Index

A

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

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

B

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

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

C

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

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

D

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

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

E

ef_construction (curate_gpt.store.db_metadata.DBSettings attribute) (curate_gpt.store.duckdb_adapter.DuckDBAdapter attribute) (curate_gpt.store.DuckDBAdapter attribute) ef_search (curate_gpt.store.db_metadata.DBSettings attribute) (curate_gpt.store.duckdb_adapter.DuckDBAdapter attribute) (curate_gpt.store.DuckDBAdapter attribute) elements (curate_gpt.wrappers.ontology.ontology.Ontology attribute) email (curate_gpt.wrappers.literature.pubmed_wrapper.PubmedWrapper attribute) (curate_gpt.wrappers.literature.PubmedWrapper attribute) embedding_model_name (curate_gpt.evaluation.evaluation_datamodel.Task attribute) embeddings (curate_gpt.store.duckdb_result.DuckDBSearchResult attribute) end (curate_gpt.agents.concept_recognition_agent.Span attribute) ESSDeepDiveWrapper (class in curate_gpt.wrappers.investigation.ess_deepdive_wrapper) estimate_num_tokens() (in module curate_gpt.utils.tokens) eutils_client (curate_gpt.wrappers.literature.eutils_wrapper.EUtilsWrapper attribute) (curate_gpt.wrappers.literature.pubmed_wrapper.PubmedWrapper attribute) (curate_gpt.wrappers.literature.PubmedWrapper attribute) eutils_db (curate_gpt.wrappers.clinical.clinvar_wrapper.ClinVarWrapper attribute) (curate_gpt.wrappers.investigation.ncbi_bioproject_wrapper.NCBIBioprojectWrapper attribute) (curate_gpt.wrappers.investigation.ncbi_biosample_wrapper.NCBIBiosampleWrapper attribute) (curate_gpt.wrappers.literature.eutils_wrapper.EUtilsWrapper attribute) (curate_gpt.wrappers.literature.pmc_wrapper.PMCWrapper attribute) EUtilsWrapper (class in curate_gpt.wrappers.literature.eutils_wrapper) evaluate() (curate_gpt.evaluation.base_evaluator.BaseEvaluator method) (curate_gpt.evaluation.dae_evaluator.DatabaseAugmentedCompletionEvaluator method) evaluate_object() (curate_gpt.evaluation.base_evaluator.BaseEvaluator method) (curate_gpt.evaluation.dae_evaluator.DatabaseAugmentedCompletionEvaluator method) evaluate_predictions() (in module curate_gpt.evaluation.calc_statistics) evidence_update_policy (curate_gpt.agents.evidence_agent.EvidenceAgent attribute) (curate_gpt.agents.EvidenceAgent attribute) EvidenceAgent (class in curate_gpt.agents) (class in curate_gpt.agents.evidence_agent) EvidenceUpdatePolicyEnum (class in curate_gpt.agents.evidence_agent) executed_on (curate_gpt.evaluation.evaluation_datamodel.Task attribute) expand_publications (curate_gpt.wrappers.clinical.hpoa_wrapper.HPOAWrapper attribute) (curate_gpt.wrappers.clinical.maxoa_wrapper.MAXOAWrapper attribute) expected (curate_gpt.utils.eval_utils.Outcome attribute)

external_search() (curate_gpt.wrappers.base_wrapper.BaseWrapper method) (curate_gpt.wrappers.BaseWrapper method) (curate_gpt.wrappers.bio.omicsdi_wrapper.OmicsDIWrapper method) (curate_gpt.wrappers.clinical.ctgov_wrapper.ClinicalTrialsWrapper method) (curate_gpt.wrappers.general.github_wrapper.GitHubWrapper method) (curate_gpt.wrappers.general.google_drive_wrapper.GoogleDriveWrapper method) (curate_gpt.wrappers.investigation.jgi_wrapper.JGIWrapper method) (curate_gpt.wrappers.literature.eutils_wrapper.EUtilsWrapper method) (curate_gpt.wrappers.literature.pubmed_wrapper.PubmedWrapper method) (curate_gpt.wrappers.literature.PubmedWrapper method) (curate_gpt.wrappers.literature.wikipedia_wrapper.WikipediaWrapper method) (curate_gpt.wrappers.literature.WikipediaWrapper method) (curate_gpt.wrappers.ontology.ontology_wrapper.OntologyWrapper method) (curate_gpt.wrappers.ontology.OntologyWrapper method) extract() (curate_gpt.agents.dase_agent.DatabaseAugmentedStructuredExtraction method) (curate_gpt.BasicExtractor method) (curate_gpt.extract.basic_extractor.BasicExtractor method) (curate_gpt.extract.BasicExtractor method) (curate_gpt.extract.Extractor method) (curate_gpt.extract.extractor.Extractor method) (curate_gpt.extract.openai_extractor.OpenAIExtractor method) (curate_gpt.extract.OpenAIExtractor method) (curate_gpt.extract.recursive_extractor.RecursiveExtractor method) (curate_gpt.extract.RecursiveExtractor method) (curate_gpt.Extractor method) extract_all_text() (in module curate_gpt.wrappers.literature.pubmed_wrapper) extract_concepts_from_text() (curate_gpt.wrappers.base_wrapper.BaseWrapper method) (curate_gpt.wrappers.BaseWrapper method) extract_text_from_xml() (in module curate_gpt.wrappers.literature.pubmed_wrapper) Extractor (class in curate_gpt) (class in curate_gpt.extract) (class in curate_gpt.extract.extractor) extractor (curate_gpt.adhoc.gocam_predictor.GOCAMPredictor attribute) (curate_gpt.agents.base_agent.BaseAgent attribute) (curate_gpt.app.state.ApplicationState attribute) (curate_gpt.evaluation.evaluation_datamodel.Task attribute) (curate_gpt.wrappers.base_wrapper.BaseWrapper attribute) (curate_gpt.wrappers.BaseWrapper attribute)

F

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

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

G

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

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

H

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

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

I

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

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

J

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

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

K

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

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

L

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

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

M

M (curate_gpt.store.db_metadata.DBSettings attribute) (curate_gpt.store.duckdb_adapter.DuckDBAdapter attribute) (curate_gpt.store.DuckDBAdapter attribute) MACRO (curate_gpt.evaluation.evaluation_datamodel.AggregationMethod attribute) main_class (curate_gpt.agents.bootstrap_agent.KnowledgeBaseSpecification attribute) map_object() (curate_gpt.views.namer.Namer method) map_reference() (curate_gpt.views.namer.Namer method) Mapping (class in curate_gpt.agents.mapping_agent) MappingAgent (class in curate_gpt.agents) (class in curate_gpt.agents.mapping_agent) MappingPredicate (class in curate_gpt.agents.mapping_agent) mappings (curate_gpt.agents.mapping_agent.MappingSet attribute) MappingSet (class in curate_gpt.agents.mapping_agent) match() (curate_gpt.agents.mapping_agent.MappingAgent method) (curate_gpt.agents.MappingAgent method) match_collections() (in module curate_gpt.utils.vectordb_operations) matches() (curate_gpt.ChromaDBAdapter method) (curate_gpt.DBAdapter method) (curate_gpt.store.chromadb_adapter.ChromaDBAdapter method) (curate_gpt.store.ChromaDBAdapter method) (curate_gpt.store.db_adapter.DBAdapter method) (curate_gpt.store.DBAdapter method) (curate_gpt.store.duckdb_adapter.DuckDBAdapter method) (curate_gpt.store.DuckDBAdapter method) (curate_gpt.store.in_memory_adapter.InMemoryAdapter method) max_background_document_size (curate_gpt.agents.dase_agent.DatabaseAugmentedStructuredExtraction attribute) (curate_gpt.agents.dragon_agent.DragonAgent attribute) (curate_gpt.agents.DragonAgent attribute) max_text_length (curate_gpt.wrappers.base_wrapper.BaseWrapper attribute) (curate_gpt.wrappers.BaseWrapper attribute) (curate_gpt.wrappers.general.filesystem_wrapper.FilesystemWrapper attribute) max_tokens (curate_gpt.extract.openai_extractor.OpenAIExtractor attribute) (curate_gpt.extract.OpenAIExtractor attribute) max_tokens_by_model() (in module curate_gpt.utils.tokens) maxo_ont_adapter() (in module curate_gpt.wrappers.clinical.maxoa_wrapper) MAXOAWrapper (class in curate_gpt.wrappers.clinical.maxoa_wrapper) MediaDiveWrapper (class in curate_gpt.wrappers.bio.mediadive_wrapper) metadata (curate_gpt.app.cart.CartItem attribute) (curate_gpt.store.in_memory_adapter.Collection attribute) metadatas (curate_gpt.store.duckdb_result.DuckDBSearchResult attribute) method (curate_gpt.evaluation.evaluation_datamodel.Task attribute) MICRO (curate_gpt.evaluation.evaluation_datamodel.AggregationMethod attribute) mmr_diversified_search() (in module curate_gpt.utils.vector_algorithms) model (curate_gpt.extract.Extractor property) (curate_gpt.extract.extractor.Extractor property) (curate_gpt.extract.openai_extractor.OpenAIExtractor attribute) (curate_gpt.extract.OpenAIExtractor attribute) (curate_gpt.Extractor property) (curate_gpt.store.CollectionMetadata attribute) (curate_gpt.store.db_metadata.DBSettings attribute) (curate_gpt.store.metadata.CollectionMetadata attribute) model_computed_fields (curate_gpt.agents.bootstrap_agent.KnowledgeBaseSpecification attribute) (curate_gpt.agents.chat_agent.ChatResponse attribute) (curate_gpt.agents.concept_recognition_agent.AnnotatedText attribute) (curate_gpt.agents.concept_recognition_agent.GroundingResult attribute) (curate_gpt.agents.concept_recognition_agent.Span attribute) (curate_gpt.agents.dase_agent.PredictedFieldValue attribute) (curate_gpt.agents.dragon_agent.PredictedFieldValue attribute) (curate_gpt.agents.mapping_agent.Mapping attribute) (curate_gpt.agents.mapping_agent.MappingSet attribute) (curate_gpt.app.cart.Cart attribute) (curate_gpt.app.cart.CartItem attribute) (curate_gpt.evaluation.evaluation_datamodel.ClassificationMetrics attribute) (curate_gpt.evaluation.evaluation_datamodel.StratifiedCollection attribute) (curate_gpt.evaluation.evaluation_datamodel.Task attribute) (curate_gpt.extract.AnnotatedObject attribute) (curate_gpt.extract.extractor.AnnotatedObject attribute) (curate_gpt.store.CollectionMetadata attribute) (curate_gpt.store.db_metadata.DBSettings attribute) (curate_gpt.store.duckdb_result.DuckDBSearchResult attribute) (curate_gpt.store.in_memory_adapter.Collection attribute) (curate_gpt.store.in_memory_adapter.CollectionIndex attribute) (curate_gpt.store.metadata.CollectionMetadata attribute) (curate_gpt.utils.eval_utils.Outcome attribute) (curate_gpt.wrappers.general.github_wrapper.Comment attribute) (curate_gpt.wrappers.general.github_wrapper.Issue attribute) (curate_gpt.wrappers.general.github_wrapper.PullRequest attribute) (curate_gpt.wrappers.ontology.ontology.Ontology attribute) (curate_gpt.wrappers.ontology.ontology.OntologyClass attribute) (curate_gpt.wrappers.ontology.ontology.Relationship attribute) model_config (curate_gpt.agents.bootstrap_agent.KnowledgeBaseSpecification attribute) (curate_gpt.agents.chat_agent.ChatResponse attribute) (curate_gpt.agents.concept_recognition_agent.AnnotatedText attribute) (curate_gpt.agents.concept_recognition_agent.GroundingResult attribute) (curate_gpt.agents.concept_recognition_agent.Span attribute) (curate_gpt.agents.dase_agent.PredictedFieldValue attribute) (curate_gpt.agents.dragon_agent.PredictedFieldValue attribute) (curate_gpt.agents.mapping_agent.Mapping attribute) (curate_gpt.agents.mapping_agent.MappingSet attribute) (curate_gpt.app.cart.Cart attribute) (curate_gpt.app.cart.CartItem attribute) (curate_gpt.BasicExtractor attribute) (curate_gpt.evaluation.evaluation_datamodel.ClassificationMetrics attribute) (curate_gpt.evaluation.evaluation_datamodel.StratifiedCollection attribute) (curate_gpt.evaluation.evaluation_datamodel.Task attribute) (curate_gpt.extract.AnnotatedObject attribute) (curate_gpt.extract.basic_extractor.BasicExtractor attribute) (curate_gpt.extract.BasicExtractor attribute) (curate_gpt.extract.extractor.AnnotatedObject attribute) (curate_gpt.store.CollectionMetadata attribute) (curate_gpt.store.db_metadata.DBSettings attribute) (curate_gpt.store.duckdb_result.DuckDBSearchResult attribute) (curate_gpt.store.in_memory_adapter.Collection attribute) (curate_gpt.store.in_memory_adapter.CollectionIndex attribute) (curate_gpt.store.metadata.CollectionMetadata attribute) (curate_gpt.store.schema_proxy.SchemaProxy attribute) (curate_gpt.store.SchemaProxy attribute) (curate_gpt.utils.eval_utils.Outcome attribute) (curate_gpt.wrappers.general.github_wrapper.Comment attribute) (curate_gpt.wrappers.general.github_wrapper.Issue attribute) (curate_gpt.wrappers.general.github_wrapper.PullRequest attribute) (curate_gpt.wrappers.ontology.ontology.Ontology attribute) (curate_gpt.wrappers.ontology.ontology.OntologyClass attribute) (curate_gpt.wrappers.ontology.ontology.Relationship attribute) model_fields (curate_gpt.agents.bootstrap_agent.KnowledgeBaseSpecification attribute) (curate_gpt.agents.chat_agent.ChatResponse attribute) (curate_gpt.agents.concept_recognition_agent.AnnotatedText attribute) (curate_gpt.agents.concept_recognition_agent.GroundingResult attribute) (curate_gpt.agents.concept_recognition_agent.Span attribute) (curate_gpt.agents.dase_agent.PredictedFieldValue attribute) (curate_gpt.agents.dragon_agent.PredictedFieldValue attribute) (curate_gpt.agents.mapping_agent.Mapping attribute) (curate_gpt.agents.mapping_agent.MappingSet attribute) (curate_gpt.app.cart.Cart attribute) (curate_gpt.app.cart.CartItem attribute) (curate_gpt.evaluation.evaluation_datamodel.ClassificationMetrics attribute) (curate_gpt.evaluation.evaluation_datamodel.StratifiedCollection attribute) (curate_gpt.evaluation.evaluation_datamodel.Task attribute) (curate_gpt.extract.AnnotatedObject attribute) (curate_gpt.extract.extractor.AnnotatedObject attribute) (curate_gpt.store.CollectionMetadata attribute) (curate_gpt.store.db_metadata.DBSettings attribute) (curate_gpt.store.duckdb_result.DuckDBSearchResult attribute) (curate_gpt.store.in_memory_adapter.Collection attribute) (curate_gpt.store.in_memory_adapter.CollectionIndex attribute) (curate_gpt.store.metadata.CollectionMetadata attribute) (curate_gpt.utils.eval_utils.Outcome attribute) (curate_gpt.wrappers.general.github_wrapper.Comment attribute) (curate_gpt.wrappers.general.github_wrapper.Issue attribute) (curate_gpt.wrappers.general.github_wrapper.PullRequest attribute) (curate_gpt.wrappers.ontology.ontology.Ontology attribute) (curate_gpt.wrappers.ontology.ontology.OntologyClass attribute) (curate_gpt.wrappers.ontology.ontology.Relationship attribute)

model_name (curate_gpt.adhoc.gocam_predictor.GOCAMPredictor attribute) (curate_gpt.BasicExtractor attribute) (curate_gpt.evaluation.evaluation_datamodel.Task attribute) (curate_gpt.extract.basic_extractor.BasicExtractor attribute) (curate_gpt.extract.BasicExtractor attribute) (curate_gpt.extract.Extractor attribute) (curate_gpt.extract.extractor.Extractor attribute) (curate_gpt.extract.recursive_extractor.RecursiveExtractor attribute) (curate_gpt.extract.RecursiveExtractor attribute) (curate_gpt.Extractor attribute) module curate_gpt curate_gpt.adhoc curate_gpt.adhoc.gocam_predictor curate_gpt.agents curate_gpt.agents.agent_utils curate_gpt.agents.base_agent curate_gpt.agents.bootstrap_agent curate_gpt.agents.chat_agent curate_gpt.agents.concept_recognition_agent curate_gpt.agents.dase_agent curate_gpt.agents.dragon_agent curate_gpt.agents.evidence_agent curate_gpt.agents.huggingface_agent curate_gpt.agents.mapping_agent curate_gpt.agents.summarization_agent curate_gpt.app curate_gpt.app.app curate_gpt.app.cart curate_gpt.app.components curate_gpt.app.helper curate_gpt.app.state curate_gpt.cli curate_gpt.conf curate_gpt.conf.prompts curate_gpt.evaluation curate_gpt.evaluation.base_evaluator curate_gpt.evaluation.calc_statistics curate_gpt.evaluation.dae_evaluator curate_gpt.evaluation.evaluation_datamodel curate_gpt.evaluation.runner curate_gpt.evaluation.splitter curate_gpt.extract curate_gpt.extract.basic_extractor curate_gpt.extract.extractor curate_gpt.extract.openai_extractor curate_gpt.extract.recursive_extractor curate_gpt.formatters curate_gpt.formatters.format_utils curate_gpt.store curate_gpt.store.chromadb_adapter curate_gpt.store.db_adapter curate_gpt.store.db_metadata curate_gpt.store.duckdb_adapter curate_gpt.store.duckdb_result curate_gpt.store.in_memory_adapter curate_gpt.store.metadata curate_gpt.store.schema_proxy curate_gpt.store.vocab curate_gpt.utils curate_gpt.utils.eval_utils curate_gpt.utils.llm_utils curate_gpt.utils.patch_utils curate_gpt.utils.search curate_gpt.utils.tokens curate_gpt.utils.vector_algorithms curate_gpt.utils.vectordb_operations curate_gpt.views curate_gpt.views.namer curate_gpt.wrappers curate_gpt.wrappers.base_wrapper curate_gpt.wrappers.bio curate_gpt.wrappers.bio.alliance_gene_wrapper curate_gpt.wrappers.bio.bacdive_wrapper curate_gpt.wrappers.bio.gocam_wrapper curate_gpt.wrappers.bio.mediadive_wrapper curate_gpt.wrappers.bio.omicsdi_wrapper curate_gpt.wrappers.bio.reactome_wrapper curate_gpt.wrappers.bio.uniprot_wrapper curate_gpt.wrappers.clinical curate_gpt.wrappers.clinical.clinvar_wrapper curate_gpt.wrappers.clinical.ctgov_wrapper curate_gpt.wrappers.clinical.hpoa_by_pub_wrapper curate_gpt.wrappers.clinical.hpoa_wrapper curate_gpt.wrappers.clinical.maxoa_wrapper curate_gpt.wrappers.general curate_gpt.wrappers.general.filesystem_wrapper curate_gpt.wrappers.general.github_wrapper curate_gpt.wrappers.general.google_drive_wrapper curate_gpt.wrappers.general.gspread_wrapper curate_gpt.wrappers.general.json_wrapper curate_gpt.wrappers.general.linkml_schema_wrapper curate_gpt.wrappers.investigation curate_gpt.wrappers.investigation.ess_deepdive_wrapper curate_gpt.wrappers.investigation.fairsharing_wrapper curate_gpt.wrappers.investigation.jgi_wrapper curate_gpt.wrappers.investigation.ncbi_bioproject_wrapper curate_gpt.wrappers.investigation.ncbi_biosample_wrapper curate_gpt.wrappers.investigation.nmdc_wrapper curate_gpt.wrappers.legal curate_gpt.wrappers.legal.reusabledata_wrapper curate_gpt.wrappers.literature curate_gpt.wrappers.literature.bioc_wrapper curate_gpt.wrappers.literature.eutils_wrapper curate_gpt.wrappers.literature.pmc_wrapper curate_gpt.wrappers.literature.pubmed_wrapper curate_gpt.wrappers.literature.wikipedia_wrapper curate_gpt.wrappers.ontology curate_gpt.wrappers.ontology.bioportal_wrapper curate_gpt.wrappers.ontology.oboformat_wrapper curate_gpt.wrappers.ontology.ontology curate_gpt.wrappers.ontology.ontology_wrapper

N

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

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

O

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

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

P

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

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

Q

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

R

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

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

S

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

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

T

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

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

U

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

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

V

validation_set (curate_gpt.evaluation.evaluation_datamodel.StratifiedCollection attribute) validation_set_collection (curate_gpt.evaluation.evaluation_datamodel.StratifiedCollection attribute)

vec_dimension (curate_gpt.store.duckdb_adapter.DuckDBAdapter attribute) (curate_gpt.store.DuckDBAdapter attribute) vectors_to_fig() (in module curate_gpt.app.components)

W

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

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