Index

A

accuracy (curategpt.evaluation.evaluation_datamodel.ClassificationMetrics attribute) add() (curategpt.app.cart.Cart method) (curategpt.store.in_memory_adapter.Collection method) add_metadata() (curategpt.store.in_memory_adapter.Collection method) additional_collections (curategpt.evaluation.evaluation_datamodel.Task attribute) additional_info() (curategpt.wrappers.bio.omicsdi_wrapper.OmicsDIWrapper method) agent (curategpt.evaluation.base_evaluator.BaseEvaluator attribute) (curategpt.evaluation.dae_evaluator.DatabaseAugmentedCompletionEvaluator attribute) (curategpt.evaluation.evaluation_datamodel.Task attribute) aggregate_metrics() (in module curategpt.evaluation.calc_statistics) AggregationMethod (class in curategpt.evaluation.evaluation_datamodel) aliases (curategpt.wrappers.ontology.ontology.OntologyClass attribute) AllianceGeneWrapper (class in curategpt.wrappers.bio.alliance_gene_wrapper) annotate() (curategpt.agents.concept_recognition_agent.ConceptRecognitionAgent method) annotate_concept_list() (curategpt.agents.concept_recognition_agent.ConceptRecognitionAgent method) annotate_inline() (curategpt.agents.concept_recognition_agent.ConceptRecognitionAgent method) annotate_two_pass() (curategpt.agents.concept_recognition_agent.ConceptRecognitionAgent method) annotated_text (curategpt.agents.concept_recognition_agent.AnnotatedText attribute) AnnotatedObject (class in curategpt.extract) (class in curategpt.extract.extractor)

AnnotatedText (class in curategpt.agents.concept_recognition_agent) AnnotationMethod (class in curategpt.agents.concept_recognition_agent) annotations (curategpt.extract.AnnotatedObject attribute) (curategpt.extract.extractor.AnnotatedObject attribute) api (curategpt.agents.huggingface_agent.HuggingFaceAgent attribute) api_key (curategpt.extract.Extractor attribute) (curategpt.extract.extractor.Extractor attribute) (curategpt.Extractor attribute) append (curategpt.agents.evidence_agent.EvidenceUpdatePolicyEnum attribute) append_outcomes() (curategpt.utils.eval_utils.Outcome method) ApplicationState (class in curategpt.app.state) as_object() (curategpt.wrappers.ontology.ontology_wrapper.OntologyWrapper method) (curategpt.wrappers.ontology.OntologyWrapper method) as_single_object() (curategpt.extract.AnnotatedObject method) (curategpt.extract.extractor.AnnotatedObject method) ask_chatbot() (in module curategpt.app.app) assignees (curategpt.wrappers.general.github_wrapper.Issue attribute) (curategpt.wrappers.general.github_wrapper.PullRequest attribute) attributes (curategpt.agents.bootstrap_agent.KnowledgeBaseSpecification attribute)

B

BacDiveWrapper (class in curategpt.wrappers.bio.bacdive_wrapper) background_document_limit (curategpt.agents.dase_agent.DatabaseAugmentedStructuredExtraction attribute) (curategpt.agents.dragon_agent.DragonAgent attribute) (curategpt.agents.DragonAgent attribute) BaseAgent (class in curategpt.agents.base_agent) BaseEvaluator (class in curategpt.evaluation.base_evaluator) BaseWrapper (class in curategpt.wrappers) (class in curategpt.wrappers.base_wrapper) BasicExtractor (class in curategpt) (class in curategpt.extract) (class in curategpt.extract.basic_extractor) best_matches() (in module curategpt.utils.eval_utils) BiocWrapper (class in curategpt.wrappers.literature) (class in curategpt.wrappers.literature.bioc_wrapper)

BioportalWrapper (class in curategpt.wrappers.ontology.bioportal_wrapper) body (curategpt.agents.chat_agent.ChatResponse attribute) (curategpt.wrappers.general.github_wrapper.Comment attribute) (curategpt.wrappers.general.github_wrapper.Issue attribute) (curategpt.wrappers.general.github_wrapper.PullRequest attribute) bootstrap_data() (curategpt.agents.bootstrap_agent.BootstrapAgent method) bootstrap_schema() (curategpt.agents.bootstrap_agent.BootstrapAgent method) BootstrapAgent (class in curategpt.agents.bootstrap_agent) branches (curategpt.wrappers.ontology.ontology_wrapper.OntologyWrapper attribute) (curategpt.wrappers.ontology.OntologyWrapper attribute) BROAD_MATCH (curategpt.agents.mapping_agent.MappingPredicate attribute) by_field (curategpt.utils.eval_utils.Outcome attribute)

C

cache_name (curategpt.wrappers.general.github_wrapper.GitHubWrapper attribute) cached_download() (curategpt.agents.huggingface_agent.HuggingFaceAgent method) calculate_metrics() (curategpt.utils.eval_utils.Outcome method) (in module curategpt.evaluation.calc_statistics) camelify() (in module curategpt.formatters.format_utils) Cart (class in curategpt.app.cart) cart (curategpt.app.state.ApplicationState attribute) CartItem (class in curategpt.app.cart) categorize_mappings() (curategpt.agents.mapping_agent.MappingAgent method) (curategpt.agents.MappingAgent method) chat() (curategpt.agents.chat_agent.ChatAgent method) (curategpt.agents.ChatAgent method) (curategpt.wrappers.base_wrapper.BaseWrapper method) (curategpt.wrappers.BaseWrapper method) chat_agent (curategpt.agents.evidence_agent.EvidenceAgent attribute) (curategpt.agents.EvidenceAgent attribute) chat_response (curategpt.app.state.PageState attribute) ChatAgent (class in curategpt.agents) (class in curategpt.agents.chat_agent) ChatResponse (class in curategpt.agents.chat_agent) ChromaDBAdapter (class in curategpt) (class in curategpt.store) (class in curategpt.store.chromadb_adapter) ClassificationMetrics (class in curategpt.evaluation.evaluation_datamodel) ClassificationOutcome (class in curategpt.evaluation.evaluation_datamodel) client (curategpt.ChromaDBAdapter attribute) (curategpt.store.chromadb_adapter.ChromaDBAdapter attribute) (curategpt.store.ChromaDBAdapter attribute) ClinicalTrialsWrapper (class in curategpt.wrappers.clinical.ctgov_wrapper) ClinVarWrapper (class in curategpt.wrappers.clinical.clinvar_wrapper) close() (curategpt.store.duckdb_connection_handler.DuckDBConnectionAndRecoveryHandler method) CLOSE_MATCH (curategpt.agents.mapping_agent.MappingPredicate attribute) Collection (class in curategpt.store.in_memory_adapter) collection (curategpt.DBAdapter attribute) (curategpt.store.db_adapter.DBAdapter attribute) (curategpt.store.DBAdapter attribute) collection_index (curategpt.store.in_memory_adapter.InMemoryAdapter attribute) collection_metadata() (curategpt.ChromaDBAdapter method) (curategpt.DBAdapter method) (curategpt.store.chromadb_adapter.ChromaDBAdapter method) (curategpt.store.ChromaDBAdapter method) (curategpt.store.db_adapter.DBAdapter method) (curategpt.store.DBAdapter method) (curategpt.store.duckdb_adapter.DuckDBAdapter method) (curategpt.store.DuckDBAdapter method) (curategpt.store.in_memory_adapter.InMemoryAdapter method) collection_name (curategpt.adhoc.gocam_predictor.GOCAMPredictor attribute) CollectionIndex (class in curategpt.store.in_memory_adapter) collections (curategpt.store.in_memory_adapter.CollectionIndex attribute) collections() (curategpt.ChromaDBAdapter method) (curategpt.store.chromadb_adapter.ChromaDBAdapter method) (curategpt.store.ChromaDBAdapter method) Comment (class in curategpt.wrappers.general.github_wrapper) comments (curategpt.wrappers.general.github_wrapper.Issue attribute) (curategpt.wrappers.general.github_wrapper.PullRequest attribute) complete() (curategpt.agents.dragon_agent.DragonAgent method) (curategpt.agents.DragonAgent method) compute_cosine_similarity() (in module curategpt.utils.vector_algorithms) concept_id (curategpt.agents.concept_recognition_agent.Span attribute) concept_label (curategpt.agents.concept_recognition_agent.Span attribute) CONCEPT_LIST (curategpt.agents.concept_recognition_agent.AnnotationMethod attribute) ConceptRecognitionAgent (class in curategpt.agents.concept_recognition_agent) concepts (curategpt.agents.concept_recognition_agent.AnnotatedText attribute) conn (curategpt.store.duckdb_adapter.DuckDBAdapter attribute) (curategpt.store.DuckDBAdapter attribute) connect() (curategpt.store.duckdb_connection_handler.DuckDBConnectionAndRecoveryHandler method) conversation (curategpt.agents.dase_agent.DatabaseAugmentedStructuredExtraction attribute) (curategpt.agents.dragon_agent.DragonAgent attribute) (curategpt.agents.DragonAgent attribute) conversation_id (curategpt.agents.chat_agent.ChatAgent attribute) (curategpt.agents.ChatAgent attribute) conversation_mode (curategpt.agents.dase_agent.DatabaseAugmentedStructuredExtraction attribute) (curategpt.agents.dragon_agent.DragonAgent attribute) (curategpt.agents.DragonAgent attribute) create_curie() (curategpt.wrappers.base_wrapper.BaseWrapper method) (curategpt.wrappers.BaseWrapper method) create_index() (curategpt.store.duckdb_adapter.DuckDBAdapter method) (curategpt.store.DuckDBAdapter method) create_view() (curategpt.DBAdapter method) (curategpt.store.db_adapter.DBAdapter method) (curategpt.store.DBAdapter method) created_at (curategpt.wrappers.general.github_wrapper.Issue attribute) (curategpt.wrappers.general.github_wrapper.PullRequest attribute) curategpt module curategpt.adhoc module curategpt.adhoc.gocam_predictor module curategpt.agents module curategpt.agents.agent_utils module curategpt.agents.base_agent module curategpt.agents.bootstrap_agent module curategpt.agents.chat_agent module curategpt.agents.concept_recognition_agent module curategpt.agents.dase_agent module curategpt.agents.dragon_agent module curategpt.agents.evidence_agent module curategpt.agents.huggingface_agent module curategpt.agents.mapping_agent module curategpt.agents.summarization_agent module curategpt.app module curategpt.app.app module curategpt.app.cart module curategpt.app.components module curategpt.app.helper module curategpt.app.state module curategpt.cli module curategpt.conf module curategpt.conf.prompts module curategpt.evaluation module curategpt.evaluation.base_evaluator module curategpt.evaluation.calc_statistics module curategpt.evaluation.dae_evaluator module curategpt.evaluation.evaluation_datamodel module curategpt.evaluation.runner module curategpt.evaluation.splitter module

curategpt.extract module curategpt.extract.basic_extractor module curategpt.extract.extractor module curategpt.extract.openai_extractor module curategpt.extract.recursive_extractor module curategpt.formatters module curategpt.formatters.format_utils module curategpt.store module curategpt.store.chromadb_adapter module curategpt.store.db_adapter module curategpt.store.db_metadata module curategpt.store.duckdb_adapter module curategpt.store.duckdb_connection_handler module curategpt.store.duckdb_result module curategpt.store.in_memory_adapter module curategpt.store.metadata module curategpt.store.schema_proxy module curategpt.store.vocab module curategpt.utils module curategpt.utils.eval_utils module curategpt.utils.llm_utils module curategpt.utils.patch_utils module curategpt.utils.search module curategpt.utils.tokens module curategpt.utils.vector_algorithms module curategpt.utils.vectordb_operations module curategpt.views module curategpt.views.namer module curategpt.wrappers module curategpt.wrappers.base_wrapper module curategpt.wrappers.bio module curategpt.wrappers.bio.alliance_gene_wrapper module curategpt.wrappers.bio.bacdive_wrapper module curategpt.wrappers.bio.gocam_wrapper module curategpt.wrappers.bio.mediadive_wrapper module curategpt.wrappers.bio.omicsdi_wrapper module curategpt.wrappers.bio.reactome_wrapper module curategpt.wrappers.bio.uniprot_wrapper module curategpt.wrappers.clinical module curategpt.wrappers.clinical.clinvar_wrapper module curategpt.wrappers.clinical.ctgov_wrapper module curategpt.wrappers.clinical.hpoa_by_pub_wrapper module curategpt.wrappers.clinical.hpoa_wrapper module curategpt.wrappers.clinical.maxoa_wrapper module curategpt.wrappers.general module curategpt.wrappers.general.filesystem_wrapper module curategpt.wrappers.general.github_wrapper module curategpt.wrappers.general.google_drive_wrapper module curategpt.wrappers.general.gspread_wrapper module curategpt.wrappers.general.json_wrapper module curategpt.wrappers.general.linkml_schema_wrapper module curategpt.wrappers.investigation module curategpt.wrappers.investigation.ess_deepdive_wrapper module curategpt.wrappers.investigation.fairsharing_wrapper module curategpt.wrappers.investigation.jgi_wrapper module curategpt.wrappers.investigation.ncbi_bioproject_wrapper module curategpt.wrappers.investigation.ncbi_biosample_wrapper module curategpt.wrappers.investigation.nmdc_wrapper module curategpt.wrappers.legal module curategpt.wrappers.legal.reusabledata_wrapper module curategpt.wrappers.literature module curategpt.wrappers.literature.bioc_wrapper module curategpt.wrappers.literature.eutils_wrapper module curategpt.wrappers.literature.pmc_wrapper module curategpt.wrappers.literature.pubmed_wrapper module curategpt.wrappers.literature.wikipedia_wrapper module curategpt.wrappers.ontology module curategpt.wrappers.ontology.bioportal_wrapper module curategpt.wrappers.ontology.oboformat_wrapper module curategpt.wrappers.ontology.ontology module curategpt.wrappers.ontology.ontology_wrapper module current_value (curategpt.agents.dase_agent.PredictedFieldValue attribute) (curategpt.agents.dragon_agent.PredictedFieldValue attribute)

D

database_path (curategpt.adhoc.gocam_predictor.GOCAMPredictor attribute) database_type (curategpt.adhoc.gocam_predictor.GOCAMPredictor attribute) DatabaseAugmentedCompletionEvaluator (class in curategpt.evaluation.dae_evaluator) DatabaseAugmentedStructuredExtraction (class in curategpt.agents.dase_agent) db (curategpt.app.state.ApplicationState attribute) DBAdapter (class in curategpt) (class in curategpt.store) (class in curategpt.store.db_adapter) DBSettings (class in curategpt.store.db_metadata) default_doc_types (curategpt.wrappers.general.google_drive_wrapper.GoogleDriveWrapper attribute) default_embedding_model (curategpt.wrappers.base_wrapper.BaseWrapper attribute) (curategpt.wrappers.BaseWrapper attribute) default_masked_fields (curategpt.agents.dase_agent.DatabaseAugmentedStructuredExtraction attribute) (curategpt.agents.dragon_agent.DragonAgent attribute) (curategpt.agents.DragonAgent attribute) default_max_document_length (curategpt.ChromaDBAdapter attribute) (curategpt.store.chromadb_adapter.ChromaDBAdapter attribute) (curategpt.store.ChromaDBAdapter attribute) (curategpt.store.duckdb_adapter.DuckDBAdapter attribute) (curategpt.store.DuckDBAdapter attribute) default_max_search_results (curategpt.wrappers.ontology.ontology_wrapper.OntologyWrapper attribute) (curategpt.wrappers.ontology.OntologyWrapper attribute) default_model (curategpt.ChromaDBAdapter attribute) (curategpt.store.chromadb_adapter.ChromaDBAdapter attribute) (curategpt.store.ChromaDBAdapter attribute) (curategpt.store.duckdb_adapter.DuckDBAdapter attribute) (curategpt.store.DuckDBAdapter attribute) default_object_type (curategpt.wrappers.base_wrapper.BaseWrapper attribute) (curategpt.wrappers.BaseWrapper attribute) (curategpt.wrappers.bio.alliance_gene_wrapper.AllianceGeneWrapper attribute) (curategpt.wrappers.bio.bacdive_wrapper.BacDiveWrapper attribute) (curategpt.wrappers.bio.gocam_wrapper.GOCAMWrapper attribute) (curategpt.wrappers.bio.mediadive_wrapper.MediaDiveWrapper attribute) (curategpt.wrappers.bio.omicsdi_wrapper.OmicsDIWrapper attribute) (curategpt.wrappers.bio.reactome_wrapper.ReactomeWrapper attribute) (curategpt.wrappers.bio.uniprot_wrapper.UniprotWrapper attribute) (curategpt.wrappers.clinical.clinvar_wrapper.ClinVarWrapper attribute) (curategpt.wrappers.clinical.ctgov_wrapper.ClinicalTrialsWrapper attribute) (curategpt.wrappers.clinical.hpoa_by_pub_wrapper.HPOAByPubWrapper attribute) (curategpt.wrappers.clinical.hpoa_wrapper.HPOAWrapper attribute) (curategpt.wrappers.clinical.maxoa_wrapper.MAXOAWrapper attribute) (curategpt.wrappers.general.github_wrapper.GitHubWrapper attribute) (curategpt.wrappers.investigation.ess_deepdive_wrapper.ESSDeepDiveWrapper attribute) (curategpt.wrappers.investigation.fairsharing_wrapper.FAIRSharingWrapper attribute) (curategpt.wrappers.investigation.ncbi_bioproject_wrapper.NCBIBioprojectWrapper attribute) (curategpt.wrappers.investigation.ncbi_biosample_wrapper.NCBIBiosampleWrapper attribute) (curategpt.wrappers.investigation.nmdc_wrapper.NMDCWrapper attribute) (curategpt.wrappers.legal.reusabledata_wrapper.ReusableDataWrapper attribute) (curategpt.wrappers.literature.bioc_wrapper.BiocWrapper attribute) (curategpt.wrappers.literature.BiocWrapper attribute) (curategpt.wrappers.literature.pmc_wrapper.PMCWrapper attribute) default_target_class (curategpt.agents.dase_agent.DatabaseAugmentedStructuredExtraction attribute) (curategpt.agents.dragon_agent.DragonAgent attribute) (curategpt.agents.DragonAgent attribute)

definition (curategpt.wrappers.ontology.ontology.OntologyClass attribute) delete() (curategpt.DBAdapter method) (curategpt.store.db_adapter.DBAdapter method) (curategpt.store.DBAdapter method) (curategpt.store.in_memory_adapter.Collection method) (curategpt.store.in_memory_adapter.InMemoryAdapter method) description (curategpt.agents.bootstrap_agent.KnowledgeBaseSpecification attribute) deserialize() (curategpt.BasicExtractor method) (curategpt.extract.basic_extractor.BasicExtractor method) (curategpt.extract.BasicExtractor method) (curategpt.extract.Extractor method) (curategpt.extract.extractor.Extractor method) (curategpt.extract.recursive_extractor.RecursiveExtractor method) (curategpt.extract.RecursiveExtractor method) (curategpt.Extractor method) deserialize_venomx_metadata_from_adapter() (curategpt.store.Metadata class method) (curategpt.store.metadata.Metadata class method) deserialize_yaml() (curategpt.BasicExtractor method) (curategpt.extract.basic_extractor.BasicExtractor method) (curategpt.extract.BasicExtractor method) determine_fields_to_include() (curategpt.store.duckdb_adapter.DuckDBAdapter static method) (curategpt.store.DuckDBAdapter static method) DIFFERENT_FROM (curategpt.agents.mapping_agent.MappingPredicate attribute) DimensionalityReductionOptions (class in curategpt.app.components) distance_metric (curategpt.store.duckdb_adapter.DuckDBAdapter attribute) (curategpt.store.DuckDBAdapter attribute) distances (curategpt.store.duckdb_result.DuckDBSearchResult attribute) diversified_search() (curategpt.ChromaDBAdapter method) (curategpt.store.chromadb_adapter.ChromaDBAdapter method) (curategpt.store.ChromaDBAdapter method) document_adapter (curategpt.agents.dase_agent.DatabaseAugmentedStructuredExtraction attribute) (curategpt.agents.dragon_agent.DragonAgent attribute) (curategpt.agents.DragonAgent attribute) document_adapter_collection (curategpt.agents.dase_agent.DatabaseAugmentedStructuredExtraction attribute) (curategpt.agents.dragon_agent.DragonAgent attribute) (curategpt.agents.DragonAgent attribute) documents (curategpt.store.duckdb_result.DuckDBSearchResult attribute) DragonAgent (class in curategpt.agents) (class in curategpt.agents.dragon_agent) DuckDBAdapter (class in curategpt.store) (class in curategpt.store.duckdb_adapter) DuckDBConnectionAndRecoveryHandler (class in curategpt.store.duckdb_connection_handler) DuckDBSearchResult (class in curategpt.store.duckdb_result) dump() (curategpt.DBAdapter method) (curategpt.store.db_adapter.DBAdapter method) (curategpt.store.DBAdapter method) dump_then_load() (curategpt.ChromaDBAdapter method) (curategpt.DBAdapter method) (curategpt.store.chromadb_adapter.ChromaDBAdapter method) (curategpt.store.ChromaDBAdapter method) (curategpt.store.db_adapter.DBAdapter method) (curategpt.store.DBAdapter method) (curategpt.store.duckdb_adapter.DuckDBAdapter method) (curategpt.store.DuckDBAdapter method)

E

ef_construction (curategpt.store.db_metadata.DBSettings attribute) (curategpt.store.duckdb_adapter.DuckDBAdapter attribute) (curategpt.store.DuckDBAdapter attribute) ef_search (curategpt.store.db_metadata.DBSettings attribute) (curategpt.store.duckdb_adapter.DuckDBAdapter attribute) (curategpt.store.DuckDBAdapter attribute) elements (curategpt.wrappers.ontology.ontology.Ontology attribute) email (curategpt.wrappers.literature.pubmed_wrapper.PubmedWrapper attribute) (curategpt.wrappers.literature.PubmedWrapper attribute) embedding_model_name (curategpt.evaluation.evaluation_datamodel.Task attribute) embeddings (curategpt.store.duckdb_result.DuckDBSearchResult attribute) end (curategpt.agents.concept_recognition_agent.Span attribute) ESSDeepDiveWrapper (class in curategpt.wrappers.investigation.ess_deepdive_wrapper) estimate_num_tokens() (in module curategpt.utils.tokens) eutils_client (curategpt.wrappers.literature.eutils_wrapper.EUtilsWrapper attribute) (curategpt.wrappers.literature.pubmed_wrapper.PubmedWrapper attribute) (curategpt.wrappers.literature.PubmedWrapper attribute) eutils_db (curategpt.wrappers.clinical.clinvar_wrapper.ClinVarWrapper attribute) (curategpt.wrappers.investigation.ncbi_bioproject_wrapper.NCBIBioprojectWrapper attribute) (curategpt.wrappers.investigation.ncbi_biosample_wrapper.NCBIBiosampleWrapper attribute) (curategpt.wrappers.literature.eutils_wrapper.EUtilsWrapper attribute) (curategpt.wrappers.literature.pmc_wrapper.PMCWrapper attribute) EUtilsWrapper (class in curategpt.wrappers.literature.eutils_wrapper) evaluate() (curategpt.evaluation.base_evaluator.BaseEvaluator method) (curategpt.evaluation.dae_evaluator.DatabaseAugmentedCompletionEvaluator method) evaluate_object() (curategpt.evaluation.base_evaluator.BaseEvaluator method) (curategpt.evaluation.dae_evaluator.DatabaseAugmentedCompletionEvaluator method) evaluate_predictions() (in module curategpt.evaluation.calc_statistics) evidence_update_policy (curategpt.agents.evidence_agent.EvidenceAgent attribute) (curategpt.agents.EvidenceAgent attribute) EvidenceAgent (class in curategpt.agents) (class in curategpt.agents.evidence_agent) EvidenceUpdatePolicyEnum (class in curategpt.agents.evidence_agent) executed_on (curategpt.evaluation.evaluation_datamodel.Task attribute) expand_publications (curategpt.wrappers.clinical.hpoa_wrapper.HPOAWrapper attribute) (curategpt.wrappers.clinical.maxoa_wrapper.MAXOAWrapper attribute) expected (curategpt.utils.eval_utils.Outcome attribute) external_search() (curategpt.wrappers.base_wrapper.BaseWrapper method) (curategpt.wrappers.BaseWrapper method) (curategpt.wrappers.bio.omicsdi_wrapper.OmicsDIWrapper method) (curategpt.wrappers.clinical.ctgov_wrapper.ClinicalTrialsWrapper method) (curategpt.wrappers.general.github_wrapper.GitHubWrapper method) (curategpt.wrappers.general.google_drive_wrapper.GoogleDriveWrapper method) (curategpt.wrappers.investigation.ess_deepdive_wrapper.ESSDeepDiveWrapper method) (curategpt.wrappers.investigation.jgi_wrapper.JGIWrapper method) (curategpt.wrappers.literature.eutils_wrapper.EUtilsWrapper method) (curategpt.wrappers.literature.pubmed_wrapper.PubmedWrapper method) (curategpt.wrappers.literature.PubmedWrapper method) (curategpt.wrappers.literature.wikipedia_wrapper.WikipediaWrapper method) (curategpt.wrappers.literature.WikipediaWrapper method) (curategpt.wrappers.ontology.ontology_wrapper.OntologyWrapper method) (curategpt.wrappers.ontology.OntologyWrapper method)

extract() (curategpt.agents.dase_agent.DatabaseAugmentedStructuredExtraction method) (curategpt.BasicExtractor method) (curategpt.extract.basic_extractor.BasicExtractor method) (curategpt.extract.BasicExtractor method) (curategpt.extract.Extractor method) (curategpt.extract.extractor.Extractor method) (curategpt.extract.openai_extractor.OpenAIExtractor method) (curategpt.extract.OpenAIExtractor method) (curategpt.extract.recursive_extractor.RecursiveExtractor method) (curategpt.extract.RecursiveExtractor method) (curategpt.Extractor method) extract_all_text() (in module curategpt.wrappers.literature.pubmed_wrapper) extract_concepts_from_text() (curategpt.wrappers.base_wrapper.BaseWrapper method) (curategpt.wrappers.BaseWrapper method) extract_text_from_xml() (in module curategpt.wrappers.literature.pubmed_wrapper) Extractor (class in curategpt) (class in curategpt.extract) (class in curategpt.extract.extractor) extractor (curategpt.adhoc.gocam_predictor.GOCAMPredictor attribute) (curategpt.agents.base_agent.BaseAgent attribute) (curategpt.app.state.ApplicationState attribute) (curategpt.evaluation.evaluation_datamodel.Task attribute) (curategpt.wrappers.base_wrapper.BaseWrapper attribute) (curategpt.wrappers.BaseWrapper attribute)

F

f1 (curategpt.utils.eval_utils.Outcome attribute) f1_score (curategpt.evaluation.evaluation_datamodel.ClassificationMetrics attribute) FAIRSharingWrapper (class in curategpt.wrappers.investigation.fairsharing_wrapper) FALSE_NEGATIVE (curategpt.evaluation.evaluation_datamodel.ClassificationOutcome attribute) false_negatives (curategpt.evaluation.evaluation_datamodel.ClassificationMetrics attribute) FALSE_POSITIVE (curategpt.evaluation.evaluation_datamodel.ClassificationOutcome attribute) false_positives (curategpt.evaluation.evaluation_datamodel.ClassificationMetrics attribute) fetch_all_objects_memory_safe() (curategpt.ChromaDBAdapter method) (curategpt.DBAdapter method) (curategpt.store.chromadb_adapter.ChromaDBAdapter method) (curategpt.store.ChromaDBAdapter method) (curategpt.store.db_adapter.DBAdapter method) (curategpt.store.DBAdapter method) (curategpt.store.duckdb_adapter.DuckDBAdapter method) (curategpt.store.DuckDBAdapter method) (curategpt.store.in_memory_adapter.InMemoryAdapter method) fetch_definitions (curategpt.wrappers.ontology.bioportal_wrapper.BioportalWrapper attribute) (curategpt.wrappers.ontology.ontology_wrapper.OntologyWrapper attribute) (curategpt.wrappers.ontology.OntologyWrapper attribute) fetch_full_text() (curategpt.wrappers.literature.pubmed_wrapper.PubmedWrapper method) (curategpt.wrappers.literature.PubmedWrapper method) fetch_pmcid() (curategpt.wrappers.literature.pubmed_wrapper.PubmedWrapper method) (curategpt.wrappers.literature.PubmedWrapper method) fetch_relationships (curategpt.wrappers.ontology.bioportal_wrapper.BioportalWrapper attribute) (curategpt.wrappers.ontology.ontology_wrapper.OntologyWrapper attribute) (curategpt.wrappers.ontology.OntologyWrapper attribute) fetch_tool (curategpt.wrappers.clinical.clinvar_wrapper.ClinVarWrapper attribute) (curategpt.wrappers.literature.eutils_wrapper.EUtilsWrapper attribute) (curategpt.wrappers.literature.pmc_wrapper.PMCWrapper attribute) field_names() (curategpt.DBAdapter method) (curategpt.store.db_adapter.DBAdapter method) (curategpt.store.DBAdapter method) field_predicted (curategpt.agents.dase_agent.PredictedFieldValue attribute) (curategpt.agents.dragon_agent.PredictedFieldValue attribute)

fields_to_mask (curategpt.evaluation.dae_evaluator.DatabaseAugmentedCompletionEvaluator attribute) (curategpt.evaluation.evaluation_datamodel.Task attribute) fields_to_predict (curategpt.evaluation.dae_evaluator.DatabaseAugmentedCompletionEvaluator attribute) (curategpt.evaluation.evaluation_datamodel.Task attribute) FilesystemWrapper (class in curategpt.wrappers.general.filesystem_wrapper) filter_header() (in module curategpt.wrappers.clinical.hpoa_wrapper) (in module curategpt.wrappers.clinical.maxoa_wrapper) filtered_collection_names() (in module curategpt.app.app) find() (curategpt.ChromaDBAdapter method) (curategpt.DBAdapter method) (curategpt.store.chromadb_adapter.ChromaDBAdapter method) (curategpt.store.ChromaDBAdapter method) (curategpt.store.db_adapter.DBAdapter method) (curategpt.store.DBAdapter method) (curategpt.store.duckdb_adapter.DuckDBAdapter method) (curategpt.store.DuckDBAdapter method) (curategpt.store.in_memory_adapter.InMemoryAdapter method) find_evidence() (curategpt.agents.evidence_agent.EvidenceAgent method) (curategpt.agents.EvidenceAgent method) find_evidence_complex() (curategpt.agents.evidence_agent.EvidenceAgent method) (curategpt.agents.EvidenceAgent method) find_evidence_simple() (curategpt.agents.evidence_agent.EvidenceAgent method) (curategpt.agents.EvidenceAgent method) find_links() (curategpt.agents.mapping_agent.MappingAgent method) (curategpt.agents.MappingAgent method) fix_yaml() (curategpt.adhoc.gocam_predictor.GOCAMPredictor method) flatten() (curategpt.utils.eval_utils.Outcome method) fn (curategpt.utils.eval_utils.Outcome attribute) format (curategpt.wrappers.bio.bacdive_wrapper.BacDiveWrapper attribute) (curategpt.wrappers.general.json_wrapper.JSONWrapper attribute) formatted_body (curategpt.agents.chat_agent.ChatResponse attribute) fp (curategpt.utils.eval_utils.Outcome attribute) from_schemaview() (curategpt.wrappers.general.linkml_schema_wrapper.LinkMLSchemarapper method) functions() (curategpt.extract.openai_extractor.OpenAIExtractor method) (curategpt.extract.OpenAIExtractor method)

G

gc (curategpt.wrappers.general.gspread_wrapper.GSpreadWrapper attribute) generate_all() (curategpt.agents.dragon_agent.DragonAgent method) (curategpt.agents.DragonAgent method) generate_background (curategpt.evaluation.evaluation_datamodel.Task attribute) generate_queries() (curategpt.agents.dragon_agent.DragonAgent method) (curategpt.agents.DragonAgent method) generic_object() (in module curategpt.wrappers.bio.reactome_wrapper) get_applicable_examples() (in module curategpt.app.helper) get_case_collection() (in module curategpt.app.helper) get_chat_agent() (in module curategpt.app.app) get_collection() (curategpt.store.in_memory_adapter.CollectionIndex method) get_page_state() (curategpt.app.state.ApplicationState method) get_raw_objects() (curategpt.store.duckdb_adapter.DuckDBAdapter method) (curategpt.store.DuckDBAdapter method) get_records() (in module curategpt.wrappers.investigation.ess_deepdive_wrapper) get_samples() (in module curategpt.wrappers.investigation.nmdc_wrapper) get_state() (in module curategpt.app.state) get_store() (in module curategpt.store)

get_token() (in module curategpt.wrappers.general.github_wrapper) get_wrapper() (in module curategpt.wrappers) GitHubWrapper (class in curategpt.wrappers.general.github_wrapper) glob (curategpt.wrappers.general.filesystem_wrapper.FilesystemWrapper attribute) (curategpt.wrappers.legal.reusabledata_wrapper.ReusableDataWrapper attribute) gocam_by_id() (curategpt.adhoc.gocam_predictor.GOCAMPredictor method) gocam_wrapper (curategpt.adhoc.gocam_predictor.GOCAMPredictor attribute) GOCAMPredictor (class in curategpt.adhoc.gocam_predictor) GOCAMWrapper (class in curategpt.wrappers.bio.gocam_wrapper) google_drive_id (curategpt.wrappers.general.google_drive_wrapper.GoogleDriveWrapper attribute) google_folder_id (curategpt.wrappers.general.google_drive_wrapper.GoogleDriveWrapper attribute) GoogleDriveWrapper (class in curategpt.wrappers.general.google_drive_wrapper) ground_concept() (curategpt.agents.concept_recognition_agent.ConceptRecognitionAgent method) GroundingResult (class in curategpt.agents.concept_recognition_agent) group_by_publication (curategpt.wrappers.clinical.hpoa_by_pub_wrapper.HPOAByPubWrapper attribute) (curategpt.wrappers.clinical.hpoa_wrapper.HPOAWrapper attribute) (curategpt.wrappers.clinical.maxoa_wrapper.MAXOAWrapper attribute) GSpreadWrapper (class in curategpt.wrappers.general.gspread_wrapper)

H

headers (curategpt.wrappers.general.github_wrapper.GitHubWrapper property) hnsw_space (curategpt.store.db_metadata.DBSettings attribute) (curategpt.store.Metadata attribute) (curategpt.store.metadata.Metadata attribute) hpo_ont_adapter() (in module curategpt.wrappers.clinical.hpoa_wrapper) (in module curategpt.wrappers.clinical.maxoa_wrapper)

HPOAByPubWrapper (class in curategpt.wrappers.clinical.hpoa_by_pub_wrapper) HPOAWrapper (class in curategpt.wrappers.clinical.hpoa_wrapper) html_table() (in module curategpt.app.app) HuggingFaceAgent (class in curategpt.agents.huggingface_agent)

I

id (curategpt.agents.dase_agent.PredictedFieldValue attribute) (curategpt.agents.dragon_agent.PredictedFieldValue attribute) (curategpt.evaluation.evaluation_datamodel.Task property) (curategpt.wrappers.general.github_wrapper.Comment attribute) (curategpt.wrappers.general.github_wrapper.Issue attribute) (curategpt.wrappers.general.github_wrapper.PullRequest attribute) (curategpt.wrappers.ontology.ontology.OntologyClass attribute) id_field (curategpt.ChromaDBAdapter attribute) (curategpt.store.chromadb_adapter.ChromaDBAdapter attribute) (curategpt.store.ChromaDBAdapter attribute) (curategpt.store.duckdb_adapter.DuckDBAdapter attribute) (curategpt.store.DuckDBAdapter attribute) id_prefix (curategpt.wrappers.clinical.clinvar_wrapper.ClinVarWrapper attribute) (curategpt.wrappers.investigation.ncbi_bioproject_wrapper.NCBIBioprojectWrapper attribute) (curategpt.wrappers.investigation.ncbi_biosample_wrapper.NCBIBiosampleWrapper attribute) (curategpt.wrappers.literature.eutils_wrapper.EUtilsWrapper attribute) (curategpt.wrappers.literature.pmc_wrapper.PMCWrapper attribute) id_to_object (curategpt.ChromaDBAdapter attribute) (curategpt.store.chromadb_adapter.ChromaDBAdapter attribute) (curategpt.store.ChromaDBAdapter attribute) (curategpt.store.duckdb_adapter.DuckDBAdapter attribute) (curategpt.store.DuckDBAdapter attribute) id_to_shorthand (curategpt.wrappers.ontology.ontology_wrapper.OntologyWrapper attribute) (curategpt.wrappers.ontology.OntologyWrapper attribute) identifier_field (curategpt.agents.concept_recognition_agent.ConceptRecognitionAgent attribute) identifier_field() (curategpt.DBAdapter method) (curategpt.store.db_adapter.DBAdapter method) (curategpt.store.DBAdapter method) (curategpt.store.duckdb_adapter.DuckDBAdapter method) (curategpt.store.DuckDBAdapter method) ids (curategpt.store.duckdb_result.DuckDBSearchResult attribute) ids_from_tree() (in module curategpt.wrappers.bio.reactome_wrapper)

ids_to_names() (curategpt.views.namer.Namer method) include (curategpt.store.duckdb_result.DuckDBSearchResult attribute) include_standard_annotations (curategpt.adhoc.gocam_predictor.GOCAMPredictor attribute) (curategpt.wrappers.bio.gocam_wrapper.GOCAMWrapper attribute) INLINE (curategpt.agents.concept_recognition_agent.AnnotationMethod attribute) InMemoryAdapter (class in curategpt.store.in_memory_adapter) input_text (curategpt.agents.concept_recognition_agent.AnnotatedText attribute) (curategpt.agents.concept_recognition_agent.GroundingResult attribute) insert() (curategpt.ChromaDBAdapter method) (curategpt.DBAdapter method) (curategpt.store.chromadb_adapter.ChromaDBAdapter method) (curategpt.store.ChromaDBAdapter method) (curategpt.store.db_adapter.DBAdapter method) (curategpt.store.DBAdapter method) (curategpt.store.duckdb_adapter.DuckDBAdapter method) (curategpt.store.DuckDBAdapter method) (curategpt.store.in_memory_adapter.InMemoryAdapter method) insert_from_huggingface() (curategpt.ChromaDBAdapter method) (curategpt.DBAdapter method) (curategpt.store.chromadb_adapter.ChromaDBAdapter method) (curategpt.store.ChromaDBAdapter method) (curategpt.store.db_adapter.DBAdapter method) (curategpt.store.DBAdapter method) (curategpt.store.duckdb_adapter.DuckDBAdapter method) (curategpt.store.DuckDBAdapter method) is_fetch_full_text (curategpt.wrappers.literature.pubmed_wrapper.PubmedWrapper attribute) (curategpt.wrappers.literature.PubmedWrapper attribute) is_rate_limit_error() (in module curategpt.utils.llm_utils) is_suspect (curategpt.agents.concept_recognition_agent.Span attribute) Issue (class in curategpt.wrappers.general.github_wrapper) issue_comments() (curategpt.wrappers.general.github_wrapper.GitHubWrapper method) items (curategpt.app.cart.Cart attribute) ixn_by_field (curategpt.utils.eval_utils.Outcome attribute)

J

JGIWrapper (class in curategpt.wrappers.investigation.jgi_wrapper) json_schema() (curategpt.store.schema_proxy.SchemaProxy method) (curategpt.store.SchemaProxy method)

JSONWrapper (class in curategpt.wrappers.general.json_wrapper) jwt (curategpt.wrappers.investigation.fairsharing_wrapper.FAIRSharingWrapper property)

K

kb_name (curategpt.agents.bootstrap_agent.KnowledgeBaseSpecification attribute) key_values (curategpt.extract.AnnotatedObject attribute) (curategpt.extract.extractor.AnnotatedObject attribute) kill_process() (curategpt.store.duckdb_adapter.DuckDBAdapter static method) (curategpt.store.DuckDBAdapter static method)

knowledge_source (curategpt.agents.base_agent.BaseAgent attribute) knowledge_source_collection (curategpt.agents.base_agent.BaseAgent attribute) KnowledgeBaseSpecification (class in curategpt.agents.bootstrap_agent)

L

label (curategpt.wrappers.ontology.ontology.OntologyClass attribute) label_adapter (curategpt.wrappers.bio.gocam_wrapper.GOCAMWrapper property) (curategpt.wrappers.investigation.nmdc_wrapper.NMDCWrapper property) (curategpt.wrappers.literature.bioc_wrapper.BiocWrapper property) (curategpt.wrappers.literature.BiocWrapper property) label_field (curategpt.agents.concept_recognition_agent.ConceptRecognitionAgent attribute) label_field() (curategpt.DBAdapter method) (curategpt.store.db_adapter.DBAdapter method) (curategpt.store.DBAdapter method) labels (curategpt.wrappers.general.github_wrapper.Issue attribute) (curategpt.wrappers.general.github_wrapper.PullRequest attribute) limit (curategpt.wrappers.investigation.ess_deepdive_wrapper.ESSDeepDiveWrapper attribute) limit_slider_component() (in module curategpt.app.components) LinkMLSchemarapper (class in curategpt.wrappers.general.linkml_schema_wrapper) list_collection_names() (curategpt.ChromaDBAdapter method) (curategpt.DBAdapter method) (curategpt.store.chromadb_adapter.ChromaDBAdapter method) (curategpt.store.ChromaDBAdapter method) (curategpt.store.db_adapter.DBAdapter method) (curategpt.store.DBAdapter method) (curategpt.store.duckdb_adapter.DuckDBAdapter method) (curategpt.store.DuckDBAdapter method) (curategpt.store.in_memory_adapter.InMemoryAdapter method)

load_config() (curategpt.store.db_metadata.DBSettings method) local_store (curategpt.wrappers.base_wrapper.BaseWrapper attribute) (curategpt.wrappers.BaseWrapper attribute) logical_definition (curategpt.wrappers.ontology.ontology.OntologyClass attribute) lookup() (curategpt.ChromaDBAdapter method) (curategpt.DBAdapter method) (curategpt.store.chromadb_adapter.ChromaDBAdapter method) (curategpt.store.ChromaDBAdapter method) (curategpt.store.db_adapter.DBAdapter method) (curategpt.store.DBAdapter method) (curategpt.store.duckdb_adapter.DuckDBAdapter method) (curategpt.store.DuckDBAdapter method) (curategpt.store.in_memory_adapter.InMemoryAdapter method) lookup_multiple() (curategpt.DBAdapter method) (curategpt.store.db_adapter.DBAdapter method) (curategpt.store.DBAdapter method)

M

M (curategpt.store.db_metadata.DBSettings attribute) (curategpt.store.duckdb_adapter.DuckDBAdapter attribute) (curategpt.store.DuckDBAdapter attribute) MACRO (curategpt.evaluation.evaluation_datamodel.AggregationMethod attribute) main_class (curategpt.agents.bootstrap_agent.KnowledgeBaseSpecification attribute) map_object() (curategpt.views.namer.Namer method) map_reference() (curategpt.views.namer.Namer method) Mapping (class in curategpt.agents.mapping_agent) MappingAgent (class in curategpt.agents) (class in curategpt.agents.mapping_agent) MappingPredicate (class in curategpt.agents.mapping_agent) mappings (curategpt.agents.mapping_agent.MappingSet attribute) MappingSet (class in curategpt.agents.mapping_agent) match() (curategpt.agents.mapping_agent.MappingAgent method) (curategpt.agents.MappingAgent method) match_collections() (in module curategpt.utils.vectordb_operations) matches() (curategpt.ChromaDBAdapter method) (curategpt.DBAdapter method) (curategpt.store.chromadb_adapter.ChromaDBAdapter method) (curategpt.store.ChromaDBAdapter method) (curategpt.store.db_adapter.DBAdapter method) (curategpt.store.DBAdapter method) (curategpt.store.duckdb_adapter.DuckDBAdapter method) (curategpt.store.DuckDBAdapter method) (curategpt.store.in_memory_adapter.InMemoryAdapter method) max_background_document_size (curategpt.agents.dase_agent.DatabaseAugmentedStructuredExtraction attribute) (curategpt.agents.dragon_agent.DragonAgent attribute) (curategpt.agents.DragonAgent attribute) max_text_length (curategpt.wrappers.base_wrapper.BaseWrapper attribute) (curategpt.wrappers.BaseWrapper attribute) (curategpt.wrappers.general.filesystem_wrapper.FilesystemWrapper attribute) max_tokens (curategpt.extract.openai_extractor.OpenAIExtractor attribute) (curategpt.extract.OpenAIExtractor attribute) max_tokens_by_model() (in module curategpt.utils.tokens) maxo_ont_adapter() (in module curategpt.wrappers.clinical.maxoa_wrapper) MAXOAWrapper (class in curategpt.wrappers.clinical.maxoa_wrapper) MediaDiveWrapper (class in curategpt.wrappers.bio.mediadive_wrapper) Metadata (class in curategpt.store) (class in curategpt.store.metadata) metadata (curategpt.app.cart.CartItem attribute) (curategpt.store.in_memory_adapter.Collection attribute) metadatas (curategpt.store.duckdb_result.DuckDBSearchResult attribute) method (curategpt.evaluation.evaluation_datamodel.Task attribute) MICRO (curategpt.evaluation.evaluation_datamodel.AggregationMethod attribute) mmr_diversified_search() (in module curategpt.utils.vector_algorithms) model (curategpt.extract.Extractor property) (curategpt.extract.extractor.Extractor property) (curategpt.extract.openai_extractor.OpenAIExtractor attribute) (curategpt.extract.OpenAIExtractor attribute) (curategpt.Extractor property) (curategpt.store.db_metadata.DBSettings attribute) model_config (curategpt.agents.bootstrap_agent.KnowledgeBaseSpecification attribute) (curategpt.agents.chat_agent.ChatResponse attribute) (curategpt.agents.concept_recognition_agent.AnnotatedText attribute) (curategpt.agents.concept_recognition_agent.GroundingResult attribute) (curategpt.agents.concept_recognition_agent.Span attribute) (curategpt.agents.dase_agent.PredictedFieldValue attribute) (curategpt.agents.dragon_agent.PredictedFieldValue attribute) (curategpt.agents.mapping_agent.Mapping attribute) (curategpt.agents.mapping_agent.MappingSet attribute) (curategpt.app.cart.Cart attribute) (curategpt.app.cart.CartItem attribute) (curategpt.BasicExtractor attribute) (curategpt.evaluation.evaluation_datamodel.ClassificationMetrics attribute) (curategpt.evaluation.evaluation_datamodel.StratifiedCollection attribute) (curategpt.evaluation.evaluation_datamodel.Task attribute) (curategpt.extract.AnnotatedObject attribute) (curategpt.extract.basic_extractor.BasicExtractor attribute) (curategpt.extract.BasicExtractor attribute) (curategpt.extract.extractor.AnnotatedObject attribute) (curategpt.store.db_metadata.DBSettings attribute) (curategpt.store.duckdb_result.DuckDBSearchResult attribute) (curategpt.store.in_memory_adapter.Collection attribute) (curategpt.store.in_memory_adapter.CollectionIndex attribute) (curategpt.store.Metadata attribute) (curategpt.store.metadata.Metadata attribute) (curategpt.store.schema_proxy.SchemaProxy attribute) (curategpt.store.SchemaProxy attribute) (curategpt.utils.eval_utils.Outcome attribute) (curategpt.wrappers.general.github_wrapper.Comment attribute) (curategpt.wrappers.general.github_wrapper.Issue attribute) (curategpt.wrappers.general.github_wrapper.PullRequest attribute) (curategpt.wrappers.ontology.ontology.Ontology attribute) (curategpt.wrappers.ontology.ontology.OntologyClass attribute) (curategpt.wrappers.ontology.ontology.Relationship attribute) model_name (curategpt.adhoc.gocam_predictor.GOCAMPredictor attribute) (curategpt.BasicExtractor attribute) (curategpt.evaluation.evaluation_datamodel.Task attribute) (curategpt.extract.basic_extractor.BasicExtractor attribute) (curategpt.extract.BasicExtractor attribute) (curategpt.extract.Extractor attribute) (curategpt.extract.extractor.Extractor attribute) (curategpt.extract.recursive_extractor.RecursiveExtractor attribute) (curategpt.extract.RecursiveExtractor attribute) (curategpt.Extractor attribute) model_post_init() (curategpt.store.Metadata method) (curategpt.store.metadata.Metadata method) module curategpt curategpt.adhoc curategpt.adhoc.gocam_predictor curategpt.agents curategpt.agents.agent_utils curategpt.agents.base_agent curategpt.agents.bootstrap_agent curategpt.agents.chat_agent curategpt.agents.concept_recognition_agent curategpt.agents.dase_agent curategpt.agents.dragon_agent curategpt.agents.evidence_agent curategpt.agents.huggingface_agent curategpt.agents.mapping_agent curategpt.agents.summarization_agent curategpt.app curategpt.app.app curategpt.app.cart curategpt.app.components curategpt.app.helper curategpt.app.state curategpt.cli curategpt.conf curategpt.conf.prompts curategpt.evaluation curategpt.evaluation.base_evaluator curategpt.evaluation.calc_statistics curategpt.evaluation.dae_evaluator curategpt.evaluation.evaluation_datamodel curategpt.evaluation.runner curategpt.evaluation.splitter curategpt.extract curategpt.extract.basic_extractor curategpt.extract.extractor curategpt.extract.openai_extractor curategpt.extract.recursive_extractor curategpt.formatters curategpt.formatters.format_utils curategpt.store curategpt.store.chromadb_adapter curategpt.store.db_adapter curategpt.store.db_metadata curategpt.store.duckdb_adapter curategpt.store.duckdb_connection_handler curategpt.store.duckdb_result curategpt.store.in_memory_adapter curategpt.store.metadata curategpt.store.schema_proxy curategpt.store.vocab curategpt.utils curategpt.utils.eval_utils curategpt.utils.llm_utils curategpt.utils.patch_utils curategpt.utils.search curategpt.utils.tokens curategpt.utils.vector_algorithms curategpt.utils.vectordb_operations curategpt.views curategpt.views.namer curategpt.wrappers curategpt.wrappers.base_wrapper curategpt.wrappers.bio curategpt.wrappers.bio.alliance_gene_wrapper curategpt.wrappers.bio.bacdive_wrapper curategpt.wrappers.bio.gocam_wrapper curategpt.wrappers.bio.mediadive_wrapper curategpt.wrappers.bio.omicsdi_wrapper curategpt.wrappers.bio.reactome_wrapper curategpt.wrappers.bio.uniprot_wrapper curategpt.wrappers.clinical curategpt.wrappers.clinical.clinvar_wrapper curategpt.wrappers.clinical.ctgov_wrapper curategpt.wrappers.clinical.hpoa_by_pub_wrapper curategpt.wrappers.clinical.hpoa_wrapper curategpt.wrappers.clinical.maxoa_wrapper curategpt.wrappers.general curategpt.wrappers.general.filesystem_wrapper curategpt.wrappers.general.github_wrapper curategpt.wrappers.general.google_drive_wrapper curategpt.wrappers.general.gspread_wrapper curategpt.wrappers.general.json_wrapper curategpt.wrappers.general.linkml_schema_wrapper curategpt.wrappers.investigation curategpt.wrappers.investigation.ess_deepdive_wrapper curategpt.wrappers.investigation.fairsharing_wrapper curategpt.wrappers.investigation.jgi_wrapper curategpt.wrappers.investigation.ncbi_bioproject_wrapper curategpt.wrappers.investigation.ncbi_biosample_wrapper curategpt.wrappers.investigation.nmdc_wrapper curategpt.wrappers.legal curategpt.wrappers.legal.reusabledata_wrapper curategpt.wrappers.literature curategpt.wrappers.literature.bioc_wrapper curategpt.wrappers.literature.eutils_wrapper curategpt.wrappers.literature.pmc_wrapper curategpt.wrappers.literature.pubmed_wrapper curategpt.wrappers.literature.wikipedia_wrapper curategpt.wrappers.ontology curategpt.wrappers.ontology.bioportal_wrapper curategpt.wrappers.ontology.oboformat_wrapper curategpt.wrappers.ontology.ontology curategpt.wrappers.ontology.ontology_wrapper

N

name (curategpt.ChromaDBAdapter attribute) (curategpt.DBAdapter attribute) (curategpt.store.chromadb_adapter.ChromaDBAdapter attribute) (curategpt.store.ChromaDBAdapter attribute) (curategpt.store.db_adapter.DBAdapter attribute) (curategpt.store.db_metadata.DBSettings attribute) (curategpt.store.DBAdapter attribute) (curategpt.store.duckdb_adapter.DuckDBAdapter attribute) (curategpt.store.DuckDBAdapter attribute) (curategpt.store.in_memory_adapter.InMemoryAdapter attribute) (curategpt.store.schema_proxy.SchemaProxy property) (curategpt.store.SchemaProxy property) (curategpt.wrappers.base_wrapper.BaseWrapper attribute) (curategpt.wrappers.BaseWrapper attribute) (curategpt.wrappers.bio.alliance_gene_wrapper.AllianceGeneWrapper attribute) (curategpt.wrappers.bio.bacdive_wrapper.BacDiveWrapper attribute) (curategpt.wrappers.bio.gocam_wrapper.GOCAMWrapper attribute) (curategpt.wrappers.bio.mediadive_wrapper.MediaDiveWrapper attribute) (curategpt.wrappers.bio.omicsdi_wrapper.OmicsDIWrapper attribute) (curategpt.wrappers.bio.reactome_wrapper.ReactomeWrapper attribute) (curategpt.wrappers.bio.uniprot_wrapper.UniprotWrapper attribute) (curategpt.wrappers.clinical.clinvar_wrapper.ClinVarWrapper attribute) (curategpt.wrappers.clinical.ctgov_wrapper.ClinicalTrialsWrapper attribute) (curategpt.wrappers.clinical.hpoa_by_pub_wrapper.HPOAByPubWrapper attribute) (curategpt.wrappers.clinical.hpoa_wrapper.HPOAWrapper attribute) (curategpt.wrappers.clinical.maxoa_wrapper.MAXOAWrapper attribute) (curategpt.wrappers.general.filesystem_wrapper.FilesystemWrapper attribute) (curategpt.wrappers.general.github_wrapper.GitHubWrapper attribute) (curategpt.wrappers.general.google_drive_wrapper.GoogleDriveWrapper attribute) (curategpt.wrappers.general.gspread_wrapper.GSpreadWrapper attribute) (curategpt.wrappers.general.json_wrapper.JSONWrapper attribute) (curategpt.wrappers.general.linkml_schema_wrapper.LinkMLSchemarapper attribute) (curategpt.wrappers.investigation.ess_deepdive_wrapper.ESSDeepDiveWrapper attribute) (curategpt.wrappers.investigation.fairsharing_wrapper.FAIRSharingWrapper attribute) (curategpt.wrappers.investigation.jgi_wrapper.JGIWrapper attribute) (curategpt.wrappers.investigation.ncbi_bioproject_wrapper.NCBIBioprojectWrapper attribute) (curategpt.wrappers.investigation.ncbi_biosample_wrapper.NCBIBiosampleWrapper attribute) (curategpt.wrappers.investigation.nmdc_wrapper.NMDCWrapper attribute) (curategpt.wrappers.legal.reusabledata_wrapper.ReusableDataWrapper attribute) (curategpt.wrappers.literature.bioc_wrapper.BiocWrapper attribute) (curategpt.wrappers.literature.BiocWrapper attribute) (curategpt.wrappers.literature.eutils_wrapper.EUtilsWrapper attribute) (curategpt.wrappers.literature.pmc_wrapper.PMCWrapper attribute) (curategpt.wrappers.literature.pubmed_wrapper.PubmedWrapper attribute) (curategpt.wrappers.literature.PubmedWrapper attribute) (curategpt.wrappers.literature.wikipedia_wrapper.WikipediaWrapper attribute) (curategpt.wrappers.literature.WikipediaWrapper attribute) (curategpt.wrappers.ontology.oboformat_wrapper.OBOFormatWrapper attribute) (curategpt.wrappers.ontology.ontology_wrapper.OntologyWrapper attribute) (curategpt.wrappers.ontology.OntologyWrapper attribute)

Namer (class in curategpt.views.namer) names_to_ids() (curategpt.views.namer.Namer method) NARROW_MATCH (curategpt.agents.mapping_agent.MappingPredicate attribute) ncbi_key (curategpt.wrappers.literature.pubmed_wrapper.PubmedWrapper attribute) (curategpt.wrappers.literature.PubmedWrapper attribute) NCBIBioprojectWrapper (class in curategpt.wrappers.investigation.ncbi_bioproject_wrapper) NCBIBiosampleWrapper (class in curategpt.wrappers.investigation.ncbi_biosample_wrapper) NMDCWrapper (class in curategpt.wrappers.investigation.nmdc_wrapper) normalize_metadata() (curategpt.ChromaDBAdapter method) (curategpt.store.chromadb_adapter.ChromaDBAdapter method) (curategpt.store.ChromaDBAdapter method) nparray_to_list() (curategpt.ChromaDBAdapter method) (curategpt.store.chromadb_adapter.ChromaDBAdapter method) (curategpt.store.ChromaDBAdapter method) num_testing (curategpt.evaluation.evaluation_datamodel.Task attribute) num_training (curategpt.evaluation.evaluation_datamodel.Task attribute) num_validation (curategpt.evaluation.evaluation_datamodel.Task attribute) number (curategpt.wrappers.general.github_wrapper.Issue attribute) (curategpt.wrappers.general.github_wrapper.PullRequest attribute)

O

oak_adapter (curategpt.wrappers.ontology.ontology_wrapper.OntologyWrapper attribute) (curategpt.wrappers.ontology.OntologyWrapper attribute) object (curategpt.app.cart.CartItem attribute) (curategpt.extract.AnnotatedObject attribute) (curategpt.extract.extractor.AnnotatedObject attribute) object_as_yaml() (in module curategpt.formatters.format_utils) object_by_id() (curategpt.wrappers.bio.gocam_wrapper.GOCAMWrapper method) (curategpt.wrappers.investigation.fairsharing_wrapper.FAIRSharingWrapper method) object_count (curategpt.store.Metadata attribute) (curategpt.store.metadata.Metadata attribute) object_from_dict() (curategpt.wrappers.bio.gocam_wrapper.GOCAMWrapper method) object_id (curategpt.agents.mapping_agent.Mapping attribute) object_ids() (curategpt.wrappers.bio.alliance_gene_wrapper.AllianceGeneWrapper method) (curategpt.wrappers.bio.mediadive_wrapper.MediaDiveWrapper method) (curategpt.wrappers.bio.reactome_wrapper.ReactomeWrapper method) (curategpt.wrappers.bio.uniprot_wrapper.UniprotWrapper method) object_type (curategpt.app.cart.CartItem attribute) (curategpt.store.Metadata attribute) (curategpt.store.metadata.Metadata attribute) objects (curategpt.store.in_memory_adapter.Collection attribute) objects() (curategpt.wrappers.base_wrapper.BaseWrapper method) (curategpt.wrappers.BaseWrapper method) (curategpt.wrappers.bio.alliance_gene_wrapper.AllianceGeneWrapper method) (curategpt.wrappers.bio.bacdive_wrapper.BacDiveWrapper method) (curategpt.wrappers.bio.gocam_wrapper.GOCAMWrapper method) (curategpt.wrappers.bio.mediadive_wrapper.MediaDiveWrapper method) (curategpt.wrappers.bio.reactome_wrapper.ReactomeWrapper method) (curategpt.wrappers.bio.uniprot_wrapper.UniprotWrapper method) (curategpt.wrappers.clinical.hpoa_wrapper.HPOAWrapper method) (curategpt.wrappers.clinical.maxoa_wrapper.MAXOAWrapper method) (curategpt.wrappers.general.filesystem_wrapper.FilesystemWrapper method) (curategpt.wrappers.general.github_wrapper.GitHubWrapper method) (curategpt.wrappers.general.gspread_wrapper.GSpreadWrapper method) (curategpt.wrappers.general.json_wrapper.JSONWrapper method) (curategpt.wrappers.general.linkml_schema_wrapper.LinkMLSchemarapper method) (curategpt.wrappers.investigation.ess_deepdive_wrapper.ESSDeepDiveWrapper method) (curategpt.wrappers.investigation.fairsharing_wrapper.FAIRSharingWrapper method) (curategpt.wrappers.investigation.nmdc_wrapper.NMDCWrapper method) (curategpt.wrappers.legal.reusabledata_wrapper.ReusableDataWrapper method) (curategpt.wrappers.literature.bioc_wrapper.BiocWrapper method) (curategpt.wrappers.literature.BiocWrapper method) (curategpt.wrappers.ontology.oboformat_wrapper.OBOFormatWrapper method) (curategpt.wrappers.ontology.ontology_wrapper.OntologyWrapper method) (curategpt.wrappers.ontology.OntologyWrapper method)

objects_by_ids() (curategpt.wrappers.base_wrapper.BaseWrapper method) (curategpt.wrappers.BaseWrapper method) (curategpt.wrappers.bio.omicsdi_wrapper.OmicsDIWrapper method) (curategpt.wrappers.bio.uniprot_wrapper.UniprotWrapper method) (curategpt.wrappers.general.google_drive_wrapper.GoogleDriveWrapper method) (curategpt.wrappers.literature.eutils_wrapper.EUtilsWrapper method) (curategpt.wrappers.literature.pubmed_wrapper.PubmedWrapper method) (curategpt.wrappers.literature.PubmedWrapper method) objects_from_dict() (curategpt.wrappers.clinical.clinvar_wrapper.ClinVarWrapper method) (curategpt.wrappers.investigation.ncbi_bioproject_wrapper.NCBIBioprojectWrapper method) (curategpt.wrappers.investigation.ncbi_biosample_wrapper.NCBIBiosampleWrapper method) (curategpt.wrappers.literature.eutils_wrapper.EUtilsWrapper method) (curategpt.wrappers.literature.pmc_wrapper.PMCWrapper method) objects_from_file() (curategpt.wrappers.clinical.hpoa_wrapper.HPOAWrapper method) (curategpt.wrappers.clinical.maxoa_wrapper.MAXOAWrapper method) objects_from_files() (curategpt.wrappers.general.google_drive_wrapper.GoogleDriveWrapper method) objects_from_list() (curategpt.wrappers.clinical.ctgov_wrapper.ClinicalTrialsWrapper method) objects_from_rows() (curategpt.wrappers.clinical.hpoa_wrapper.HPOAWrapper method) (curategpt.wrappers.clinical.maxoa_wrapper.MAXOAWrapper method) OBOFormatWrapper (class in curategpt.wrappers.ontology.oboformat_wrapper) OmicsDIWrapper (class in curategpt.wrappers.bio.omicsdi_wrapper) Ontology (class in curategpt.wrappers.ontology.ontology) OntologyClass (class in curategpt.wrappers.ontology.ontology) OntologyWrapper (class in curategpt.wrappers.ontology) (class in curategpt.wrappers.ontology.ontology_wrapper) openai_client (curategpt.store.duckdb_adapter.DuckDBAdapter attribute) (curategpt.store.DuckDBAdapter attribute) OpenAIExtractor (class in curategpt.extract) (class in curategpt.extract.openai_extractor) original_id (curategpt.agents.dase_agent.PredictedFieldValue attribute) (curategpt.agents.dragon_agent.PredictedFieldValue attribute) (curategpt.wrappers.ontology.ontology.OntologyClass attribute) Outcome (class in curategpt.utils.eval_utils) owner (curategpt.wrappers.general.github_wrapper.GitHubWrapper attribute)

P

page (curategpt.app.state.ApplicationState attribute) page_states (curategpt.app.state.ApplicationState attribute) PageState (class in curategpt.app.state) parameters (curategpt.utils.eval_utils.Outcome attribute) parse_annotations() (in module curategpt.agents.concept_recognition_agent) parse_duckdb_result() (curategpt.store.duckdb_adapter.DuckDBAdapter static method) (curategpt.store.DuckDBAdapter static method) parse_spans() (in module curategpt.agents.concept_recognition_agent) partially_serialize() (curategpt.extract.recursive_extractor.RecursiveExtractor method) (curategpt.extract.RecursiveExtractor method) password (curategpt.wrappers.investigation.fairsharing_wrapper.FAIRSharingWrapper attribute) patches_to_oak_commands() (in module curategpt.utils.patch_utils) path (curategpt.DBAdapter attribute) (curategpt.store.db_adapter.DBAdapter attribute) (curategpt.store.DBAdapter attribute) path_expression (curategpt.wrappers.bio.bacdive_wrapper.BacDiveWrapper attribute) (curategpt.wrappers.general.json_wrapper.JSONWrapper attribute) PCA (curategpt.app.components.DimensionalityReductionOptions attribute) peek() (curategpt.ChromaDBAdapter method) (curategpt.DBAdapter method) (curategpt.store.chromadb_adapter.ChromaDBAdapter method) (curategpt.store.ChromaDBAdapter method) (curategpt.store.db_adapter.DBAdapter method) (curategpt.store.DBAdapter method) (curategpt.store.duckdb_adapter.DuckDBAdapter method) (curategpt.store.DuckDBAdapter method) (curategpt.store.in_memory_adapter.InMemoryAdapter method) pmc_full_text() (curategpt.wrappers.literature.pubmed_wrapper.PubmedWrapper method) (curategpt.wrappers.literature.PubmedWrapper method) pmc_xml() (curategpt.wrappers.literature.pubmed_wrapper.PubmedWrapper method) (curategpt.wrappers.literature.PubmedWrapper method) PMCWrapper (class in curategpt.wrappers.literature.pmc_wrapper) populate_venomx() (curategpt.ChromaDBAdapter static method) (curategpt.store.chromadb_adapter.ChromaDBAdapter static method) (curategpt.store.ChromaDBAdapter static method) (curategpt.store.duckdb_adapter.DuckDBAdapter static method) (curategpt.store.DuckDBAdapter static method) (curategpt.store.in_memory_adapter.InMemoryAdapter static method)

pr_comments() (curategpt.wrappers.general.github_wrapper.GitHubWrapper method) (in module curategpt.wrappers.general.github_wrapper) precision (curategpt.evaluation.evaluation_datamodel.ClassificationMetrics attribute) (curategpt.utils.eval_utils.Outcome attribute) predicate (curategpt.wrappers.ontology.ontology.Relationship attribute) predicate_id (curategpt.agents.mapping_agent.Mapping attribute) predict_activity_unit() (curategpt.adhoc.gocam_predictor.GOCAMPredictor method) predicted_object (curategpt.app.state.PageState attribute) predicted_value (curategpt.agents.dase_agent.PredictedFieldValue attribute) (curategpt.agents.dragon_agent.PredictedFieldValue attribute) PredictedFieldValue (class in curategpt.agents.dase_agent) (class in curategpt.agents.dragon_agent) prediction (curategpt.utils.eval_utils.Outcome attribute) prefix (curategpt.wrappers.base_wrapper.BaseWrapper attribute) (curategpt.wrappers.BaseWrapper attribute) (curategpt.wrappers.bio.bacdive_wrapper.BacDiveWrapper attribute) (curategpt.wrappers.bio.reactome_wrapper.ReactomeWrapper attribute) prefixes (curategpt.agents.concept_recognition_agent.ConceptRecognitionAgent attribute) prompt (curategpt.agents.chat_agent.ChatResponse attribute) (curategpt.agents.concept_recognition_agent.AnnotatedText attribute) (curategpt.agents.mapping_agent.MappingSet attribute) pub_object() (in module curategpt.wrappers.bio.reactome_wrapper) pubmed_wrapper (curategpt.wrappers.bio.gocam_wrapper.GOCAMWrapper attribute) (curategpt.wrappers.clinical.hpoa_wrapper.HPOAWrapper attribute) (curategpt.wrappers.clinical.maxoa_wrapper.MAXOAWrapper attribute) PubmedWrapper (class in curategpt.wrappers.literature) (class in curategpt.wrappers.literature.pubmed_wrapper) PullRequest (class in curategpt.wrappers.general.github_wrapper) pydantic_root_model (curategpt.extract.Extractor property) (curategpt.extract.extractor.Extractor property) (curategpt.Extractor property) (curategpt.store.schema_proxy.SchemaProxy property) (curategpt.store.SchemaProxy property)

Q

query_model() (in module curategpt.utils.llm_utils)

R

raise_error_if_unparsable (curategpt.extract.Extractor attribute) (curategpt.extract.extractor.Extractor attribute) (curategpt.Extractor attribute) ReactomeWrapper (class in curategpt.wrappers.bio.reactome_wrapper) recall (curategpt.evaluation.evaluation_datamodel.ClassificationMetrics attribute) (curategpt.utils.eval_utils.Outcome attribute) RecursiveExtractor (class in curategpt.extract) (class in curategpt.extract.recursive_extractor) references (curategpt.agents.chat_agent.ChatResponse attribute) RELATED_MATCH (curategpt.agents.mapping_agent.MappingPredicate attribute) Relationship (class in curategpt.wrappers.ontology.ontology) relationships (curategpt.wrappers.ontology.ontology.OntologyClass attribute) relationships_as_fields (curategpt.wrappers.ontology.ontology_wrapper.OntologyWrapper attribute) (curategpt.wrappers.ontology.OntologyWrapper attribute) relevance_factor (curategpt.agents.chat_agent.ChatAgent attribute) (curategpt.agents.ChatAgent attribute) (curategpt.agents.concept_recognition_agent.ConceptRecognitionAgent attribute) (curategpt.agents.dase_agent.DatabaseAugmentedStructuredExtraction attribute) (curategpt.agents.dragon_agent.DragonAgent attribute) (curategpt.agents.DragonAgent attribute) (curategpt.agents.mapping_agent.MappingAgent attribute) (curategpt.agents.MappingAgent attribute) remove() (curategpt.app.cart.Cart method) remove_collection() (curategpt.ChromaDBAdapter method) (curategpt.DBAdapter method) (curategpt.store.chromadb_adapter.ChromaDBAdapter method) (curategpt.store.ChromaDBAdapter method) (curategpt.store.db_adapter.DBAdapter method) (curategpt.store.DBAdapter method) (curategpt.store.duckdb_adapter.DuckDBAdapter method) (curategpt.store.DuckDBAdapter method) (curategpt.store.in_memory_adapter.InMemoryAdapter method)

remove_formatting() (in module curategpt.formatters.format_utils) replace (curategpt.agents.evidence_agent.EvidenceUpdatePolicyEnum attribute) replace_references_with_links() (in module curategpt.agents.chat_agent) repo (curategpt.wrappers.general.github_wrapper.GitHubWrapper attribute) repo_description (curategpt.wrappers.general.github_wrapper.GitHubWrapper property) report_path (curategpt.evaluation.evaluation_datamodel.Task attribute) reset() (curategpt.ChromaDBAdapter method) (curategpt.store.chromadb_adapter.ChromaDBAdapter method) (curategpt.store.ChromaDBAdapter method) response_text (curategpt.agents.mapping_agent.MappingSet attribute) results (curategpt.app.state.PageState attribute) (curategpt.evaluation.evaluation_datamodel.Task attribute) retrieve_shorthand_to_id_from_store() (curategpt.wrappers.ontology.ontology_wrapper.OntologyWrapper method) (curategpt.wrappers.ontology.OntologyWrapper method) ReusableDataWrapper (class in curategpt.wrappers.legal.reusabledata_wrapper) review() (curategpt.agents.dragon_agent.DragonAgent method) (curategpt.agents.DragonAgent method) ro_adapter (curategpt.wrappers.bio.gocam_wrapper.GOCAMWrapper attribute) root_directory (curategpt.wrappers.general.filesystem_wrapper.FilesystemWrapper attribute) run_task() (in module curategpt.evaluation.runner)

S

SAME_AS (curategpt.agents.mapping_agent.MappingPredicate attribute) schema (curategpt.store.schema_proxy.SchemaProxy property) (curategpt.store.SchemaProxy property) schema_proxy (curategpt.DBAdapter attribute) (curategpt.extract.Extractor attribute) (curategpt.extract.extractor.Extractor attribute) (curategpt.Extractor attribute) (curategpt.store.db_adapter.DBAdapter attribute) (curategpt.store.DBAdapter attribute) schema_source (curategpt.store.schema_proxy.SchemaProxy attribute) (curategpt.store.SchemaProxy attribute) SchemaProxy (class in curategpt.store) (class in curategpt.store.schema_proxy) schemaview (curategpt.extract.Extractor property) (curategpt.extract.extractor.Extractor property) (curategpt.Extractor property) (curategpt.store.schema_proxy.SchemaProxy property) (curategpt.store.SchemaProxy property) score (curategpt.agents.concept_recognition_agent.GroundingResult attribute) score_prediction() (in module curategpt.utils.eval_utils) search() (curategpt.agents.base_agent.BaseAgent method) (curategpt.ChromaDBAdapter method) (curategpt.DBAdapter method) (curategpt.store.chromadb_adapter.ChromaDBAdapter method) (curategpt.store.ChromaDBAdapter method) (curategpt.store.db_adapter.DBAdapter method) (curategpt.store.DBAdapter method) (curategpt.store.duckdb_adapter.DuckDBAdapter method) (curategpt.store.DuckDBAdapter method) (curategpt.store.in_memory_adapter.InMemoryAdapter method) (curategpt.wrappers.base_wrapper.BaseWrapper method) (curategpt.wrappers.BaseWrapper method) search_limit_multiplier (curategpt.wrappers.base_wrapper.BaseWrapper attribute) (curategpt.wrappers.BaseWrapper attribute) (curategpt.wrappers.general.filesystem_wrapper.FilesystemWrapper attribute) (curategpt.wrappers.general.google_drive_wrapper.GoogleDriveWrapper attribute) select_from_options_prompt() (in module curategpt.agents.agent_utils) selected (curategpt.app.state.PageState attribute) serialization_format (curategpt.BasicExtractor attribute) (curategpt.extract.basic_extractor.BasicExtractor attribute) (curategpt.extract.BasicExtractor attribute) (curategpt.extract.recursive_extractor.RecursiveExtractor attribute) (curategpt.extract.RecursiveExtractor attribute) serialize() (curategpt.BasicExtractor method) (curategpt.extract.basic_extractor.BasicExtractor method) (curategpt.extract.BasicExtractor method) serialize_venomx_metadata_for_adapter() (curategpt.store.Metadata method) (curategpt.store.metadata.Metadata method) service (curategpt.wrappers.general.google_drive_wrapper.GoogleDriveWrapper attribute) (curategpt.wrappers.general.gspread_wrapper.GSpreadWrapper attribute) session (curategpt.wrappers.bio.gocam_wrapper.GOCAMWrapper attribute) (curategpt.wrappers.bio.uniprot_wrapper.UniprotWrapper attribute) (curategpt.wrappers.clinical.ctgov_wrapper.ClinicalTrialsWrapper attribute) (curategpt.wrappers.general.github_wrapper.GitHubWrapper attribute) (curategpt.wrappers.investigation.ess_deepdive_wrapper.ESSDeepDiveWrapper attribute) (curategpt.wrappers.investigation.fairsharing_wrapper.FAIRSharingWrapper attribute) (curategpt.wrappers.literature.eutils_wrapper.EUtilsWrapper attribute) (curategpt.wrappers.literature.pubmed_wrapper.PubmedWrapper attribute) (curategpt.wrappers.literature.PubmedWrapper attribute)

set_cache() (curategpt.wrappers.clinical.ctgov_wrapper.ClinicalTrialsWrapper method) (curategpt.wrappers.literature.eutils_wrapper.EUtilsWrapper method) (curategpt.wrappers.literature.pubmed_wrapper.PubmedWrapper method) (curategpt.wrappers.literature.PubmedWrapper method) set_collection() (curategpt.DBAdapter method) (curategpt.store.db_adapter.DBAdapter method) (curategpt.store.DBAdapter method) set_collection_metadata() (curategpt.ChromaDBAdapter method) (curategpt.DBAdapter method) (curategpt.store.chromadb_adapter.ChromaDBAdapter method) (curategpt.store.ChromaDBAdapter method) (curategpt.store.db_adapter.DBAdapter method) (curategpt.store.DBAdapter method) (curategpt.store.duckdb_adapter.DuckDBAdapter method) (curategpt.store.DuckDBAdapter method) (curategpt.store.in_memory_adapter.InMemoryAdapter method) sheet_name (curategpt.wrappers.general.gspread_wrapper.GSpreadWrapper attribute) shorthand_to_id (curategpt.wrappers.ontology.ontology_wrapper.OntologyWrapper attribute) (curategpt.wrappers.ontology.OntologyWrapper attribute) simple_entity_object() (in module curategpt.wrappers.bio.reactome_wrapper) size (curategpt.app.cart.Cart property) skip (curategpt.agents.evidence_agent.EvidenceUpdatePolicyEnum attribute) skip_unprocessable (curategpt.wrappers.general.filesystem_wrapper.FilesystemWrapper attribute) source (curategpt.app.cart.CartItem attribute) (curategpt.evaluation.evaluation_datamodel.StratifiedCollection attribute) (curategpt.wrappers.bio.omicsdi_wrapper.OmicsDIWrapper attribute) source_collection (curategpt.evaluation.evaluation_datamodel.Task attribute) source_db_path (curategpt.evaluation.evaluation_datamodel.Task attribute) source_locator (curategpt.wrappers.base_wrapper.BaseWrapper attribute) (curategpt.wrappers.BaseWrapper attribute) source_url (curategpt.wrappers.clinical.hpoa_wrapper.HPOAWrapper attribute) (curategpt.wrappers.clinical.maxoa_wrapper.MAXOAWrapper attribute) Span (class in curategpt.agents.concept_recognition_agent) spans (curategpt.agents.concept_recognition_agent.AnnotatedText attribute) (curategpt.agents.concept_recognition_agent.GroundingResult attribute) specificity (curategpt.evaluation.evaluation_datamodel.ClassificationMetrics attribute) split_input_text (curategpt.agents.concept_recognition_agent.ConceptRecognitionAgent attribute) split_objects() (curategpt.wrappers.base_wrapper.BaseWrapper method) (curategpt.wrappers.BaseWrapper method) start (curategpt.agents.concept_recognition_agent.Span attribute) state (curategpt.wrappers.general.github_wrapper.Issue attribute) (curategpt.wrappers.general.github_wrapper.PullRequest attribute) store (curategpt.adhoc.gocam_predictor.GOCAMPredictor attribute) stores (curategpt.views.namer.Namer attribute) stratified_collection (curategpt.evaluation.evaluation_datamodel.Task attribute) StratifiedCollection (class in curategpt.evaluation.evaluation_datamodel) stratify_collection() (in module curategpt.evaluation.splitter) stratify_collection_to_store() (in module curategpt.evaluation.splitter) stream_filtered_lines() (in module curategpt.wrappers.clinical.hpoa_wrapper) (in module curategpt.wrappers.clinical.maxoa_wrapper) strict (curategpt.adhoc.gocam_predictor.GOCAMPredictor attribute) subject_id (curategpt.agents.mapping_agent.Mapping attribute) SummarizationAgent (class in curategpt.agents.summarization_agent) summarize() (curategpt.agents.summarization_agent.SummarizationAgent method) summary (curategpt.agents.concept_recognition_agent.AnnotatedText attribute)

T

target (curategpt.wrappers.ontology.ontology.Relationship attribute) target_db_path (curategpt.evaluation.evaluation_datamodel.Task attribute) Task (class in curategpt.evaluation.evaluation_datamodel) task_finished (curategpt.evaluation.evaluation_datamodel.Task attribute) task_started (curategpt.evaluation.evaluation_datamodel.Task attribute) taxon_id (curategpt.wrappers.bio.alliance_gene_wrapper.AllianceGeneWrapper attribute) (curategpt.wrappers.bio.reactome_wrapper.ReactomeWrapper attribute) (curategpt.wrappers.bio.uniprot_wrapper.UniprotWrapper attribute) term_label() (in module curategpt.wrappers.clinical.hpoa_wrapper) (in module curategpt.wrappers.clinical.maxoa_wrapper) term_object() (in module curategpt.wrappers.bio.reactome_wrapper) testing_set (curategpt.evaluation.evaluation_datamodel.StratifiedCollection attribute) testing_set_collection (curategpt.evaluation.evaluation_datamodel.StratifiedCollection attribute) text (curategpt.agents.concept_recognition_agent.Span attribute) (curategpt.extract.AnnotatedObject property) (curategpt.extract.extractor.AnnotatedObject property) text_field (curategpt.wrappers.ontology.ontology_wrapper.OntologyWrapper property) (curategpt.wrappers.ontology.OntologyWrapper property) text_lookup (curategpt.ChromaDBAdapter attribute) (curategpt.store.chromadb_adapter.ChromaDBAdapter attribute) (curategpt.store.ChromaDBAdapter attribute) (curategpt.store.duckdb_adapter.DuckDBAdapter attribute) (curategpt.store.DuckDBAdapter attribute)

text_overlap (curategpt.wrappers.base_wrapper.BaseWrapper attribute) (curategpt.wrappers.BaseWrapper attribute) (curategpt.wrappers.general.filesystem_wrapper.FilesystemWrapper attribute) title (curategpt.wrappers.general.github_wrapper.Issue attribute) (curategpt.wrappers.general.github_wrapper.PullRequest attribute) tn (curategpt.utils.eval_utils.Outcome attribute) to_dict() (curategpt.store.duckdb_result.DuckDBSearchResult method) to_json() (curategpt.store.duckdb_result.DuckDBSearchResult method) top_matches() (in module curategpt.utils.vector_algorithms) top_n_matches() (in module curategpt.utils.vector_algorithms) tp (curategpt.utils.eval_utils.Outcome attribute) training_set (curategpt.evaluation.evaluation_datamodel.StratifiedCollection attribute) training_set_collection (curategpt.evaluation.evaluation_datamodel.StratifiedCollection attribute) transform_issue() (curategpt.wrappers.general.github_wrapper.GitHubWrapper method) TRUE_NEGATIVE (curategpt.evaluation.evaluation_datamodel.ClassificationOutcome attribute) true_negatives (curategpt.evaluation.evaluation_datamodel.ClassificationMetrics attribute) TRUE_POSITIVE (curategpt.evaluation.evaluation_datamodel.ClassificationOutcome attribute) true_positives (curategpt.evaluation.evaluation_datamodel.ClassificationMetrics attribute) TSNE (curategpt.app.components.DimensionalityReductionOptions attribute) TWO_PASS (curategpt.agents.concept_recognition_agent.AnnotationMethod attribute) type (curategpt.wrappers.general.github_wrapper.Issue attribute)

U

UMAP (curategpt.app.components.DimensionalityReductionOptions attribute) uncited_references (curategpt.agents.chat_agent.ChatResponse attribute) UniprotWrapper (class in curategpt.wrappers.bio.uniprot_wrapper) UNKNOWN (curategpt.agents.mapping_agent.MappingPredicate attribute) unwrap_object() (curategpt.wrappers.base_wrapper.BaseWrapper method) (curategpt.wrappers.BaseWrapper method) (curategpt.wrappers.ontology.ontology_wrapper.OntologyWrapper method) (curategpt.wrappers.ontology.OntologyWrapper method) unwrap_objects() (curategpt.wrappers.ontology.ontology_wrapper.OntologyWrapper method) (curategpt.wrappers.ontology.OntologyWrapper method) update() (curategpt.ChromaDBAdapter method) (curategpt.DBAdapter method) (curategpt.store.chromadb_adapter.ChromaDBAdapter method) (curategpt.store.ChromaDBAdapter method) (curategpt.store.db_adapter.DBAdapter method) (curategpt.store.DBAdapter method) (curategpt.store.duckdb_adapter.DuckDBAdapter method) (curategpt.store.DuckDBAdapter method) (curategpt.store.in_memory_adapter.InMemoryAdapter method) update_collection_metadata() (curategpt.ChromaDBAdapter method) (curategpt.DBAdapter method) (curategpt.store.chromadb_adapter.ChromaDBAdapter method) (curategpt.store.ChromaDBAdapter method) (curategpt.store.db_adapter.DBAdapter method) (curategpt.store.DBAdapter method) (curategpt.store.duckdb_adapter.DuckDBAdapter method) (curategpt.store.DuckDBAdapter method) (curategpt.store.in_memory_adapter.InMemoryAdapter method)

update_or_create_venomx() (curategpt.store.duckdb_adapter.DuckDBAdapter method) (curategpt.store.DuckDBAdapter method) upload() (curategpt.agents.huggingface_agent.HuggingFaceAgent method) upload_duckdb() (curategpt.agents.huggingface_agent.HuggingFaceAgent method) upsert() (curategpt.ChromaDBAdapter method) (curategpt.DBAdapter method) (curategpt.store.chromadb_adapter.ChromaDBAdapter method) (curategpt.store.ChromaDBAdapter method) (curategpt.store.db_adapter.DBAdapter method) (curategpt.store.DBAdapter method) (curategpt.store.duckdb_adapter.DuckDBAdapter method) (curategpt.store.DuckDBAdapter method) (curategpt.store.in_memory_adapter.InMemoryAdapter method) user (curategpt.wrappers.general.github_wrapper.Comment attribute) (curategpt.wrappers.general.github_wrapper.Issue attribute) (curategpt.wrappers.general.github_wrapper.PullRequest attribute) (curategpt.wrappers.investigation.fairsharing_wrapper.FAIRSharingWrapper attribute)

V

validation_set (curategpt.evaluation.evaluation_datamodel.StratifiedCollection attribute) validation_set_collection (curategpt.evaluation.evaluation_datamodel.StratifiedCollection attribute) vec_dimension (curategpt.store.duckdb_adapter.DuckDBAdapter attribute) (curategpt.store.DuckDBAdapter attribute)

vectors_to_fig() (in module curategpt.app.components) venomx (curategpt.store.Metadata attribute) (curategpt.store.metadata.Metadata attribute)

W

WEIGHTED (curategpt.evaluation.evaluation_datamodel.AggregationMethod attribute) where (curategpt.wrappers.clinical.ctgov_wrapper.ClinicalTrialsWrapper attribute) (curategpt.wrappers.literature.pubmed_wrapper.PubmedWrapper attribute) (curategpt.wrappers.literature.PubmedWrapper attribute) WikipediaWrapper (class in curategpt.wrappers.literature) (class in curategpt.wrappers.literature.wikipedia_wrapper)

working_directory (curategpt.evaluation.evaluation_datamodel.Task attribute) worksheet_name (curategpt.wrappers.general.gspread_wrapper.GSpreadWrapper attribute) wrap_object() (curategpt.wrappers.base_wrapper.BaseWrapper method) (curategpt.wrappers.BaseWrapper method) (curategpt.wrappers.bio.bacdive_wrapper.BacDiveWrapper method) (curategpt.wrappers.general.json_wrapper.JSONWrapper method) (curategpt.wrappers.ontology.oboformat_wrapper.OBOFormatWrapper method)