Index

A

Acetylation (class in indra.statements.statements) Activation (class in indra.statements.statements) ActiveForm (class in indra.statements.statements) activities_by_target() (in module indra.databases.chembl_client) ActivityCondition (class in indra.statements.statements) add_activity_form() (indra.assemblers.pysb.base_agents.BaseAgent method) add_activity_type() (indra.assemblers.pysb.base_agents.BaseAgent method) add_agent() (indra.assemblers.kami.assembler.Nugget method) add_default_initial_conditions() (indra.assemblers.pysb.assembler.PysbAssembler method) add_edge() (indra.assemblers.cx.assembler.NiceCxAssembler method) (indra.assemblers.kami.assembler.Nugget method) add_entry() (indra.preassembler.hierarchy_manager.YamlHierarchyManager method) add_image() (indra.tools.reading.util.reporter.Reporter method) add_node() (indra.assemblers.cx.assembler.NiceCxAssembler method) (indra.assemblers.kami.assembler.Nugget method) add_result() (indra.tools.reading.readers.Reader method) add_reverse_effects() (indra.assemblers.pysb.preassembler.PysbPreassembler method) add_rule_to_model() (in module indra.assemblers.pysb.assembler) add_section() (indra.tools.reading.util.reporter.Reporter method) add_site_states() (indra.assemblers.pysb.base_agents.BaseAgent method) add_statements() (indra.assemblers.cag.assembler.CAGAssembler method) (indra.assemblers.cx.assembler.CxAssembler method) (indra.assemblers.cyjs.assembler.CyJSAssembler method) (indra.assemblers.english.assembler.EnglishAssembler method) (indra.assemblers.graph.assembler.GraphAssembler method) (indra.assemblers.html.assembler.HtmlAssembler method) (indra.assemblers.index_card.assembler.IndexCardAssembler method) (indra.assemblers.indranet.assembler.IndraNetAssembler method) (indra.assemblers.pysb.assembler.PysbAssembler method) (indra.assemblers.pysb.preassembler.PysbPreassembler method) (indra.assemblers.sbgn.assembler.SBGNAssembler method) (indra.explanation.model_checker.model_checker.ModelChecker method) (indra.mechlinker.MechLinker method) (indra.preassembler.Preassembler method) (indra.tools.incremental_model.IncrementalModel method)

add_text() (indra.tools.reading.util.reporter.Reporter method) add_typing() (indra.assemblers.kami.assembler.Nugget method) AddModification (class in indra.statements.statements) Agent (class in indra.statements.statements) agent_from_entity() (indra.sources.medscan.processor.MedscanProcessor method) agent_list() (indra.statements.statements.Association method) (indra.statements.statements.Influence method) (indra.statements.statements.Statement method) agent_set (indra.assemblers.pysb.assembler.PysbAssembler attribute) agent_texts() (in module indra.preassembler.grounding_mapper.analysis) agent_texts_with_grounding() (in module indra.preassembler.grounding_mapper.analysis) AgentState (class in indra.mechlinker) align_statements() (in module indra.tools.assemble_corpus) all_agents() (in module indra.preassembler.grounding_mapper.analysis) all_direct_stmts (indra.sources.bel.rdf_processor.BelRdfProcessor attribute) all_events (indra.sources.reach.processor.ReachProcessor attribute) all_indirect_stmts (indra.sources.bel.rdf_processor.BelRdfProcessor attribute) analyze_db_reading() (in module indra.tools.reading.util.log_analysis_tools) analyze_reach_log() (in module indra.tools.reading.util.log_analysis_tools) api_ruler (indra.sources.reach.reader.ReachReader attribute) append_warning() (indra.assemblers.html.assembler.HtmlAssembler method) apply_to() (indra.mechlinker.AgentState method) assembled_stmts (indra.tools.incremental_model.IncrementalModel attribute) Association (class in indra.statements.statements) Autophosphorylation (class in indra.statements.statements)

B

BaseAgent (class in indra.assemblers.pysb.base_agents) (class in indra.mechlinker) BaseAgentSet (class in indra.assemblers.pysb.base_agents) (class in indra.mechlinker) basename (indra.tools.gene_network.GeneNetwork attribute) BatchReadingError BayesianScorer (class in indra.belief) BeliefEngine (class in indra.belief) BeliefPackage (class in indra.belief)

BeliefScorer (class in indra.belief) BelRdfProcessor (class in indra.sources.bel.rdf_processor) BioContext (class in indra.statements.statements) BiogridProcessor (class in indra.sources.biogrid) BiopaxProcessor (class in indra.sources.biopax.processor) BMIModel (class in indra.assemblers.pysb.bmi_wrapper) bound_conditions (indra.mechlinker.AgentState attribute) BoundCondition (class in indra.statements.statements) build_transitive_closure() (indra.preassembler.hierarchy_manager.HierarchyManager method) build_transitive_closures() (indra.preassembler.hierarchy_manager.HierarchyManager method)

C

CAG (indra.assemblers.cag.assembler.CAGAssembler attribute) CAGAssembler (class in indra.assemblers.cag.assembler) ch_end (indra.sources.medscan.processor.MedscanEntity attribute) ch_start (indra.sources.medscan.processor.MedscanEntity attribute) change_format() (indra.tools.reading.readers.Content method) change_id() (indra.tools.reading.readers.Content method) check_entitlement() (in module indra.literature.elsevier_client) check_grounding_map() (indra.preassembler.grounding_mapper.mapper.GroundingMapper static method) check_model() (indra.explanation.model_checker.model_checker.ModelChecker method) check_prior_probs() (indra.belief.BeliefScorer method) (indra.belief.SimpleScorer method) check_statement() (indra.explanation.model_checker.model_checker.ModelChecker method) citation (indra.sources.reach.processor.ReachProcessor attribute) clear_input() (indra.tools.reading.readers.ReachReader method) cm_json_to_graph() (in module indra.assemblers.pysb.kappa_util) combine_duplicate_stmts() (indra.preassembler.Preassembler method) combine_duplicates() (indra.preassembler.Preassembler method) combine_related() (indra.preassembler.Preassembler method) Complex (class in indra.statements.statements) complex_monomers_default() (in module indra.assemblers.pysb.assembler) complex_monomers_one_step() (in module indra.assemblers.pysb.assembler)

Concept (class in indra.statements.statements) concept (indra.statements.statements.Event attribute) connected_subgraph() (indra.sources.tees.processor.TEESProcessor method) Content (class in indra.tools.reading.readers) Context (class in indra.statements.statements) context (indra.statements.statements.Event attribute) Conversion (class in indra.statements.statements) convert_unit() (indra.statements.statements.QuantitativeState static method) converted_direct_stmts (indra.sources.bel.rdf_processor.BelRdfProcessor attribute) converted_indirect_stmts (indra.sources.bel.rdf_processor.BelRdfProcessor attribute) copy_default_config() (in module indra.tools.machine) Corpus (class in indra.tools.live_curation) create_mod_site() (indra.assemblers.pysb.base_agents.BaseAgent method) create_network() (in module indra.databases.ndex_client) create_site() (indra.assemblers.pysb.base_agents.BaseAgent method) curations (indra.tools.live_curation.Corpus attribute) CWMSError CWMSProcessor (class in indra.sources.cwms.processor) CWMSRDFProcessor (class in indra.sources.cwms.rdf_processor) cx (indra.assemblers.cx.assembler.CxAssembler attribute) CxAssembler (class in indra.assemblers.cx.assembler) CyJSAssembler (class in indra.assemblers.cyjs.assembler)

D

db_rest_url (indra.assemblers.html.assembler.HtmlAssembler attribute) Deacetylation (class in indra.statements.statements) DecreaseAmount (class in indra.statements.statements) Defarnesylation (class in indra.statements.statements) degenerate_stmts (indra.sources.bel.rdf_processor.BelRdfProcessor attribute) Degeranylgeranylation (class in indra.statements.statements) Deglycosylation (class in indra.statements.statements) Dehydroxylation (class in indra.statements.statements) delta (indra.statements.statements.Event attribute) Demethylation (class in indra.statements.statements) Demyristoylation (class in indra.statements.statements) Depalmitoylation (class in indra.statements.statements) Dephosphorylation (class in indra.statements.statements) Deribosylation (class in indra.statements.statements) Desumoylation (class in indra.statements.statements) determine_reach_subtype() (in module indra.sources.reach.processor)

Deubiquitination (class in indra.statements.statements) df (indra.sources.trrust.processor.TrrustProcessor attribute) digraph_from_df() (indra.assemblers.indranet.net.IndraNet class method) directly_or_indirectly_related() (indra.preassembler.hierarchy_manager.HierarchyManager method) doc_id (indra.sources.cwms.processor.CWMSProcessor attribute) (indra.sources.trips.processor.TripsProcessor attribute) doi_query() (in module indra.literature.crossref_client) download_article() (in module indra.literature.elsevier_client) download_article_from_ids() (in module indra.literature.elsevier_client) download_from_search() (in module indra.literature.elsevier_client) draw_im() (indra.explanation.model_checker.pysb.PysbModelChecker method) draw_stmt_graph() (in module indra.statements.statements) drum_system (indra.sources.trips.drum_reader.DrumReader attribute) DrumReader (class in indra.sources.trips.drum_reader) dump_logs() (in module indra.util.aws) dump_statements() (in module indra.tools.assemble_corpus) dump_stmt_strings() (in module indra.tools.assemble_corpus)

E

edge_properties (indra.assemblers.graph.assembler.GraphAssembler attribute) eidos_reader (indra.sources.eidos.reader.EidosReader attribute) EidosProcessor (class in indra.sources.eidos.processor) EidosReader (class in indra.sources.eidos.reader) eliminate_exact_duplicates() (indra.sources.biopax.processor.BiopaxProcessor method) EmptyReader (class in indra.tools.reading.readers) english_join() (in module indra.assemblers.english.assembler) EnglishAssembler (class in indra.assemblers.english.assembler) entities (indra.sources.medscan.processor.MedscanRelation attribute) entity_matches_key() (indra.statements.statements.Agent method) ev_totals (indra.assemblers.html.assembler.HtmlAssembler attribute) Event (class in indra.statements.statements) event_from_event() (indra.sources.cwms.processor.CWMSProcessor method) Evidence (class in indra.statements.statements) evidence_random_noise_prior() (in module indra.belief) evidences (indra.belief.BeliefPackage attribute) existing_edges (indra.assemblers.graph.assembler.GraphAssembler attribute) existing_nodes (indra.assemblers.graph.assembler.GraphAssembler attribute) expand_families() (in module indra.tools.assemble_corpus) expand_pagination() (in module indra.literature.pubmed_client)

export_dict() (indra.util.nested_dict.NestedDict method) export_into_python() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) export_model() (indra.assemblers.pysb.assembler.PysbAssembler method) export_to_cytoscapejs() (indra.assemblers.cag.assembler.CAGAssembler method) extend_with() (indra.preassembler.hierarchy_manager.HierarchyManager method) extract_and_process() (in module indra.sources.eidos.cli) extract_causal_relations() (indra.sources.cwms.processor.CWMSProcessor method) (indra.sources.eidos.processor.EidosProcessor method) extract_events() (indra.sources.cwms.processor.CWMSProcessor method) extract_from_directory() (in module indra.sources.eidos.cli) extract_output() (in module indra.sources.tees.api) extract_paragraphs() (in module indra.literature.elsevier_client) (in module indra.literature.pmc_client) extract_statement_from_query_result() (indra.sources.cwms.rdf_processor.CWMSRDFProcessor method) extract_statements() (indra.sources.cwms.rdf_processor.CWMSRDFProcessor method) (indra.sources.rlimsp.processor.RlimspProcessor method) (indra.sources.trrust.processor.TrrustProcessor method) extract_text() (in module indra.literature.elsevier_client) (in module indra.literature.pmc_client) extracted_events (indra.sources.trips.processor.TripsProcessor attribute) extractions (indra.sources.trips.drum_reader.DrumReader attribute)

F

Farnesylation (class in indra.statements.statements) filename (in module indra.sources.medscan.api) filter_belief() (in module indra.tools.assemble_corpus) filter_by_db_refs() (in module indra.tools.assemble_corpus) filter_by_type() (in module indra.tools.assemble_corpus) filter_concept_names() (in module indra.tools.assemble_corpus) filter_direct() (in module indra.tools.assemble_corpus) filter_enzyme_kinase() (in module indra.tools.assemble_corpus) filter_evidence_source() (in module indra.tools.assemble_corpus) filter_gene_list() (in module indra.tools.assemble_corpus) filter_genes_only() (in module indra.tools.assemble_corpus) filter_grounded_only() (in module indra.tools.assemble_corpus) filter_human_only() (in module indra.tools.assemble_corpus) filter_inconsequential_acts() (in module indra.tools.assemble_corpus) filter_inconsequential_mods() (in module indra.tools.assemble_corpus) filter_mod_nokinase() (in module indra.tools.assemble_corpus) filter_mutation_status() (in module indra.tools.assemble_corpus) filter_no_hypothesis() (in module indra.tools.assemble_corpus) filter_no_negated() (in module indra.tools.assemble_corpus) filter_paragraphs() (in module indra.literature.adeft_tools) filter_pmids() (in module indra.literature.pmc_client)

filter_top_level() (in module indra.tools.assemble_corpus) filter_transcription_factor() (in module indra.tools.assemble_corpus) filter_uuid_list() (in module indra.tools.assemble_corpus) finalize() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) find_arg() (in module indra.sources.eidos.processor) find_args() (in module indra.sources.eidos.processor) find_contradicts() (indra.preassembler.Preassembler method) find_entity (indra.preassembler.hierarchy_manager.HierarchyManager attribute) find_event_parent_with_event_child() (indra.sources.tees.processor.TEESProcessor method) find_event_with_outgoing_edges() (indra.sources.tees.processor.TEESProcessor method) find_paths() (indra.explanation.model_checker.model_checker.ModelChecker method) flatten_evidence() (in module indra.preassembler) flatten_stmts() (in module indra.preassembler) flip_polarity() (indra.statements.statements.Association method) (indra.statements.statements.Event method) (indra.statements.statements.Influence method) (indra.statements.statements.Statement method) format_axis() (in module indra.util.plot_formatting) from_df() (indra.assemblers.indranet.net.IndraNet class method) from_file() (indra.tools.reading.readers.Content class method) from_seconds() (indra.statements.statements.QuantitativeState static method) from_string() (indra.tools.reading.readers.Content class method)

G

g (indra.sources.bel.rdf_processor.BelRdfProcessor attribute) Gap (class in indra.statements.statements) gather_explicit_activities() (indra.mechlinker.MechLinker method) gather_implicit_activities() (indra.mechlinker.MechLinker method) Gef (class in indra.statements.statements) gene_list (indra.tools.gene_network.GeneNetwork attribute) GeneNetwork (class in indra.tools.gene_network) general_node_label() (indra.sources.tees.processor.TEESProcessor method) generate_im() (indra.explanation.model_checker.pysb.PysbModelChecker method) generate_jupyter_js() (indra.assemblers.cag.assembler.CAGAssembler method) geneways_action_to_indra_statement_type() (in module indra.sources.geneways.processor) GenewaysProcessor (class in indra.sources.geneways.processor) geo_context_from_ref() (indra.sources.eidos.processor.EidosProcessor method) Geranylgeranylation (class in indra.statements.statements) get() (indra.util.nested_dict.NestedDict method) get_abstract() (in module indra.literature.elsevier_client) (in module indra.literature.pubmed_client) get_activating_mods() (indra.sources.bel.rdf_processor.BelRdfProcessor method) get_activating_subs() (indra.sources.bel.rdf_processor.BelRdfProcessor method) get_activation() (indra.sources.bel.rdf_processor.BelRdfProcessor method) (indra.sources.reach.processor.ReachProcessor method) get_activations() (indra.sources.trips.processor.TripsProcessor method) get_activations_causal() (indra.sources.trips.processor.TripsProcessor method) get_activations_stimulate() (indra.sources.trips.processor.TripsProcessor method) get_active_forms() (indra.sources.trips.processor.TripsProcessor method) get_active_forms_state() (indra.sources.trips.processor.TripsProcessor method) get_activity_modification() (indra.sources.biopax.processor.BiopaxProcessor method) get_ag_ns_id() (in module indra.assemblers.indranet.assembler) get_agent_from_entity_info() (in module indra.sources.rlimsp.processor) get_agent_rule_str() (in module indra.assemblers.pysb.assembler) get_agents() (indra.sources.ndex_cx.processor.NdexCxProcessor method) (indra.sources.trips.processor.TripsProcessor method) get_agents_with_name() (in module indra.preassembler.grounding_mapper.analysis) get_all_descendants() (in module indra.statements.statements) get_all_direct_statements() (indra.sources.bel.rdf_processor.BelRdfProcessor method) get_all_events() (indra.sources.reach.processor.ReachProcessor method) (indra.sources.trips.processor.TripsProcessor method) get_all_indirect_statements() (indra.sources.bel.rdf_processor.BelRdfProcessor method) get_annotation() (in module indra.assemblers.pysb.assembler) get_api_ruler() (indra.sources.reach.reader.ReachReader method) get_article() (in module indra.literature.elsevier_client) get_article_xml (in module indra.literature.pubmed_client) get_attribute() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) get_batch_command() (in module indra.util.aws) get_bel_stmts() (indra.tools.gene_network.GeneNetwork method) get_bio_hierarchies() (in module indra.preassembler.hierarchy_manager) get_biopax_stmts() (indra.tools.gene_network.GeneNetwork method) get_cancer_studies() (in module indra.databases.cbio_client) get_cancer_types() (in module indra.databases.cbio_client) get_case_lists() (in module indra.databases.cbio_client) get_causal_edge() (in module indra.assemblers.pybel.assembler) get_ccle_cna() (in module indra.databases.cbio_client) get_ccle_lines_for_mutation() (in module indra.databases.cbio_client) get_ccle_mrna() (in module indra.databases.cbio_client) get_ccle_mutations() (in module indra.databases.cbio_client) get_chebi_entry_from_web (in module indra.databases.chebi_client) get_chebi_id_from_cas() (in module indra.databases.chebi_client) get_chebi_id_from_hmdb() (in module indra.databases.chebi_client) get_chebi_id_from_name() (in module indra.databases.chebi_client) get_chebi_id_from_pubchem() (in module indra.databases.chebi_client) get_chebi_name_from_id() (in module indra.databases.chebi_client) get_chebi_name_from_id_web() (in module indra.databases.chebi_client) get_chembl_id() (in module indra.databases.chebi_client) (in module indra.databases.chembl_client) get_children() (indra.preassembler.hierarchy_manager.HierarchyManager method) get_complexes() (indra.sources.bel.rdf_processor.BelRdfProcessor method) (indra.sources.biopax.processor.BiopaxProcessor method) (indra.sources.hprd.processor.HprdProcessor method) (indra.sources.reach.processor.ReachProcessor method) (indra.sources.trips.processor.TripsProcessor method) get_concept() (indra.sources.eidos.processor.EidosProcessor method) get_conversions() (indra.sources.bel.rdf_processor.BelRdfProcessor method) (indra.sources.biopax.processor.BiopaxProcessor method) get_corpus() (indra.tools.live_curation.LiveCurator method) get_create_base_agent() (indra.assemblers.pysb.base_agents.BaseAgentSet method) (indra.mechlinker.BaseAgentSet method) get_create_parameter() (in module indra.assemblers.pysb.assembler) get_current_hgnc_id() (in module indra.databases.hgnc_client) get_current_time() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) get_default_ndex_cred() (in module indra.databases.ndex_client) get_degenerate_statements() (indra.sources.bel.rdf_processor.BelRdfProcessor method) get_degradations() (indra.sources.trips.processor.TripsProcessor method) get_doid_id_from_doid_alt_id() (in module indra.databases.doid_client) get_doid_id_from_doid_name() (in module indra.databases.doid_client) get_doid_name_from_doid_id() (in module indra.databases.doid_client) get_dois (in module indra.literature.elsevier_client) get_drug_inhibition_stmts() (in module indra.databases.chembl_client) get_drug_target_data() (in module indra.databases.lincs_client) get_ecs_cluster_for_queue() (in module indra.tools.reading.submit_reading_pipeline) get_efo_id_from_efo_name() (in module indra.databases.efo_client) get_efo_name_from_efo_id() (in module indra.databases.efo_client) get_ensembl_id() (in module indra.databases.hgnc_client) get_entity_text_for_relation() (indra.sources.tees.processor.TEESProcessor method) get_entrez_id() (in module indra.databases.hgnc_client) get_evidence() (in module indra.databases.chembl_client) (indra.sources.eidos.processor.EidosProcessor method) get_filename() (indra.tools.reading.readers.Content method) get_filepath() (indra.tools.reading.readers.Content method) get_full_text() (in module indra.literature) get_fulltext_links() (in module indra.literature.crossref_client) get_gap() (indra.sources.biopax.processor.BiopaxProcessor method) get_gef() (indra.sources.biopax.processor.BiopaxProcessor method) get_gene_names() (indra.assemblers.cyjs.assembler.CyJSAssembler method) get_genetic_profiles() (in module indra.databases.cbio_client) get_git_info() (in module indra.util.get_version) get_go_id_from_label() (in module indra.databases.go_client) get_go_label() (in module indra.databases.go_client) get_graph() (indra.explanation.model_checker.model_checker.ModelChecker method) (indra.explanation.model_checker.pybel.PybelModelChecker method) (indra.explanation.model_checker.pysb.PysbModelChecker method) (indra.explanation.model_checker.signed_graph.SignedGraphModelChecker method) (indra.explanation.model_checker.unsigned_graph.UnsignedGraphModelChecker method) get_grounded_agent() (in module indra.sources.trrust.processor) get_grounding() (indra.statements.statements.Agent method) get_groundings() (indra.sources.eidos.processor.EidosProcessor method) get_hash() (indra.statements.statements.Statement method) get_heat_kernel() (in module indra.databases.relevance_client) get_hedging() (indra.sources.eidos.processor.EidosProcessor static method) get_hgnc_entry (in module indra.databases.hgnc_client) get_hgnc_from_ensembl() (in module indra.databases.hgnc_client) get_hgnc_from_entrez() (in module indra.databases.hgnc_client) get_hgnc_from_mouse() (in module indra.databases.hgnc_client) get_hgnc_from_rat() (in module indra.databases.hgnc_client) get_hgnc_id() (in module indra.databases.hgnc_client) get_hgnc_id_from_mirbase_id() (in module indra.databases.mirbase_client) get_hgnc_name() (in module indra.databases.hgnc_client) get_hp_id_from_hp_name() (in module indra.databases.hp_client) get_hp_name_from_hp_id() (in module indra.databases.hp_client) get_id_count() (in module indra.literature.pubmed_client) get_ids (in module indra.literature.pubmed_client) get_ids_for_gene (in module indra.literature.pubmed_client) get_ids_for_mesh() (in module indra.literature.pubmed_client)

get_im() (indra.explanation.model_checker.pysb.PysbModelChecker method) get_inchi_key (in module indra.databases.pubchem_client) get_inchi_key() (in module indra.databases.chebi_client) get_input_var_names() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) get_issns_for_journal (in module indra.literature.pubmed_client) get_job_log() (in module indra.util.aws) get_jobs() (in module indra.util.aws) get_kinetics() (in module indra.databases.chembl_client) get_leaves() (indra.util.nested_dict.NestedDict method) get_log_by_name() (in module indra.util.aws) get_logs_from_db_reading() (in module indra.tools.reading.util.log_analysis_tools) get_mesh_id() (in module indra.databases.chembl_client) get_mesh_id_name() (in module indra.databases.mesh_client) get_mesh_id_name_from_web() (in module indra.databases.mesh_client) get_mesh_name() (in module indra.databases.mesh_client) get_mesh_name_from_web (in module indra.databases.mesh_client) get_metadata (in module indra.literature.crossref_client) get_metadata_for_ids() (in module indra.literature.pubmed_client) get_metadata_from_xml_tree() (in module indra.literature.pubmed_client) get_mirbase_id_from_hgnc_id() (in module indra.databases.mirbase_client) get_mirbase_id_from_hgnc_symbol() (in module indra.databases.mirbase_client) get_mirbase_id_from_mirbase_name() (in module indra.databases.mirbase_client) get_mirbase_name_from_mirbase_id() (in module indra.databases.mirbase_client) get_model_agents() (indra.tools.incremental_model.IncrementalModel method) get_modifications() (indra.sources.bel.rdf_processor.BelRdfProcessor method) (indra.sources.biopax.processor.BiopaxProcessor method) (indra.sources.reach.processor.ReachProcessor method) (indra.sources.trips.processor.TripsProcessor method) get_modifications_indirect() (indra.sources.trips.processor.TripsProcessor method) get_monomer_pattern() (in module indra.assemblers.pysb.assembler) get_mouse_id() (in module indra.databases.hgnc_client) get_mutations() (in module indra.databases.cbio_client) (in module indra.databases.context_client) get_negation() (indra.sources.eidos.processor.EidosProcessor static method) get_node_names() (indra.sources.ndex_cx.processor.NdexCxProcessor method) get_nugget_dict() (indra.assemblers.kami.assembler.Nugget method) get_num_sequenced() (in module indra.databases.cbio_client) get_output() (indra.tools.reading.readers.ReachReader method) (indra.tools.reading.readers.SparserReader method) get_output_var_names() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) get_parents() (indra.preassembler.hierarchy_manager.HierarchyManager method) get_parser() (in module indra.tools.reading.util.script_tools) get_path() (indra.util.nested_dict.NestedDict method) get_paths() (indra.util.nested_dict.NestedDict method) get_pcid() (in module indra.databases.chembl_client) get_piis() (in module indra.literature.elsevier_client) get_piis_for_date (in module indra.literature.elsevier_client) get_pmid() (in module indra.databases.chembl_client) get_pmids() (indra.sources.ndex_cx.processor.NdexCxProcessor method) get_ppis() (indra.sources.hprd.processor.HprdProcessor method) get_profile_data() (in module indra.databases.cbio_client) get_protein_expression() (in module indra.databases.context_client) get_protein_refs() (indra.databases.lincs_client.LincsClient method) get_protein_targets_only() (in module indra.databases.chembl_client) get_ptms() (indra.sources.hprd.processor.HprdProcessor method) get_pubchem_id() (in module indra.databases.chebi_client) get_publications() (in module indra.databases.biogrid_client) get_rat_id() (in module indra.databases.hgnc_client) get_reader() (in module indra.tools.reading.readers) get_reader_class() (in module indra.tools.reading.readers) get_reader_classes() (in module indra.tools.reading.readers) get_regulate_activities() (indra.sources.biopax.processor.BiopaxProcessor method) get_regulate_amounts() (indra.sources.biopax.processor.BiopaxProcessor method) (indra.sources.reach.processor.ReachProcessor method) (indra.sources.trips.processor.TripsProcessor method) get_related_node() (indra.sources.tees.processor.TEESProcessor method) get_relevant_nodes() (in module indra.databases.relevance_client) get_s3_file_tree() (in module indra.util.aws) get_sentences_for_agent() (in module indra.preassembler.grounding_mapper.analysis) get_site_pattern() (in module indra.assemblers.pysb.assembler) get_sites() (indra.sources.medscan.processor.ProteinSiteInfo method) get_small_molecule_name() (indra.databases.lincs_client.LincsClient method) get_small_molecule_refs() (indra.databases.lincs_client.LincsClient method) get_source_hash() (indra.statements.statements.Evidence method) get_specific_id() (in module indra.databases.chebi_client) get_start_time() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) get_statement_by_name() (in module indra.statements.statements) get_statements() (in module indra.sources.indra_db_rest.api) (indra.sources.isi.processor.IsiProcessor method) (indra.sources.ndex_cx.processor.NdexCxProcessor method) (indra.tools.gene_network.GeneNetwork method) (indra.tools.incremental_model.IncrementalModel method) (indra.tools.reading.readers.ReadingData method) get_statements_by_hash() (in module indra.sources.indra_db_rest.api) get_statements_for_paper() (in module indra.sources.indra_db_rest.api) get_statements_noprior() (indra.tools.incremental_model.IncrementalModel method) get_statements_prior() (indra.tools.incremental_model.IncrementalModel method) get_status() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) get_stmts() (in module indra.tools.reading.pmid_reading.read_pmids) get_string() (indra.assemblers.graph.assembler.GraphAssembler method) get_subnetwork() (in module indra.tools.executable_subnetwork) get_syntheses() (indra.sources.trips.processor.TripsProcessor method) get_target_chemblid() (in module indra.databases.chembl_client) get_term_agents() (indra.sources.trips.processor.TripsProcessor method) get_text() (indra.tools.reading.readers.Content method) get_text_content_for_gene() (in module indra.literature.adeft_tools) get_text_content_for_pmids() (in module indra.literature.adeft_tools) get_time_step() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) get_time_units() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) get_title() (in module indra.literature.pubmed_client) get_transcription() (indra.sources.bel.rdf_processor.BelRdfProcessor method) get_translocation() (indra.sources.reach.processor.ReachProcessor method) get_typing_dict() (indra.assemblers.kami.assembler.Nugget method) get_uncond_agent() (in module indra.assemblers.pysb.assembler) get_uniprot_id() (in module indra.databases.hgnc_client) get_unresolved_support_uuids() (in module indra.statements.statements) get_unyielding_tcids() (in module indra.tools.reading.util.log_analysis_tools) get_valid_location() (in module indra.statements.statements), [1] get_valid_residue() (in module indra.statements.statements) get_value() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) get_values() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) get_var_name() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) get_var_rank() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) get_var_type() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) get_var_units() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) get_version() (in module indra.sources.sparser.api) (in module indra.util.get_version) get_wm_hierarchies() (in module indra.preassembler.hierarchy_manager) get_xml() (in module indra.literature.pmc_client) (in module indra.sources.trips.client) GetReadingStatsError gets() (indra.util.nested_dict.NestedDict method) Glycosylation (class in indra.statements.statements) graph (indra.assemblers.graph.assembler.GraphAssembler attribute) (indra.assemblers.sif.assembler.SifAssembler attribute) (indra.explanation.model_checker.model_checker.ModelChecker attribute) (indra.preassembler.hierarchy_manager.HierarchyManager attribute) graph_properties (indra.assemblers.graph.assembler.GraphAssembler attribute) graph_query() (in module indra.sources.biopax.pathway_commons_client) GraphAssembler (class in indra.assemblers.graph.assembler) grounded_monomer_patterns() (in module indra.assemblers.pysb.assembler) GroundingMapper (class in indra.preassembler.grounding_mapper.mapper) GtpActivation (class in indra.statements.statements)

H

HasActivity (class in indra.statements.statements) hierarchies (indra.preassembler.Preassembler attribute) HierarchyManager (class in indra.preassembler.hierarchy_manager)

HprdProcessor (class in indra.sources.hprd.processor) HtmlAssembler (class in indra.assemblers.html.assembler) HumeJsonLdProcessor (class in indra.sources.hume.processor) Hydroxylation (class in indra.statements.statements)

I

id_df (indra.sources.hprd.processor.HprdProcessor attribute) id_lookup() (in module indra.literature) (in module indra.literature.pmc_client) im_json_to_graph() (in module indra.assemblers.pysb.kappa_util) IncreaseAmount (class in indra.statements.statements) IncrementalModel (class in indra.tools.incremental_model) IndexCardAssembler (class in indra.assemblers.index_card.assembler) indirect_stmts (indra.sources.bel.rdf_processor.BelRdfProcessor attribute) indra.assemblers.cag.assembler (module) indra.assemblers.cx.assembler (module) indra.assemblers.cyjs.assembler (module) indra.assemblers.english.assembler (module) indra.assemblers.graph.assembler (module) indra.assemblers.html.assembler (module) indra.assemblers.index_card.assembler (module) indra.assemblers.indranet (module) indra.assemblers.indranet.assembler (module) indra.assemblers.indranet.net (module) indra.assemblers.kami.assembler (module) indra.assemblers.pybel.assembler (module) indra.assemblers.pysb.assembler (module) indra.assemblers.pysb.base_agents (module) indra.assemblers.pysb.bmi_wrapper (module) indra.assemblers.pysb.kappa_util (module) indra.assemblers.pysb.preassembler (module) indra.assemblers.sbgn.assembler (module) indra.assemblers.sif.assembler (module) indra.assemblers.tsv.assembler (module) indra.belief (module) indra.databases.biogrid_client (module) indra.databases.cbio_client (module) indra.databases.chebi_client (module) indra.databases.chembl_client (module) indra.databases.context_client (module) indra.databases.doid_client (module) indra.databases.efo_client (module) indra.databases.go_client (module) indra.databases.hgnc_client (module) indra.databases.hp_client (module) indra.databases.lincs_client (module) indra.databases.mesh_client (module) indra.databases.mirbase_client (module) indra.databases.ndex_client (module) indra.databases.pubchem_client (module) indra.databases.relevance_client (module) indra.databases.uniprot_client (module) indra.explanation.model_checker.model_checker (module) indra.explanation.model_checker.pybel (module) indra.explanation.model_checker.pysb (module) indra.explanation.model_checker.signed_graph (module) indra.explanation.model_checker.unsigned_graph (module) indra.literature (module) indra.literature.adeft_tools (module) indra.literature.crossref_client (module) indra.literature.elsevier_client (module) indra.literature.newsapi_client (module) indra.literature.pmc_client (module) indra.literature.pubmed_client (module) indra.mechlinker (module) indra.preassembler (module) indra.preassembler.grounding_mapper (module) indra.preassembler.grounding_mapper.adeft (module) indra.preassembler.grounding_mapper.analysis (module) indra.preassembler.grounding_mapper.mapper (module) indra.preassembler.hierarchy_manager (module) indra.preassembler.ontology_mapper (module) indra.preassembler.sitemapper (module) indra.sources.bel.api (module) indra.sources.bel.processor (module) indra.sources.bel.rdf_processor (module) indra.sources.biogrid (module) indra.sources.biopax.api (module) indra.sources.biopax.pathway_commons_client (module) indra.sources.biopax.processor (module) indra.sources.cwms (module) indra.sources.cwms.api (module) indra.sources.cwms.processor (module) indra.sources.cwms.rdf_processor (module) indra.sources.eidos (module) indra.sources.eidos.api (module) indra.sources.eidos.cli (module) indra.sources.eidos.processor (module) indra.sources.eidos.reader (module) indra.sources.eidos.server (module) indra.sources.geneways.api (module) indra.sources.geneways.processor (module) indra.sources.hprd (module) indra.sources.hprd.api (module) indra.sources.hprd.processor (module) indra.sources.hume (module) indra.sources.hume.api (module) indra.sources.hume.processor (module)

indra.sources.indra_db_rest (module) indra.sources.indra_db_rest.api (module) indra.sources.indra_db_rest.processor (module) indra.sources.isi (module) indra.sources.isi.api (module) indra.sources.isi.processor (module) indra.sources.lincs_drug (module) indra.sources.lincs_drug.api (module) indra.sources.lincs_drug.processor (module) indra.sources.medscan (module) indra.sources.medscan.api (module) indra.sources.medscan.processor (module) indra.sources.ndex_cx.api (module) indra.sources.ndex_cx.processor (module) indra.sources.reach.api (module) indra.sources.reach.processor (module) indra.sources.reach.reader (module) indra.sources.rlimsp (module) indra.sources.rlimsp.api (module) indra.sources.rlimsp.processor (module) indra.sources.signor.api (module) indra.sources.signor.processor (module) indra.sources.sofia (module) indra.sources.sofia.api (module) indra.sources.sofia.processor (module) indra.sources.sparser (module) indra.sources.sparser.api (module) indra.sources.tas (module) indra.sources.tas.api (module) indra.sources.tas.processor (module) indra.sources.tees.api (module) indra.sources.tees.processor (module) indra.sources.trips.api (module) indra.sources.trips.client (module) indra.sources.trips.drum_reader (module) indra.sources.trips.processor (module) indra.sources.trrust (module) indra.sources.trrust.api (module) indra.sources.trrust.processor (module) indra.statements.statements (module) indra.tools.assemble_corpus (module) indra.tools.executable_subnetwork (module) indra.tools.gene_network (module) indra.tools.incremental_model (module) indra.tools.live_curation (module) indra.tools.machine (module) indra.tools.reading.pmid_reading.read_pmids (module) indra.tools.reading.read_files (module) indra.tools.reading.readers (module) indra.tools.reading.run_drum_reading (module) indra.tools.reading.submit_reading_pipeline (module) indra.tools.reading.util.export_stmts_by_reach_rule (module) indra.tools.reading.util.log_analysis_tools (module) indra.tools.reading.util.reporter (module) indra.tools.reading.util.script_tools (module) indra.util.aws (module) indra.util.get_version (module) indra.util.nested_dict (module) indra.util.plot_formatting (module) IndraDBRestHashProcessor (class in indra.sources.indra_db_rest.processor) IndraDBRestSearchProcessor (class in indra.sources.indra_db_rest.processor) IndraNet (class in indra.assemblers.indranet.net) IndraNetAssembler (class in indra.assemblers.indranet.assembler) infer_activations() (indra.mechlinker.MechLinker static method) infer_active_forms() (indra.mechlinker.MechLinker static method) infer_complexes() (indra.mechlinker.MechLinker static method) infer_modifications() (indra.mechlinker.MechLinker static method) Influence (class in indra.statements.statements) influence_from_event() (indra.sources.cwms.processor.CWMSProcessor method) influence_from_relation() (indra.sources.cwms.processor.CWMSProcessor method) Inhibition (class in indra.statements.statements) initialize() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) initialize_reader() (in module indra.sources.eidos.api) (indra.sources.eidos.reader.EidosReader method) InputError interval (in module indra.sources.medscan.api) invalid_site_pos (indra.sources.hprd.processor.HprdProcessor attribute) InvalidCorpusError InvalidLocationError InvalidResidueError is_equal() (indra.preassembler.hierarchy_manager.HierarchyManager method) is_format() (indra.tools.reading.readers.Content method) is_kinase() (in module indra.databases.hgnc_client) is_opposite() (indra.preassembler.hierarchy_manager.HierarchyManager method) is_phosphatase() (in module indra.databases.hgnc_client) is_transcription_factor() (in module indra.databases.hgnc_client) is_working() (indra.sources.indra_db_rest.processor.IndraDBRestSearchProcessor method) isa() (indra.preassembler.hierarchy_manager.HierarchyManager method) isa_or_partof() (indra.preassembler.hierarchy_manager.HierarchyManager method) IsiProcessor (class in indra.sources.isi.processor) items() (indra.assemblers.pysb.base_agents.BaseAgentSet method) iter_s3_keys() (in module indra.util.aws)

J

join_json_files() (in module indra.tools.reading.pmid_reading.read_pmids)

K

KamiAssembler (class in indra.assemblers.kami.assembler)

kill_all() (in module indra.util.aws)

L

last_site_info_in_sentence (indra.sources.medscan.processor.MedscanProcessor attribute) lazy (in module indra.sources.medscan.api) length (indra.explanation.model_checker.model_checker.PathMetric attribute) LincsClient (class in indra.databases.lincs_client) LincsProcessor (class in indra.sources.lincs_drug.processor) LinkedStatement (class in indra.mechlinker) LiveCurator (class in indra.tools.live_curation) load_from_rdf_file() (indra.preassembler.hierarchy_manager.HierarchyManager method)

load_from_rdf_graph() (indra.preassembler.hierarchy_manager.HierarchyManager method) load_from_rdf_string() (indra.preassembler.hierarchy_manager.HierarchyManager method) load_go_graph() (in module indra.databases.go_client) load_grounding_map() (in module indra.preassembler.grounding_mapper.mapper) load_lincs_csv() (in module indra.databases.lincs_client) load_prior() (indra.tools.incremental_model.IncrementalModel method) load_statements() (in module indra.tools.assemble_corpus) location (indra.mechlinker.AgentState attribute)

M

make_df() (indra.assemblers.indranet.assembler.IndraNetAssembler method) make_generic_copy() (indra.statements.statements.Statement method) make_hash() (in module indra.statements.statements) make_model() (indra.assemblers.cag.assembler.CAGAssembler method) (indra.assemblers.cx.assembler.CxAssembler method) (indra.assemblers.cx.assembler.NiceCxAssembler method) (indra.assemblers.cyjs.assembler.CyJSAssembler method) (indra.assemblers.english.assembler.EnglishAssembler method) (indra.assemblers.graph.assembler.GraphAssembler method) (indra.assemblers.html.assembler.HtmlAssembler method) (indra.assemblers.index_card.assembler.IndexCardAssembler method) (indra.assemblers.indranet.assembler.IndraNetAssembler method) (indra.assemblers.kami.assembler.KamiAssembler method) (indra.assemblers.pysb.assembler.PysbAssembler method) (indra.assemblers.sbgn.assembler.SBGNAssembler method) (indra.assemblers.sif.assembler.SifAssembler method) (indra.assemblers.tsv.assembler.TsvAssembler method) make_nxml_from_text() (in module indra.sources.sparser.api) make_parser() (in module indra.tools.reading.read_files) make_report() (indra.tools.reading.util.reporter.Reporter method) make_repository_component() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) make_statement() (indra.sources.geneways.processor.GenewaysProcessor method) make_statement_camel() (in module indra.statements.statements) make_stmt() (in module indra.sources.trrust.processor) many_ups_for_refseq (indra.sources.hprd.processor.HprdProcessor attribute) map_agent() (indra.preassembler.grounding_mapper.mapper.GroundingMapper method) map_agents_for_stmt() (indra.preassembler.grounding_mapper.mapper.GroundingMapper method) map_grounding() (in module indra.tools.assemble_corpus) map_sequence() (in module indra.tools.assemble_corpus) map_sites() (indra.preassembler.sitemapper.SiteMapper method) map_statements() (indra.preassembler.ontology_mapper.OntologyMapper method)

map_stmts() (indra.preassembler.grounding_mapper.mapper.GroundingMapper method) MappedStatement (class in indra.preassembler.sitemapper) matches_key() (indra.statements.statements.Agent method) max_path_length (indra.explanation.model_checker.model_checker.PathResult attribute) max_paths (indra.explanation.model_checker.model_checker.PathResult attribute) MechLinker (class in indra.mechlinker) MedscanEntity (class in indra.sources.medscan.processor) MedscanProcessor (class in indra.sources.medscan.processor) MedscanProperty (class in indra.sources.medscan.processor) MedscanRelation (class in indra.sources.medscan.processor) merge_deltas() (in module indra.tools.assemble_corpus) merge_groundings() (in module indra.tools.assemble_corpus) merge_results() (indra.sources.indra_db_rest.processor.IndraDBRestSearchProcessor method) metadata (indra.assemblers.html.assembler.HtmlAssembler attribute) Methylation (class in indra.statements.statements) Migration (class in indra.statements.statements) migration_from_event() (indra.sources.cwms.processor.CWMSProcessor method) ModCondition (class in indra.statements.statements) model (indra.assemblers.english.assembler.EnglishAssembler attribute) (indra.assemblers.html.assembler.HtmlAssembler attribute) (indra.assemblers.indranet.assembler.IndraNetAssembler attribute) (indra.assemblers.pysb.assembler.PysbAssembler attribute) (indra.sources.biopax.processor.BiopaxProcessor attribute) model_to_owl() (in module indra.sources.biopax.pathway_commons_client) ModelChecker (class in indra.explanation.model_checker.model_checker) Modification (class in indra.statements.statements) mods (indra.mechlinker.AgentState attribute) motif_window (indra.sources.hprd.processor.HprdProcessor attribute) MovementContext (class in indra.statements.statements) mutations (indra.mechlinker.AgentState attribute) MutCondition (class in indra.statements.statements) Myristoylation (class in indra.statements.statements)

N

name (indra.assemblers.pysb.assembler.Param attribute) (indra.assemblers.pysb.assembler.Policy attribute) (indra.sources.medscan.processor.MedscanEntity attribute) (indra.sources.medscan.processor.MedscanProperty attribute) namespace_from_uri() (in module indra.sources.bel.rdf_processor) NdexCxProcessor (class in indra.sources.ndex_cx.processor) NestedDict (class in indra.util.nested_dict) network (indra.assemblers.cx.assembler.NiceCxAssembler attribute) network_name (indra.assemblers.cx.assembler.CxAssembler attribute) NiceCxAssembler (class in indra.assemblers.cx.assembler) no_hgnc_for_egid (indra.sources.hprd.processor.HprdProcessor attribute)

no_mech_ctr (indra.sources.signor.processor.SignorProcessor attribute) no_mech_rows (indra.sources.signor.processor.SignorProcessor attribute) no_up_for_hgnc (indra.sources.hprd.processor.HprdProcessor attribute) no_up_for_refseq (indra.sources.hprd.processor.HprdProcessor attribute) node_has_edge_with_label() (indra.sources.tees.processor.TEESProcessor method) node_properties (indra.assemblers.graph.assembler.GraphAssembler attribute) node_to_evidence() (indra.sources.tees.processor.TEESProcessor method) normalize_medscan_name() (in module indra.sources.medscan.processor) NotAStatementName Nugget (class in indra.assemblers.kami.assembler) num_entities (indra.sources.medscan.processor.MedscanProcessor attribute) num_entities_not_found (indra.sources.medscan.processor.MedscanProcessor attribute)

O

obj (indra.sources.medscan.processor.MedscanRelation attribute) off_by_one (indra.sources.hprd.processor.HprdProcessor attribute)

OntologyMapper (class in indra.preassembler.ontology_mapper) owl_str_to_model() (in module indra.sources.biopax.pathway_commons_client) owl_to_model() (in module indra.sources.biopax.pathway_commons_client)

P

Palmitoylation (class in indra.statements.statements) par_to_sec (indra.sources.cwms.processor.CWMSProcessor attribute) (indra.sources.trips.processor.TripsProcessor attribute) paragraphs (indra.sources.cwms.processor.CWMSProcessor attribute) (indra.sources.trips.processor.TripsProcessor attribute) Param (class in indra.assemblers.pysb.assembler) parameters (indra.assemblers.pysb.assembler.Policy attribute) parse_identifiers_url() (in module indra.assemblers.pysb.assembler) partof() (indra.preassembler.hierarchy_manager.HierarchyManager method) path_found (indra.explanation.model_checker.model_checker.PathResult attribute) path_metrics (indra.explanation.model_checker.model_checker.PathResult attribute) PathMetric (class in indra.explanation.model_checker.model_checker) PathResult (class in indra.explanation.model_checker.model_checker) paths (indra.explanation.model_checker.model_checker.PathResult attribute) Phosphorylation (class in indra.statements.statements) physical_only (indra.sources.biogrid.BiogridProcessor attribute) pmid (indra.sources.medscan.processor.MedscanRelation attribute) policies (indra.assemblers.pysb.assembler.PysbAssembler attribute) Policy (class in indra.assemblers.pysb.assembler) position (indra.sources.reach.processor.Site attribute) preassemble() (indra.tools.incremental_model.IncrementalModel method) Preassembler (class in indra.preassembler) prep_input() (indra.tools.reading.readers.ReachReader method) (indra.tools.reading.readers.SparserReader method) print_boolean_net() (indra.assemblers.sif.assembler.SifAssembler method) print_cx() (indra.assemblers.cx.assembler.CxAssembler method) print_cyjs_context() (indra.assemblers.cyjs.assembler.CyJSAssembler method) print_cyjs_graph() (indra.assemblers.cyjs.assembler.CyJSAssembler method) print_event_statistics() (indra.sources.reach.processor.ReachProcessor method) print_loopy() (indra.assemblers.sif.assembler.SifAssembler method) print_model() (indra.assemblers.cx.assembler.NiceCxAssembler method) (indra.assemblers.index_card.assembler.IndexCardAssembler method) (indra.assemblers.pysb.assembler.PysbAssembler method) (indra.assemblers.sbgn.assembler.SBGNAssembler method) (indra.assemblers.sif.assembler.SifAssembler method) print_parent_and_children_info() (indra.sources.tees.processor.TEESProcessor method) print_statement_coverage() (indra.sources.bel.rdf_processor.BelRdfProcessor method) print_statements() (indra.sources.bel.rdf_processor.BelRdfProcessor method) (indra.sources.biopax.processor.BiopaxProcessor method) process_belrdf() (in module indra.sources.bel.api) process_belscript() (in module indra.sources.bel.api) process_binding_statements() (indra.sources.tees.processor.TEESProcessor method) process_cbn_jgif_file() (in module indra.sources.bel.api) process_csv() (in module indra.sources.tas.api) process_csxml_file() (indra.sources.medscan.processor.MedscanProcessor method) process_cx() (in module indra.sources.ndex_cx.api) process_cx_file() (in module indra.sources.ndex_cx.api) process_decrease_expression_amount() (indra.sources.tees.processor.TEESProcessor method) process_directory() (in module indra.sources.medscan.api) process_directory_statements_sorted_by_pmid() (in module indra.sources.medscan.api) process_ekb() (in module indra.sources.cwms.api) process_ekb_file() (in module indra.sources.cwms.api) process_file() (in module indra.sources.medscan.api) process_file_sorted_by_pmid() (in module indra.sources.medscan.api) process_flat_files() (in module indra.sources.hprd.api) process_from_file() (in module indra.sources.signor.api) process_from_json_file() (in module indra.sources.rlimsp.api) process_from_jsonish_str() (in module indra.sources.rlimsp.api) process_from_web() (in module indra.sources.lincs_drug.api) (in module indra.sources.trrust.api) process_from_webservice() (in module indra.sources.rlimsp.api) process_geneways_files() (in module indra.sources.geneways.api) process_increase_expression_amount() (indra.sources.tees.processor.TEESProcessor method) process_json() (in module indra.sources.eidos.api) (in module indra.sources.sofia.api) process_json_dict() (in module indra.sources.sparser.api) process_json_file() (in module indra.sources.bel.api) (in module indra.sources.eidos.api) (in module indra.sources.isi.api) (in module indra.sources.reach.api) (in module indra.sources.sofia.api)

process_json_str() (in module indra.sources.eidos.api) (in module indra.sources.reach.api) process_jsonld() (in module indra.sources.hume.api) process_jsonld_file() (in module indra.sources.hume.api) process_large_corpus() (in module indra.sources.bel.api) process_model() (in module indra.sources.biopax.api) process_ndex_network() (in module indra.sources.ndex_cx.api) process_nxml() (in module indra.sources.isi.api) process_nxml_file() (in module indra.sources.reach.api) (in module indra.sources.sparser.api) process_nxml_str() (in module indra.sources.reach.api) (in module indra.sources.sparser.api) process_output_folder() (in module indra.sources.isi.api) process_owl() (in module indra.sources.biopax.api) process_owl_str() (in module indra.sources.biopax.api) process_pc_neighborhood() (in module indra.sources.biopax.api) process_pc_pathsbetween() (in module indra.sources.biopax.api) process_pc_pathsfromto() (in module indra.sources.biopax.api) process_phosphorylation_statements() (indra.sources.tees.processor.TEESProcessor method) process_pmc() (in module indra.sources.reach.api) process_preprocessed() (in module indra.sources.isi.api) process_pubmed_abstract() (in module indra.sources.reach.api) process_pybel_graph (in module indra.sources.bel.api) process_pybel_neighborhood() (in module indra.sources.bel.api) process_pybel_network() (in module indra.sources.bel.api) process_rdf_file() (in module indra.sources.cwms.api) process_relation() (indra.sources.medscan.processor.MedscanProcessor method) process_small_corpus() (in module indra.sources.bel.api) process_sparser_output() (in module indra.sources.sparser.api) process_statement() (indra.explanation.model_checker.model_checker.ModelChecker method) (indra.explanation.model_checker.pybel.PybelModelChecker method) (indra.explanation.model_checker.pysb.PysbModelChecker method) (indra.explanation.model_checker.signed_graph.SignedGraphModelChecker method) (indra.explanation.model_checker.unsigned_graph.UnsignedGraphModelChecker method) process_subject() (indra.explanation.model_checker.model_checker.ModelChecker method) (indra.explanation.model_checker.pybel.PybelModelChecker method) (indra.explanation.model_checker.pysb.PysbModelChecker method) (indra.explanation.model_checker.signed_graph.SignedGraphModelChecker method) (indra.explanation.model_checker.unsigned_graph.UnsignedGraphModelChecker method) process_table() (in module indra.sources.sofia.api) process_text() (in module indra.sources.cwms.api) (in module indra.sources.eidos.api) (in module indra.sources.isi.api) (in module indra.sources.reach.api) (in module indra.sources.sofia.api) (in module indra.sources.sparser.api) (in module indra.sources.tees.api) (in module indra.sources.trips.api) (indra.sources.eidos.reader.EidosReader method) process_xml() (in module indra.sources.sparser.api) (in module indra.sources.trips.api) process_xml_file() (in module indra.sources.trips.api) properties (indra.sources.medscan.processor.MedscanEntity attribute) protein_map_from_twg() (in module indra.preassembler.grounding_mapper.analysis) ProteinSiteInfo (class in indra.sources.medscan.processor) prune_influence_map() (indra.explanation.model_checker.pysb.PysbModelChecker method) prune_influence_map_degrade_bind_positive() (indra.explanation.model_checker.pysb.PysbModelChecker method) prune_influence_map_subj_obj() (indra.explanation.model_checker.pysb.PysbModelChecker method) prune_nodes() (indra.explanation.model_checker.model_checker.ModelChecker method) PybelAssembler (class in indra.assemblers.pybel.assembler) PybelModelChecker (class in indra.explanation.model_checker.pybel) PybelProcessor (class in indra.sources.bel.processor) PysbAssembler (class in indra.assemblers.pysb.assembler) PysbModelChecker (class in indra.explanation.model_checker.pysb) PysbPreassembler (class in indra.assemblers.pysb.preassembler)

Q

QualitativeDelta (class in indra.statements.statements)

QuantitativeState (class in indra.statements.statements) query_target() (in module indra.databases.chembl_client)

R

ReachError ReachOfflineReadingError ReachProcessor (class in indra.sources.reach.processor) ReachReader (class in indra.sources.reach.reader) (class in indra.tools.reading.readers) read() (indra.tools.reading.readers.ReachReader method) (indra.tools.reading.readers.Reader method) (indra.tools.reading.readers.SparserReader method) (indra.tools.reading.readers.TripsReader method) read_files() (in module indra.tools.reading.read_files) read_pmc() (indra.sources.trips.drum_reader.DrumReader method) read_pmid() (in module indra.tools.reading.pmid_reading.read_pmids) read_pmid_sentences() (in module indra.tools.reading.run_drum_reading) read_some() (indra.tools.reading.readers.SparserReader method) read_text() (in module indra.tools.reading.run_drum_reading) (indra.sources.trips.drum_reader.DrumReader method) Reader (class in indra.tools.reading.readers) ReadingData (class in indra.tools.reading.readers) ReadingError receive_reply() (indra.sources.trips.drum_reader.DrumReader method) reduce_activities() (in module indra.tools.assemble_corpus) (indra.mechlinker.MechLinker method) ref_context_from_geoloc() (in module indra.sources.eidos.processor) RefContext (class in indra.statements.statements) RegulateActivity (class in indra.statements.statements) RegulateAmount (class in indra.statements.statements) related_stmts (indra.preassembler.Preassembler attribute)

remove_im_params() (in module indra.explanation.model_checker.pysb) RemoveModification (class in indra.statements.statements) rename_agents() (indra.preassembler.grounding_mapper.mapper.GroundingMapper static method) rename_db_ref() (in module indra.tools.assemble_corpus) render_stmt_graph() (in module indra.preassembler) replace_activations() (indra.mechlinker.MechLinker method) replace_activities() (indra.assemblers.pysb.preassembler.PysbPreassembler method) replace_complexes() (indra.mechlinker.MechLinker method) Reporter (class in indra.tools.reading.util.reporter) require_active_forms() (indra.mechlinker.MechLinker method) reset_scorer() (indra.tools.live_curation.LiveCurator method) residue (indra.sources.reach.processor.Site attribute) result_code (indra.explanation.model_checker.model_checker.PathResult attribute) results (indra.tools.gene_network.GeneNetwork attribute) Ribosylation (class in indra.statements.statements) RlimspParagraph (class in indra.sources.rlimsp.processor) RlimspProcessor (class in indra.sources.rlimsp.processor) run_adeft_disambiguation() (in module indra.preassembler.grounding_mapper.adeft) run_eidos() (in module indra.sources.eidos.cli) run_on_text() (in module indra.sources.tees.api) run_preassembly() (in module indra.tools.assemble_corpus) (indra.tools.gene_network.GeneNetwork method) run_preassembly_duplicate() (in module indra.tools.assemble_corpus) run_preassembly_related() (in module indra.tools.assemble_corpus) run_reach() (in module indra.tools.reading.pmid_reading.read_pmids) run_sparser() (in module indra.sources.sparser.api) (in module indra.tools.reading.pmid_reading.read_pmids)

S

s2a() (in module indra.sources.tees.processor) s3_get() (indra.tools.live_curation.Corpus method) s3_put() (indra.tools.live_curation.Corpus method) sample_statements() (in module indra.belief) save() (indra.tools.incremental_model.IncrementalModel method) save_base_map() (in module indra.preassembler.grounding_mapper.analysis) save_dot() (indra.assemblers.graph.assembler.GraphAssembler method) save_json() (indra.assemblers.cyjs.assembler.CyJSAssembler method) save_model() (indra.assemblers.cx.assembler.CxAssembler method) (indra.assemblers.cyjs.assembler.CyJSAssembler method) (indra.assemblers.html.assembler.HtmlAssembler method) (indra.assemblers.index_card.assembler.IndexCardAssembler method) (indra.assemblers.pybel.assembler.PybelAssembler method) (indra.assemblers.pysb.assembler.PysbAssembler method) (indra.assemblers.sbgn.assembler.SBGNAssembler method) (indra.assemblers.sif.assembler.SifAssembler method) (indra.sources.biopax.processor.BiopaxProcessor method) save_pdf() (indra.assemblers.graph.assembler.GraphAssembler method) save_rst() (indra.assemblers.pysb.assembler.PysbAssembler method) save_sentences() (in module indra.preassembler.grounding_mapper.analysis) save_xml() (in module indra.sources.trips.client) sbgn (indra.assemblers.sbgn.assembler.SBGNAssembler attribute) SBGNAssembler (class in indra.assemblers.sbgn.assembler) score_evidence_list() (indra.belief.SimpleScorer method) score_paths() (indra.explanation.model_checker.pysb.PysbModelChecker method) score_statement() (indra.belief.BeliefScorer method) (indra.belief.SimpleScorer method) scorer (indra.belief.BeliefEngine attribute) search_science_direct (in module indra.literature.elsevier_client) sec (indra.sources.medscan.processor.MedscanRelation attribute) SelfModification (class in indra.statements.statements) send_query() (in module indra.databases.chembl_client) (in module indra.sources.trips.client) send_request (in module indra.databases.cbio_client) send_request() (in module indra.databases.ndex_client) (in module indra.literature.newsapi_client) sentence_statements (indra.sources.medscan.processor.MedscanProcessor attribute) sentences (indra.sources.cwms.processor.CWMSProcessor attribute) (indra.sources.trips.processor.TripsProcessor attribute) separate_reach_logs() (in module indra.tools.reading.util.log_analysis_tools) seq_dict (indra.sources.hprd.processor.HprdProcessor attribute) set_base_initial_condition() (in module indra.assemblers.pysb.assembler) set_CCLE_context() (indra.assemblers.cyjs.assembler.CyJSAssembler method) set_context() (indra.assemblers.cx.assembler.CxAssembler method) (indra.assemblers.pysb.assembler.PysbAssembler method) set_expression() (indra.assemblers.pysb.assembler.PysbAssembler method) set_extended_initial_condition() (in module indra.assemblers.pysb.assembler) set_fig_params() (in module indra.util.plot_formatting) set_hierarchy_probs() (indra.belief.BeliefEngine method) set_linked_probs() (indra.belief.BeliefEngine method) set_location() (indra.tools.reading.readers.Content method) set_prior_probs() (indra.belief.BeliefEngine method) set_section_order() (indra.tools.reading.util.reporter.Reporter method) set_style() (in module indra.databases.ndex_client) set_title() (indra.tools.reading.util.reporter.Reporter method) set_value() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) set_values() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) SifAssembler (class in indra.assemblers.sif.assembler) signed_edges_to_signed_nodes() (indra.explanation.model_checker.model_checker.ModelChecker method) signed_from_df() (indra.assemblers.indranet.net.IndraNet class method) SignedGraphModelChecker (class in indra.explanation.model_checker.signed_graph) SignorProcessor (class in indra.sources.signor.processor) SimpleScorer (class in indra.belief)

Site (class in indra.sources.reach.processor) SiteMapper (class in indra.preassembler.sitemapper) sites (indra.assemblers.pysb.assembler.Policy attribute) source_node (indra.explanation.model_checker.model_checker.PathMetric attribute) SparserError SparserReader (class in indra.tools.reading.readers) standardize_agent_name() (indra.preassembler.grounding_mapper.mapper.GroundingMapper static method) standardize_db_refs() (indra.preassembler.grounding_mapper.mapper.GroundingMapper static method) standardize_names_groundings() (in module indra.tools.assemble_corpus) state_matches_key() (indra.statements.statements.Agent method) Statement (class in indra.statements.statements) statement_base_verb() (in module indra.assemblers.english.assembler) statement_key (indra.belief.BeliefPackage attribute) statement_passive_verb() (in module indra.assemblers.english.assembler) statement_present_verb() (in module indra.assemblers.english.assembler) statements (indra.assemblers.cag.assembler.CAGAssembler attribute) (indra.assemblers.cx.assembler.CxAssembler attribute) (indra.assemblers.cyjs.assembler.CyJSAssembler attribute) (indra.assemblers.english.assembler.EnglishAssembler attribute) (indra.assemblers.graph.assembler.GraphAssembler attribute) (indra.assemblers.html.assembler.HtmlAssembler attribute) (indra.assemblers.index_card.assembler.IndexCardAssembler attribute) (indra.assemblers.pysb.assembler.PysbAssembler attribute) (indra.assemblers.sbgn.assembler.SBGNAssembler attribute) (indra.assemblers.tsv.assembler.TsvAssembler attribute) (indra.sources.bel.processor.PybelProcessor attribute) (indra.sources.bel.rdf_processor.BelRdfProcessor attribute) (indra.sources.biogrid.BiogridProcessor attribute) (indra.sources.biopax.processor.BiopaxProcessor attribute) (indra.sources.cwms.processor.CWMSProcessor attribute) (indra.sources.cwms.rdf_processor.CWMSRDFProcessor attribute) (indra.sources.eidos.processor.EidosProcessor attribute) (indra.sources.geneways.processor.GenewaysProcessor attribute) (indra.sources.hprd.processor.HprdProcessor attribute) (indra.sources.hume.processor.HumeJsonLdProcessor attribute) (indra.sources.indra_db_rest.processor.IndraDBRestHashProcessor attribute) (indra.sources.indra_db_rest.processor.IndraDBRestSearchProcessor attribute) (indra.sources.isi.processor.IsiProcessor attribute) (indra.sources.lincs_drug.processor.LincsProcessor attribute) (indra.sources.medscan.processor.MedscanProcessor attribute) (indra.sources.ndex_cx.processor.NdexCxProcessor attribute) (indra.sources.reach.processor.ReachProcessor attribute) (indra.sources.signor.processor.SignorProcessor attribute) (indra.sources.tees.processor.TEESProcessor attribute) (indra.sources.trips.processor.TripsProcessor attribute) (indra.sources.trrust.processor.TrrustProcessor attribute) (indra.tools.live_curation.Corpus attribute) statements_sample (indra.sources.indra_db_rest.processor.IndraDBRestSearchProcessor attribute) stmt_type() (in module indra.statements.statements) stmts (indra.preassembler.Preassembler attribute) (indra.tools.incremental_model.IncrementalModel attribute) stmts_from_json() (in module indra.statements.statements) stmts_from_json_file() (in module indra.statements.statements) stmts_to_json() (in module indra.statements.statements) stmts_to_json_file() (in module indra.statements.statements) strip_agent_context() (in module indra.tools.assemble_corpus) subj (indra.sources.medscan.processor.MedscanRelation attribute) submit_combine() (in module indra.tools.reading.submit_reading_pipeline) submit_curation() (in module indra.sources.indra_db_rest.api) (indra.tools.live_curation.LiveCurator method) submit_reading() (in module indra.tools.reading.submit_reading_pipeline) Sumoylation (class in indra.statements.statements) svo_type (indra.sources.medscan.processor.MedscanRelation attribute)

T

tag_evidence_subtype() (in module indra.belief) tag_instance() (in module indra.util.aws) tag_instances_on_cluster() (in module indra.tools.reading.submit_reading_pipeline) tag_myself() (in module indra.util.aws) tag_text() (in module indra.assemblers.html.assembler) tagged_sentence (indra.sources.medscan.processor.MedscanRelation attribute) target_node (indra.explanation.model_checker.model_checker.PathMetric attribute) TasProcessor (class in indra.sources.tas.processor) TEESProcessor (class in indra.sources.tees.processor) term_from_uri() (in module indra.sources.bel.rdf_processor) time_context_from_ref() (indra.sources.eidos.processor.EidosProcessor method) time_context_from_timex() (in module indra.sources.eidos.processor) TimeContext (class in indra.statements.statements) to_database() (indra.assemblers.pybel.assembler.PybelAssembler method) to_digraph() (indra.assemblers.indranet.net.IndraNet method) to_graph() (indra.statements.statements.Statement method) to_impl() (in module indra.sources.biopax.processor) to_json() (indra.statements.statements.ActiveForm method) (indra.statements.statements.Association method) (indra.statements.statements.Complex method) (indra.statements.statements.Conversion method) (indra.statements.statements.Event method) (indra.statements.statements.Evidence method) (indra.statements.statements.Gap method) (indra.statements.statements.Gef method) (indra.statements.statements.Influence method) (indra.statements.statements.Modification method) (indra.statements.statements.RegulateActivity method) (indra.statements.statements.RegulateAmount method) (indra.statements.statements.SelfModification method) (indra.statements.statements.Statement method) (indra.statements.statements.Translocation method)

to_signed_graph() (indra.assemblers.indranet.net.IndraNet method) to_web() (indra.assemblers.pybel.assembler.PybelAssembler method) Translocation (class in indra.statements.statements) Transphosphorylation (class in indra.statements.statements) tree (indra.sources.cwms.processor.CWMSProcessor attribute) (indra.sources.hume.processor.HumeJsonLdProcessor attribute) (indra.sources.reach.processor.ReachProcessor attribute) (indra.sources.trips.processor.TripsProcessor attribute) TripsProcessor (class in indra.sources.trips.processor) TripsReader (class in indra.tools.reading.readers) TrrustProcessor (class in indra.sources.trrust.processor) TsvAssembler (class in indra.assemblers.tsv.assembler) type (indra.sources.medscan.processor.MedscanEntity attribute) (indra.sources.medscan.processor.MedscanProperty attribute)

U

Ubiquitination (class in indra.statements.statements) ungrounded_texts() (in module indra.preassembler.grounding_mapper.analysis) unique (indra.assemblers.pysb.assembler.Param attribute) unique_stmts (indra.preassembler.Preassembler attribute) universal_extract_paragraphs() (in module indra.literature.adeft_tools) universal_extract_text() (in module indra.literature.adeft_tools) UnknownNamespaceException UnknownPolicyError Unresolved (class in indra.statements.statements) UnresolvedUuidError UnsignedGraphModelChecker (class in indra.explanation.model_checker.unsigned_graph)

update() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) update_agent_db_refs() (indra.preassembler.grounding_mapper.mapper.GroundingMapper method) update_beliefs() (indra.tools.live_curation.LiveCurator method) update_counts() (indra.belief.BayesianScorer method) update_id_mappings() (in module indra.databases.go_client) update_network() (in module indra.databases.ndex_client) update_probs() (indra.belief.BayesianScorer method) update_secondary_mappings() (in module indra.databases.go_client) upload_model() (indra.assemblers.cx.assembler.CxAssembler method) urn (indra.sources.medscan.processor.MedscanEntity attribute) (indra.sources.medscan.processor.MedscanProperty attribute)

V

value (indra.assemblers.pysb.assembler.Param attribute) value_per_second() (indra.statements.statements.QuantitativeState static method)

verb (indra.sources.medscan.processor.MedscanRelation attribute) verbs (indra.sources.isi.processor.IsiProcessor attribute)

W

wait_for_complete() (in module indra.tools.reading.submit_reading_pipeline)

wait_until_done() (indra.sources.indra_db_rest.processor.IndraDBRestSearchProcessor method) WorldContext (class in indra.statements.statements)

Y

YamlHierarchyManager (class in indra.preassembler.hierarchy_manager)