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_default_initial_conditions() (indra.assemblers.pysb.assembler.PysbAssembler method) add_image() (indra.tools.reading.util.reporter.Reporter 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.pysb.assembler.PysbAssembler method) (indra.assemblers.pysb.preassembler.PysbPreassembler method) (indra.assemblers.sbgn.assembler.SBGNAssembler method) (indra.explanation.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) 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.Statement method) agent_map (indra.preassembler.grounding_mapper.GroundingMapper attribute) agent_set (indra.assemblers.pysb.assembler.PysbAssembler attribute) agent_texts() (in module indra.preassembler.grounding_mapper) agent_texts_with_grounding() (in module indra.preassembler.grounding_mapper) AgentState (class in indra.mechlinker) align_statements() (in module indra.tools.assemble_corpus) all_agents() (in module indra.preassembler.grounding_mapper) 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_model() (indra.explanation.model_checker.ModelChecker method) check_prior_probs() (indra.belief.BeliefScorer method) (indra.belief.SimpleScorer method) check_statement() (indra.explanation.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.util.kappa_util) combine_duplicate_stmts() (indra.preassembler.Preassembler static 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) connected_subgraph() (indra.sources.tees.processor.TEESProcessor method) Content (class in indra.tools.reading.readers) Context (class in indra.statements.statements) Conversion (class in indra.statements.statements) 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) 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) 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) default_mapper (in module indra.preassembler.sitemapper) 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) 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) 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.ModelChecker 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) 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) 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) extra_annotations (indra.sources.isi.processor.IsiProcessor attribute) extract_and_process() (in module indra.sources.eidos.cli) extract_from_directory() (in module indra.sources.eidos.cli) extract_noun_relations() (indra.sources.cwms.processor.CWMSProcessor method) extract_output() (in module indra.sources.tees.api) 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) 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_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() (indra.sources.eidos.processor.EidosProcessor static method) find_args() (indra.sources.eidos.processor.EidosProcessor static method) 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) flatten_evidence() (in module indra.preassembler) flatten_stmts() (in module indra.preassembler) format_axis() (in module indra.util.plot_formatting) from_file() (indra.tools.reading.readers.Content class 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.ModelChecker 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_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) 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_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_relations() (indra.sources.eidos.processor.EidosProcessor method) 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_id_from_cas() (in module indra.databases.chebi_client) get_chebi_id_from_pubchem() (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_cols() (indra.tools.reading.readers.ReadingData static method) (indra.tools.reading.util.script_tools.StatementData class method) get_complexes() (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_concept() (indra.sources.eidos.processor.EidosProcessor static method) get_conversions() (indra.sources.bel.rdf_processor.BelRdfProcessor method) (indra.sources.biopax.processor.BiopaxProcessor 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_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_documents() (indra.sources.hume.processor.HumeJsonLdProcessor method) 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_entity_text_for_relation() (indra.sources.tees.processor.TEESProcessor method) get_entrez_id() (in module indra.databases.hgnc_client) get_ev_count() (indra.sources.indra_db_rest.processor.IndraDBRestProcessor method) get_ev_count_by_hash() (indra.sources.indra_db_rest.processor.IndraDBRestProcessor method) get_ev_counts() (indra.sources.indra_db_rest.processor.IndraDBRestProcessor method) get_evidence() (in module indra.databases.chembl_client) (indra.sources.eidos.processor.EidosProcessor method) get_family_members() (in module indra.databases.uniprot_client) 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_function() (in module indra.databases.uniprot_client) get_gap() (indra.sources.biopax.processor.BiopaxProcessor method) get_gef() (indra.sources.biopax.processor.BiopaxProcessor method) get_gene_name() (in module indra.databases.uniprot_client) get_gene_names() (indra.assemblers.cyjs.assembler.CyJSAssembler method) get_gene_synonyms() (in module indra.databases.uniprot_client) get_genetic_profiles() (in module indra.databases.cbio_client) get_git_info() (in module indra.util.get_version) get_go_label() (in module indra.databases.go_client) get_groundings() (indra.sources.eidos.processor.EidosProcessor static method) get_hash() (indra.statements.statements.Statement method) get_hash_statements_dict() (indra.sources.indra_db_rest.processor.IndraDBRestProcessor 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_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_name() (in module indra.databases.hgnc_client) get_id_count() (in module indra.literature.pubmed_client) get_id_from_mgi() (in module indra.databases.uniprot_client) get_id_from_mnemonic() (in module indra.databases.uniprot_client) get_id_from_rgd() (in module indra.databases.uniprot_client) get_ids (in module indra.literature.pubmed_client) get_ids_for_gene (in module indra.literature.pubmed_client) get_im() (indra.explanation.model_checker.ModelChecker method) 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_length() (in module indra.databases.uniprot_client) 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_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_mgi_id() (in module indra.databases.uniprot_client) get_mnemonic() (in module indra.databases.uniprot_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) (in module indra.databases.uniprot_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_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_primary_id() (in module indra.databases.uniprot_client) 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_synonyms() (in module indra.databases.uniprot_client) get_protein_targets_only() (in module indra.databases.chembl_client) 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) (in module indra.databases.uniprot_client) get_reader() (in module indra.tools.reading.readers) get_reader_class() (in module indra.tools.reading.readers) get_readers() (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_rgd_id() (in module indra.databases.uniprot_client) get_s3_file_tree() (in module indra.util.aws) get_sentences_for_agent() (in module indra.preassembler.grounding_mapper) 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_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_synonyms() (in module indra.databases.uniprot_client) get_syntheses() (indra.sources.trips.processor.TripsProcessor method) get_target_chemblid() (in module indra.databases.chembl_client) get_text() (indra.tools.reading.readers.Content method) 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_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_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) gm (indra.preassembler.grounding_mapper.GroundingMapper attribute) graph (indra.assemblers.graph.assembler.GraphAssembler attribute) (indra.assemblers.sif.assembler.SifAssembler 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) 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)

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

I

id_lookup() (in module indra.literature) (in module indra.literature.pmc_client) im_json_to_graph() (in module indra.util.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.pysb.assembler (module) indra.assemblers.pysb.base_agents (module) indra.assemblers.pysb.bmi_wrapper (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.go_client (module) indra.databases.hgnc_client (module) indra.databases.lincs_client (module) indra.databases.mesh_client (module) indra.databases.ndex_client (module) indra.databases.relevance_client (module) indra.databases.uniprot_client (module) indra.explanation.model_checker (module) indra.literature (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.hierarchy_manager (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.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 (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.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.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.kappa_util (module) indra.util.nested_dict (module) indra.util.plot_formatting (module) IndraDBRestProcessor (class in indra.sources.indra_db_rest.processor) 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) Inhibition (class in indra.statements.statements) initialize() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) initialize_reader() (in module indra.sources.eidos.api) InputError InvalidLocationError InvalidResidueError is_format() (indra.tools.reading.readers.Content method) is_human() (in module indra.databases.uniprot_client) is_mouse() (in module indra.databases.uniprot_client) is_opposite() (indra.preassembler.hierarchy_manager.HierarchyManager method) is_rat() (in module indra.databases.uniprot_client) is_secondary() (in module indra.databases.uniprot_client) is_statement_in_list() (in module indra.sources.medscan.processor) is_working() (indra.sources.indra_db_rest.processor.IndraDBRestProcessor 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)

J

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

K

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

L

last_site_info_in_sentence (indra.sources.medscan.processor.MedscanProcessor attribute) length (indra.explanation.model_checker.PathMetric attribute) LincsClient (class in indra.databases.lincs_client) LincsProcessor (class in indra.sources.lincs_drug.processor) LinkedStatement (class in indra.mechlinker) load_go_graph() (in module indra.databases.go_client)

load_grounding_map() (in module indra.preassembler.grounding_mapper) load_lincs_csv() (in module indra.databases.lincs_client) load_prior() (indra.tools.incremental_model.IncrementalModel method) load_site_map() (in module indra.preassembler.sitemapper) load_statements() (in module indra.tools.assemble_corpus) location (indra.mechlinker.AgentState attribute)

M

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.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.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_statements() (in module indra.tools.reading.util.script_tools) make_tuple() (indra.tools.reading.readers.ReadingData method) (indra.tools.reading.util.script_tools.StatementData method) map_agent() (indra.preassembler.grounding_mapper.GroundingMapper method) map_agents() (indra.preassembler.grounding_mapper.GroundingMapper method) map_agents_for_stmt() (indra.preassembler.grounding_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) MappedStatement (class in indra.preassembler.sitemapper) matches() (indra.tools.reading.readers.ReadingData method) matches_key() (indra.statements.statements.Agent method) max_path_length (indra.explanation.model_checker.PathResult attribute) max_paths (indra.explanation.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.IndraDBRestProcessor method) metadata (indra.assemblers.html.assembler.HtmlAssembler attribute) Methylation (class in indra.statements.statements) ModCondition (class in indra.statements.statements) model (indra.assemblers.english.assembler.EnglishAssembler attribute) (indra.assemblers.html.assembler.HtmlAssembler 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) Modification (class in indra.statements.statements) mods (indra.mechlinker.AgentState attribute) 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_name (indra.assemblers.cx.assembler.CxAssembler 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 num_documents (in module indra.sources.medscan.api) 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)

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.PathResult attribute) path_metrics (indra.explanation.model_checker.PathResult attribute) PathMetric (class in indra.explanation.model_checker) PathResult (class in indra.explanation.model_checker) paths (indra.explanation.model_checker.PathResult attribute) Phosphorylation (class in indra.statements.statements) physical_only (indra.sources.biogrid.BiogridProcessor attribute) pmid (indra.sources.isi.processor.IsiProcessor attribute) polarity (indra.explanation.model_checker.PathMetric 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.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_csv() (in module indra.sources.tas.api) process_csxml_from_file_handle() (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_from_web() (in module indra.sources.lincs_drug.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) process_json_ld() (in module indra.sources.eidos.api) process_json_ld_file() (in module indra.sources.eidos.api) process_json_ld_str() (in module indra.sources.eidos.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_model() (in module indra.sources.biopax.api) process_ndex_neighborhood() (in module indra.sources.bel.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_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_rdf_file() (in module indra.sources.cwms.api) process_relation() (indra.sources.medscan.processor.MedscanProcessor method) process_sparser_output() (in module indra.sources.sparser.api) 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) ProteinSiteInfo (class in indra.sources.medscan.processor) prune_influence_map() (indra.explanation.model_checker.ModelChecker method) prune_influence_map_subj_obj() (indra.explanation.model_checker.ModelChecker method) PybelProcessor (class in indra.sources.bel.processor) PysbAssembler (class in indra.assemblers.pysb.assembler) PysbPreassembler (class in indra.assemblers.pysb.preassembler)

Q

query_protein (in module indra.databases.uniprot_client)

query_target() (in module indra.databases.chembl_client)

R

ReachError 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) 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) reader_output (indra.sources.isi.processor.IsiProcessor attribute) 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() (indra.sources.eidos.processor.EidosProcessor static method) 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) RemoveModification (class in indra.statements.statements) rename_agents() (indra.preassembler.grounding_mapper.GroundingMapper 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) residue (indra.sources.reach.processor.Site attribute) result_code (indra.explanation.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_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) sample_statements() (in module indra.belief) save() (indra.tools.incremental_model.IncrementalModel method) save_base_map() (in module indra.preassembler.grounding_mapper) 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.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) 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.ModelChecker method) score_statement() (indra.belief.BeliefScorer method) (indra.belief.SimpleScorer method) scorer (indra.belief.BeliefEngine attribute) 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) 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)

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.PathMetric attribute) SparserError SparserReader (class in indra.tools.reading.readers) state_matches_key() (indra.statements.statements.Agent method) Statement (class in indra.statements.statements) statement_key (indra.belief.BeliefPackage attribute) StatementData (class in indra.tools.reading.util.script_tools) 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.hume.processor.HumeJsonLdProcessor attribute) (indra.sources.indra_db_rest.processor.IndraDBRestProcessor 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.tees.processor.TEESProcessor attribute) (indra.sources.trips.processor.TripsProcessor attribute) statements_sample (indra.sources.indra_db_rest.processor.IndraDBRestProcessor attribute) stmt_from_rule() (in module indra.explanation.model_checker) 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) 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.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_dct() (indra.sources.eidos.processor.EidosProcessor static method) time_context_from_ref() (indra.sources.eidos.processor.EidosProcessor method) time_context_from_timex() (indra.sources.eidos.processor.EidosProcessor static method) TimeContext (class in indra.statements.statements) to_graph() (indra.statements.statements.Statement method) to_json() (indra.statements.statements.ActiveForm method) (indra.statements.statements.Complex method) (indra.statements.statements.Conversion 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)

Translocation (class in indra.statements.statements) Transphosphorylation (class in indra.statements.statements) tree (indra.sources.cwms.processor.CWMSProcessor attribute) (indra.sources.eidos.processor.EidosProcessor 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) 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) unique (indra.assemblers.pysb.assembler.Param attribute) unique_stmts (indra.preassembler.Preassembler attribute) UnknownNamespaceException UnknownPolicyError Unresolved (class in indra.statements.statements) UnresolvedUuidError update() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)

update_agent_db_refs() (indra.preassembler.grounding_mapper.GroundingMapper 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) upload_model() (indra.assemblers.cx.assembler.CxAssembler method) uri (indra.sources.medscan.processor.MedscanRelation attribute) urn (indra.sources.medscan.processor.MedscanEntity attribute) (indra.sources.medscan.processor.MedscanProperty attribute)

V

value (indra.assemblers.pysb.assembler.Param attribute) verb (indra.sources.medscan.processor.MedscanRelation attribute)

verbs (indra.sources.isi.processor.IsiProcessor attribute) verify_location() (in module indra.databases.uniprot_client) verify_modification() (in module indra.databases.uniprot_client)

W

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

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

Z

zip_content() (indra.tools.reading.readers.ReadingData method)