse.MEMETool method) (tooluniverse.UniProtIDMappingTool method) _list_datasets() (tooluniverse.CryoETTool method) (tooluniverse.HarmonizomeTool method) (tooluniverse.NextstrainTool method) (tooluniverse.PharmacoDBTool method) (tooluniverse.SYNERGxDBTool method) _list_drugs() (tooluniverse.SYNERGxDBTool method) _list_experiments() (tooluniverse.GxATool method) (tooluniverse.SCExpressionAtlasTool method) _list_foods() (tooluniverse.FoodDataCentralTool method) _list_funfams() (tooluniverse.CATHTool method) _list_libraries() (tooluniverse.EnrichrExtTool method) (tooluniverse.LINCSSignatureTool method) _list_models() (tooluniverse.BiGGModelsTool method) _list_modifications() (tooluniverse.MODOMICSTool method) _list_namespaces() (tooluniverse.IdentifiersOrgTool method) _list_org() (tooluniverse.AHAACCGuidelineTool method) _list_organs() (tooluniverse.HuBMAPTool method) _list_page_size (tooluniverse.smcp.SMCP attribute) _LIST_PARAM_MAP (tooluniverse.biogrid_tool.BioGRIDRESTTool attribute) (tooluniverse.BioGRIDRESTTool attribute) _list_pathways() (tooluniverse.SIGNORTool method) _list_patient_guidelines() (tooluniverse.NCCNGuidelineTool method) _list_phenotypes() (tooluniverse.FinnGenTool method) _list_products() (tooluniverse.NEBTmTool method) _list_programs() (tooluniverse.PDCTool method) _list_proteins() (tooluniverse.GPCRdbTool method) _list_response() (tooluniverse.ClueTool method) _list_runs() (tooluniverse.CryoETTool method) _list_sections() (tooluniverse.ADAStandardsTool method) _list_sources() (tooluniverse.UniChemTool method) _list_species() (tooluniverse.PlantReactomeTool method) _list_studies() (tooluniverse.GWASSumStatsTool method) _list_tissues() (tooluniverse.ProteomicsDBTool method) _list_tomograms() (tooluniverse.CryoETTool method) _load_all_therapeutics() (tooluniverse.TheraSAbDabTool method) _load_auto_discovered_configs() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _load_by_categories() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) _load_code_from_file() (tooluniverse.compose_tool.ComposeTool method) (tooluniverse.ComposeTool method) _load_dataset() (tooluniverse.dataset_tool.DatasetTool method) (tooluniverse.DatasetTool method) (tooluniverse.xml_tool.XMLDatasetTool method) (tooluniverse.XMLDatasetTool method) _load_embedded_code() (tooluniverse.custom_tool.CustomTool method) (tooluniverse.CustomTool method) _load_external_code() (tooluniverse.custom_tool.CustomTool method) (tooluniverse.CustomTool method) _load_from_file() (tooluniverse.ProfileLoader method) _load_from_hf() (tooluniverse.ProfileLoader method) _load_from_url() (tooluniverse.ProfileLoader method) _load_hook_config() (tooluniverse.output_hook.HookManager method) _load_hooks() (tooluniverse.output_hook.HookManager method) _load_missing_dependencies() (tooluniverse.compose_tool.ComposeTool method) (tooluniverse.ComposeTool method) _load_pending_tools() (tooluniverse.output_hook.HookManager method) _load_profile_configs() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) _load_raw() (tooluniverse.ProfileLoader method) _load_tool_names_from_file() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _load_tools_from_mcp_server() (in module tooluniverse.mcp_integration) (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _load_tools_from_sources() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _load_tools_with_filters() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) _load_user_json_configs() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _local() (tooluniverse.europe_pmc_tool.EuropePMCStructuredFullTextTool static method) (tooluniverse.EuropePMCStructuredFullTextTool static method) _local_name() (tooluniverse.europe_pmc_tool.EuropePMCTool method) (tooluniverse.EuropePMCTool method) _local_provider (tooluniverse.smcp.SMCP attribute) _locus_go() (tooluniverse.SGDTool method) _locus_interactions() (tooluniverse.SGDTool method) _locus_overview() (tooluniverse.SGDTool method) _locus_phenotypes() (tooluniverse.SGDTool method) _log_rank_test() (tooluniverse.SurvivalTool method) _logger (tooluniverse.logging_config.ToolUniverseLogger attribute) _lookup_allele() (tooluniverse.ClinGenARTool method) _lookup_chembl_id_by_name() (tooluniverse.chem_tool.ChEMBLRESTTool method) (tooluniverse.ChEMBLRESTTool method) _lookup_compound() (tooluniverse.MculeTool method) _lookup_gene_id() (tooluniverse.CIViCTool method) _lookup_hgvs() (tooluniverse.ClinGenAlleleTool method) _make_api_request() (tooluniverse.hpa_tool.HPAJsonApiTool method) (tooluniverse.hpa_tool.HPASearchApiTool method) (tooluniverse.hpa_tool.HPAXmlApiTool method) (tooluniverse.HPAJsonApiTool method) (tooluniverse.HPASearchApiTool method) (tooluniverse.HPAXmlApiTool method) _make_cache_key() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _make_get_request() (tooluniverse.FoodDataCentralTool method) _make_mcp_request() (tooluniverse.BaseMCPClient method) (tooluniverse.mcp_client_tool.BaseMCPClient method) _make_request() (tooluniverse.alphafold_tool.AlphaFoldRESTTool method) (tooluniverse.AlphaFoldRESTTool method) (tooluniverse.biogrid_tool.BioGRIDRESTTool method) (tooluniverse.BioGRIDRESTTool method) (tooluniverse.BVBRCTool method) (tooluniverse.cdc_tool.CDCRESTTool method) (tooluniverse.CDCRESTTool method) (tooluniverse.CellPaintingTool method) (tooluniverse.clinvar_tool.ClinVarRESTTool method) (tooluniverse.ClinVarRESTTool method) (tooluniverse.ClueTool method) (tooluniverse.GTDBTool method) (tooluniverse.gwas_tool.GWASRESTTool method) (tooluniverse.GWASRESTTool method) (tooluniverse.ICD10Tool method) (tooluniverse.ICDTool method) (tooluniverse.kegg_tool.KEGGRESTTool method) (tooluniverse.KEGGRESTTool method) (tooluniverse.LipidMapsTool method) (tooluniverse.LOINCTool method) (tooluniverse.LOVDTool method) (tooluniverse.MculeTool method) (tooluniverse.MetabolomicsWorkbenchTool method) (tooluniverse.ncbi_eutils_tool.NCBIEUtilsTool method) (tooluniverse.NCBIEUtilsTool method) (tooluniverse.odphp_tool.ODPHPRESTTool method) (tooluniverse.ODPHPRESTTool method) (tooluniverse.OmniPathTool method) (tooluniverse.OncoKBTool method) (tooluniverse.OpenFDAApprovalTool method) (tooluniverse.ORCIDTool method) (tooluniverse.string_tool.STRINGRESTTool method) (tooluniverse.STRINGRESTTool method) (tooluniverse.SYNERGxDBTool method) (tooluniverse.umls_tool.UMLSRESTTool method) (tooluniverse.UMLSRESTTool method) (tooluniverse.who_gho_tool.WHOGHORESTTool method) (tooluniverse.WHOGHORESTTool method) (tooluniverse.ZincTool method) _make_request_for_data() (tooluniverse.who_gho_tool.WHOGHORESTTool method) (tooluniverse.WHOGHORESTTool method) _make_rma_query() (tooluniverse.AllenBrainTool method) _map_param_names() (tooluniverse.ClinicalTrialsTool method) (tooluniverse.ctg_tool.ClinicalTrialsTool method) _map_term_to_field() (tooluniverse.cellosaurus_tool.CellosaurusQueryConverterTool method) (tooluniverse.CellosaurusQueryConverterTool method) _map_value() (tooluniverse.FDADrugAdverseEventDetailTool method) (tooluniverse.FDADrugAdverseEventTool method) (tooluniverse.FDADrugInteractionDetailTool method) (tooluniverse.openfda_adv_tool.FDADrugAdverseEventDetailTool method) (tooluniverse.openfda_adv_tool.FDADrugAdverseEventTool method) (tooluniverse.openfda_adv_tool.FDADrugInteractionDetailTool method) _mask_error_details (tooluniverse.smcp.SMCP attribute) _match_names() (tooluniverse.OpenTreeTool method) _matched_molecular_pair() (tooluniverse.RDKitCheminfoTool method) _max_retries (tooluniverse.agentic_tool.AgenticTool attribute) _maybe_refresh_embeddings() (tooluniverse.tool_finder_embedding.ToolFinderEmbedding method) (tooluniverse.ToolFinderEmbedding method) _mcp_server (tooluniverse.smcp.SMCP attribute) _meta_analyze() (tooluniverse.MetaAnalysisTool method) _michaelis_menten() (tooluniverse.ScientificCalculatorTool method) _model_id (tooluniverse.agentic_tool.AgenticTool attribute) _mondo_get_disease() (tooluniverse.MonarchV3Tool method) _mondo_get_phenotypes() (tooluniverse.MonarchV3Tool method) _mondo_search() (tooluniverse.MonarchV3Tool method) _motif_features() (tooluniverse.EnsemblRegulationTool method) _motif_search() (tooluniverse.RCSBAdvancedSearchTool method) _name_to_id() (tooluniverse.MetaboAnalystTool method) _ncbi_get() (tooluniverse.MedGenTool method) _nnt() (tooluniverse.EpidemiologyTool method) _normalize() (tooluniverse.MutalyzerTool method) (tooluniverse.openaire_tool.OpenAIRETool method) (tooluniverse.OpenAIRETool method) _normalize_accessions() (tooluniverse.NCBISRATool static method) _normalize_article_id() (tooluniverse.EuroPMCAnnotationsTool static method) _normalize_doi() (tooluniverse.openalex_tool.OpenAlexRESTTool static method) (tooluniverse.OpenAlexRESTTool static method) _normalize_gene_id() (tooluniverse.AllianceGenomeTool static method) _normalize_numeric_fields() (tooluniverse.MetabolomicsWorkbenchTool method) _normalize_openalex_id() (tooluniverse.openalex_tool.OpenAlexRESTTool static method) (tooluniverse.OpenAlexRESTTool static method) _normalize_path() (tooluniverse.file_download_tool.FileDownloadTool method) (tooluniverse.FileDownloadTool method) _normalize_pmcid() (in module tooluniverse.europe_pmc_tool) (tooluniverse.pmc_tool.PMCTool method) (tooluniverse.PMCTool method) _normalize_protein() (tooluniverse.GPCRdbTool method) _normalize_temperature() (tooluniverse.llm_clients.AzureOpenAIClient method) _normalize_value() (in module tooluniverse.build_optimizer) _normalize_variant() (tooluniverse.ProtVarMapTool static method) (tooluniverse.SpliceAITool method) _obo_id_to_efo_iri() (tooluniverse.efo_tool.OLSRESTTool static method) (tooluniverse.OLSRESTTool static method) _on_duplicate (tooluniverse.smcp.SMCP attribute) _ontology_children() (tooluniverse.ChEBITool method) _OPERATION_HANDLERS (tooluniverse.SwissDockTool attribute) _OPERATION_MAP (tooluniverse.LOINCTool attribute) _OPERATION_URLS (tooluniverse.ClinicalTrialsTool attribute) (tooluniverse.ctg_tool.ClinicalTrialsTool attribute) _OPERATIONS (tooluniverse.NCBISRATool attribute) (tooluniverse.ols_tool.OLSTool attribute) (tooluniverse.OLSTool attribute) _ORGANISM_ALIASES (tooluniverse.EpigenomicsTool attribute) _ORGANISM_MAP (tooluniverse.biogrid_tool.BioGRIDRESTTool attribute) (tooluniverse.BioGRIDRESTTool attribute) _ortholog() (tooluniverse.PANTHERTool method) _ot_resolve_id() (in module tooluniverse.graphql_tool) _overlap_gene() (tooluniverse.EnsemblOverlapTool method) _overlap_region() (tooluniverse.EnsemblOverlapTool method) _pains_filter() (tooluniverse.DrugPropertiesTool method) _parse_accessions() (tooluniverse.ProteinsAPIRESTTool method) _parse_adverse_reactions() (tooluniverse.dailymed_tool.DailyMedSPLParserTool method) (tooluniverse.DailyMedSPLParserTool method) _parse_article_xml() (tooluniverse.europe_pmc_tool.EuropePMCStructuredFullTextTool method) (tooluniverse.EuropePMCStructuredFullTextTool method) _parse_blast_results() (tooluniverse.blast_tool.NCBIBlastTool method) (tooluniverse.NCBIBlastTool method) _parse_clinical_pharmacology() (tooluniverse.dailymed_tool.DailyMedSPLParserTool method) (tooluniverse.DailyMedSPLParserTool method) _parse_contraindications() (tooluniverse.dailymed_tool.DailyMedSPLParserTool method) (tooluniverse.DailyMedSPLParserTool method) _parse_csv() (tooluniverse.ClinGenTool method) _parse_csv_row() (tooluniverse.SwissADMETool method) _parse_cv_groups() (tooluniverse.MassIVETool method) _parse_dataset() (tooluniverse.MassIVETool method) _parse_dblinks() (tooluniverse.MetaboAnalystTool static method) _parse_dosing() (tooluniverse.dailymed_tool.DailyMedSPLParserTool method) (tooluniverse.DailyMedSPLParserTool method) _parse_drug_interactions() (tooluniverse.dailymed_tool.DailyMedSPLParserTool method) (tooluniverse.DailyMedSPLParserTool method) _parse_efetch_xml() (tooluniverse.pubmed_tool.PubMedRESTTool method) (tooluniverse.PubMedRESTTool method) _parse_esummary_item() (tooluniverse.pmc_tool.PMCTool method) (tooluniverse.PMCTool method) _parse_esummary_xml() (tooluniverse.pmc_tool.PMCTool method) (tooluniverse.PMCTool method) _parse_fimo_tsv() (tooluniverse.MEMETool method) _parse_gene_list() (tooluniverse.GProfilerTool method) _parse_gene_xml() (tooluniverse.hpa_tool.HPAGetGenePageDetailsTool method) (tooluniverse.HPAGetGenePageDetailsTool method) _parse_html_table() (tooluniverse.FDAPharmacogenomicBiomarkersTool method) _parse_int_param() (in module tooluniverse.core_tool) _parse_location() (tooluniverse.UniProtLocationsTool method) _parse_meme_text() (tooluniverse.MEMETool method) _parse_prosite_text() (tooluniverse.PROSITETool method) _parse_response() (tooluniverse.NvidiaNIMTool method) _parse_result_table() (tooluniverse.SwissTargetTool method) _parse_results() (tooluniverse.FoldseekTool method) _parse_search_results() (tooluniverse.LOINCTool method) (tooluniverse.rcsb_search_tool.RCSBSearchTool method) (tooluniverse.RCSBSearchTool method) (tooluniverse.TheraSAbDabTool method) _parse_smiles() (tooluniverse.DrugPropertiesTool method) (tooluniverse.RDKitCheminfoTool method) _parse_sra_summary() (tooluniverse.SRATool method) _parse_sra_xml() (tooluniverse.NCBISRATool method) _parse_tomtom_tsv() (tooluniverse.MEMETool method) _parse_tsv() (tooluniverse.ELMTool method) (tooluniverse.IEDBPredictionTool method) (tooluniverse.RheaTool method) _parse_tsv_attributes() (tooluniverse.BridgeDbTool method) _parse_tsv_response() (tooluniverse.string_tool.STRINGRESTTool method) (tooluniverse.STRINGRESTTool method) _parse_tsv_xrefs() (tooluniverse.BridgeDbTool method) _parse_variant_args() (tooluniverse.InterVarTool static method) _parse_variant_summary() (tooluniverse.clinvar_tool.ClinVarRESTTool method) (tooluniverse.ClinVarRESTTool method) _parse_xml_field() (tooluniverse.MetaCycTool method) _parse_xml_frameids() (tooluniverse.MetaCycTool method) _patch_tooluniverse() (in module tooluniverse.mcp_integration) _patch_torch_load() (in module tooluniverse.admetai_tool) _paths() (tooluniverse.EmbeddingDatabase method) _pathway_enrichment() (tooluniverse.MetaboAnalystTool method) (tooluniverse.ReactomeAnalysisTool method) _perform_tool_search() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) _pharmacophore_features() (tooluniverse.RDKitCheminfoTool method) _phenotype_gene() (tooluniverse.EnsemblPhenotypeTool method) _phenotype_region() (tooluniverse.EnsemblPhenotypeTool method) _phenotype_variant() (tooluniverse.EnsemblPhenotypeTool method) _PLACEHOLDER_KEYS (tooluniverse.ICDTool attribute) _poll_for_result() (tooluniverse.NvidiaNIMTool method) _poll_job() (tooluniverse.MEMETool method) _poll_job_status() (tooluniverse.DynaMut2Tool method) _post_process() (tooluniverse.FDADrugAdverseEventTool method) (tooluniverse.openfda_adv_tool.FDADrugAdverseEventTool method) _post_search() (tooluniverse.VDJDBTool method) _predict() (tooluniverse.admetai_tool.ADMETAITool method) (tooluniverse.ADMETAITool method) (tooluniverse.SwissTargetTool method) _predict_function() (tooluniverse.DeepGOTool method) _predict_mhci() (tooluniverse.IEDBPredictionTool method) _predict_mhcii() (tooluniverse.IEDBPredictionTool method) _predict_splice() (tooluniverse.SpliceAITool method) _predict_splice_pangolin() (tooluniverse.SpliceAITool method) _predict_stability() (tooluniverse.DynaMut2Tool method) _prefilter_tools_by_keywords() (tooluniverse.tool_finder_llm.ToolFinderLLM method) (tooluniverse.ToolFinderLLM method) _prepare_api_params() (tooluniverse.ClinicalTrialsTool method) (tooluniverse.ctg_tool.ClinicalTrialsTool method) _prepare_ligand() (tooluniverse.SwissDockTool method) _prepare_target() (tooluniverse.SwissDockTool method) _preprocess_drug_name() (tooluniverse.rxnorm_tool.RxNormTool method) (tooluniverse.RxNormTool method) _prime_batch_cache() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _primer_design() (tooluniverse.DNATool method) _print_tooluniverse_banner() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) _process_mcp_auto_loaders() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _process_response() (tooluniverse.BaseRESTTool method) (tooluniverse.biomodels_tool.BioModelsRESTTool method) (tooluniverse.BioModelsRESTTool method) (tooluniverse.crossref_tool.CrossrefRESTTool method) (tooluniverse.CrossrefRESTTool method) (tooluniverse.DataCiteRESTTool method) (tooluniverse.zenodo_tool.ZenodoRESTTool method) (tooluniverse.ZenodoRESTTool method) _prompt_template (tooluniverse.agentic_tool.AgenticTool attribute) _protein_detail() (tooluniverse.GlyGenTool method) _protein_search() (tooluniverse.GlyGenTool method) _query() (tooluniverse.AllianceGenomeTool method) (tooluniverse.BgeeTool method) (tooluniverse.BioImageArchiveTool method) (tooluniverse.BioPortalTool method) (tooluniverse.BVBRCTool method) (tooluniverse.CATHTool method) (tooluniverse.CellxGeneDiscoveryTool method) (tooluniverse.ClinGenARTool method) (tooluniverse.CTDTool method) (tooluniverse.CTGovAPITool method) (tooluniverse.DfamTool method) (tooluniverse.DiseaseOntologyTool method) (tooluniverse.DisProtTool method) (tooluniverse.EBIProteinsCoordinatesTool method) (tooluniverse.EBIProteinsExtTool method) (tooluniverse.EBIProteinsInteractionsTool method) (tooluniverse.EBITaxonomyTool method) (tooluniverse.EnsemblArchiveTool method) (tooluniverse.EnsemblComparaTool method) (tooluniverse.EnsemblInfoTool method) (tooluniverse.EnsemblMapTool method) (tooluniverse.EnsemblOverlapTool method) (tooluniverse.EnsemblSequenceTool method) (tooluniverse.EnsemblVariationExtTool method) (tooluniverse.EnsemblVEPTool method) (tooluniverse.EnsemblXrefsTool method) (tooluniverse.EOLTool method) (tooluniverse.EpiGraphDBTool method) (tooluniverse.EPMCAnnotationsTool method) (tooluniverse.FoldseekTool method) (tooluniverse.GenomeNexusTool method) (tooluniverse.GOAPITool method) (tooluniverse.GProfilerTool method) (tooluniverse.GxATool method) (tooluniverse.HarmonizomeTool method) (tooluniverse.HGNCTool method) (tooluniverse.HPOTool method) (tooluniverse.IdentifiersOrgTool method) (tooluniverse.INaturalistTool method) (tooluniverse.InterProDomainArchTool method) (tooluniverse.InterProEntryTool method) (tooluniverse.InterProExtTool method) (tooluniverse.IntOGenTool method) (tooluniverse.ITISTool method) (tooluniverse.KEGGExtTool method) (tooluniverse.LINCSSignatureTool method) (tooluniverse.MedGenTool method) (tooluniverse.MeSHTool method) (tooluniverse.MobiDBTool method) (tooluniverse.MODOMICSTool method) (tooluniverse.MonarchV3Tool method) (tooluniverse.MutalyzerTool method) (tooluniverse.MyDiseaseTool method) (tooluniverse.NCBIDatasetsTool method) (tooluniverse.NCBIVariationTool method) (tooluniverse.NCIThesaurusTool method) (tooluniverse.NDExTool method) (tooluniverse.OMATool method) (tooluniverse.OmniPathTool method) (tooluniverse.OpenTreeTool method) (tooluniverse.OrthoDBTool method) (tooluniverse.OxOTool method) (tooluniverse.PDBe_KB_Tool method) (tooluniverse.PDBECompoundTool method) (tooluniverse.PDBeLigandsTool method) (tooluniverse.PDBeSIFTSTool method) (tooluniverse.PDBeValidationTool method) (tooluniverse.PfamTool method) (tooluniverse.PlantReactomeTool method) (tooluniverse.ProgenetixTool method) (tooluniverse.PubChemBioAssayTool method) (tooluniverse.PubChemToxTool method) (tooluniverse.QuickGOTool method) (tooluniverse.RCSBAdvancedSearchTool method) (tooluniverse.RCSBDataTool method) (tooluniverse.RCSBGraphQLTool method) (tooluniverse.ReactomeAnalysisTool method) (tooluniverse.ReactomeContentTool method) (tooluniverse.ReactomeInteractorsTool method) (tooluniverse.RheaTool method) (tooluniverse.STRINGExtTool method) (tooluniverse.SynBioHubTool method) (tooluniverse.ThreeDBeaconsTool method) (tooluniverse.UniParcTool method) (tooluniverse.UniProtLocationsTool method) (tooluniverse.UniProtRefTool method) (tooluniverse.UniProtTaxonomyTool method) (tooluniverse.UniRefTool method) (tooluniverse.WikiPathwaysExtTool method) _query_batch() (tooluniverse.MyGeneTool method) _query_by_coordinates() (tooluniverse.SIMBADTool method) _query_by_identifier() (tooluniverse.SIMBADTool method) _query_by_name() (tooluniverse.SIMBADTool method) _query_chemicals() (tooluniverse.MyChemTool method) _query_compound() (tooluniverse.LipidMapsTool method) (tooluniverse.MetabolomicsWorkbenchTool method) _query_drug_fields() (tooluniverse.FDALabelTool method) _query_gene() (tooluniverse.LipidMapsTool method) _query_genes() (tooluniverse.MyGeneTool method) _query_params() (tooluniverse.pubtator_tool.PubTatorTool method) (tooluniverse.PubTatorTool method) _query_protein() (tooluniverse.LipidMapsTool method) _query_refmet() (tooluniverse.MetabolomicsWorkbenchTool method) _query_study() (tooluniverse.MetabolomicsWorkbenchTool method) _query_variants() (tooluniverse.MyVariantTool method) _r0_herd() (tooluniverse.EpidemiologyTool method) _rank_packages() (tooluniverse.DynamicPackageDiscovery method) (tooluniverse.package_discovery_tool.DynamicPackageDiscovery method) _rate_limit_lock (tooluniverse.ICiteSearchPublicationsTool attribute) (tooluniverse.pubmed_tool.PubMedRESTTool attribute) (tooluniverse.PubMedRESTTool attribute) (tooluniverse.semantic_scholar_tool.SemanticScholarTool attribute) (tooluniverse.SemanticScholarTool attribute) _read_profile_yaml() (in module tooluniverse.tool_registry) _read_tools_from_file() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _reconstruct_abstract() (tooluniverse.OpenAlexGuidelinesTool method) (tooluniverse.unified_guideline_tools.OpenAlexGuidelinesTool method) _register_custom_mcp_methods() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) _remove_empty_values() (tooluniverse.ClinicalTrialsDetailsTool method) (tooluniverse.ctg_tool.ClinicalTrialsDetailsTool method) _request_json() (tooluniverse.PharmGKBTool method) _required_arguments (tooluniverse.agentic_tool.AgenticTool attribute) _resolve() (tooluniverse.IdentifiersOrgTool method) _resolve_aliases() (tooluniverse.CPICSearchPairsTool method) _resolve_api_version() (tooluniverse.llm_clients.AzureOpenAIClient method) _resolve_cid() (tooluniverse.PubChemToxTool method) _resolve_compound_id() (tooluniverse.PharmacoDBTool method) _resolve_ctd_term() (tooluniverse.MetaboliteTool method) _resolve_default_max_tokens() (tooluniverse.llm_clients.AzureOpenAIClient method) (tooluniverse.llm_clients.OpenRouterClient method) _resolve_drug_id_by_name() (tooluniverse.SYNERGxDBTool method) _resolve_ec_from_name() (tooluniverse.BRENDATool method) _resolve_extends() (tooluniverse.ProfileLoader method) _resolve_filename() (tooluniverse.nhanes_tool.NHANESTool method) (tooluniverse.NHANESTool method) _resolve_gene_id() (in module tooluniverse.gtex_tool) _resolve_gene_symbol() (tooluniverse.KEGGExtTool method) (tooluniverse.OrphanetTool method) _resolve_github_to_dir() (tooluniverse.ProfileLoader method) _resolve_hf_to_dir() (tooluniverse.ProfileLoader method) _resolve_http_file_to_dir() (tooluniverse.ProfileLoader method) _resolve_identifiers() (tooluniverse.STITCHTool method) _resolve_local_to_dir() (tooluniverse.ProfileLoader method) _resolve_molecule_name() (tooluniverse.Molecule2DTool method) (tooluniverse.molecule_2d_tool.Molecule2DTool method) _resolve_multiple() (tooluniverse.NCICACTUSTool method) _resolve_name_to_id() (tooluniverse.DrugCentralTool method) _resolve_oneof_type() (tooluniverse.SMCP static method) (tooluniverse.smcp.SMCP static method) _resolve_param_type() (tooluniverse.SMCP class method) (tooluniverse.smcp.SMCP class method) _resolve_pmid_to_pmcid() (tooluniverse.europe_pmc_tool.EuropePMCStructuredFullTextTool method) (tooluniverse.EuropePMCStructuredFullTextTool method) _resolve_reference() (tooluniverse.BioregistryTool method) _resolve_rxcui() (tooluniverse.RxNormExtendedTool method) _resolve_sequence() (tooluniverse.SequenceAnalyzeTool method) _resolve_single() (tooluniverse.NCICACTUSTool method) _resolve_single_type() (in module tooluniverse.generate_tools) _resolve_study() (tooluniverse.CancerPrognosisTool method) (tooluniverse.TIMERTool method) _resolve_system_code() (tooluniverse.BridgeDbTool method) _resolve_term_iri() (tooluniverse.efo_tool.OLSRESTTool method) (tooluniverse.OLSRESTTool method) _resolve_to_cid() (tooluniverse.MetaboliteTool method) _resolve_tool_name() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _resolve_trait_or_error() (tooluniverse.gwas_tool.GWASRESTTool method) (tooluniverse.GWASRESTTool method) _resolve_trait_to_efo_id() (tooluniverse.gwas_tool.GWASRESTTool method) (tooluniverse.GWASRESTTool method) _resolve_workspace() (tooluniverse.execute_function.ToolUniverse static method) (tooluniverse.ToolUniverse static method) _respect_rate_limit() (tooluniverse.arxiv_tool.ArXivTool method) (tooluniverse.ArXivTool method) _rest_url_for_input_id() (tooluniverse.rcsb_pdb_tool.RCSBTool method) (tooluniverse.RCSBTool method) _retrieve_results() (tooluniverse.SwissDockTool method) _retrieve_results_operation() (tooluniverse.SwissDockTool method) _retry_delay (tooluniverse.agentic_tool.AgenticTool attribute) _return_json (tooluniverse.agentic_tool.AgenticTool attribute) _reverse_complement() (tooluniverse.DNATool method) (tooluniverse.SequenceAnalyzeTool method) _rollup_meddra_hierarchy() (tooluniverse.FAERSAnalyticsTool method) _rsid_lookup() (tooluniverse.NCBIVariationTool method) _run() (tooluniverse.AgingCohortSearchTool method) (tooluniverse.OncoTreeGetTypeTool method) (tooluniverse.OncoTreeListTissuesTool method) (tooluniverse.OncoTreeSearchTool method) _run_async() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _run_call_tool() (tooluniverse.mcp_client_tool.MCPClientTool method) (tooluniverse.MCPClientTool method) _run_field_values() (tooluniverse.ClinicalTrialsTool method) (tooluniverse.ctg_tool.ClinicalTrialsTool method) _run_get_prompt() (tooluniverse.mcp_client_tool.MCPClientTool method) (tooluniverse.MCPClientTool method) _run_get_study() (tooluniverse.ClinicalTrialsTool method) (tooluniverse.ctg_tool.ClinicalTrialsTool method) _run_json_search() (tooluniverse.tool_finder_keyword.ToolFinderKeyword method) (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_search() (tooluniverse.ClinicalTrialsTool method) (tooluniverse.ctg_tool.ClinicalTrialsTool method) _run_stats_size() (tooluniverse.ClinicalTrialsTool method) (tooluniverse.ctg_tool.ClinicalTrialsTool method) _run_sync() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _run_sync_request() (tooluniverse.ProteinsPlusRESTTool method) _run_via_rest() (tooluniverse.rcsb_pdb_tool.RCSBTool method) (tooluniverse.RCSBTool method) _run_with_cleanup() (tooluniverse.BaseMCPClient method) (tooluniverse.mcp_client_tool.BaseMCPClient method) _sa_score() (tooluniverse.ChemComputeTool method) _safe_import() (in module tooluniverse.smolagent_tool) _sanitize_schema_for_openai() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _save_full_response() (in module tooluniverse.smcp) _scan_all_json_files() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _scan_predefined_files() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _scan_sequence() (tooluniverse.InterProScanTool method) (tooluniverse.PROSITETool method) _score_sequence() (tooluniverse.ESMTool method) _scrape_topic_publications() (tooluniverse.unified_guideline_tools.WHOGuidelinesTool method) (tooluniverse.WHOGuidelinesTool method) _search() (tooluniverse.ADAStandardsTool method) (tooluniverse.AHAACCGuidelineTool method) (tooluniverse.arxiv_tool.ArXivTool method) (tooluniverse.ArXivTool method) (tooluniverse.BiGGModelsTool method) (tooluniverse.BioImageArchiveTool method) (tooluniverse.BioPortalTool method) (tooluniverse.BioSamplesTool method) (tooluniverse.BridgeDbTool method) (tooluniverse.ChEBITool method) (tooluniverse.core_tool.CoreTool method) (tooluniverse.CoreTool method) (tooluniverse.dblp_tool.DBLPTool method) (tooluniverse.DBLPTool method) (tooluniverse.DisProtTool method) (tooluniverse.efo_tool.EFOTool method) (tooluniverse.EFOTool method) (tooluniverse.EmbeddingDatabase method) (tooluniverse.EMoleculesTool method) (tooluniverse.EOLTool method) (tooluniverse.europe_pmc_tool.EuropePMCTool method) (tooluniverse.EuropePMCTool method) (tooluniverse.FDADrugAdverseEventDetailTool method) (tooluniverse.FDADrugAdverseEventTool method) (tooluniverse.FDADrugInteractionDetailTool method) (tooluniverse.FDALabelTool method) (tooluniverse.FourDNTool method) (tooluniverse.hal_tool.HALTool method) (tooluniverse.HALTool method) (tooluniverse.HarmonizomeTool method) (tooluniverse.HGNCTool method) (tooluniverse.iPTMnetTool method) (tooluniverse.MaveDBTool method) (tooluniverse.MedGenTool method) (tooluniverse.MetaboliteTool method) (tooluniverse.MonarchV3Tool method) (tooluniverse.NCCNGuidelineTool method) (tooluniverse.NCIThesaurusTool method) (tooluniverse.OMIMTool method) (tooluniverse.openfda_adv_tool.FDADrugAdverseEventDetailTool method) (tooluniverse.openfda_adv_tool.FDADrugAdverseEventTool method) (tooluniverse.openfda_adv_tool.FDADrugInteractionDetailTool method) (tooluniverse.OrthoDBTool method) (tooluniverse.PathwayCommonsTool method) (tooluniverse.PharmacoDBTool method) (tooluniverse.PlantReactomeTool method) (tooluniverse.pmc_tool.PMCTool method) (tooluniverse.PMCTool method) (tooluniverse.PROSITETool method) (tooluniverse.ReactomeContentTool method) (tooluniverse.semantic_scholar_tool.SemanticScholarTool method) (tooluniverse.SemanticScholarTool method) (tooluniverse.SGDTool method) (tooluniverse.SRATool method) (tooluniverse.SynBioHubTool method) (tooluniverse.UCSCGenomeTool method) (tooluniverse.UniParcTool method) (tooluniverse.UniProtTaxonomyTool method) (tooluniverse.xml_tool.XMLDatasetTool method) (tooluniverse.XMLDatasetTool method) _search_actionability() (tooluniverse.ClinGenTool method) _search_amr() (tooluniverse.BVBRCTool method) _search_annotations() (tooluniverse.GOAPITool method) _search_approvals() (tooluniverse.OpenFDAApprovalTool method) _search_bioimages() (tooluniverse.BioImageArchiveTool method) _search_by_cell_type() (tooluniverse.CellMarkerTool method) _search_by_chebi() (tooluniverse.RheaTool method) _search_by_ec() (tooluniverse.RheaTool method) _search_by_filter() (tooluniverse.BioSamplesTool method) _search_by_gene() (tooluniverse.CellMarkerTool method) (tooluniverse.PubChemBioAssayTool method) _search_by_name() (tooluniverse.OrphanetTool method) _search_by_organism() (tooluniverse.PDBeSearchTool method) _search_by_properties() (tooluniverse.ZincTool method) _search_by_smiles() (tooluniverse.ZincTool method) _search_by_substrate() (tooluniverse.TCDBTool method) _search_by_target() (tooluniverse.TheraSAbDabTool method) _search_cancer_markers() (tooluniverse.CellMarkerTool method) _search_catalog() (tooluniverse.EnamineTool method) _search_cdr3() (tooluniverse.VDJDBTool method) _search_cell_lines() (tooluniverse.cellosaurus_tool.CellosaurusSearchTool method) (tooluniverse.CellosaurusSearchTool method) (tooluniverse.DepMapTool method) _search_clans() (tooluniverse.PfamTool method) _search_clusters() (tooluniverse.UniRefTool method) _search_cma_guidelines() (tooluniverse.CMAGuidelinesTool method) (tooluniverse.unified_guideline_tools.CMAGuidelinesTool method) _search_combos() (tooluniverse.SYNERGxDBTool method) _search_common() (tooluniverse.ITISTool method) _search_complexes() (tooluniverse.ComplexPortalTool method) _search_compound() (tooluniverse.UniChemTool method) _search_compounds() (tooluniverse.ClueTool method) (tooluniverse.ZincTool method) _search_datasets() (tooluniverse.CellxGeneDiscoveryTool method) (tooluniverse.ChIPAtlasTool method) (tooluniverse.HuBMAPTool method) (tooluniverse.MassIVETool method) (tooluniverse.nhanes_tool.NHANESTool method) (tooluniverse.NHANESTool method) (tooluniverse.ProteomeXchangeTool method) _search_depositors() (tooluniverse.AddgeneTool method) _search_descriptors() (tooluniverse.MeSHTool method) _search_differential_experiments() (tooluniverse.ExpressionAtlasTool method) _search_disease() (tooluniverse.DisGeNETTool method) (tooluniverse.GenCCTool method) (tooluniverse.KEGGExtTool method) _search_diseases() (tooluniverse.MyDiseaseTool method) (tooluniverse.OrphanetTool method) (tooluniverse.UniProtRefTool method) _search_dosage_sensitivity() (tooluniverse.ClinGenTool method) _search_drug() (tooluniverse.FDAOrangeBookTool method) (tooluniverse.KEGGExtTool method) (tooluniverse.SiderTool method) _search_drugs() (tooluniverse.DrugCentralTool method) _search_entity() (tooluniverse.PharmGKBTool method) (tooluniverse.ReactomeInteractorsTool method) _search_entries() (tooluniverse.EMPIARTool method) (tooluniverse.InterProEntryTool method) _search_epitopes() (tooluniverse.BVBRCTool method) _search_europepmc_guidelines() (tooluniverse.EuropePMCGuidelinesTool method) (tooluniverse.unified_guideline_tools.EuropePMCGuidelinesTool method) _search_exactmass() (tooluniverse.MetabolomicsWorkbenchTool method) _search_experiments() (tooluniverse.ExpressionAtlasTool method) (tooluniverse.MaveDBTool method) _search_families() (tooluniverse.DfamTool method) (tooluniverse.PfamTool method) _search_family() (tooluniverse.TCDBTool method) _search_features() (tooluniverse.BVBRCTool method) _SEARCH_FIELDS (tooluniverse.NCBISRATool attribute) _search_foods() (tooluniverse.FoodDataCentralTool method) _search_forms() (tooluniverse.LOINCTool method) _search_gene() (tooluniverse.DisGeNETTool method) (tooluniverse.EpiGraphDBTool method) (tooluniverse.GenCCTool method) (tooluniverse.SCExpressionAtlasTool method) _search_gene_validity() (tooluniverse.ClinGenTool method) _search_genes() (tooluniverse.AllenBrainTool method) (tooluniverse.AllianceGenomeTool method) (tooluniverse.DepMapTool method) (tooluniverse.HarmonizomeTool method) (tooluniverse.IMGTTool method) (tooluniverse.IMPCTool method) (tooluniverse.RGDTool method) (tooluniverse.XenbaseTool method) _search_genes_by_species() (tooluniverse.AllianceGenomeTool method) _search_genomes() (tooluniverse.BVBRCTool method) (tooluniverse.GTDBTool method) _search_gin_guidelines() (tooluniverse.GINGuidelinesTool method) (tooluniverse.unified_guideline_tools.GINGuidelinesTool method) _search_keywords() (tooluniverse.UniProtRefTool method) _search_locations() (tooluniverse.UniProtLocationsTool method) _search_loinc_items() (tooluniverse.LOINCTool method) _search_mappings() (tooluniverse.OxOTool method) _search_modifications() (tooluniverse.MODOMICSTool method) _search_motifs() (tooluniverse.HocomocoTool method) _search_moverz() (tooluniverse.LipidMapsTool method) (tooluniverse.MetabolomicsWorkbenchTool method) _search_mutations() (tooluniverse.COSMICTool method) _search_namespaces() (tooluniverse.IdentifiersOrgTool method) _search_network() (tooluniverse.KEGGExtTool method) _search_networks() (tooluniverse.NDExTool method) _search_neurons() (tooluniverse.NeuroMorphoTool method) _search_nice_guidelines_real() (tooluniverse.NICEWebScrapingTool method) (tooluniverse.unified_guideline_tools.NICEWebScrapingTool method) _search_nucleotide() (tooluniverse.NCBINucleotideSearchTool method) _search_observations() (tooluniverse.INaturalistTool method) _search_openalex_guidelines() (tooluniverse.OpenAlexGuidelinesTool method) (tooluniverse.unified_guideline_tools.OpenAlexGuidelinesTool method) _search_opengwas() (tooluniverse.EpiGraphDBTool method) _search_pathways() (tooluniverse.BVBRCTool method) (tooluniverse.MetaCycTool method) _search_plasmids() (tooluniverse.AddgeneTool method) _search_populations() (tooluniverse.IGSRTool method) _search_protacs() (tooluniverse.ProtacDBTool method) _search_protein_structures() (tooluniverse.BVBRCTool method) _search_proteins() (tooluniverse.ProteomicsDBTool method) _search_proteomes() (tooluniverse.UniProtRefTool method) _search_pubmed() (tooluniverse.ICiteSearchPublicationsTool method) _search_pubmed_guidelines() (tooluniverse.PubMedGuidelinesTool method) (tooluniverse.unified_guideline_tools.PubMedGuidelinesTool method) _search_pypi_via_web() (tooluniverse.DynamicPackageDiscovery method) (tooluniverse.package_discovery_tool.DynamicPackageDiscovery method) _search_reactions() (tooluniverse.RheaTool method) (tooluniverse.SABIORKTool method) _search_registries() (tooluniverse.BioregistryTool method) _search_repositories() (tooluniverse.Re3DataTool method) _search_researchers() (tooluniverse.ORCIDTool method) _search_samples() (tooluniverse.ENAPortalTool method) (tooluniverse.IGSRTool method) _search_scientific() (tooluniverse.ITISTool method) _search_screens() (tooluniverse.CellPaintingTool method) _search_sequence() (tooluniverse.RfamTool method) _search_side_effect() (tooluniverse.SiderTool method) _search_signatures() (tooluniverse.ClueTool method) (tooluniverse.LINCSSignatureTool method) _search_similar_molecules() (tooluniverse.chem_tool.ChEMBLTool method) (tooluniverse.ChEMBLTool method) _search_smiles() (tooluniverse.EMoleculesTool method) (tooluniverse.EnamineTool method) _search_specialty_genes() (tooluniverse.BVBRCTool method) _search_species() (tooluniverse.GmrepoTool method) _search_sra_runs() (tooluniverse.NCBISRATool method) _search_structures() (tooluniverse.AllenBrainTool method) (tooluniverse.PDBeSearchTool method) (tooluniverse.SAbDabTool method) _search_studies() (tooluniverse.CancerPrognosisTool method) (tooluniverse.CTGovAPITool method) (tooluniverse.ENAPortalTool method) (tooluniverse.ImmPortTool method) (tooluniverse.PDCTool method) _search_substances() (tooluniverse.FDAGSRSTool method) _search_subsystems() (tooluniverse.BVBRCTool method) _search_surveillance() (tooluniverse.BVBRCTool method) _search_targets() (tooluniverse.PharosTool method) (tooluniverse.ProtacDBTool method) _search_targets_by_abbreviation_variants() (tooluniverse.gtopdb_tool.GtoPdbRESTTool method) (tooluniverse.GtoPdbRESTTool method) _search_taxa() (tooluniverse.INaturalistTool method) _search_taxon() (tooluniverse.GTDBTool method) _search_taxonomy() (tooluniverse.BVBRCTool method) _search_terms() (tooluniverse.HPOTool method) (tooluniverse.MeSHTool method) _search_therapeutics() (tooluniverse.TheraSAbDabTool method) _search_toxins() (tooluniverse.T3DBTool method) _search_trip_database() (tooluniverse.TRIPDatabaseTool method) (tooluniverse.unified_guideline_tools.TRIPDatabaseTool method) _search_variant() (tooluniverse.KEGGExtTool method) _search_variants() (tooluniverse.LOVDTool method) _search_who_guidelines() (tooluniverse.unified_guideline_tools.WHOGuidelinesTool method) (tooluniverse.WHOGuidelinesTool method) _search_with_ddgs() (tooluniverse.web_search_tool.WebSearchTool method) (tooluniverse.WebSearchTool method) _search_with_duckduckgo_html() (tooluniverse.web_search_tool.WebSearchTool method) (tooluniverse.WebSearchTool method) _search_with_fallback() (tooluniverse.web_search_tool.WebSearchTool method) (tooluniverse.WebSearchTool method) _search_with_wikipedia_api() (tooluniverse.web_search_tool.WebSearchTool method) (tooluniverse.WebSearchTool method) _SECTION_KEYWORDS (tooluniverse.europe_pmc_tool.EuropePMCStructuredFullTextTool attribute) (tooluniverse.EuropePMCStructuredFullTextTool attribute) _sections_array() (in module tooluniverse.odphp_tool) _select_search_tool() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) _semsim_search() (tooluniverse.MonarchV3Tool method) _set_docking_parameters() (tooluniverse.SwissDockTool method) _set_nested_value() (tooluniverse.FDADrugAdverseEventDetailTool method) (tooluniverse.FDADrugInteractionDetailTool method) (tooluniverse.openfda_adv_tool.FDADrugAdverseEventDetailTool method) (tooluniverse.openfda_adv_tool.FDADrugInteractionDetailTool method) _setup_logger() (tooluniverse.logging_config.ToolUniverseLogger method) _setup_smcp_tools() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) _SIENA_OPTIONAL_KEYS (tooluniverse.ProteinsPlusRESTTool attribute) _sig_search() (tooluniverse.L1000FWDTool method) _SIMPLE_TYPE_MAP (tooluniverse.SMCP attribute) (tooluniverse.smcp.SMCP attribute) _simplify_output() (tooluniverse.ClinicalTrialsDetailsTool method) (tooluniverse.ClinicalTrialsSearchTool method) (tooluniverse.ctg_tool.ClinicalTrialsDetailsTool method) (tooluniverse.ctg_tool.ClinicalTrialsSearchTool method) _site_detail() (tooluniverse.GlyGenTool method) _snpense() (tooluniverse.GProfilerTool method) _solr_query() (tooluniverse.IMPCTool method) _spdi_canonical() (tooluniverse.NCBIVariationTool method) _spdi_equivalents() (tooluniverse.NCBIVariationTool method) _spdi_to_hgvs() (tooluniverse.NCBIVariationTool method) _species_comparison() (tooluniverse.ReactomeAnalysisTool method) _species_list() (tooluniverse.BgeeTool method) _split_composite_id() (tooluniverse.rcsb_pdb_tool.RCSBTool method) (tooluniverse.RCSBTool method) _start_docking() (tooluniverse.SwissDockTool method) _start_server_for_port() (in module tooluniverse.mcp_tool_registry) _started (tooluniverse.smcp.SMCP attribute) _state_storage (tooluniverse.smcp.SMCP attribute) _state_store (tooluniverse.smcp.SMCP attribute) _stats() (tooluniverse.SequenceAnalyzeTool method) _STATUS_KEYWORD_MAP (tooluniverse.SwissDockTool attribute) _store_profile_metadata() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _stores() (tooluniverse.EmbeddingDatabase method) _stratify_by_demographics() (tooluniverse.FAERSAnalyticsTool method) _stream_supports_unicode() (in module tooluniverse.logging_config) _strip_html() (in module tooluniverse.gtopdb_tool) (tooluniverse.EOLTool static method) (tooluniverse.PfamTool method) (tooluniverse.PubChemToxTool method) (tooluniverse.ReactomeContentTool static method) _strip_html_to_text() (in module tooluniverse.odphp_tool) _study_detail() (tooluniverse.MGnifyExpandedTool method) _submit_and_get_csv() (tooluniverse.SwissADMETool method) _submit_and_poll() (tooluniverse.UniProtIDMappingTool method) _submit_genes() (tooluniverse.EnrichrExtTool method) _submit_search() (tooluniverse.FoldseekTool method) _support_tasks_by_default (tooluniverse.smcp.SMCP attribute) _survival_association() (tooluniverse.TIMERTool method) _t_test() (tooluniverse.ScientificCalculatorTool method) _temperature (tooluniverse.agentic_tool.AgenticTool attribute) _term_children() (tooluniverse.QuickGOTool method) _term_detail() (tooluniverse.QuickGOTool method) _therapeutics_cache (tooluniverse.TheraSAbDabTool attribute) _TISSUE_ALIASES (tooluniverse.SYNERGxDBTool attribute) _to_pdb() (tooluniverse.UniProtIDMappingTool method) _token_result() (tooluniverse.ReactomeAnalysisTool method) _tokenize_and_normalize() (tooluniverse.tool_finder_keyword.ToolFinderKeyword method) (tooluniverse.ToolFinderKeyword method) _tomtom_compare() (tooluniverse.MEMETool method) _tools_find_middleware() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) _topic_slug() (tooluniverse.unified_guideline_tools.WHOGuidelinesTool method) (tooluniverse.WHOGuidelinesTool method) _transform_params() (tooluniverse.ProteinsPlusRESTTool method) _transforms (tooluniverse.smcp.SMCP attribute) _translate_coords() (tooluniverse.EnsemblMapTool method) _translate_reading_frames() (tooluniverse.ScientificCalculatorTool method) _translate_sequence() (tooluniverse.DNATool method) _traverse() (tooluniverse.PathwayCommonsTool method) _truncate_response() (in module tooluniverse.smcp) _try_api() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) _try_initialize_api() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) _try_pk_unit_conversion() (tooluniverse.NCATool method) _ucsc_get_track() (tooluniverse.UCSCEpigenomicsTool method) _unwrap_list() (tooluniverse.ClueTool method) _upload() (tooluniverse.EmbeddingSync method) _upload_asset() (tooluniverse.NvidiaNIMTool method) _use_complex_web_service() (tooluniverse.IntActRESTTool method) _use_ebi_search() (tooluniverse.IntActRESTTool method) _use_global_fallback (tooluniverse.agentic_tool.AgenticTool attribute) _vaccine_coverage() (tooluniverse.EpidemiologyTool method) _VALID_API_PARAMS (tooluniverse.openfda_tool.OpenFDADrugEventsTool attribute) (tooluniverse.OpenFDADrugEventsTool attribute) _VALID_SORT_BY (tooluniverse.arxiv_tool.ArXivTool attribute) (tooluniverse.ArXivTool attribute) _validate() (tooluniverse.CrystalStructureTool method) _validate_api_key (tooluniverse.agentic_tool.AgenticTool attribute) _validate_api_key() (tooluniverse.NvidiaNIMTool method) _validate_arguments() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) _validate_context() (tooluniverse.hpa_tool.HPAGetContextualBiologicalProcessTool method) (tooluniverse.HPAGetContextualBiologicalProcessTool method) _validate_dna_sequence() (tooluniverse.DNATool method) _validate_doc_args() (tooluniverse.EmbeddingDatabase static method) _validate_llm_api_keys() (tooluniverse.output_hook.HookManager method) _validate_model_config() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) _validate_output() (tooluniverse.extended_hooks.ValidationHook method) _validate_parameters() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) _validate_pdb_id() (tooluniverse.rcsb_search_tool.RCSBSearchTool method) (tooluniverse.RCSBSearchTool method) _validate_required() (tooluniverse.ProteinsPlusRESTTool method) _validate_sequence() (tooluniverse.IDTTool method) (tooluniverse.rcsb_search_tool.RCSBSearchTool method) (tooluniverse.RCSBSearchTool method) _validate_solr_query() (tooluniverse.cellosaurus_tool.CellosaurusQueryConverterTool method) (tooluniverse.CellosaurusQueryConverterTool method) _validate_variant() (tooluniverse.SpliceAITool method) _variant_recoder() (tooluniverse.EnsemblVEPTool method) _vep_hgvs() (tooluniverse.EnsemblVEPTool method) _vep_id() (tooluniverse.EnsemblVEPTool method) _virtual_digest() (tooluniverse.DNATool method) _with_data_payload() (tooluniverse.dailymed_tool.DailyMedSPLParserTool method) (tooluniverse.DailyMedSPLParserTool method) (tooluniverse.FAERSAnalyticsTool method) (tooluniverse.FDAOrangeBookTool method) _workspace_dir (tooluniverse.execute_function.ToolUniverse attribute) _workspace_profile_config (tooluniverse.execute_function.ToolUniverse attribute) _write_data_to_file() (tooluniverse.output_hook.FileSaveHook method) _write_log() (tooluniverse.extended_hooks.LoggingHook method)

A

acquire() (tooluniverse.cache.memory_cache.SingleFlight method) ADAStandardsTool (class in tooluniverse) add_3d_controls_script() (tooluniverse.visualization_tool.VisualizationTool method) (tooluniverse.VisualizationTool method) add_agent_result() (tooluniverse.memory_manager.MemoryManager method) add_annotations_to_tool_config() (in module tooluniverse.tool_defaults) add_custom_tool() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) add_embeddings() (tooluniverse.database_setup.vector_store.VectorStore method) (tooluniverse.database_setup.VectorStore method) add_tool() (in module tooluniverse.database_setup.cli) AddgeneTool (class in tooluniverse) ADMETAITool (class in tooluniverse) (class in tooluniverse.admetai_tool) Agentic Tool AgenticTool (class in tooluniverse) (class in tooluniverse.agentic_tool) AgingCohortSearchTool (class in tooluniverse) AHAACCGuidelineTool (class in tooluniverse) AI Scientist AI-Tool Interaction Protocol all_tool_dict (tooluniverse.execute_function.ToolUniverse attribute), [1] (tooluniverse.ToolUniverse attribute) all_tools (tooluniverse.execute_function.ToolUniverse attribute), [1] (tooluniverse.ToolUniverse attribute) AllenBrainTool (class in tooluniverse)

AllianceGenomeTool (class in tooluniverse) AlphaFold AlphaFold2 AlphaFoldRESTTool (class in tooluniverse) (class in tooluniverse.alphafold_tool) AlphaMissenseTool (class in tooluniverse) AOPWikiDetailTool (class in tooluniverse) AOPWikiListTool (class in tooluniverse) API Endpoint API_VERSION (tooluniverse.DeepGOTool attribute) apply_hooks() (tooluniverse.output_hook.HookManager method) APPRISTool (class in tooluniverse) ARCHS4Tool (class in tooluniverse) arguments (tooluniverse.execute_function._BatchJob attribute) ArrayExpressRESTTool (class in tooluniverse) ArXivPDFSnippetsTool (class in tooluniverse) (class in tooluniverse.arxiv_tool) ArXivTool (class in tooluniverse) (class in tooluniverse.arxiv_tool) ASSETS_URL (tooluniverse.NvidiaNIMTool attribute) assign_by_path() (tooluniverse.uspto_tool.USPTOOpenDataPortalTool method) (tooluniverse.USPTOOpenDataPortalTool method) auth (tooluniverse.smcp.SMCP attribute) 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

BASE_URL (tooluniverse.APPRISTool attribute) (tooluniverse.BindingDBTool attribute) (tooluniverse.clinical_trials_tool.ClinicalTrialsGovTool attribute) (tooluniverse.ClinicalTrialsGovTool attribute) (tooluniverse.DeepGOTool attribute) (tooluniverse.hca_tool.HCATool attribute) (tooluniverse.HCATool attribute) (tooluniverse.IDTTool attribute) (tooluniverse.NEBTmTool attribute) (tooluniverse.pathway_commons_tool.PathwayCommonsTool attribute) (tooluniverse.Re3DataTool attribute) BaseLLMClient (class in tooluniverse.llm_clients) BaseMCPClient (class in tooluniverse) (class in tooluniverse.mcp_client_tool) BasePythonExecutor (class in tooluniverse) (class in tooluniverse.python_executor_tool) BaseRESTTool (class in tooluniverse) BaseTool (class in tooluniverse) (class in tooluniverse.base_tool) BENIGN_THRESHOLD (tooluniverse.AlphaMissenseTool attribute) BgeeTool (class in tooluniverse) BiGGModelsTool (class in tooluniverse) BinaryDownloadTool (class in tooluniverse) (class in tooluniverse.file_download_tool)

BindingDBTool (class in tooluniverse) BioGRIDRESTTool (class in tooluniverse) (class in tooluniverse.biogrid_tool) BioImageArchiveTool (class in tooluniverse) BioModelsRESTTool (class in tooluniverse) (class in tooluniverse.biomodels_tool) BioPortalTool (class in tooluniverse) BioregistryTool (class in tooluniverse) BioRxivTool (class in tooluniverse) (class in tooluniverse.biorxiv_tool) BioSamplesTool (class in tooluniverse) BioStudiesRESTTool (class in tooluniverse) Boltz2DockingTool (class in tooluniverse) (class in tooluniverse.boltz_tool) BRENDATool (class in tooluniverse) BridgeDbTool (class in tooluniverse) build_collection() (in module tooluniverse.database_setup) (in module tooluniverse.database_setup.pipeline) build_graph() (tooluniverse.enrichr_tool.EnrichrTool method) (tooluniverse.EnrichrTool method) build_lazy_registry() (in module tooluniverse.tool_registry) bulk_get() (tooluniverse.cache.result_cache_manager.ResultCacheManager method) BVBRCTool (class in tooluniverse)

C

Cache Fingerprint 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) CADDTool (class in tooluniverse) calculate_tool_hash() (in module tooluniverse.build_optimizer) call (tooluniverse.execute_function._BatchJob attribute) 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) CancerPrognosisTool (class in tooluniverse) CancerVarTool (class in tooluniverse) category_overrides (tooluniverse.tool_defaults.ToolDefaultsConfig attribute) CATHTool (class in tooluniverse) CBioPortalRESTTool (class in tooluniverse) (class in tooluniverse.cbioportal_tool) CDCRESTTool (class in tooluniverse) (class in tooluniverse.cdc_tool) CellMarkerTool (class in tooluniverse) 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) CellPaintingTool (class in tooluniverse) CELLxGENECensusTool (class in tooluniverse) CellxGeneDiscoveryTool (class in tooluniverse) ChEBITool (class in tooluniverse) 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) check_status() (tooluniverse.ProteinsPlusRESTTool method) (tooluniverse.SwissDockTool method) ChEMBL ChEMBL ID ChEMBLRESTTool (class in tooluniverse) (class in tooluniverse.chem_tool) ChEMBLTool (class in tooluniverse) (class in tooluniverse.chem_tool) ChemComputeTool (class in tooluniverse) ChIPAtlasTool (class in tooluniverse) chunk_size (tooluniverse.output_hook.SummarizationHook attribute) (tooluniverse.output_hook.SummarizationHookConfig attribute) CIViCTool (class in tooluniverse) 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) clear_lazy_cache() (in module tooluniverse.tool_registry) clear_tools() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) client_log_level (tooluniverse.smcp.SMCP attribute) ClinGenAlleleTool (class in tooluniverse) ClinGenARTool (class in tooluniverse) ClinGenDosageTool (class in tooluniverse) ClinGenTool (class in tooluniverse) ClinicalTrialsDetailsTool (class in tooluniverse) (class in tooluniverse.ctg_tool) ClinicalTrialsGovTool (class in tooluniverse) (class in tooluniverse.clinical_trials_tool) ClinicalTrialsSearchTool (class in tooluniverse) (class in tooluniverse.ctg_tool) ClinicalTrialsTool (class in tooluniverse) (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) (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) (tooluniverse.ToolUniverseClient method) close_session() (tooluniverse.memory_manager.MemoryManager method) ClueTool (class in tooluniverse) CMAGuidelinesTool (class in tooluniverse) (class in tooluniverse.unified_guideline_tools) CODTool (class in tooluniverse) COLORS (tooluniverse.logging_config.ToolUniverseFormatter attribute) Compact Mode compare_function_calls() (in module tooluniverse.utils) ComplexPortalTool (class in tooluniverse) 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) 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) (tooluniverse.VisualizationTool method) CorePDFSnippetsTool (class in tooluniverse) (class in tooluniverse.core_tool) CoreTool (class in tooluniverse) (class in tooluniverse.core_tool) COSMICTool (class in tooluniverse) CPICGetRecommendationsTool (class in tooluniverse) CPICListGuidelinesTool (class in tooluniverse) CPICSearchPairsTool (class in tooluniverse) create_error_response() (tooluniverse.visualization_tool.VisualizationTool method) (tooluniverse.VisualizationTool method) create_mcp_tools_config() (tooluniverse.mcp_client_tool.MCPServerDiscovery static method) (tooluniverse.MCPServerDiscovery static method) create_molecule_2d_html() (tooluniverse.visualization_tool.VisualizationTool method) (tooluniverse.VisualizationTool method) create_plotly_html() (tooluniverse.visualization_tool.VisualizationTool method) (tooluniverse.VisualizationTool method) create_py3dmol_html() (tooluniverse.visualization_tool.VisualizationTool method) (tooluniverse.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) (tooluniverse.VisualizationTool method) created_at (tooluniverse.cache.sqlite_backend.CacheEntry attribute) critical() (in module tooluniverse.logging_config) CrossrefRESTTool (class in tooluniverse) (class in tooluniverse.crossref_tool) CryoETTool (class in tooluniverse) CrystalStructureTool (class in tooluniverse) CTDTool (class in tooluniverse) CTFPHCListGuidelinesTool (class in tooluniverse) (class in tooluniverse.unified_guideline_tools) CTFPHCSearchGuidelinesTool (class in tooluniverse) (class in tooluniverse.unified_guideline_tools) CTGovAPITool (class in tooluniverse) CustomTool (class in tooluniverse) (class in tooluniverse.custom_tool)

D

DailyMedSPLParserTool (class in tooluniverse) (class in tooluniverse.dailymed_tool) DataCiteRESTTool (class in tooluniverse) DataGovTool (class in tooluniverse) DataQualityTool (class in tooluniverse) DatasetTool (class in tooluniverse) (class in tooluniverse.dataset_tool) DbfetchRESTTool (class in tooluniverse) DBLPTool (class in tooluniverse) (class in tooluniverse.dblp_tool) DBpediaSPARQLTool (class in tooluniverse) (class in tooluniverse.dbpedia_tool) dbSNPGetFrequencies (class in tooluniverse) (class in tooluniverse.dbsnp_tool) dbSNPGetVariantByRsID (class in tooluniverse) (class in tooluniverse.dbsnp_tool) dbSNPRESTTool (class in tooluniverse) (class in tooluniverse.dbsnp_tool) dbSNPSearchByGene (class in tooluniverse) (class in tooluniverse.dbsnp_tool) debug() (in module tooluniverse.logging_config) DeepGOTool (class in tooluniverse) DEFAULT_ALLOWED_MODULES (tooluniverse.BasePythonExecutor attribute) (tooluniverse.python_executor_tool.BasePythonExecutor attribute) default_annotations (tooluniverse.tool_defaults.ToolDefaultsConfig attribute) DEFAULT_BASE_URL (tooluniverse.efo_tool.OLSRESTTool attribute) (tooluniverse.NvidiaNIMTool attribute) (tooluniverse.OLSRESTTool attribute) DEFAULT_MODEL_LIMITS (tooluniverse.llm_clients.AzureOpenAIClient attribute) (tooluniverse.llm_clients.OpenRouterClient attribute) DEFAULT_POLL_SECONDS (tooluniverse.NvidiaNIMTool attribute) DEFAULT_TIMEOUT (tooluniverse.NvidiaNIMTool attribute) DEFAULT_VERSION (tooluniverse.CADDTool attribute) DegreesOfUnsaturationTool (class in tooluniverse) delete() (tooluniverse.cache.memory_cache.LRUCache method) (tooluniverse.cache.result_cache_manager.ResultCacheManager method) (tooluniverse.cache.sqlite_backend.PersistentCache method) DepMapTool (class in tooluniverse) description (tooluniverse.DetailedTermInfo attribute) (tooluniverse.ols_tool.DetailedTermInfo attribute) (tooluniverse.ols_tool.OntologyInfo attribute) (tooluniverse.OntologyInfo attribute)

destructiveHint (tooluniverse.tool_defaults.ToolAnnotations attribute), [1] DetailedTermInfo (class in tooluniverse) (class in tooluniverse.ols_tool) details (tooluniverse.exceptions.ToolError attribute) DfamTool (class in tooluniverse) DGIdbTool (class in tooluniverse) 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) (tooluniverse.MCPServerDiscovery static method) discover_tools() (tooluniverse.mcp_client_tool.MCPAutoLoaderTool method) (tooluniverse.MCPAutoLoaderTool method) DiseaseOntologyTool (class in tooluniverse) DiseaseTargetScoreTool (class in tooluniverse) (class in tooluniverse.graphql_tool) DisGeNETTool (class in tooluniverse) DisProtTool (class in tooluniverse) DNATool (class in tooluniverse) DOAJTool (class in tooluniverse) (class in tooluniverse.doaj_tool) domain (tooluniverse.ols_tool.OntologyInfo attribute) (tooluniverse.OntologyInfo attribute) DoseResponseTool (class in tooluniverse) download() (in module tooluniverse.database_setup) download_from_hf() (in module tooluniverse.utils) DrugCentralTool (class in tooluniverse) DrugPropertiesTool (class in tooluniverse) DrugSynergyTool (class in tooluniverse) dump() (tooluniverse.cache.result_cache_manager.ResultCacheManager method) dump_cache() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) DynamicPackageDiscovery (class in tooluniverse) (class in tooluniverse.package_discovery_tool) DynaMut2Tool (class in tooluniverse)

E

eager_load() (tooluniverse.execute_function.ToolNamespace method) eager_load_tools() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) EBI_SEARCH_BASE (tooluniverse.EMPIARTool attribute) EBIProteinsCoordinatesTool (class in tooluniverse) EBIProteinsEpitopeTool (class in tooluniverse) EBIProteinsExtTool (class in tooluniverse) EBIProteinsFeaturesTool (class in tooluniverse) EBIProteinsInteractionsTool (class in tooluniverse) EBISearchRESTTool (class in tooluniverse) EBITaxonomyTool (class in tooluniverse) EFO EFO ID EFOTool (class in tooluniverse) (class in tooluniverse.efo_tool) ELMTool (class in tooluniverse) 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 Embedding Search embedding_search() (tooluniverse.database_setup.search.SearchEngine method) (tooluniverse.database_setup.SearchEngine method) EmbeddingCollectionSearchTool (class in tooluniverse) (class in tooluniverse.database_setup) (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) EMDBRESTTool (class in tooluniverse) (class in tooluniverse.emdb_tool) EMOJI_PREFIX (tooluniverse.logging_config.ToolUniverseFormatter attribute) EMoleculesTool (class in tooluniverse) EMPIAR_API_BASE (tooluniverse.EMPIARTool attribute) EMPIARTool (class in tooluniverse) 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) ENABrowserRESTTool (class in tooluniverse) EnamineTool (class in tooluniverse) ENAPortalTool (class in tooluniverse) ENCODEFilesTool (in module tooluniverse) (in module tooluniverse.encode_tool) ENCODERESTTool (class in tooluniverse) (class in tooluniverse.encode_tool) ENCODESearchBiosamplesTool (in module tooluniverse) (in module tooluniverse.encode_tool) ENCODESearchTool (class in tooluniverse) (class in tooluniverse.encode_tool) endpoint_template (tooluniverse.biogrid_tool.BioGRIDRESTTool attribute) enrichr_api() (tooluniverse.enrichr_tool.EnrichrTool method) (tooluniverse.EnrichrTool method) EnrichrExtTool (class in tooluniverse) EnrichrTool (class in tooluniverse) (class in tooluniverse.enrichr_tool) EnsemblArchiveTool (class in tooluniverse) EnsemblComparaTool (class in tooluniverse) EnsemblGetSequence (class in tooluniverse) (class in tooluniverse.ensembl_tool)

EnsemblGetVariants (class in tooluniverse) (class in tooluniverse.ensembl_tool) EnsemblInfoTool (class in tooluniverse) EnsemblLDTool (class in tooluniverse) EnsemblLookupGene (class in tooluniverse) (class in tooluniverse.ensembl_tool) EnsemblMapTool (class in tooluniverse) EnsemblOverlapTool (class in tooluniverse) EnsemblPhenotypeTool (class in tooluniverse) EnsemblRegulationTool (class in tooluniverse) EnsemblRESTTool (class in tooluniverse) (class in tooluniverse.ensembl_tool) EnsemblSequenceTool (class in tooluniverse) EnsemblVariationExtTool (class in tooluniverse) EnsemblVEPTool (class in tooluniverse) EnsemblXrefsTool (class in tooluniverse) EOLTool (class in tooluniverse) EpidemiologyTool (class in tooluniverse) EpigenomicsTool (class in tooluniverse) EpiGraphDBTool (class in tooluniverse) EPMCAnnotationsTool (class in tooluniverse) error() (in module tooluniverse.logging_config) error_type (tooluniverse.exceptions.ToolError attribute) ESMFoldTool (class in tooluniverse) ESMTool (class in tooluniverse) estimate_token_usage() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) EuHealthDeepDiveTool (class in tooluniverse) EuHealthTopicSearchTool (class in tooluniverse) EuropePMCFullTextFetchTool (class in tooluniverse) (class in tooluniverse.europe_pmc_tool) EuropePMCFullTextSnippetsTool (class in tooluniverse) (class in tooluniverse.europe_pmc_tool) EuropePMCGuidelinesTool (class in tooluniverse) (class in tooluniverse.unified_guideline_tools) EuropePMCRESTTool (class in tooluniverse) (class in tooluniverse.europe_pmc_tool) EuropePMCStructuredFullTextTool (class in tooluniverse) (class in tooluniverse.europe_pmc_tool) EuropePMCTool (class in tooluniverse) (class in tooluniverse.europe_pmc_tool) EuroPMCAnnotationsTool (class in tooluniverse) evaluate() (tooluniverse.output_hook.HookRule method) evaluate_function_call() (in module tooluniverse.utils) evaluate_function_call_from_toolbox() (in module tooluniverse.utils) EVETool (class in tooluniverse) execute_query() (in module tooluniverse.graphql_tool) execute_RESTful_query() (in module tooluniverse.restful_tool) ExecuteTool (in module tooluniverse) ExecuteToolTool (class in tooluniverse) (class in tooluniverse.tool_discovery_tools) expires_at (tooluniverse.cache.result_cache_manager.CacheRecord attribute) (tooluniverse.cache.sqlite_backend.CacheEntry attribute) export_tool_names() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) ExpressionAtlasTool (class in tooluniverse) 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 FAERSAnalyticsTool (class in tooluniverse) FatcatMetadataParser (class in tooluniverse) (class in tooluniverse.fatcat_tool) FatcatResultParser (class in tooluniverse) (class in tooluniverse.fatcat_tool) FatcatScholarTool (class in tooluniverse) (class in tooluniverse.fatcat_tool) FDA_URL (tooluniverse.FDAPharmacogenomicBiomarkersTool attribute) FDACountAdditiveReactionsTool (class in tooluniverse) (class in tooluniverse.openfda_adv_tool) FDADrugAdverseEventDetailTool (class in tooluniverse) (class in tooluniverse.openfda_adv_tool) FDADrugAdverseEventTool (class in tooluniverse) (class in tooluniverse.openfda_adv_tool) FDADrugInteractionDetailTool (class in tooluniverse) (class in tooluniverse.openfda_adv_tool) FDADrugLabel (in module tooluniverse) FDADrugLabelAggregated (in module tooluniverse) FDADrugLabelFieldValueTool (class in tooluniverse) (class in tooluniverse.openfda_tool) FDADrugLabelGetDrugGenericNameTool (class in tooluniverse) (class in tooluniverse.openfda_tool) FDADrugLabelGetDrugNamesByIndicationAggregated (class in tooluniverse) (class in tooluniverse.openfda_tool) FDADrugLabelGetDrugNamesByIndicationStats (class in tooluniverse) (class in tooluniverse.openfda_tool) FDADrugLabelSearchIDTool (class in tooluniverse) (class in tooluniverse.openfda_tool) FDADrugLabelSearchTool (class in tooluniverse) (class in tooluniverse.openfda_tool) FDADrugLabelStats (in module tooluniverse) FDADrugLabelTool (class in tooluniverse) (class in tooluniverse.openfda_tool) FDAGSRSTool (class in tooluniverse) FDALabelTool (class in tooluniverse) FDAOrangeBookTool (class in tooluniverse) FDAPharmacogenomicBiomarkersTool (class in tooluniverse) FDATool (class in tooluniverse) (class in tooluniverse.openfda_tool) FederalRegisterTool (class in tooluniverse) 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)

FileDownloadTool (class in tooluniverse) (class in tooluniverse.file_download_tool) FileSaveHook (class in tooluniverse.output_hook) fill_defaults() (in module tooluniverse.profile) (in module tooluniverse.profile.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) Fingerprint FinnGenTool (class in tooluniverse) flush() (tooluniverse.cache.result_cache_manager.ResultCacheManager method) focus_areas (tooluniverse.output_hook.SummarizationHook attribute) (tooluniverse.output_hook.SummarizationHookConfig attribute) FoldseekTool (class in tooluniverse) FoodDataCentralTool (class in tooluniverse) FORBIDDEN_AST_NODES (tooluniverse.BasePythonExecutor attribute) (tooluniverse.python_executor_tool.BasePythonExecutor 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) format_health_answer() (tooluniverse.who_gho_tool.WHOGHORESTTool static method) (tooluniverse.WHOGHORESTTool static method) format_result() (tooluniverse.ProteinsPlusRESTTool method) (tooluniverse.SwissDockTool method) FormattingHook (class in tooluniverse.extended_hooks) FourDNTool (class in tooluniverse) from_tooluniverse() (tooluniverse.smolagent_tool.ToolUniverseTool class method) (tooluniverse.ToolUniverseTool class method) function_name (tooluniverse.execute_function._BatchJob attribute)

G

GBIFOccurrenceTool (class in tooluniverse) (class in tooluniverse.gbif_tool) GBIFTool (class in tooluniverse) (class in tooluniverse.gbif_tool) GDCCasesTool (class in tooluniverse) (class in tooluniverse.gdc_tool) GDCClinicalDataTool (class in tooluniverse) (class in tooluniverse.gdc_tool) GDCCNVTool (class in tooluniverse) (class in tooluniverse.gdc_tool) GDCFilesTool (class in tooluniverse) (class in tooluniverse.gdc_tool) GDCGeneExpressionTool (class in tooluniverse) (class in tooluniverse.gdc_tool) GDCMutationFrequencyTool (class in tooluniverse) (class in tooluniverse.gdc_tool) GDCProjectsTool (class in tooluniverse) (class in tooluniverse.gdc_tool) GDCSSMTool (class in tooluniverse) (class in tooluniverse.gdc_tool) GDCSurvivalTool (class in tooluniverse) (class in tooluniverse.gdc_tool) GeminiClient (class in tooluniverse.llm_clients) GenCCTool (class in tooluniverse) GeneOntologyTool (class in tooluniverse) (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) GenomeNexusTool (class in tooluniverse) GEOGetDatasetInfo (class in tooluniverse) (class in tooluniverse.geo_tool) GEOGetSampleInfo (class in tooluniverse) (class in tooluniverse.geo_tool) GEORESTTool (class in tooluniverse) (class in tooluniverse.geo_tool) GEOSearchDatasets (class in tooluniverse) (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_annotations_for_tool() (in module tooluniverse.tool_defaults) 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_annotations() (in module tooluniverse.tool_defaults) 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) (tooluniverse.EnrichrTool method) get_entrez_ids() (tooluniverse.humanbase_tool.HumanBaseTool method) (tooluniverse.HumanBaseTool method) get_entry_by_accession() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) get_file_manifest() (tooluniverse.hca_tool.HCATool method) (tooluniverse.HCATool method) get_function_by_accession() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) get_genes_for_term() (tooluniverse.gene_ontology_tool.GeneOntologyTool method) (tooluniverse.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_interaction_graph() (tooluniverse.pathway_commons_tool.PathwayCommonsTool method) get_lazy_loading_status() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) get_list_config_registry() (in module tooluniverse.tool_registry) 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.EnrichrTool method) (tooluniverse.humanbase_tool.HumanBaseTool method) (tooluniverse.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) (tooluniverse.OpenAlexTool method)

get_papers_by_author() (tooluniverse.openalex_tool.OpenAlexTool method) (tooluniverse.OpenAlexTool method) get_parameter_schema() (in module tooluniverse.utils) get_profile_llm_config() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) get_profile_metadata() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) 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) (tooluniverse.RemoteTool method) get_required_parameters() (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseTool method) (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) get_schema_const_operation() (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseTool method) get_sequence_isoforms_by_accession() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) get_server_info() (tooluniverse.remote_tool.RemoteTool method) (tooluniverse.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_study_details() (tooluniverse.clinical_trials_tool.ClinicalTrialsGovTool method) (tooluniverse.ClinicalTrialsGovTool method) get_subcellular_location_by_accession() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) get_term_details() (tooluniverse.gene_ontology_tool.GeneOntologyTool method) (tooluniverse.GeneOntologyTool method) get_terms_for_gene() (tooluniverse.gene_ontology_tool.GeneOntologyTool method) (tooluniverse.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_defaults() (in module tooluniverse.tool_defaults) get_tool_description() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) get_tool_errors() (in module tooluniverse.tool_registry) get_tool_files_from_dir() (tooluniverse.profile.loader.ProfileLoader static method) (tooluniverse.profile.ProfileLoader static method) (tooluniverse.ProfileLoader static method) 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_tools() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) get_user_cache_dir() (in module tooluniverse.utils) GetSPLBySetIDTool (class in tooluniverse) (class in tooluniverse.dailymed_tool) GetToolInfo (in module tooluniverse) GetToolInfoTool (class in tooluniverse) (class in tooluniverse.tool_discovery_tools) GINGuidelinesTool (class in tooluniverse) (class in tooluniverse.unified_guideline_tools) GlyGenTool (class in tooluniverse) GmrepoTool (class in tooluniverse) gnomADGetGeneConstraints (class in tooluniverse) (class in tooluniverse.gnomad_tool) gnomADGraphQLQueryTool (class in tooluniverse) (class in tooluniverse.gnomad_tool) gnomADGraphQLTool (class in tooluniverse) (class in tooluniverse.gnomad_tool) GNPSTool (class in tooluniverse) GOAPITool (class in tooluniverse) GPCRdbTool (class in tooluniverse) GProfilerTool (class in tooluniverse) GraphQLTool (class in tooluniverse) (class in tooluniverse.graphql_tool) GrepTools (in module tooluniverse) GrepToolsTool (class in tooluniverse) (class in tooluniverse.tool_discovery_tools) GTDBTool (class in tooluniverse) GTExEQTLTool (class in tooluniverse) (class in tooluniverse.gtex_tool) GTExExpressionTool (class in tooluniverse) (class in tooluniverse.gtex_tool) GTExV2Tool (class in tooluniverse) GtoPdbRESTTool (class in tooluniverse) (class in tooluniverse.gtopdb_tool) 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) (class in tooluniverse.genomics_gene_search_tool) GWASRESTTool (class in tooluniverse) (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) GWASSumStatsTool (class in tooluniverse) GWASVariantsForTrait (class in tooluniverse) (class in tooluniverse.gwas_tool) GxATool (class in tooluniverse)

H

HALTool (class in tooluniverse) (class in tooluniverse.hal_tool) handle_data() (tooluniverse.fatcat_tool.FatcatResultParser method) (tooluniverse.FatcatResultParser method) handle_endtag() (tooluniverse.fatcat_tool.FatcatResultParser method) (tooluniverse.FatcatResultParser method) handle_error() (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseTool method) (tooluniverse.encode_tool.ENCODESearchTool method) (tooluniverse.ENCODESearchTool method) handle_starttag() (tooluniverse.fatcat_tool.FatcatMetadataParser method) (tooluniverse.fatcat_tool.FatcatResultParser method) (tooluniverse.FatcatMetadataParser method) (tooluniverse.FatcatResultParser method) handle_tasks_cancel() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) handle_tasks_get() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) handle_tasks_list() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) handle_tasks_result() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) HarmonizomeTool (class in tooluniverse) has_any_api_keys() (tooluniverse.agentic_tool.AgenticTool static method) (tooluniverse.AgenticTool static method) HCATool (class in tooluniverse) (class in tooluniverse.hca_tool) HEADERS (tooluniverse.FDAPharmacogenomicBiomarkersTool attribute) health_check() (tooluniverse.ToolUniverseClient method) HealthDisparitiesTool (class in tooluniverse) (class in tooluniverse.health_disparities_tool) help() (tooluniverse.ToolUniverseClient method) HGNCTool (class in tooluniverse) hit_count (tooluniverse.cache.sqlite_backend.CacheEntry attribute) HocomocoTool (class in tooluniverse) homepage (tooluniverse.ols_tool.OntologyInfo attribute) (tooluniverse.OntologyInfo attribute) Hook HookManager (class in tooluniverse.output_hook) HookRule (class in tooluniverse.output_hook) hooks (tooluniverse.output_hook.HookManager attribute)

HPAGetBiologicalProcessTool (class in tooluniverse) (class in tooluniverse.hpa_tool) HPAGetCancerPrognosticsTool (class in tooluniverse) (class in tooluniverse.hpa_tool) HPAGetComparativeExpressionTool (class in tooluniverse) (class in tooluniverse.hpa_tool) HPAGetContextualBiologicalProcessTool (class in tooluniverse) (class in tooluniverse.hpa_tool) HPAGetDiseaseExpressionTool (class in tooluniverse) (class in tooluniverse.hpa_tool) HPAGetGeneJSONTool (class in tooluniverse) (class in tooluniverse.hpa_tool) HPAGetGenePageDetailsTool (class in tooluniverse) (class in tooluniverse.hpa_tool) HPAGetGeneXMLTool (class in tooluniverse) (class in tooluniverse.hpa_tool) HPAGetProteinInteractionsTool (class in tooluniverse) (class in tooluniverse.hpa_tool) HPAGetRnaExpressionBySourceTool (class in tooluniverse) (class in tooluniverse.hpa_tool) HPAGetRnaExpressionByTissueTool (class in tooluniverse) (class in tooluniverse.hpa_tool) HPAGetSubcellularLocationTool (class in tooluniverse) (class in tooluniverse.hpa_tool) HPAJsonApiTool (class in tooluniverse) (class in tooluniverse.hpa_tool) HPASearchApiTool (class in tooluniverse) (class in tooluniverse.hpa_tool) HPASearchGenesTool (class in tooluniverse) (class in tooluniverse.hpa_tool) HPASearchTool (class in tooluniverse) (class in tooluniverse.hpa_tool) HPAXmlApiTool (class in tooluniverse) (class in tooluniverse.hpa_tool) HPOTool (class in tooluniverse) HuBMAPTool (class in tooluniverse) humanbase_ppi_retrieve() (tooluniverse.humanbase_tool.HumanBaseTool method) (tooluniverse.HumanBaseTool method) HumanBaseTool (class in tooluniverse) (class in tooluniverse.humanbase_tool) hybrid_search() (tooluniverse.database_setup.search.SearchEngine method) (tooluniverse.database_setup.SearchEngine method)

I

ICD10Tool (class in tooluniverse) ICDTool (class in tooluniverse) ICITE_API (tooluniverse.ICiteSearchPublicationsTool attribute) ICiteSearchPublicationsTool (class in tooluniverse) id (tooluniverse.ols_tool.OntologyInfo attribute) (tooluniverse.OntologyInfo attribute) IdentifiersOrgTool (class in tooluniverse) IDTTool (class in tooluniverse) IEDBPredictionTool (class in tooluniverse) IEDBTool (class in tooluniverse) (class in tooluniverse.iedb_tool) IGSRTool (class in tooluniverse) IMGTTool (class in tooluniverse) ImmPortTool (class in tooluniverse) IMPCTool (class in tooluniverse) INaturalistTool (class in tooluniverse) indices (tooluniverse.execute_function._BatchJob attribute) INDRADBTool (class in tooluniverse) 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) IntActRESTTool (class in tooluniverse) INTERPRO_BASE_URL (tooluniverse.PROSITETool attribute) InterProDomainArchTool (class in tooluniverse) InterProEntryTool (class in tooluniverse) InterProExtTool (class in tooluniverse) InterProRESTTool (class in tooluniverse) (class in tooluniverse.interpro_tool) InterProScanTool (class in tooluniverse) InterVarTool (class in tooluniverse) IntOGenTool (class in tooluniverse) iPTMnetTool (class in tooluniverse) iri (tooluniverse.ols_tool.DetailedTermInfo attribute) (tooluniverse.ols_tool.TermInfo attribute) (tooluniverse.TermInfo attribute) is_available() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) is_available_locally() (tooluniverse.remote_tool.RemoteTool method) (tooluniverse.RemoteTool method) is_obsolete (tooluniverse.ols_tool.DetailedTermInfo attribute) (tooluniverse.ols_tool.TermInfo attribute) (tooluniverse.TermInfo attribute) is_value_available() (tooluniverse.who_gho_tool.WHOGHORESTTool static method) (tooluniverse.WHOGHORESTTool static 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) ITISTool (class in tooluniverse)

J

JASPARRESTTool (class in tooluniverse) (class in tooluniverse.jaspar_tool)

JSON-RPC json_type_to_python() (in module tooluniverse.generate_tools)

K

KEGGExtTool (class in tooluniverse) KEGGFindGenes (class in tooluniverse) (class in tooluniverse.kegg_tool) KEGGGetGeneInfo (class in tooluniverse) (class in tooluniverse.kegg_tool) KEGGGetPathwayInfo (class in tooluniverse) (class in tooluniverse.kegg_tool) KEGGListOrganisms (class in tooluniverse) (class in tooluniverse.kegg_tool)

KEGGRESTTool (class in tooluniverse) (class in tooluniverse.kegg_tool) KEGGSearchPathway (class in tooluniverse) (class in tooluniverse.kegg_tool) key (tooluniverse.cache.sqlite_backend.CacheEntry attribute) keyword_search() (tooluniverse.database_setup.search.SearchEngine method) (tooluniverse.database_setup.SearchEngine method)

L

L1000FWDTool (class in tooluniverse) label (tooluniverse.ols_tool.DetailedTermInfo attribute) (tooluniverse.ols_tool.TermInfo attribute) (tooluniverse.TermInfo attribute) last_accessed (tooluniverse.cache.sqlite_backend.CacheEntry attribute) lazy_import_tool() (in module tooluniverse.tool_registry) LINCSSignatureTool (class in tooluniverse) LipidMapsTool (class in tooluniverse) list_available_methods() (tooluniverse.ToolUniverseClient method) 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) ListTools (in module tooluniverse) ListToolsTool (class in tooluniverse) (class in tooluniverse.tool_discovery_tools)

load() (tooluniverse.profile.loader.ProfileLoader method) (tooluniverse.profile.ProfileLoader method) (tooluniverse.ProfileLoader 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_profile() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) load_rag_model() (tooluniverse.tool_finder_embedding.ToolFinderEmbedding method) (tooluniverse.ToolFinderEmbedding 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) LOINCTool (class in tooluniverse) LOVDTool (class in tooluniverse) LRU Cache LRUCache (class in tooluniverse.cache.memory_cache)

M

main() (in module tooluniverse.database_setup.cli) (in module tooluniverse.doctor) (in module tooluniverse.generate_lazy_registry) (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) (class in tooluniverse.markitdown_tool) MassIVETool (class in tooluniverse) MaveDBTool (class in tooluniverse) max_duration (tooluniverse.SwissDockTool attribute) MAX_POLL_ATTEMPTS (tooluniverse.InterProScanTool attribute) (tooluniverse.NvidiaNIMTool attribute) max_summary_length (tooluniverse.output_hook.SummarizationHook attribute) (tooluniverse.output_hook.SummarizationHookConfig attribute) MAX_TOOL_NAME_LENGTH (tooluniverse.execute_function.ToolUniverse attribute) (tooluniverse.ToolUniverse attribute) MCP MCPAutoLoaderTool (class in tooluniverse) (class in tooluniverse.mcp_client_tool) MCPClientTool (class in tooluniverse) (class in tooluniverse.mcp_client_tool) MCPProxyTool (class in tooluniverse) (class in tooluniverse.mcp_client_tool) MCPServerDiscovery (class in tooluniverse) (class in tooluniverse.mcp_client_tool) MculeTool (class in tooluniverse) MedGenTool (class in tooluniverse) MedlinePlusRESTTool (class in tooluniverse) (class in tooluniverse.medlineplus_tool) MEMETool (class in tooluniverse) MemoryManager (class in tooluniverse.memory_manager) MeSHTool (class in tooluniverse) MetaAnalysisTool (class in tooluniverse) MetaboAnalystTool (class in tooluniverse) MetaboLightsRESTTool (class in tooluniverse) MetaboliteTool (class in tooluniverse) MetabolomicsWorkbenchTool (class in tooluniverse) MetaCycTool (class in tooluniverse) MGnifyAnalysesTool (class in tooluniverse) (class in tooluniverse.mgnify_tool) MGnifyExpandedTool (class in tooluniverse) MGnifyStudiesTool (class in tooluniverse) (class in tooluniverse.mgnify_tool) middleware (tooluniverse.smcp.SMCP attribute) minimal() (in module tooluniverse.logging_config) miRNAGetTool (class in tooluniverse) miRNASearchTool (class in tooluniverse) MobiDBTool (class in tooluniverse) Model Context Protocol model_config (tooluniverse.DetailedTermInfo attribute) (tooluniverse.ols_tool.DetailedTermInfo attribute) (tooluniverse.ols_tool.OntologyInfo attribute) (tooluniverse.ols_tool.OntologySearchResponse attribute) (tooluniverse.ols_tool.TermInfo attribute) (tooluniverse.ols_tool.TermSearchResponse attribute) (tooluniverse.OntologyInfo attribute) (tooluniverse.OntologySearchResponse attribute) (tooluniverse.PagedResponse attribute) (tooluniverse.TermInfo attribute) (tooluniverse.TermSearchResponse attribute) MODOMICSTool (class in tooluniverse) module tooluniverse tooluniverse._lazy_registry_static tooluniverse.admetai_tool tooluniverse.agentic_tool tooluniverse.alphafold_tool tooluniverse.arxiv_tool tooluniverse.base_tool tooluniverse.biogrid_tool tooluniverse.biomodels_tool tooluniverse.biorxiv_tool tooluniverse.blast_tool tooluniverse.boltz_tool tooluniverse.build_optimizer tooluniverse.cache tooluniverse.cache.memory_cache tooluniverse.cache.result_cache_manager tooluniverse.cache.sqlite_backend tooluniverse.cbioportal_tool tooluniverse.cdc_tool tooluniverse.cellosaurus_tool tooluniverse.chem_tool tooluniverse.clinical_trials_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.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.dbpedia_tool tooluniverse.dbsnp_tool tooluniverse.default_config tooluniverse.doaj_tool tooluniverse.doctor tooluniverse.efo_tool tooluniverse.emdb_tool tooluniverse.encode_tool tooluniverse.enrichr_tool tooluniverse.ensembl_tool tooluniverse.europe_pmc_tool tooluniverse.exceptions tooluniverse.execute_function tooluniverse.extended_hooks tooluniverse.fatcat_tool tooluniverse.file_download_tool tooluniverse.gbif_tool tooluniverse.gdc_tool tooluniverse.gene_ontology_tool tooluniverse.generate_lazy_registry tooluniverse.generate_tools tooluniverse.genomics_gene_search_tool tooluniverse.geo_tool tooluniverse.gnomad_tool tooluniverse.graphql_tool tooluniverse.gtex_tool tooluniverse.gtopdb_tool tooluniverse.gwas_tool tooluniverse.hal_tool tooluniverse.hca_tool tooluniverse.health_disparities_tool tooluniverse.hpa_tool tooluniverse.humanbase_tool tooluniverse.iedb_tool tooluniverse.interpro_tool tooluniverse.jaspar_tool tooluniverse.kegg_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.memory_manager tooluniverse.mgnify_tool tooluniverse.molecule_2d_tool tooluniverse.molecule_3d_tool tooluniverse.mpd_tool tooluniverse.ncbi_eutils_tool tooluniverse.nhanes_tool tooluniverse.obis_tool tooluniverse.odphp_tool tooluniverse.ols_tool tooluniverse.openaire_tool tooluniverse.openalex_tool tooluniverse.openfda_adv_tool tooluniverse.openfda_tool tooluniverse.osf_preprints_tool tooluniverse.output_hook tooluniverse.package_discovery_tool tooluniverse.package_tool tooluniverse.paleobiology_tool tooluniverse.pathway_commons_tool tooluniverse.pmc_tool tooluniverse.pride_tool tooluniverse.profile tooluniverse.profile.loader tooluniverse.profile.validator tooluniverse.protein_structure_3d_tool tooluniverse.pubchem_tool tooluniverse.pubmed_tool tooluniverse.pubtator_tool tooluniverse.pypi_package_inspector_tool tooluniverse.python_executor_tool tooluniverse.rcsb_pdb_tool tooluniverse.rcsb_search_tool tooluniverse.reactome_tool tooluniverse.regulomedb_tool tooluniverse.remap_tool tooluniverse.remote_tool tooluniverse.restful_tool tooluniverse.rnacentral_tool tooluniverse.rxnorm_tool tooluniverse.screen_tool tooluniverse.semantic_scholar_tool tooluniverse.smcp tooluniverse.smcp_server tooluniverse.smolagent_tool tooluniverse.string_tool tooluniverse.tool_defaults tooluniverse.tool_discovery_tools tooluniverse.tool_finder_embedding tooluniverse.tool_finder_keyword tooluniverse.tool_finder_llm tooluniverse.tool_graph_web_ui tooluniverse.tool_registry tooluniverse.umls_tool tooluniverse.unified_guideline_tools tooluniverse.uniprot_tool tooluniverse.unpaywall_tool tooluniverse.url_tool tooluniverse.uspto_tool tooluniverse.utils tooluniverse.visualization_tool tooluniverse.web_search_tool tooluniverse.who_gho_tool tooluniverse.wikidata_sparql_tool tooluniverse.wikipathways_tool tooluniverse.wikipedia_tool tooluniverse.worms_tool tooluniverse.xml_tool tooluniverse.zenodo_tool

Molecule2DTool (class in tooluniverse) (class in tooluniverse.molecule_2d_tool) Molecule3DTool (class in tooluniverse) (class in tooluniverse.molecule_3d_tool) Monarch (in module tooluniverse) MonarchDiseasesForMultiplePheno (in module tooluniverse) MonarchDiseasesForMultiplePhenoTool (class in tooluniverse) (class in tooluniverse.restful_tool) MonarchTool (class in tooluniverse) (class in tooluniverse.restful_tool) MonarchV3Tool (class in tooluniverse) MPDRESTTool (class in tooluniverse) (class in tooluniverse.mpd_tool) multi_collection_search() (tooluniverse.database_setup.search.SearchEngine method) (tooluniverse.database_setup.SearchEngine method) MutalyzerTool (class in tooluniverse) MYCHEM_BASE_URL (tooluniverse.MyChemTool attribute) MyChemTool (class in tooluniverse) MyDiseaseTool (class in tooluniverse) MyGeneTool (class in tooluniverse) MYVARIANT_BASE_URL (tooluniverse.MyVariantTool attribute) MyVariantTool (class in tooluniverse)

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) NCATool (class in tooluniverse) NCBI NCBIBlastTool (class in tooluniverse) (class in tooluniverse.blast_tool) NCBIDatasetsTool (class in tooluniverse) NCBIEUtilsTool (class in tooluniverse) (class in tooluniverse.ncbi_eutils_tool) NCBINucleotideSearchTool (class in tooluniverse) NCBISRATool (class in tooluniverse) NCBIVariationTool (class in tooluniverse) NCCNGuidelineTool (class in tooluniverse) NCICACTUSTool (class in tooluniverse) NCIThesaurusTool (class in tooluniverse) NDExTool (class in tooluniverse)

NEBTmTool (class in tooluniverse) NeuroMorphoTool (class in tooluniverse) next_steps (tooluniverse.exceptions.ToolError attribute) NextstrainTool (class in tooluniverse) NHANESTool (class in tooluniverse) (class in tooluniverse.nhanes_tool) NICEGuidelineFullTextTool (class in tooluniverse) (class in tooluniverse.unified_guideline_tools) NICEWebScrapingTool (class in tooluniverse) (class in tooluniverse.unified_guideline_tools) normalize_gene_symbol() (in module tooluniverse.utils) normalize_text() (in module tooluniverse.database_setup.sqlite_store) num_found (tooluniverse.ols_tool.TermSearchResponse attribute) (tooluniverse.TermSearchResponse attribute) number_of_classes (tooluniverse.ols_tool.OntologyInfo attribute) (tooluniverse.OntologyInfo attribute) number_of_terms (tooluniverse.ols_tool.OntologyInfo attribute) (tooluniverse.OntologyInfo attribute) NvidiaNIMTool (class in tooluniverse)

O

OBISOccurrenceTool (class in tooluniverse) (class in tooluniverse.obis_tool) OBISTaxaTool (class in tooluniverse) (class in tooluniverse.obis_tool) obo_id (tooluniverse.ols_tool.DetailedTermInfo attribute) (tooluniverse.ols_tool.TermInfo attribute) (tooluniverse.TermInfo attribute) 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) (class in tooluniverse.odphp_tool) ODPHPTopicSearch (class in tooluniverse) (class in tooluniverse.odphp_tool) OLSRESTTool (class in tooluniverse) (class in tooluniverse.efo_tool) OLSTool (class in tooluniverse) (class in tooluniverse.ols_tool) OMATool (class in tooluniverse) OMIMTool (class in tooluniverse) OmniPathTool (class in tooluniverse) OncoKBTool (class in tooluniverse) OncoTreeBaseTool (class in tooluniverse) OncoTreeGetTypeTool (class in tooluniverse) OncoTreeListTissuesTool (class in tooluniverse) OncoTreeSearchTool (class in tooluniverse) ontologies (tooluniverse.ols_tool.OntologySearchResponse attribute) (tooluniverse.OntologySearchResponse attribute) Ontology ontology_name (tooluniverse.ols_tool.DetailedTermInfo attribute) (tooluniverse.ols_tool.TermInfo attribute) (tooluniverse.TermInfo attribute) OntologyInfo (class in tooluniverse) (class in tooluniverse.ols_tool)

OntologySearchResponse (class in tooluniverse) (class in tooluniverse.ols_tool) OpenAIREDatasetTool (class in tooluniverse) OpenAIRETool (class in tooluniverse) (class in tooluniverse.openaire_tool) OpenAlexGuidelinesTool (class in tooluniverse) (class in tooluniverse.unified_guideline_tools) OpenAlexRESTTool (class in tooluniverse) (class in tooluniverse.openalex_tool) OpenAlexTool (class in tooluniverse) (class in tooluniverse.openalex_tool) OpenCRAVATTool (class in tooluniverse) OpenFDAApprovalTool (class in tooluniverse) OpenFDADrugEventsTool (class in tooluniverse) (class in tooluniverse.openfda_tool) OpenNeuroTool (class in tooluniverse) OpenRouterClient (class in tooluniverse.llm_clients) OpenTarget (in module tooluniverse) OpenTargetGenetics (in module tooluniverse) OpentargetGeneticsTool (class in tooluniverse) (class in tooluniverse.graphql_tool) OpenTargets OpentargetTool (class in tooluniverse) (class in tooluniverse.graphql_tool) OpentargetToolDrugNameMatch (class in tooluniverse) (class in tooluniverse.graphql_tool) OpenTreeTool (class in tooluniverse) optimize_code() (in module tooluniverse.compose_scripts.tool_discover) ORCIDTool (class in tooluniverse) OrphanetTool (class in tooluniverse) OrthoDBTool (class in tooluniverse) OSFPreprintsTool (class in tooluniverse) (class in tooluniverse.osf_preprints_tool) output_format (tooluniverse.biogrid_tool.BioGRIDRESTTool attribute) OutputHook (class in tooluniverse.output_hook) OxOTool (class in tooluniverse)

P

pack_folder() (in module tooluniverse.database_setup.packager) PackageTool (class in tooluniverse) (class in tooluniverse.package_tool) page (tooluniverse.ols_tool.OntologySearchResponse attribute) (tooluniverse.ols_tool.TermSearchResponse attribute) (tooluniverse.PagedResponse attribute) PagedResponse (class in tooluniverse) PaleobiologyRESTTool (class in tooluniverse) (class in tooluniverse.paleobiology_tool) PANTHERTool (class in tooluniverse) parse_query() (tooluniverse.who_gho_tool.WHOGHORESTTool static method) (tooluniverse.WHOGHORESTTool static method) PATHOGENIC_THRESHOLD (tooluniverse.AlphaMissenseTool attribute) (tooluniverse.EVETool attribute) PathwayCommonsTool (class in tooluniverse) (class in tooluniverse.pathway_commons_tool) PDBe_KB_Tool (class in tooluniverse) PDBeAPIRESTTool (class in tooluniverse) PDBECompoundTool (class in tooluniverse) PDBeLigandsTool (class in tooluniverse) PDBePISATool (class in tooluniverse) PDBeSearchTool (class in tooluniverse) PDBeSIFTSTool (class in tooluniverse) PDBeValidationTool (class in tooluniverse) PDCTool (class in tooluniverse) PersistentCache (class in tooluniverse.cache.sqlite_backend) PfamTool (class in tooluniverse) PharmacoDBTool (class in tooluniverse) PharmGKBTool (class in tooluniverse) PharosTool (class in tooluniverse) PlantReactomeTool (class in tooluniverse) PMCTool (class in tooluniverse) (class in tooluniverse.pmc_tool) POLL_INTERVAL (tooluniverse.InterProScanTool attribute) (tooluniverse.NvidiaNIMTool attribute) poll_interval (tooluniverse.SwissDockTool attribute) PomBaseTool (class in tooluniverse) PopGenTool (class in tooluniverse) preferred_prefix (tooluniverse.ols_tool.OntologyInfo attribute) (tooluniverse.OntologyInfo attribute) 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) PRIDERESTTool (class in tooluniverse) (class in tooluniverse.pride_tool)

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) Profile ProfileLoader (class in tooluniverse) (class in tooluniverse.profile) (class in tooluniverse.profile.loader) ProgenetixTool (class in tooluniverse) progress() (in module tooluniverse.logging_config) progress_log() (in module tooluniverse.logging_config) prop_to_python_type() (in module tooluniverse.generate_tools) PROSITE_BASE_URL (tooluniverse.PROSITETool attribute) PROSITETool (class in tooluniverse) ProtacDBTool (class in tooluniverse) ProteinsAPIRESTTool (class in tooluniverse) ProteinsPlusRESTTool (class in tooluniverse) ProteinStructure3DTool (class in tooluniverse) (class in tooluniverse.protein_structure_3d_tool) ProteomeXchangeTool (class in tooluniverse) ProteomicsDBTool (class in tooluniverse) ProtParamTool (class in tooluniverse) ProtVarFunctionTool (class in tooluniverse) ProtVarMapTool (class in tooluniverse) ProtVarPopulationTool (class in tooluniverse) ProtVarTool (in module tooluniverse) providers (tooluniverse.smcp.SMCP attribute) prune_item() (tooluniverse.uspto_tool.USPTOOpenDataPortalTool method) (tooluniverse.USPTOOpenDataPortalTool method) PubChem CID PubChemBioAssayTool (class in tooluniverse) PubChemRESTTool (class in tooluniverse) (class in tooluniverse.pubchem_tool) PubChemToxTool (class in tooluniverse) PUBMED_ESEARCH (tooluniverse.ICiteSearchPublicationsTool attribute) PubMedGuidelinesTool (class in tooluniverse) (class in tooluniverse.unified_guideline_tools) PubMedRESTTool (class in tooluniverse) (class in tooluniverse.pubmed_tool) PubTatorTool (class in tooluniverse) (class in tooluniverse.pubtator_tool) PyPIPackageInspector (class in tooluniverse) (class in tooluniverse.pypi_package_inspector_tool) PythonCodeExecutor (class in tooluniverse) (class in tooluniverse.python_executor_tool) PythonScriptRunner (class in tooluniverse) (class in tooluniverse.python_executor_tool)

Q

QUERY_API_URL (tooluniverse.iedb_tool.IEDBTool attribute) (tooluniverse.IEDBTool attribute)

QuickGOTool (class in tooluniverse)

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_indicators() (tooluniverse.who_gho_tool.WHOGHORESTTool static method) (tooluniverse.WHOGHORESTTool static method) rank_paths_by_weight() (tooluniverse.enrichr_tool.EnrichrTool method) (tooluniverse.EnrichrTool method) rank_paths_to_term() (tooluniverse.enrichr_tool.EnrichrTool method) (tooluniverse.EnrichrTool method) Rate Limit RCSBAdvancedSearchTool (class in tooluniverse) RCSBDataTool (class in tooluniverse) RCSBGraphQLTool (class in tooluniverse) RCSBSearchTool (class in tooluniverse) (class in tooluniverse.rcsb_search_tool) RCSBTool (class in tooluniverse) (class in tooluniverse.rcsb_pdb_tool) RDKitCheminfoTool (class in tooluniverse) Re3DataTool (class in tooluniverse) ReactomeAnalysisTool (class in tooluniverse) ReactomeContentTool (class in tooluniverse) ReactomeInteractorsTool (class in tooluniverse) 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) readOnlyHint (tooluniverse.tool_defaults.ToolAnnotations attribute), [1] reconfigure_for_quiet() (in module tooluniverse.logging_config) 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_tool_configs() (in module tooluniverse.tool_registry) register_tools_in_engine() (tooluniverse.mcp_client_tool.MCPAutoLoaderTool method) (tooluniverse.MCPAutoLoaderTool method) RegulomeDBRESTTool (class in tooluniverse) (class in tooluniverse.regulomedb_tool) reload_config() (tooluniverse.output_hook.HookManager method) ReMapRESTTool (class in tooluniverse) (class in tooluniverse.remap_tool) remote_info (tooluniverse.remote_tool.RemoteTool attribute) (tooluniverse.RemoteTool attribute) RemoteTool (class in tooluniverse) (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) repository (tooluniverse.ols_tool.OntologyInfo attribute) (tooluniverse.OntologyInfo attribute) required (tooluniverse.biogrid_tool.BioGRIDRESTTool attribute) reset_plugin_discovery() (in module tooluniverse.tool_registry) reset_server() (tooluniverse.ToolUniverseClient method) 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) resolve_to_local_dir() (tooluniverse.profile.loader.ProfileLoader method) (tooluniverse.profile.ProfileLoader method) (tooluniverse.ProfileLoader method) RESTfulTool (class in tooluniverse) (class in tooluniverse.restful_tool) ResultCacheManager (class in tooluniverse.cache.result_cache_manager) 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) RfamTool (class in tooluniverse) RGDTool (class in tooluniverse) RheaTool (class in tooluniverse) RNAcentralGetTool (class in tooluniverse) (class in tooluniverse.rnacentral_tool) RNAcentralSearchTool (class in tooluniverse) (class in tooluniverse.rnacentral_tool) rule (tooluniverse.output_hook.OutputHook attribute) run() (tooluniverse.ADAStandardsTool method) (tooluniverse.AddgeneTool method) (tooluniverse.admetai_tool.ADMETAITool method) (tooluniverse.ADMETAITool method) (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) (tooluniverse.AgingCohortSearchTool method) (tooluniverse.AHAACCGuidelineTool method) (tooluniverse.AllenBrainTool method) (tooluniverse.AllianceGenomeTool method) (tooluniverse.alphafold_tool.AlphaFoldRESTTool method) (tooluniverse.AlphaFoldRESTTool method) (tooluniverse.AlphaMissenseTool method) (tooluniverse.AOPWikiDetailTool method) (tooluniverse.AOPWikiListTool method) (tooluniverse.APPRISTool method) (tooluniverse.ARCHS4Tool method) (tooluniverse.ArrayExpressRESTTool method) (tooluniverse.arxiv_tool.ArXivPDFSnippetsTool method) (tooluniverse.arxiv_tool.ArXivTool method) (tooluniverse.ArXivPDFSnippetsTool method) (tooluniverse.ArXivTool method) (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseRESTTool method) (tooluniverse.BaseTool method) (tooluniverse.BgeeTool method) (tooluniverse.BiGGModelsTool method) (tooluniverse.BinaryDownloadTool method) (tooluniverse.BindingDBTool method) (tooluniverse.biogrid_tool.BioGRIDRESTTool method) (tooluniverse.BioGRIDRESTTool method) (tooluniverse.BioImageArchiveTool method) (tooluniverse.BioPortalTool method) (tooluniverse.BioregistryTool method) (tooluniverse.biorxiv_tool.BioRxivTool method) (tooluniverse.BioRxivTool method) (tooluniverse.BioSamplesTool method) (tooluniverse.BioStudiesRESTTool method) (tooluniverse.blast_tool.NCBIBlastTool method) (tooluniverse.Boltz2DockingTool method) (tooluniverse.boltz_tool.Boltz2DockingTool method) (tooluniverse.BRENDATool method) (tooluniverse.BridgeDbTool method) (tooluniverse.BVBRCTool method) (tooluniverse.CADDTool method) (tooluniverse.CancerPrognosisTool method) (tooluniverse.CancerVarTool method) (tooluniverse.CATHTool method) (tooluniverse.cbioportal_tool.CBioPortalRESTTool method) (tooluniverse.CBioPortalRESTTool method) (tooluniverse.cdc_tool.CDCRESTTool method) (tooluniverse.CDCRESTTool method) (tooluniverse.CellMarkerTool 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.CellPaintingTool method) (tooluniverse.CELLxGENECensusTool method) (tooluniverse.CellxGeneDiscoveryTool method) (tooluniverse.ChEBITool method) (tooluniverse.chem_tool.ChEMBLRESTTool method) (tooluniverse.chem_tool.ChEMBLTool method) (tooluniverse.ChEMBLRESTTool method) (tooluniverse.ChEMBLTool method) (tooluniverse.ChemComputeTool method) (tooluniverse.ChIPAtlasTool method) (tooluniverse.CIViCTool method) (tooluniverse.ClinGenAlleleTool method) (tooluniverse.ClinGenARTool method) (tooluniverse.ClinGenDosageTool method) (tooluniverse.ClinGenTool method) (tooluniverse.clinical_trials_tool.ClinicalTrialsGovTool method) (tooluniverse.ClinicalTrialsDetailsTool method) (tooluniverse.ClinicalTrialsGovTool method) (tooluniverse.ClinicalTrialsSearchTool method) (tooluniverse.ClinicalTrialsTool 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.ClinVarRESTTool method) (tooluniverse.ClinVarSearchVariants method) (tooluniverse.ClueTool method) (tooluniverse.CMAGuidelinesTool method) (tooluniverse.CODTool method) (tooluniverse.ComplexPortalTool method) (tooluniverse.compose_tool.ComposeTool method) (tooluniverse.ComposeTool method) (tooluniverse.core_tool.CorePDFSnippetsTool method) (tooluniverse.core_tool.CoreTool method) (tooluniverse.CorePDFSnippetsTool method) (tooluniverse.CoreTool method) (tooluniverse.COSMICTool method) (tooluniverse.CPICGetRecommendationsTool method) (tooluniverse.CPICListGuidelinesTool method) (tooluniverse.CryoETTool 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(tooluniverse.HPAGetDiseaseExpressionTool method) (tooluniverse.HPAGetGeneJSONTool method) (tooluniverse.HPAGetGenePageDetailsTool method) (tooluniverse.HPAGetGeneXMLTool method) (tooluniverse.HPAGetProteinInteractionsTool method) (tooluniverse.HPAGetRnaExpressionBySourceTool method) (tooluniverse.HPAGetRnaExpressionByTissueTool method) (tooluniverse.HPAGetSubcellularLocationTool method) (tooluniverse.HPASearchGenesTool method) (tooluniverse.HPASearchTool method) (tooluniverse.HPOTool method) (tooluniverse.HuBMAPTool method) (tooluniverse.humanbase_tool.HumanBaseTool method) (tooluniverse.HumanBaseTool method) (tooluniverse.ICD10Tool method) (tooluniverse.ICDTool method) (tooluniverse.ICiteSearchPublicationsTool method) (tooluniverse.IdentifiersOrgTool method) (tooluniverse.IDTTool method) (tooluniverse.iedb_tool.IEDBTool method) (tooluniverse.IEDBPredictionTool method) (tooluniverse.IEDBTool method) (tooluniverse.IGSRTool method) (tooluniverse.IMGTTool method) (tooluniverse.ImmPortTool method) (tooluniverse.IMPCTool method) (tooluniverse.INaturalistTool method) (tooluniverse.INDRADBTool method) (tooluniverse.IntActRESTTool method) (tooluniverse.interpro_tool.InterProRESTTool method) (tooluniverse.InterProDomainArchTool method) (tooluniverse.InterProEntryTool method) (tooluniverse.InterProExtTool method) (tooluniverse.InterProRESTTool method) (tooluniverse.InterProScanTool method) (tooluniverse.InterVarTool method) (tooluniverse.IntOGenTool method) (tooluniverse.iPTMnetTool method) (tooluniverse.ITISTool method) (tooluniverse.jaspar_tool.JASPARRESTTool method) (tooluniverse.JASPARRESTTool method) (tooluniverse.kegg_tool.KEGGFindGenes method) (tooluniverse.kegg_tool.KEGGGetGeneInfo method) (tooluniverse.kegg_tool.KEGGGetPathwayInfo method) (tooluniverse.kegg_tool.KEGGListOrganisms method) (tooluniverse.kegg_tool.KEGGRESTTool method) (tooluniverse.kegg_tool.KEGGSearchPathway method) (tooluniverse.KEGGExtTool method) (tooluniverse.KEGGFindGenes 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method) (tooluniverse.MEMETool method) (tooluniverse.MeSHTool method) (tooluniverse.MetaAnalysisTool method) (tooluniverse.MetaboAnalystTool method) (tooluniverse.MetaboLightsRESTTool method) (tooluniverse.MetaboliteTool method) (tooluniverse.MetabolomicsWorkbenchTool method) (tooluniverse.MetaCycTool method) (tooluniverse.mgnify_tool.MGnifyAnalysesTool method) (tooluniverse.mgnify_tool.MGnifyStudiesTool method) (tooluniverse.MGnifyAnalysesTool method) (tooluniverse.MGnifyExpandedTool method) (tooluniverse.MGnifyStudiesTool method) (tooluniverse.miRNAGetTool method) (tooluniverse.miRNASearchTool method) (tooluniverse.MobiDBTool method) (tooluniverse.MODOMICSTool method) (tooluniverse.Molecule2DTool method) (tooluniverse.Molecule3DTool method) (tooluniverse.molecule_2d_tool.Molecule2DTool method) (tooluniverse.molecule_3d_tool.Molecule3DTool method) (tooluniverse.MonarchDiseasesForMultiplePhenoTool method) (tooluniverse.MonarchTool method) (tooluniverse.MonarchV3Tool method) (tooluniverse.mpd_tool.MPDRESTTool method) (tooluniverse.MPDRESTTool method) (tooluniverse.MutalyzerTool method) (tooluniverse.MyChemTool method) (tooluniverse.MyDiseaseTool method) (tooluniverse.MyGeneTool method) (tooluniverse.MyVariantTool method) (tooluniverse.NCATool method) (tooluniverse.ncbi_eutils_tool.NCBIEUtilsTool method) (tooluniverse.NCBIBlastTool method) (tooluniverse.NCBIDatasetsTool method) (tooluniverse.NCBIEUtilsTool method) (tooluniverse.NCBINucleotideSearchTool method) (tooluniverse.NCBISRATool method) (tooluniverse.NCBIVariationTool method) (tooluniverse.NCCNGuidelineTool method) (tooluniverse.NCICACTUSTool method) (tooluniverse.NCIThesaurusTool method) (tooluniverse.NDExTool method) (tooluniverse.NEBTmTool method) (tooluniverse.NeuroMorphoTool method) (tooluniverse.NextstrainTool method) (tooluniverse.nhanes_tool.NHANESTool method) (tooluniverse.NHANESTool method) (tooluniverse.NICEGuidelineFullTextTool method) (tooluniverse.NICEWebScrapingTool method) (tooluniverse.NvidiaNIMTool method) (tooluniverse.obis_tool.OBISOccurrenceTool method) (tooluniverse.obis_tool.OBISTaxaTool method) (tooluniverse.OBISOccurrenceTool method) (tooluniverse.OBISTaxaTool 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.ols_tool.OLSTool method) (tooluniverse.OLSRESTTool method) (tooluniverse.OLSTool method) (tooluniverse.OMATool method) (tooluniverse.OMIMTool method) (tooluniverse.OmniPathTool method) (tooluniverse.OncoKBTool method) (tooluniverse.OncoTreeGetTypeTool method) (tooluniverse.OncoTreeListTissuesTool method) (tooluniverse.OncoTreeSearchTool method) (tooluniverse.openaire_tool.OpenAIRETool method) (tooluniverse.OpenAIREDatasetTool method) (tooluniverse.OpenAIRETool method) (tooluniverse.openalex_tool.OpenAlexRESTTool method) (tooluniverse.openalex_tool.OpenAlexTool method) (tooluniverse.OpenAlexGuidelinesTool method) (tooluniverse.OpenAlexRESTTool method) (tooluniverse.OpenAlexTool method) (tooluniverse.OpenCRAVATTool 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.FDADrugLabelFieldValueTool method) (tooluniverse.openfda_tool.FDADrugLabelGetDrugGenericNameTool method) (tooluniverse.openfda_tool.FDADrugLabelGetDrugNamesByIndicationAggregated method) (tooluniverse.openfda_tool.FDADrugLabelGetDrugNamesByIndicationStats method) (tooluniverse.openfda_tool.FDADrugLabelSearchIDTool method) 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(tooluniverse.PythonCodeExecutor method) (tooluniverse.PythonScriptRunner method) (tooluniverse.QuickGOTool method) (tooluniverse.rcsb_pdb_tool.RCSBTool method) (tooluniverse.rcsb_search_tool.RCSBSearchTool method) (tooluniverse.RCSBAdvancedSearchTool method) (tooluniverse.RCSBDataTool method) (tooluniverse.RCSBGraphQLTool method) (tooluniverse.RCSBSearchTool method) (tooluniverse.RCSBTool method) (tooluniverse.RDKitCheminfoTool method) (tooluniverse.Re3DataTool method) (tooluniverse.reactome_tool.ReactomeRESTTool method) (tooluniverse.ReactomeAnalysisTool method) (tooluniverse.ReactomeContentTool method) (tooluniverse.ReactomeInteractorsTool method) (tooluniverse.ReactomeRESTTool method) (tooluniverse.regulomedb_tool.RegulomeDBRESTTool method) (tooluniverse.RegulomeDBRESTTool method) (tooluniverse.remap_tool.ReMapRESTTool method) (tooluniverse.ReMapRESTTool method) (tooluniverse.remote_tool.RemoteTool method) (tooluniverse.RemoteTool method) (tooluniverse.restful_tool.MonarchDiseasesForMultiplePhenoTool method) (tooluniverse.restful_tool.MonarchTool method) (tooluniverse.restful_tool.RESTfulTool method) (tooluniverse.RESTfulTool method) (tooluniverse.RfamTool method) (tooluniverse.RGDTool method) (tooluniverse.RheaTool method) (tooluniverse.rnacentral_tool.RNAcentralGetTool method) (tooluniverse.rnacentral_tool.RNAcentralSearchTool method) (tooluniverse.RNAcentralGetTool method) (tooluniverse.RNAcentralSearchTool method) (tooluniverse.RxClassTool method) (tooluniverse.rxnorm_tool.RxNormTool method) (tooluniverse.RxNormExtendedTool method) (tooluniverse.RxNormTool method) (tooluniverse.SAbDabTool method) (tooluniverse.SABIORKTool method) (tooluniverse.SASBDBRESTTool method) (tooluniverse.SASBDBSearchTool method) (tooluniverse.SASBDBTextSearchTool method) (tooluniverse.SCExpressionAtlasTool method) (tooluniverse.ScientificCalculatorTool method) (tooluniverse.screen_tool.SCREENRESTTool method) (tooluniverse.SCREENRESTTool method) (tooluniverse.SearchSPLTool method) (tooluniverse.semantic_scholar_tool.SemanticScholarPDFSnippetsTool method) (tooluniverse.semantic_scholar_tool.SemanticScholarTool method) (tooluniverse.SemanticScholarPDFSnippetsTool method) (tooluniverse.SemanticScholarTool method) (tooluniverse.SequenceAnalyzeTool method) (tooluniverse.SGDTool method) (tooluniverse.SiderTool method) (tooluniverse.SIGNListGuidelinesTool method) (tooluniverse.SIGNORTool method) (tooluniverse.SIGNSearchGuidelinesTool method) (tooluniverse.SIMBADAdvancedTool method) (tooluniverse.SIMBADTool method) (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) (tooluniverse.SMILESVerifyTool method) (tooluniverse.smolagent_tool.SmolAgentTool method) (tooluniverse.SmolAgentTool method) (tooluniverse.SpliceAITool method) (tooluniverse.SRATool method) (tooluniverse.STITCHTool method) (tooluniverse.string_tool.STRINGRESTTool method) (tooluniverse.STRINGExtTool method) (tooluniverse.STRINGRESTTool method) (tooluniverse.SurvivalTool method) (tooluniverse.SwissADMETool method) (tooluniverse.SwissDockTool method) (tooluniverse.SwissModelTool method) (tooluniverse.SwissTargetTool method) (tooluniverse.SynBioHubTool method) (tooluniverse.SYNERGxDBTool method) (tooluniverse.T3DBTool method) (tooluniverse.TCDBTool method) (tooluniverse.TextDownloadTool method) (tooluniverse.TheraSAbDabTool method) (tooluniverse.ThreeDBeaconsTool method) (tooluniverse.TIMERTool method) (tooluniverse.tool_discovery_tools.ExecuteToolTool method) (tooluniverse.tool_discovery_tools.GetToolInfoTool method) (tooluniverse.tool_discovery_tools.GrepToolsTool method) (tooluniverse.tool_discovery_tools.ListToolsTool method) (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) (tooluniverse.ToolUniverse method) (tooluniverse.ToolUniversePageTool method) (tooluniverse.TRIPDatabaseTool method) (tooluniverse.UCSCEpigenomicsTool method) (tooluniverse.UCSCGenomeTool method) (tooluniverse.umls_tool.UMLSRESTTool method) (tooluniverse.UMLSRESTTool method) (tooluniverse.UniChemTool method) (tooluniverse.unified_guideline_tools.CMAGuidelinesTool method) (tooluniverse.unified_guideline_tools.CTFPHCListGuidelinesTool method) (tooluniverse.unified_guideline_tools.CTFPHCSearchGuidelinesTool 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.SIGNListGuidelinesTool method) (tooluniverse.unified_guideline_tools.SIGNSearchGuidelinesTool method) (tooluniverse.unified_guideline_tools.TRIPDatabaseTool method) (tooluniverse.unified_guideline_tools.WHOGuidelineFullTextTool method) (tooluniverse.unified_guideline_tools.WHOGuidelinesTool method) (tooluniverse.UniParcTool method) (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtIDMappingTool method) (tooluniverse.UniProtLocationsTool method) (tooluniverse.UniProtRefTool method) (tooluniverse.UniProtRESTTool method) (tooluniverse.UniProtTaxonomyTool method) (tooluniverse.UniRefTool 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.UsageTipsTool method) (tooluniverse.uspto_tool.USPTOOpenDataPortalTool method) (tooluniverse.USPTOOpenDataPortalTool method) (tooluniverse.VDJDBTool method) (tooluniverse.web_search_tool.WebAPIDocumentationSearchTool method) (tooluniverse.web_search_tool.WebSearchTool method) (tooluniverse.WebAPIDocumentationSearchTool method) (tooluniverse.WebSearchTool method) (tooluniverse.WFGYPromptBundleTool method) (tooluniverse.who_gho_tool.WHOGHOQueryTool method) (tooluniverse.who_gho_tool.WHOGHORESTTool method) (tooluniverse.who_gho_tool.WHOGHOStatisticTool method) (tooluniverse.who_gho_tool.WHOGHOTopicTool method) (tooluniverse.WHOGHOQueryTool method) (tooluniverse.WHOGHORESTTool method) (tooluniverse.WHOGHOStatisticTool method) (tooluniverse.WHOGHOTopicTool method) (tooluniverse.WHOGuidelineFullTextTool method) (tooluniverse.WHOGuidelinesTool method) (tooluniverse.wikidata_sparql_tool.WikidataSPARQLTool method) (tooluniverse.WikidataSPARQLTool method) (tooluniverse.wikipathways_tool.WikiPathwaysGetTool method) (tooluniverse.wikipathways_tool.WikiPathwaysSearchTool method) (tooluniverse.WikiPathwaysExtTool method) (tooluniverse.WikiPathwaysGetTool method) (tooluniverse.WikiPathwaysSearchTool method) (tooluniverse.wikipedia_tool.WikipediaContentTool method) (tooluniverse.wikipedia_tool.WikipediaSearchTool method) (tooluniverse.wikipedia_tool.WikipediaSummaryTool method) (tooluniverse.WikipediaContentTool method) (tooluniverse.WikipediaSearchTool method) (tooluniverse.WikipediaSummaryTool method) (tooluniverse.WormBaseTool method) (tooluniverse.worms_tool.WoRMSRESTTool method) (tooluniverse.WoRMSRESTTool method) (tooluniverse.XenbaseTool method) (tooluniverse.xml_tool.XMLDatasetTool method) (tooluniverse.XMLDatasetTool method) (tooluniverse.ZincTool method)

run_default_stdio_server() (in module tooluniverse.smcp_server) run_http_server() (in module tooluniverse.smcp_server) run_one_function() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) run_one_function_async() (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) RxClassTool (class in tooluniverse) RxNormExtendedTool (class in tooluniverse) RxNormTool (class in tooluniverse) (class in tooluniverse.rxnorm_tool)

S

SAbDabTool (class in tooluniverse) SABIORKTool (class in tooluniverse) SAFE_BUILTINS (tooluniverse.BasePythonExecutor attribute) (tooluniverse.python_executor_tool.BasePythonExecutor attribute) safe_for_fts() (in module tooluniverse.database_setup.sqlite_store) sampling_handler (tooluniverse.smcp.SMCP attribute) sampling_handler_behavior (tooluniverse.smcp.SMCP attribute) sanitize_param_name() (in module tooluniverse.generate_tools) SASBDBRESTTool (class in tooluniverse) SASBDBSearchTool (class in tooluniverse) SASBDBTextSearchTool (class in tooluniverse) save_index() (tooluniverse.database_setup.vector_store.VectorStore method) (tooluniverse.database_setup.VectorStore method) save_metadata() (in module tooluniverse.build_optimizer) SCANPROSITE_URL (tooluniverse.PROSITETool attribute) SCExpressionAtlasTool (class in tooluniverse) Scientific Model Context Protocol ScientificCalculatorTool (class in tooluniverse) SCREENRESTTool (class in tooluniverse) (class in tooluniverse.screen_tool) 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) (tooluniverse.OpenAlexTool method) search_openfda() (in module tooluniverse.openfda_tool) search_pathways() (tooluniverse.pathway_commons_tool.PathwayCommonsTool method) search_projects() (tooluniverse.hca_tool.HCATool method) (tooluniverse.HCATool method) search_studies() (tooluniverse.clinical_trials_tool.ClinicalTrialsGovTool method) (tooluniverse.ClinicalTrialsGovTool method) search_terms() (tooluniverse.gene_ontology_tool.GeneOntologyTool method) (tooluniverse.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) SemanticScholarPDFSnippetsTool (class in tooluniverse) (class in tooluniverse.semantic_scholar_tool) SemanticScholarTool (class in tooluniverse) (class in tooluniverse.semantic_scholar_tool) SequenceAnalyzeTool (class in tooluniverse) 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) SGDTool (class in tooluniverse) short_form (tooluniverse.ols_tool.DetailedTermInfo attribute) (tooluniverse.ols_tool.TermInfo attribute) (tooluniverse.TermInfo attribute) should_trigger() (tooluniverse.output_hook.OutputHook method) SiderTool (class in tooluniverse) signature (tooluniverse.execute_function._BatchJob attribute) SIGNListGuidelinesTool (class in tooluniverse) (class in tooluniverse.unified_guideline_tools)

SIGNORTool (class in tooluniverse) SIGNSearchGuidelinesTool (class in tooluniverse) (class in tooluniverse.unified_guideline_tools) SIMBADAdvancedTool (class in tooluniverse) SIMBADTool (class in tooluniverse) SingleFlight (class in tooluniverse.cache.memory_cache) singleflight_guard() (tooluniverse.cache.result_cache_manager.ResultCacheManager method) size (tooluniverse.ols_tool.OntologySearchResponse attribute) (tooluniverse.ols_tool.TermSearchResponse attribute) (tooluniverse.PagedResponse attribute) skip_execution (tooluniverse.execute_function._BatchJob attribute) SMCP (class in tooluniverse) (class in tooluniverse.smcp) SMILESVerifyTool (class in tooluniverse) SmolAgentTool (class in tooluniverse) (class in tooluniverse.smolagent_tool) special_tools_name (tooluniverse.tool_finder_embedding.ToolFinderEmbedding attribute) (tooluniverse.ToolFinderEmbedding attribute) SpliceAITool (class in tooluniverse) SQLiteStore (class in tooluniverse.database_setup) (class in tooluniverse.database_setup.sqlite_store) SRATool (class in tooluniverse) SSE start_mcp_server() (in module tooluniverse.mcp_tool_registry) start_mcp_server_for_tool() (in module tooluniverse.mcp_tool_registry) STATEMENT_TYPES (tooluniverse.INDRADBTool attribute) 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) STATUS_URL (tooluniverse.NvidiaNIMTool attribute) STDIO Transport STEMMING_RULES (tooluniverse.tool_finder_keyword.ToolFinderKeyword attribute) (tooluniverse.ToolFinderKeyword attribute) STITCHTool (class in tooluniverse) 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) strict_input_validation (tooluniverse.smcp.SMCP attribute) STRINGExtTool (class in tooluniverse) STRINGRESTTool (class in tooluniverse) (class in tooluniverse.string_tool) submit_gene_list() (tooluniverse.enrichr_tool.EnrichrTool method) (tooluniverse.EnrichrTool method) submit_job() (tooluniverse.ProteinsPlusRESTTool method) (tooluniverse.SwissDockTool 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) SurvivalTool (class in tooluniverse) SwissADMETool (class in tooluniverse) SwissDockTool (class in tooluniverse) SwissModelTool (class in tooluniverse) SwissTargetTool (class in tooluniverse) SynBioHubTool (class in tooluniverse) SYNERGxDBTool (class in tooluniverse) synonyms (tooluniverse.DetailedTermInfo attribute) (tooluniverse.ols_tool.DetailedTermInfo attribute)

T

T3DBTool (class in tooluniverse) TCDBTool (class in tooluniverse) TermInfo (class in tooluniverse) (class in tooluniverse.ols_tool) terms (tooluniverse.ols_tool.TermSearchResponse attribute) (tooluniverse.TermSearchResponse attribute) TermSearchResponse (class in tooluniverse) (class in tooluniverse.ols_tool) 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) TextDownloadTool (class in tooluniverse) (class in tooluniverse.file_download_tool) TheraSAbDabTool (class in tooluniverse) ThreeDBeaconsTool (class in tooluniverse) TIMERTool (class in tooluniverse) title (tooluniverse.ols_tool.OntologyInfo attribute) (tooluniverse.OntologyInfo attribute) to_dict() (tooluniverse.exceptions.ToolError method) toggle_hooks() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.output_hook.HookManager method) (tooluniverse.ToolUniverse method) Tool Category Tool Composition Tool Finder Tool Specification Tool Type tool_category_dicts (tooluniverse.execute_function.ToolUniverse attribute), [1] (tooluniverse.ToolUniverse attribute) tool_config (tooluniverse.remote_tool.RemoteTool attribute) (tooluniverse.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_instance (tooluniverse.execute_function._BatchJob attribute) tool_name (tooluniverse.tool_finder_embedding.ToolFinderEmbedding attribute) (tooluniverse.ToolFinderEmbedding attribute) tool_specification() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) tool_to_str() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.ToolUniverse method) tool_type_overrides (tooluniverse.tool_defaults.ToolDefaultsConfig attribute) ToolAnnotations (class in tooluniverse.tool_defaults) ToolAuthError ToolCallable (class in tooluniverse.execute_function) ToolConfigError ToolDefaultsConfig (class in tooluniverse.tool_defaults) ToolDependencyError 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) ToolNamespace (class in tooluniverse.execute_function) ToolRateLimitError ToolServerError ToolSpace Toolspace 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._lazy_registry_static module 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.biomodels_tool module tooluniverse.biorxiv_tool module tooluniverse.blast_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.cbioportal_tool module tooluniverse.cdc_tool module tooluniverse.cellosaurus_tool module tooluniverse.chem_tool module tooluniverse.clinical_trials_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.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.dbpedia_tool module tooluniverse.dbsnp_tool module tooluniverse.default_config module tooluniverse.doaj_tool module tooluniverse.doctor module tooluniverse.efo_tool module tooluniverse.emdb_tool module tooluniverse.encode_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.file_download_tool module tooluniverse.gbif_tool module tooluniverse.gdc_tool module tooluniverse.gene_ontology_tool module tooluniverse.generate_lazy_registry module tooluniverse.generate_tools module tooluniverse.genomics_gene_search_tool module tooluniverse.geo_tool module tooluniverse.gnomad_tool module tooluniverse.graphql_tool module tooluniverse.gtex_tool module tooluniverse.gtopdb_tool module tooluniverse.gwas_tool module tooluniverse.hal_tool module tooluniverse.hca_tool module tooluniverse.health_disparities_tool module tooluniverse.hpa_tool module tooluniverse.humanbase_tool module tooluniverse.iedb_tool module tooluniverse.interpro_tool module tooluniverse.jaspar_tool module tooluniverse.kegg_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.memory_manager module tooluniverse.mgnify_tool module tooluniverse.molecule_2d_tool module tooluniverse.molecule_3d_tool module tooluniverse.mpd_tool module tooluniverse.ncbi_eutils_tool module tooluniverse.nhanes_tool module tooluniverse.obis_tool module tooluniverse.odphp_tool module tooluniverse.ols_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_discovery_tool module tooluniverse.package_tool module tooluniverse.paleobiology_tool module tooluniverse.pathway_commons_tool module tooluniverse.pmc_tool module tooluniverse.pride_tool module tooluniverse.profile module tooluniverse.profile.loader module tooluniverse.profile.validator module tooluniverse.protein_structure_3d_tool module tooluniverse.pubchem_tool module tooluniverse.pubmed_tool module tooluniverse.pubtator_tool module tooluniverse.pypi_package_inspector_tool module tooluniverse.python_executor_tool module tooluniverse.rcsb_pdb_tool module tooluniverse.rcsb_search_tool module tooluniverse.reactome_tool module tooluniverse.regulomedb_tool module tooluniverse.remap_tool module tooluniverse.remote_tool module tooluniverse.restful_tool module tooluniverse.rnacentral_tool module tooluniverse.rxnorm_tool module tooluniverse.screen_tool module tooluniverse.semantic_scholar_tool module tooluniverse.smcp module tooluniverse.smcp_server module tooluniverse.smolagent_tool module tooluniverse.string_tool module tooluniverse.tool_defaults module tooluniverse.tool_discovery_tools 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.umls_tool module tooluniverse.unified_guideline_tools module tooluniverse.uniprot_tool module tooluniverse.unpaywall_tool module tooluniverse.url_tool module tooluniverse.uspto_tool module tooluniverse.utils module tooluniverse.visualization_tool module tooluniverse.web_search_tool module tooluniverse.who_gho_tool module tooluniverse.wikidata_sparql_tool module tooluniverse.wikipathways_tool module tooluniverse.wikipedia_tool module tooluniverse.worms_tool module tooluniverse.xml_tool module tooluniverse.zenodo_tool module ToolUniverseClient (class in tooluniverse) ToolUniverseFormatter (class in tooluniverse.logging_config) ToolUniverseLogger (class in tooluniverse.logging_config) ToolUniversePageTool (class in tooluniverse) ToolUniverseTool (class in tooluniverse) (class in tooluniverse.smolagent_tool) ToolValidationError total_elements (tooluniverse.ols_tool.OntologySearchResponse attribute) (tooluniverse.ols_tool.TermSearchResponse attribute) (tooluniverse.PagedResponse attribute) total_pages (tooluniverse.ols_tool.OntologySearchResponse attribute) (tooluniverse.ols_tool.TermSearchResponse attribute) (tooluniverse.PagedResponse attribute) TRIPDatabaseTool (class in tooluniverse) (class in tooluniverse.unified_guideline_tools) TTL ttl (tooluniverse.cache.sqlite_backend.CacheEntry attribute)

U

UCSCEpigenomicsTool (class in tooluniverse) UCSCGenomeTool (class in tooluniverse) UMLSRESTTool (class in tooluniverse) (class in tooluniverse.umls_tool) UniChemTool (class in tooluniverse) UniParcTool (class in tooluniverse) UniProt Accession UniProtIDMappingTool (class in tooluniverse) UniProtLocationsTool (class in tooluniverse) UniProtRefTool (class in tooluniverse) UniProtRESTTool (class in tooluniverse) (class in tooluniverse.uniprot_tool) UniProtTaxonomyTool (class in tooluniverse) UniRefTool (class in tooluniverse)

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) url_encode_iri() (in module tooluniverse.ols_tool) URLHTMLTagTool (class in tooluniverse) (class in tooluniverse.url_tool) URLToPDFTextTool (class in tooluniverse) (class in tooluniverse.url_tool) UsageTipsTool (class in tooluniverse) USPTOOpenDataPortalTool (class in tooluniverse) (class in tooluniverse.uspto_tool)

V

VALID_METHODS (tooluniverse.APPRISTool attribute) validate() (tooluniverse.output_hook.SummarizationHookConfig method) validate_configuration() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) validate_enum_arguments() (tooluniverse.FDADrugAdverseEventDetailTool method) (tooluniverse.FDADrugAdverseEventTool method) (tooluniverse.FDADrugInteractionDetailTool 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_profile_config() (in module tooluniverse) (in module tooluniverse.profile) (in module tooluniverse.profile.validator) validate_query() (in module tooluniverse.graphql_tool) (in module tooluniverse.utils) validate_with_schema() (in module tooluniverse) (in module tooluniverse.profile) (in module tooluniverse.profile.validator)

validate_yaml_file() (in module tooluniverse.profile) (in module tooluniverse.profile.validator) validate_yaml_file_with_schema() (in module tooluniverse) (in module tooluniverse.profile) (in module tooluniverse.profile.validator) validate_yaml_format_by_template() (in module tooluniverse) (in module tooluniverse.profile) (in module tooluniverse.profile.validator) ValidationError, [1] ValidationHook (class in tooluniverse.extended_hooks) value (tooluniverse.cache.result_cache_manager.CacheRecord attribute) (tooluniverse.cache.sqlite_backend.CacheEntry attribute) VDJDBTool (class in tooluniverse) 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) (tooluniverse.ols_tool.OntologyInfo attribute) (tooluniverse.OntologyInfo attribute) VisualizationTool (class in tooluniverse) (class in tooluniverse.visualization_tool) VLLMClient (class in tooluniverse.llm_clients)

W

warning() (in module tooluniverse.logging_config) WebAPIDocumentationSearchTool (class in tooluniverse) (class in tooluniverse.web_search_tool) WebSearchTool (class in tooluniverse) (class in tooluniverse.web_search_tool) WFGYPromptBundleTool (class in tooluniverse) WHOGHOQueryTool (class in tooluniverse) (class in tooluniverse.who_gho_tool) WHOGHORESTTool (class in tooluniverse) (class in tooluniverse.who_gho_tool) WHOGHOStatisticTool (class in tooluniverse) (class in tooluniverse.who_gho_tool) WHOGHOTopicTool (class in tooluniverse) (class in tooluniverse.who_gho_tool) WHOGuidelineFullTextTool (class in tooluniverse) (class in tooluniverse.unified_guideline_tools) WHOGuidelinesTool (class in tooluniverse) (class in tooluniverse.unified_guideline_tools)

WikidataSPARQLTool (class in tooluniverse) (class in tooluniverse.wikidata_sparql_tool) WikiPathwaysExtTool (class in tooluniverse) WikiPathwaysGetTool (class in tooluniverse) (class in tooluniverse.wikipathways_tool) WikiPathwaysSearchTool (class in tooluniverse) (class in tooluniverse.wikipathways_tool) WikipediaContentTool (class in tooluniverse) (class in tooluniverse.wikipedia_tool) WikipediaSearchTool (class in tooluniverse) (class in tooluniverse.wikipedia_tool) WikipediaSummaryTool (class in tooluniverse) (class in tooluniverse.wikipedia_tool) Workspace Configuration WormBaseTool (class in tooluniverse) WoRMSRESTTool (class in tooluniverse) (class in tooluniverse.worms_tool)

X

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

XMLTool (in module tooluniverse)

Y

yaml_to_dict() (in module tooluniverse.utils)

Z

ZenodoRESTTool (class in tooluniverse) (class in tooluniverse.zenodo_tool)

ZincTool (class in tooluniverse)