Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W A ACTIVATES (ExposoGraph.models.EdgeType attribute) activation_edges (ExposoGraph.graph_analysis.MetabolismChain property) activity_score (ExposoGraph.graph_analysis.VariantImpact attribute) add_edge() (ExposoGraph.engine.GraphEngine method) add_node() (ExposoGraph.engine.GraphEngine method) adduct_edges (ExposoGraph.graph_analysis.MetabolismChain property) ALIAS (ExposoGraph.models.MatchStatus attribute) ALL (ExposoGraph.config.GraphVisibility attribute) all_chemicals (ExposoGraph.db_clients.iarc.IARCClassifier property) all_shortest_paths() (in module ExposoGraph.graph_analysis) apply_viewer_filters() (in module ExposoGraph.viewer_dash) AppMode (class in ExposoGraph.config) APPROVED (ExposoGraph.models.CurationStatus attribute) ArchitectureInventoryGroup (class in ExposoGraph.example_graphs) ArchitectureSummary (class in ExposoGraph.example_graphs) B BREADTHFIRST (ExposoGraph.cytoscape_adapter.ViewerLayoutMode attribute) build_androgen_module_engine() (in module ExposoGraph.example_graphs) build_androgen_module_graph() (in module ExposoGraph.example_graphs) build_cytoscape_bundle() (in module ExposoGraph.cytoscape_adapter) build_cytoscape_elements() (in module ExposoGraph.cytoscape_adapter) build_cytoscape_metadata() (in module ExposoGraph.cytoscape_adapter) build_default_grounding_index() (in module ExposoGraph.grounding) build_detail_payload() (in module ExposoGraph.viewer_dash) build_full_legends_architecture_summary() (in module ExposoGraph.example_graphs) build_full_legends_engine() (in module ExposoGraph.example_graphs) build_full_legends_graph() (in module ExposoGraph.example_graphs) build_full_panel() (in module ExposoGraph.reference_data) build_graph_grounding_index() (in module ExposoGraph.grounding) build_iarc_grounding_index() (in module ExposoGraph.grounding) build_tier1_panel() (in module ExposoGraph.reference_data) build_tier2_panel() (in module ExposoGraph.reference_data) bundle_to_html_string() (in module ExposoGraph.exporter) C CANONICAL (ExposoGraph.models.MatchStatus attribute) canonical_id (ExposoGraph.grounding.GroundingMatch attribute) canonical_label (ExposoGraph.grounding.GroundingMatch attribute) canonical_namespace (ExposoGraph.grounding.GroundingMatch attribute) CARCINOGEN (ExposoGraph.models.NodeType attribute) carcinogen_id (ExposoGraph.graph_analysis.MetabolismChain attribute) centrality() (in module ExposoGraph.graph_analysis) chemical_id (ExposoGraph.db_clients.ctd.ChemicalGeneInteraction attribute) chemical_name (ExposoGraph.db_clients.ctd.ChemicalGeneInteraction attribute) ChemicalGeneInteraction (class in ExposoGraph.db_clients.ctd) CIRCLE (ExposoGraph.cytoscape_adapter.ViewerLayoutMode attribute) classify() (ExposoGraph.db_clients.iarc.IARCClassifier method) clear() (ExposoGraph.engine.GraphEngine method) close() (ExposoGraph.storage.GraphRepository method) compute_edge_weights() (in module ExposoGraph.graph_analysis) compute_viewer_positions() (in module ExposoGraph.cytoscape_adapter) connection (ExposoGraph.storage.GraphRepository property) COSE (ExposoGraph.cytoscape_adapter.ViewerLayoutMode attribute) create_dash_viewer_app() (in module ExposoGraph.viewer_dash) created_at (ExposoGraph.storage.GraphRevisionSummary attribute) CTDClient (class in ExposoGraph.db_clients.ctd) CurationConfidence (class in ExposoGraph.models) CurationRecord (class in ExposoGraph.models) CurationStatus (class in ExposoGraph.models) CUSTOM (ExposoGraph.models.EdgeType attribute) (ExposoGraph.models.MatchStatus attribute) CytoscapeBundle (class in ExposoGraph.cytoscape_adapter) D detox_edges (ExposoGraph.graph_analysis.MetabolismChain property) DETOXIFIES (ExposoGraph.models.EdgeType attribute) DNA_ADDUCT (ExposoGraph.models.NodeType attribute) downstream_adduct_count (ExposoGraph.graph_analysis.VariantImpact attribute) downstream_repair_count (ExposoGraph.graph_analysis.VariantImpact attribute) DRAFT (ExposoGraph.models.CurationStatus attribute) E Edge (class in ExposoGraph.models) edge_count (ExposoGraph.engine.GraphEngine property) (ExposoGraph.storage.GraphRevisionSummary attribute) edge_type_counts (ExposoGraph.viewer_dash.ViewerState attribute) edges (ExposoGraph.graph_analysis.MetabolismChain attribute) EdgeType (class in ExposoGraph.models) elements (ExposoGraph.cytoscape_adapter.CytoscapeBundle attribute) (ExposoGraph.viewer_dash.ViewerState attribute) ENCODES (ExposoGraph.models.EdgeType attribute) ensure_viewer_bundle() (in module ExposoGraph.exporter) ENZYME (ExposoGraph.models.NodeType attribute) EXPLORATORY (ExposoGraph.config.GraphMode attribute) EXPLORATORY_ONLY (ExposoGraph.config.GraphVisibility attribute) export_viewer_bundle() (in module ExposoGraph.exporter) ExposoGraph.cytoscape_adapter module ExposoGraph.db_clients.ctd module ExposoGraph.db_clients.iarc module ExposoGraph.db_clients.kegg module ExposoGraph.exporter module ExposoGraph.graph_analysis module ExposoGraph.graph_filters module ExposoGraph.grounding module ExposoGraph.llm_extractor.EXAMPLE_INPUT (built-in variable) ExposoGraph.llm_extractor.SYSTEM_PROMPT (built-in variable) ExposoGraph.reference_data.ACTIVITY_SCORE_METADATA (built-in variable) ExposoGraph.reference_data.ACTIVITY_SCORES (built-in variable) ExposoGraph.reference_data.CURATION_SOURCE_MANIFEST (built-in variable) ExposoGraph.reference_data.REFERENCE_KEGG_PATHWAYS (built-in variable) ExposoGraph.reference_data.TIER1_GENES (built-in variable) ExposoGraph.reference_data.TIER2_GENES (built-in variable) ExposoGraph.seeder module ExposoGraph.viewer_dash module EXPRESSED_IN (ExposoGraph.models.EdgeType attribute) extra_fields (ExposoGraph.grounding.GroundingMatch attribute) extract_graph() (in module ExposoGraph.llm_extractor) F filter_knowledge_graph() (in module ExposoGraph.graph_filters) filtered_engine() (in module ExposoGraph.graph_filters) find_genes() (ExposoGraph.db_clients.kegg.KEGGClient method) FORMS_ADDUCT (ExposoGraph.models.EdgeType attribute) from_dict() (ExposoGraph.cytoscape_adapter.CytoscapeBundle class method) G GENE (ExposoGraph.models.NodeType attribute) gene_id (ExposoGraph.db_clients.ctd.ChemicalGeneInteraction attribute) (ExposoGraph.db_clients.kegg.KEGGGene attribute) (ExposoGraph.graph_analysis.VariantImpact attribute) gene_symbol (ExposoGraph.db_clients.ctd.ChemicalGeneInteraction attribute) generate_id() (ExposoGraph.models.Node class method) genes (ExposoGraph.db_clients.kegg.KEGGPathway attribute) get_activity_score_metadata() (in module ExposoGraph.reference_data) get_activity_score_references() (in module ExposoGraph.reference_data) get_activity_scores() (in module ExposoGraph.reference_data) get_app_mode() (in module ExposoGraph.config) get_chemical_gene_interactions() (ExposoGraph.db_clients.ctd.CTDClient method) get_entry() (ExposoGraph.db_clients.iarc.IARCClassifier method) get_gene() (ExposoGraph.db_clients.kegg.KEGGClient method) get_gene_interactions() (ExposoGraph.db_clients.ctd.CTDClient method) get_latest_revision() (ExposoGraph.storage.GraphRepository method) get_node() (ExposoGraph.engine.GraphEngine method) get_pathway() (ExposoGraph.db_clients.kegg.KEGGClient method) get_revision() (ExposoGraph.storage.GraphRepository method) graph_json (ExposoGraph.storage.GraphRevision attribute) graph_key (ExposoGraph.storage.GraphRevisionSummary attribute) graph_name (ExposoGraph.storage.GraphRevisionSummary attribute) graph_visibility_label() (in module ExposoGraph.graph_filters) GraphEngine (class in ExposoGraph.engine) GraphMode (class in ExposoGraph.config) GraphRepository (class in ExposoGraph.storage) GraphRevision (class in ExposoGraph.storage) GraphRevisionSummary (class in ExposoGraph.storage) GraphVisibility (class in ExposoGraph.config) ground_knowledge_graph() (in module ExposoGraph.grounding) ground_node() (in module ExposoGraph.grounding) GroundingMatch (class in ExposoGraph.grounding) GROUP_1 (ExposoGraph.db_clients.iarc.IARCGroup attribute) GROUP_2A (ExposoGraph.db_clients.iarc.IARCGroup attribute) GROUP_2B (ExposoGraph.db_clients.iarc.IARCGroup attribute) GROUP_3 (ExposoGraph.db_clients.iarc.IARCGroup attribute) H HIGH (ExposoGraph.models.CurationConfidence attribute) html (ExposoGraph.storage.GraphRevision attribute) I IARCClassifier (class in ExposoGraph.db_clients.iarc) IARCGroup (class in ExposoGraph.db_clients.iarc) IMPORTED (ExposoGraph.models.RecordOrigin attribute) IN_REVIEW (ExposoGraph.models.CurationStatus attribute) INDUCES (ExposoGraph.models.EdgeType attribute) INHIBITS (ExposoGraph.models.EdgeType attribute) interaction (ExposoGraph.db_clients.ctd.ChemicalGeneInteraction attribute) K KEGGClient (class in ExposoGraph.db_clients.kegg) KEGGGene (class in ExposoGraph.db_clients.kegg) KEGGPathway (class in ExposoGraph.db_clients.kegg) KnowledgeGraph (class in ExposoGraph.models) L launch_dash_viewer() (in module ExposoGraph.viewer_dash) layout (ExposoGraph.cytoscape_adapter.CytoscapeBundle attribute) (ExposoGraph.viewer_dash.ViewerState attribute) list_by_category() (ExposoGraph.db_clients.iarc.IARCClassifier method) list_by_group() (ExposoGraph.db_clients.iarc.IARCClassifier method) list_graphs() (ExposoGraph.storage.GraphRepository method) list_pathway_genes() (ExposoGraph.db_clients.kegg.KEGGClient method) list_revisions() (ExposoGraph.storage.GraphRepository method) LLM (ExposoGraph.models.RecordOrigin attribute) load() (ExposoGraph.engine.GraphEngine method) load_cytoscape_bundle() (in module ExposoGraph.cytoscape_adapter) load_viewer_positions() (in module ExposoGraph.cytoscape_adapter) LOCAL (ExposoGraph.config.AppMode attribute) LOW (ExposoGraph.models.CurationConfidence attribute) M match_status (ExposoGraph.grounding.GroundingMatch attribute) MatchStatus (class in ExposoGraph.models) MEDIUM (ExposoGraph.models.CurationConfidence attribute) merge() (ExposoGraph.engine.GraphEngine method) metabolism_chain() (in module ExposoGraph.graph_analysis) MetabolismChain (class in ExposoGraph.graph_analysis) METABOLITE (ExposoGraph.models.NodeType attribute) metadata (ExposoGraph.cytoscape_adapter.CytoscapeBundle attribute) model_config (ExposoGraph.models.CurationRecord attribute) (ExposoGraph.models.Edge attribute) (ExposoGraph.models.KnowledgeGraph attribute) (ExposoGraph.models.Node attribute) (ExposoGraph.models.ProvenanceRecord attribute) module ExposoGraph.cytoscape_adapter ExposoGraph.db_clients.ctd ExposoGraph.db_clients.iarc ExposoGraph.db_clients.kegg ExposoGraph.exporter ExposoGraph.graph_analysis ExposoGraph.graph_filters ExposoGraph.grounding ExposoGraph.seeder ExposoGraph.viewer_dash N name (ExposoGraph.db_clients.kegg.KEGGGene attribute) (ExposoGraph.db_clients.kegg.KEGGPathway attribute) neighbors() (ExposoGraph.engine.GraphEngine method) Node (class in ExposoGraph.models) node_count (ExposoGraph.engine.GraphEngine property) (ExposoGraph.storage.GraphRevisionSummary attribute) node_ids (ExposoGraph.graph_analysis.MetabolismChain attribute) node_type_counts (ExposoGraph.viewer_dash.ViewerState attribute) nodes_by_type() (ExposoGraph.engine.GraphEngine method) NodeType (class in ExposoGraph.models) normalize_app_mode() (in module ExposoGraph.config) normalize_graph_mode() (in module ExposoGraph.config) normalize_graph_visibility() (in module ExposoGraph.config) normalize_grounding_key() (in module ExposoGraph.grounding) normalize_viewer_layout_mode() (in module ExposoGraph.cytoscape_adapter) note (ExposoGraph.storage.GraphRevisionSummary attribute) O organism (ExposoGraph.db_clients.ctd.ChemicalGeneInteraction attribute) P parse_graph_artifact() (in module ExposoGraph.exporter) parse_graph_data_js() (in module ExposoGraph.exporter) parse_graph_data_text() (in module ExposoGraph.exporter) parse_graph_html() (in module ExposoGraph.exporter) PATHWAY (ExposoGraph.models.EdgeType attribute) (ExposoGraph.models.NodeType attribute) pathway_id (ExposoGraph.db_clients.kegg.KEGGPathway attribute) pathway_subgraph() (in module ExposoGraph.graph_analysis) pathways (ExposoGraph.db_clients.kegg.KEGGGene attribute) persistence_enabled() (in module ExposoGraph.config) positions (ExposoGraph.cytoscape_adapter.CytoscapeBundle attribute) prepare_knowledge_graph() (in module ExposoGraph.grounding) PRESET (ExposoGraph.cytoscape_adapter.ViewerLayoutMode attribute) ProvenanceRecord (class in ExposoGraph.models) pubmed_ids (ExposoGraph.db_clients.ctd.ChemicalGeneInteraction attribute) R RecordOrigin (class in ExposoGraph.models) REJECTED (ExposoGraph.models.CurationStatus attribute) remove_edge() (ExposoGraph.engine.GraphEngine method) remove_node() (ExposoGraph.engine.GraphEngine method) repair_edges (ExposoGraph.graph_analysis.MetabolismChain property) REPAIRS (ExposoGraph.models.EdgeType attribute) REVIEWED (ExposoGraph.models.CurationStatus attribute) revision_id (ExposoGraph.storage.GraphRevisionSummary attribute) revision_number (ExposoGraph.storage.GraphRevisionSummary attribute) S save_engine() (ExposoGraph.storage.GraphRepository method) save_graph() (ExposoGraph.storage.GraphRepository method) score (ExposoGraph.graph_analysis.VariantImpact attribute) seed_from_ctd() (in module ExposoGraph.seeder) seed_from_kegg_pathway() (in module ExposoGraph.seeder) seed_iarc_classification() (in module ExposoGraph.seeder) SEEDED (ExposoGraph.models.RecordOrigin attribute) shortest_path() (in module ExposoGraph.graph_analysis) STATELESS (ExposoGraph.config.AppMode attribute) STRICT (ExposoGraph.config.GraphMode attribute) stylesheet (ExposoGraph.cytoscape_adapter.CytoscapeBundle attribute) symbol (ExposoGraph.db_clients.kegg.KEGGGene attribute) T TISSUE (ExposoGraph.models.NodeType attribute) to_dict() (ExposoGraph.cytoscape_adapter.CytoscapeBundle method) (ExposoGraph.engine.GraphEngine method) to_gexf() (in module ExposoGraph.exporter) to_graph_data_js() (in module ExposoGraph.exporter) to_interactive_html() (in module ExposoGraph.exporter) to_interactive_html_string() (in module ExposoGraph.exporter) to_json() (ExposoGraph.engine.GraphEngine method) (in module ExposoGraph.exporter) to_knowledge_graph() (ExposoGraph.engine.GraphEngine method) (ExposoGraph.storage.GraphRevision method) to_plotly_figure() (in module ExposoGraph.exporter) to_plotly_html() (in module ExposoGraph.exporter) to_plotly_html_string() (in module ExposoGraph.exporter) TRANSPORTS (ExposoGraph.models.EdgeType attribute) U UNKNOWN (ExposoGraph.models.MatchStatus attribute) UNMATCHED (ExposoGraph.models.MatchStatus attribute) USER (ExposoGraph.models.RecordOrigin attribute) V validate() (ExposoGraph.engine.GraphEngine method) VALIDATED_ONLY (ExposoGraph.config.GraphVisibility attribute) variant_impact_score() (in module ExposoGraph.graph_analysis) VariantImpact (class in ExposoGraph.graph_analysis) viewer_layout() (in module ExposoGraph.cytoscape_adapter) viewer_stylesheet() (in module ExposoGraph.cytoscape_adapter) ViewerLayoutMode (class in ExposoGraph.cytoscape_adapter) ViewerState (class in ExposoGraph.viewer_dash) visibility (ExposoGraph.storage.GraphRevisionSummary attribute) visible_edge_count (ExposoGraph.viewer_dash.ViewerState attribute) visible_node_count (ExposoGraph.viewer_dash.ViewerState attribute) W write_cytoscape_bundle() (in module ExposoGraph.cytoscape_adapter) write_full_legends_exports() (in module ExposoGraph.example_graphs) write_viewer_positions() (in module ExposoGraph.cytoscape_adapter)