Index

A

Acetylation (class in indra.statements.statements) AcsnProcessor (class in indra.sources.acsn.processor) 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.agent) (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_edges_from() (indra.ontology.bio.BioOntology method) (indra.ontology.bio.ontology.BioOntology method) add_node() (indra.assemblers.cx.assembler.NiceCxAssembler method) (indra.assemblers.kami.assembler.Nugget method) add_nodes_from() (indra.ontology.bio.BioOntology method) (indra.ontology.bio.ontology.BioOntology method) add_reverse_effects() (indra.assemblers.pysb.preassembler.PysbPreassembler method) add_rule_to_model() (in module indra.assemblers.pysb.assembler) add_site_states() (indra.assemblers.pysb.base_agents.BaseAgent method) add_statements() (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_stats() (indra.util.statement_presentation.StmtGroup method) add_typing() (indra.assemblers.kami.assembler.Nugget method) AddModification (class in indra.statements.statements) Agent (class in indra.statements.agent) (class in indra.statements.statements) agent_grounding_matches() (in module indra.preassembler.custom_preassembly) agent_list() (indra.statements.statements.Association method) (indra.statements.statements.Influence method) (indra.statements.statements.Statement method)

agent_name_matches() (in module indra.preassembler.custom_preassembly) agent_name_polarity_matches() (in module indra.preassembler.custom_preassembly) agent_name_stmt_matches() (in module indra.preassembler.custom_preassembly) agent_name_stmt_type_matches() (in module indra.preassembler.custom_preassembly) 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) agents (indra.assemblers.english.assembler.SentenceBuilder attribute) agents_stmt_type_matches() (in module indra.preassembler.custom_preassembly) AgentState (class in indra.mechlinker) AgentWithCoordinates (class in indra.assemblers.english.assembler) AggregatorMeta (class in indra.util.statement_presentation) align_statements() (in module indra.tools.assemble_corpus) all_agents() (in module indra.preassembler.grounding_mapper.analysis) all_events (indra.sources.reach.processor.ReachProcessor attribute) all_nodes (indra.explanation.model_checker.model_checker.NodesContainer attribute) all_sources (in module indra.util.statement_presentation) And (class in indra.sources.indra_db_rest.query) annotate_paper_from_db() (in module indra.tools.hypothesis_annotator) api_ruler (indra.sources.reach.reader.ReachReader attribute) append() (indra.assemblers.english.assembler.SentenceBuilder method) (indra.pipeline.pipeline.AssemblyPipeline method) append_as_list() (indra.assemblers.english.assembler.SentenceBuilder method) append_as_sentence() (indra.assemblers.english.assembler.SentenceBuilder method) append_warning() (indra.assemblers.html.assembler.HtmlAssembler method) apply_to() (indra.mechlinker.AgentState method) assembled_stmts (indra.tools.incremental_model.IncrementalModel attribute) AssemblyPipeline (class in indra.pipeline.pipeline) assert_no_cycle() (in module indra.belief) assert_valid_agent() (in module indra.statements.validate) assert_valid_bio_context() (in module indra.statements.validate) assert_valid_context() (in module indra.statements.validate) assert_valid_db_refs() (in module indra.statements.validate) assert_valid_evidence() (in module indra.statements.validate) assert_valid_id() (in module indra.statements.validate) assert_valid_ns() (in module indra.statements.validate) assert_valid_pmid_text_refs() (in module indra.statements.validate) assert_valid_statement() (in module indra.statements.validate) assert_valid_statement_semantics() (in module indra.statements.validate) assert_valid_statements() (in module indra.statements.validate) assert_valid_text_refs() (in module indra.statements.validate) Association (class in indra.statements.statements) Autophosphorylation (class in indra.statements.statements) available_sources_src_counts() (in module indra.util.statement_presentation) available_sources_stmts() (in module indra.util.statement_presentation) AveAggregator (class in indra.util.statement_presentation)

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) BasicAggregator (class in indra.util.statement_presentation) BayesianScorer (class in indra.belief) BeliefEngine (class in indra.belief) beliefs (indra.assemblers.html.assembler.HtmlAssembler attribute) BeliefScorer (class in indra.belief) bfs_search() (in module indra.explanation.pathfinding.pathfinding) bfs_search_multiple_nodes() (in module indra.explanation.pathfinding.pathfinding)

BioContext (class in indra.statements.context) (class in indra.statements.statements) BioFactoidProcessor (class in indra.sources.biofactoid.processor) BiogridProcessor (class in indra.sources.biogrid) BioOntology (class in indra.ontology.bio) (class in indra.ontology.bio.ontology) BiopaxProcessor (class in indra.sources.biopax.processor) BioregistryValidator (class in indra.statements.validate) BMIModel (class in indra.assemblers.pysb.bmi_wrapper) bound_conditions (indra.mechlinker.AgentState attribute) BoundCondition (class in indra.statements.agent) (class in indra.statements.statements) build_refinements_graph() (in module indra.belief)

C

cancel() (indra.sources.indra_db_rest.processor.IndraDBQueryProcessor method) check_entitlement() (in module indra.literature.elsevier_client) check_extra_evidence() (in module indra.belief) 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) (indra.belief.skl.HybridScorer method) (indra.belief.skl.SklearnScorer method) check_statement() (indra.explanation.model_checker.model_checker.ModelChecker method) citation (indra.sources.reach.processor.ReachProcessor attribute) cli() (indra.sources.utils.Processor class method) cm_json_to_graph() (in module indra.assemblers.pysb.kappa_util) cm_json_to_networkx() (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) common_target (indra.explanation.model_checker.model_checker.NodesContainer attribute) 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) compositional_sort_key() (in module indra.statements.concept) Concept (class in indra.statements.concept) (class in indra.statements.statements) concept (indra.statements.statements.Event attribute)

connected_subgraph() (indra.sources.tees.processor.TEESProcessor method) Context (class in indra.statements.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) copy() (indra.sources.indra_db_rest.query.Query method) copy_default_config() (in module indra.tools.machine) correspondence_dict (indra.sources.acsn.processor.AcsnProcessor attribute) CountsScorer (class in indra.belief.skl) create_mod_site() (indra.assemblers.pysb.base_agents.BaseAgent method) create_network() (in module indra.databases.ndex_client) create_new_step() (indra.pipeline.pipeline.AssemblyPipeline method) create_site() (indra.assemblers.pysb.base_agents.BaseAgent method) CREEDSChemicalProcessor (class in indra.sources.creeds.processor) CREEDSDiseaseProcessor (class in indra.sources.creeds.processor) CREEDSGeneProcessor (class in indra.sources.creeds.processor) CrogProcessor (class in indra.sources.crog.processor) CTDChemicalDiseaseProcessor (class in indra.sources.ctd.processor) CTDChemicalGeneProcessor (class in indra.sources.ctd.processor) CTDGeneDiseaseProcessor (class in indra.sources.ctd.processor) CTDProcessor (class in indra.sources.ctd.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) db_sources (in module indra.util.statement_presentation) DB_TEXT_COLOR (in module indra.assemblers.html.assembler) DBQueryHashProcessor (class in indra.sources.indra_db_rest.processor) DBQueryStatementProcessor (class in indra.sources.indra_db_rest.processor) Deacetylation (class in indra.statements.statements) DecreaseAmount (class in indra.statements.statements) Defarnesylation (class in indra.statements.statements) 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) (indra.sources.virhostnet.processor.VirhostnetProcessor attribute)

df_to_matrix() (indra.belief.skl.CountsScorer method) (indra.belief.skl.SklearnScorer method) DGIProcessor (class in indra.sources.dgi.processor) digraph_from_df() (indra.assemblers.indranet.net.IndraNet class method) DisambManager (class in indra.preassembler.grounding_mapper.disambiguate) doc_id (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.io) (in module indra.statements.statements) DrugbankProcessor (class in indra.sources.drugbank.processor) drum_system (indra.sources.trips.drum_reader.DrumReader attribute) DrumReader (class in indra.sources.trips.drum_reader) dump() (indra.util.aws.JobLog method) 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) EidosBioProcessor (class in indra.sources.eidos.bio_processor) EidosProcessor (class in indra.sources.eidos.processor) EidosReader (class in indra.sources.eidos.reader) eliminate_exact_duplicates() (indra.sources.biopax.processor.BiopaxProcessor method) EmptyQuery (class in indra.sources.indra_db_rest.query) english_join() (in module indra.assemblers.english.assembler) EnglishAssembler (class in indra.assemblers.english.assembler) ensure_chebi_prefix() (in module indra.databases.identifiers) ensure_chembl_prefix() (in module indra.databases.identifiers) ensure_prefix() (in module indra.databases.identifiers) ensure_prefix_if_needed() (in module indra.databases.bioregistry_client) (in module indra.databases.identifiers) entity_matches_key() (indra.statements.agent.Agent method) (indra.statements.statements.Agent method) entries_from_graph() (indra.databases.obo_client.OboClient static method) entry_from_term() (indra.databases.owl_client.OwlClient static method) ev_counts (indra.assemblers.html.assembler.HtmlAssembler attribute) Event (class in indra.statements.statements) Evidence (class in indra.statements.evidence) (class in indra.statements.statements) evidence_random_noise_prior() (in module indra.belief) existing_edges (indra.assemblers.graph.assembler.GraphAssembler attribute) existing_nodes (indra.assemblers.graph.assembler.GraphAssembler attribute) ExistingFunctionError 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) extend() (indra.preassembler.refinement.OntologyRefinementFilter method) (indra.preassembler.refinement.RefinementFilter method) extend_refinements_graph() (in module indra.belief) extract_all_events() (indra.sources.eidos.processor.EidosProcessor method) extract_and_process() (in module indra.sources.eidos.cli) extract_causal_relations() (indra.sources.eidos.processor.EidosProcessor method) extract_correlations() (indra.sources.eidos.processor.EidosProcessor method) extract_events() (indra.sources.eidos.processor.EidosProcessor method) extract_from_directory() (in module indra.sources.eidos.cli) extract_groundings() (indra.sources.hypothesis.processor.HypothesisProcessor method) extract_output() (in module indra.sources.tees.api) extract_paragraphs() (in module indra.literature.elsevier_client) (in module indra.literature.pmc_client) extract_predication() (indra.sources.semrep.processor.SemRepXmlProcessor method) extract_statements() (indra.sources.acsn.processor.AcsnProcessor method) (indra.sources.crog.processor.CrogProcessor method) (indra.sources.dgi.processor.DGIProcessor method) (indra.sources.hypothesis.processor.HypothesisProcessor method) (indra.sources.rlimsp.processor.RlimspProcessor method) (indra.sources.trrust.processor.TrrustProcessor method) (indra.sources.utils.Processor method) (indra.sources.utils.RemoteProcessor method) extract_stmts() (indra.sources.gnbr.processor.GnbrProcessor 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) feature_delta() (indra.sources.biopax.processor.BiopaxProcessor method) fill_from_stmt_stats() (indra.util.statement_presentation.StmtGroup method) filter_belief() (in module indra.tools.assemble_corpus) filter_by_curation() (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_complexes_by_size() (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() (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_event_parent_with_event_child() (indra.sources.tees.processor.TEESProcessor method) find_event_with_outgoing_edges() (indra.sources.tees.processor.TEESProcessor method) find_matching_entities() (indra.sources.biopax.processor.BiopaxProcessor static method) find_matching_left_right() (indra.sources.biopax.processor.BiopaxProcessor static method) find_paths() (indra.explanation.model_checker.model_checker.ModelChecker method) find_refinements_for_statement() (in module indra.preassembler) find_sources() (in module indra.explanation.pathfinding.pathfinding) finish() (indra.util.statement_presentation.StmtGroup method) fit() (indra.belief.skl.SklearnScorer method) fix_invalidities() (in module indra.tools.assemble_corpus) (in module indra.tools.fix_invalidities) fix_invalidities_agent() (in module indra.tools.fix_invalidities) fix_invalidities_context() (in module indra.tools.fix_invalidities) fix_invalidities_db_refs() (in module indra.tools.fix_invalidities) fix_invalidities_evidence() (in module indra.tools.fix_invalidities) fix_invalidities_stmt() (in module indra.tools.fix_invalidities) 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_dicts() (indra.util.statement_presentation.StmtGroup class method) (indra.util.statement_presentation.StmtStat class method) from_json_file() (indra.pipeline.pipeline.AssemblyPipeline class method) from_seconds() (indra.statements.statements.QuantitativeState static method) from_stmt_stats() (indra.util.statement_presentation.StmtGroup class method) from_stmts() (indra.util.statement_presentation.StmtStat class method) FromMeshIds (class in indra.sources.indra_db_rest.query) FromPapers (class in indra.sources.indra_db_rest.query)

G

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_source_css() (in module indra.assemblers.html.assembler) geneways_action_to_indra_statement_type() (in module indra.sources.geneways.processor) GenewaysProcessor (class in indra.sources.geneways.processor) Geranylgeranylation (class in indra.statements.statements) get() (indra.sources.indra_db_rest.query.Query method) (indra.util.nested_dict.NestedDict method) get_abstract() (in module indra.literature.elsevier_client) (in module indra.literature.pubmed_client) get_activation() (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() (in module indra.sources.bel.processor) (in module indra.sources.minerva.processor) (indra.sources.acsn.processor.AcsnProcessor method) get_agent_from_entity() (indra.sources.semrep.processor.SemRepXmlProcessor method) get_agent_from_entity_info() (in module indra.sources.rlimsp.processor) get_agent_from_grounding() (in module indra.sources.virhostnet.processor) get_agent_from_refs() (in module indra.sources.minerva.processor) get_agent_key() (in module indra.preassembler.refinement) 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_from_entities() (indra.sources.reach.processor.ReachProcessor method) get_agents_from_entities_with_coords() (indra.sources.reach.processor.ReachProcessor method) get_agents_with_name() (in module indra.preassembler.grounding_mapper.analysis) get_all_descendants() (in module indra.statements.statements) get_all_entities() (indra.sources.reach.processor.ReachProcessor method) get_all_events() (indra.sources.eidos.processor.EidosProcessor method) (indra.sources.reach.processor.ReachProcessor method) (indra.sources.trips.processor.TripsProcessor method) get_all_mps() (indra.explanation.model_checker.pysb.PysbModelChecker method) get_all_nodes() (indra.explanation.model_checker.model_checker.NodesContainer method) get_all_sources() (indra.belief.skl.CountsScorer static method) get_annotation() (in module indra.assemblers.pysb.assembler) get_annotations() (in module indra.sources.hypothesis.api) get_api_ruler() (indra.sources.reach.reader.ReachReader method) get_argument_value() (indra.pipeline.pipeline.AssemblyPipeline 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_belief_score_by_hash() (indra.sources.indra_db_rest.processor.DBQueryStatementProcessor method) get_belief_score_by_stmt() (indra.sources.indra_db_rest.processor.DBQueryStatementProcessor method) get_belief_scores() (indra.sources.indra_db_rest.processor.IndraDBQueryProcessor method) get_biopax_stmts() (indra.tools.gene_network.GeneNetwork method) get_bioregistry_curie() (in module indra.databases.bioregistry_client) get_bioregistry_prefix() (in module indra.databases.bioregistry_client) get_bioregistry_url() (in module indra.databases.bioregistry_client) 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() (in module indra.databases.drugbank_client) get_chebi_id_from_cas() (in module indra.databases.chebi_client) get_chebi_id_from_chembl() (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) (in module indra.databases.drugbank_client) get_chembl_name() (in module indra.databases.chembl_client) get_children() (indra.ontology.ontology_graph.IndraOntology method) get_citation_count_for_doi() (in module indra.literature.coci_client) get_citation_count_for_pmid() (in module indra.literature.coci_client) get_cli() (indra.sources.utils.Processor class method) get_cm_cycles() (in module indra.assemblers.pysb.kappa_util) get_collection_dois() (in module indra.literature.biorxiv_client) get_collection_pubs() (in module indra.literature.biorxiv_client) get_complexes() (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_content_from_pub_json() (in module indra.literature.biorxiv_client) get_conversions() (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_curations() (in module indra.sources.indra_db_rest.api) get_current_hgnc_id() (in module indra.databases.hgnc_client) get_current_time() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) get_date_from_str() (in module indra.util.aws) get_db_mapping() (in module indra.databases.drugbank_client) (in module indra.databases.mesh_client) get_default_ndex_cred() (in module indra.databases.ndex_client) get_degradations() (indra.sources.trips.processor.TripsProcessor method) get_dict() (indra.util.statement_presentation.AggregatorMeta method) (indra.util.statement_presentation.BasicAggregator method) (indra.util.statement_presentation.MultiAggregator 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_drugbank_id_from_chebi_id() (in module indra.databases.drugbank_client) get_drugbank_id_from_chembl_id() (in module indra.databases.drugbank_client) get_drugbank_id_from_db_id() (in module indra.databases.drugbank_client) get_drugbank_name() (in module indra.databases.drugbank_client) 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_enzymes() (in module indra.databases.hgnc_client) get_ev_count() (indra.sources.indra_db_rest.processor.DBQueryStatementProcessor method) get_ev_count_by_hash() (indra.sources.indra_db_rest.processor.DBQueryStatementProcessor method) get_ev_counts() (indra.sources.indra_db_rest.processor.IndraDBQueryProcessor method) get_ev_for_stmts_from_hashes() (in module indra.belief) get_ev_for_stmts_from_supports() (in module indra.belief) get_evidence() (in module indra.databases.chembl_client) (in module indra.sources.gnbr.processor) (indra.sources.eidos.processor.EidosProcessor method) get_family() (in module indra.sources.minerva.processor) get_formats() (in module indra.literature.biorxiv_client) get_full_text() (in module indra.literature) get_full_xml() (in module indra.literature.pubmed_client) get_fulltext_links() (in module indra.literature.crossref_client) get_function_from_name() (indra.pipeline.pipeline.AssemblyPipeline static method) get_function_parameters() (indra.pipeline.pipeline.AssemblyPipeline static method) get_gap_gef() (indra.sources.biopax.processor.BiopaxProcessor method) get_gene_names() (indra.assemblers.cyjs.assembler.CyJSAssembler method) get_gene_type() (in module indra.databases.hgnc_client) get_genetic_profiles() (in module indra.databases.cbio_client) get_gilda_models() (in module indra.preassembler.grounding_mapper.gilda) get_git_info() (in module indra.util.get_version) get_go_id() (in module indra.databases.mesh_client) get_go_id_from_label() (in module indra.databases.go_client) get_go_id_from_label_or_synonym() (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_grounded_agents() (in module indra.assemblers.pysb.assembler) get_grounding() (in module indra.preassembler.grounding_mapper.gilda) (indra.statements.agent.Agent method) (indra.statements.statements.Agent method) get_groundings() (indra.sources.eidos.processor.EidosProcessor method) get_hash() (indra.statements.statements.Statement method) get_hash_statements_dict() (indra.sources.indra_db_rest.processor.DBQueryStatementProcessor method) 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_mgi_name() (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_hgnc_name_from_mgi_name() (in module indra.databases.hgnc_client) get_hgncs_from_enzyme() (in module indra.databases.hgnc_client) get_hierarchy_probs() (indra.belief.BeliefEngine method) get_hierarchy_probs_from_hashes() (indra.belief.BeliefEngine method) 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() (indra.ontology.ontology_graph.IndraOntology static method) get_id_count() (in module indra.literature.pubmed_client) get_id_from_alt_id() (in module indra.databases.mondo_client) (indra.databases.obo_client.OntologyClient method) get_id_from_name() (in module indra.databases.ec_client) (in module indra.databases.mgi_client) (in module indra.databases.mondo_client) (indra.databases.obo_client.OntologyClient method) (indra.ontology.ontology_graph.IndraOntology method) (indra.ontology.virtual.ontology.VirtualOntology method) get_id_from_name_or_synonym() (indra.databases.obo_client.OntologyClient method) get_id_from_name_synonym() (in module indra.databases.mgi_client) get_identifiers_ns() (in module indra.databases.identifiers) get_identifiers_url() (in module indra.databases.identifiers) get_ido_id_from_ido_name() (in module indra.databases.ido_client) get_ido_name_from_ido_id() (in module indra.databases.ido_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.chebi_client) (in module indra.databases.pubchem_client) get_input_var_names() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) get_issn_info() (in module indra.literature.pubmed_client) get_issns_for_journal() (in module indra.literature.pubmed_client)

get_jobs() (in module indra.util.aws) get_json_record() (in module indra.databases.pubchem_client) get_kinetics() (in module indra.databases.chembl_client) get_leaves() (indra.util.nested_dict.NestedDict method) get_less_specifics() (indra.preassembler.refinement.RefinementFilter method) get_mappings() (indra.ontology.ontology_graph.IndraOntology method) get_mesh_annotations() (in module indra.literature.pubmed_client) get_mesh_id() (in module indra.databases.chembl_client) (in module indra.databases.pubchem_client) get_mesh_id_from_db_id() (in module indra.databases.mesh_client) get_mesh_id_from_go_id() (in module indra.databases.mesh_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_mesh_tree_numbers() (in module indra.databases.mesh_client) get_mesh_tree_numbers_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.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_more_specifics() (indra.preassembler.refinement.RefinementFilter method) get_mouse_id() (in module indra.databases.hgnc_client) get_mutations() (in module indra.databases.cbio_client) (in module indra.databases.context_client) get_name() (in module indra.databases.biolookup_client) (indra.ontology.ontology_graph.IndraOntology method) get_name_from_id() (in module indra.databases.ec_client) (in module indra.databases.mgi_client) (in module indra.databases.mondo_client) (indra.databases.obo_client.OntologyClient method) get_namespace() (in module indra.databases.go_client) get_negation() (indra.sources.eidos.processor.EidosProcessor static method) get_new_instance() (indra.util.statement_presentation.StmtGroup method) get_node_names() (indra.sources.ndex_cx.processor.NdexCxProcessor method) get_node_property() (indra.ontology.ontology_graph.IndraOntology method) (indra.ontology.virtual.ontology.VirtualOntology method) get_nodes() (indra.explanation.model_checker.pybel.PybelModelChecker method) (indra.explanation.model_checker.signed_graph.SignedGraphModelChecker method) (indra.explanation.model_checker.unsigned_graph.UnsignedGraphModelChecker method) get_nodes_to_agents() (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_ns() (indra.ontology.ontology_graph.IndraOntology static method) get_ns_from_bioregistry() (in module indra.databases.bioregistry_client) get_ns_from_identifiers() (in module indra.databases.identifiers) get_ns_id() (indra.ontology.ontology_graph.IndraOntology static method) get_ns_id_from_bioregistry() (in module indra.databases.bioregistry_client) get_ns_id_from_bioregistry_curie() (in module indra.databases.bioregistry_client) get_ns_id_from_identifiers() (in module indra.databases.identifiers) get_nugget_dict() (indra.assemblers.kami.assembler.Nugget method) get_num_sequenced() (in module indra.databases.cbio_client) get_output_var_names() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) get_parents() (indra.databases.obo_client.OntologyClient method) (indra.ontology.ontology_graph.IndraOntology method) get_path() (indra.util.nested_dict.NestedDict method) get_path_iter() (in module indra.explanation.pathfinding.pathfinding) get_paths() (indra.util.nested_dict.NestedDict method) get_pcid() (in module indra.databases.chembl_client) get_pdf_xml_url_base() (in module indra.literature.biorxiv_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() (in module indra.databases.pubchem_client) (indra.sources.ndex_cx.processor.NdexCxProcessor method) get_polarity() (indra.ontology.ontology_graph.IndraOntology method) get_ppis() (indra.sources.hprd.processor.HprdProcessor method) get_preferred_compound_ids() (in module indra.databases.pubchem_client) get_primary_id() (in module indra.databases.chebi_client) (in module indra.databases.go_client) get_primary_mappings() (in module indra.databases.mesh_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_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_query_english() (indra.sources.indra_db_rest.query.Query method) get_query_json() (indra.sources.indra_db_rest.query.Query method) get_ranked_stmts() (in module indra.belief) get_rat_id() (in module indra.databases.hgnc_client) get_ref() (indra.explanation.model_checker.model_checker.ModelChecker method) get_refinements() (indra.explanation.model_checker.pysb.PysbModelChecker method) 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() (indra.preassembler.refinement.OntologyRefinementFilter method) (indra.preassembler.refinement.RefinementConfirmationFilter method) (indra.preassembler.refinement.RefinementFilter method) (indra.preassembler.refinement.SplitGroupFilter method) get_related_node() (indra.sources.tees.processor.TEESProcessor method) get_relation() (indra.databases.obo_client.OntologyClient method) get_relations() (indra.databases.obo_client.OntologyClient method) get_relevant_keys() (in module indra.preassembler.refinement) get_replacement() (indra.ontology.ontology_graph.IndraOntology method) get_resource_path() (in module indra.resources) get_s3_client() (in module indra.util.aws) 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_small_molecule_name() (indra.databases.lincs_client.LincsClient method) get_small_molecule_refs() (indra.databases.lincs_client.LincsClient method) get_sorted_compositional_groundings() (in module indra.statements.concept) get_sorted_neighbors() (in module indra.explanation.pathfinding.util) get_source_count() (indra.sources.indra_db_rest.processor.DBQueryStatementProcessor method) get_source_count_by_hash() (indra.sources.indra_db_rest.processor.DBQueryStatementProcessor method) get_source_counts() (indra.sources.indra_db_rest.processor.IndraDBQueryProcessor method) get_source_hash() (indra.statements.evidence.Evidence method) (indra.statements.statements.Evidence method) get_specific_id() (in module indra.databases.chebi_client) get_standard_agent() (in module indra.ontology.standardize) get_standard_name() (in module indra.ontology.standardize) 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) get_statements_by_hash() (in module indra.sources.indra_db_rest.api) get_statements_for_papers() (in module indra.sources.indra_db_rest.api) get_statements_from_query() (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_std_chemical() (in module indra.sources.gnbr.processor) get_std_disease() (in module indra.sources.gnbr.processor) get_std_gene() (in module indra.sources.gnbr.processor) get_stmt_evidence() (in module indra.belief) get_stmt_type() (in module indra.sources.acsn.processor) get_string() (indra.assemblers.graph.assembler.GraphAssembler method) get_subgraph() (in module indra.explanation.pathfinding.util) get_subnetwork() (in module indra.tools.executable_subnetwork) get_substance_annotations() (in module indra.literature.pubmed_client) get_synonyms() (in module indra.databases.mgi_client) get_syntheses() (indra.sources.trips.processor.TripsProcessor method) get_target_chemblid() (in module indra.databases.chembl_client) get_taxonomy_id() (in module indra.databases.taxonomy_client) get_term_agents() (indra.sources.trips.processor.TripsProcessor method) get_text_content_for_gene() (in module indra.literature.adeft_tools) get_text_content_for_pmids() (in module indra.literature.adeft_tools) get_text_from_rxiv_text() (in module indra.literature.biorxiv_client) get_text_from_rxiv_xml() (in module indra.literature.biorxiv_client) get_text_refs() (in module indra.sources.hypothesis.processor) get_text_url_base() (in module indra.literature.biorxiv_client) 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_top_compositional_grounding() (in module indra.statements.concept) get_top_level_parents() (indra.ontology.ontology_graph.IndraOntology method) get_total_nodes() (indra.explanation.model_checker.model_checker.NodesContainer method) get_translocation() (indra.sources.reach.processor.ReachProcessor method) get_type() (indra.ontology.ontology_graph.IndraOntology 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_url_prefix() (in module indra.databases.identifiers) get_valid_location() (in module indra.databases.go_client) get_valid_residue() (in module indra.statements.resources) (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_version_df() (in module indra.sources.dgi.api) get_xml() (in module indra.literature.pmc_client) (in module indra.sources.trips.client) gets() (indra.util.nested_dict.NestedDict method) Glycosylation (class in indra.statements.statements) GnbrProcessor (class in indra.sources.gnbr.processor) graph (indra.assemblers.graph.assembler.GraphAssembler attribute) (indra.assemblers.sif.assembler.SifAssembler attribute) (indra.explanation.model_checker.model_checker.ModelChecker attribute) (indra.explanation.model_checker.pybel.PybelModelChecker attribute) (indra.explanation.model_checker.pysb.PysbModelChecker attribute) (indra.explanation.model_checker.signed_graph.SignedGraphModelChecker attribute) (indra.explanation.model_checker.unsigned_graph.UnsignedGraphModelChecker attribute) graph_properties (indra.assemblers.graph.assembler.GraphAssembler attribute) GraphAssembler (class in indra.assemblers.graph.assembler) ground_agent() (in module indra.preassembler.grounding_mapper.gilda) ground_statement() (in module indra.preassembler.grounding_mapper.gilda) ground_statements() (in module indra.preassembler.grounding_mapper.gilda) grounded_monomer_patterns() (in module indra.assemblers.pysb.assembler) GroundingMapper (class in indra.preassembler.grounding_mapper.mapper) groundings (indra.sources.hypothesis.processor.HypothesisProcessor attribute) groundings_from_annotation() (indra.sources.hypothesis.processor.HypothesisProcessor static method) group_and_sort_statements() (in module indra.util.statement_presentation) GtpActivation (class in indra.statements.statements)

H

has_tree_prefix() (in module indra.databases.mesh_client) HasActivity (class in indra.statements.statements) HasAgent (class in indra.sources.indra_db_rest.query) HasDatabases (class in indra.sources.indra_db_rest.query) HasEvidenceBound (class in indra.sources.indra_db_rest.query) HasHash (class in indra.sources.indra_db_rest.query) HasNumAgents (class in indra.sources.indra_db_rest.query) HasNumEvidence (class in indra.sources.indra_db_rest.query)

HasOnlySource (class in indra.sources.indra_db_rest.query) HasReadings (class in indra.sources.indra_db_rest.query) HasSources (class in indra.sources.indra_db_rest.query) HasType (class in indra.sources.indra_db_rest.query) HprdProcessor (class in indra.sources.hprd.processor) HtmlAssembler (class in indra.assemblers.html.assembler) HybridScorer (class in indra.belief.skl) Hydroxylation (class in indra.statements.statements) HypothesisProcessor (class in indra.sources.hypothesis.processor)

I

id_df (indra.sources.hprd.processor.HprdProcessor attribute) id_lookup() (in module indra.literature) (in module indra.literature.pmc_client) IdentifiersValidator (class in indra.statements.validate) im_json_to_graph() (in module indra.assemblers.pysb.kappa_util) include() (indra.util.statement_presentation.AggregatorMeta method) (indra.util.statement_presentation.BasicAggregator method) (indra.util.statement_presentation.MultiAggregator method) IncreaseAmount (class in indra.statements.statements) IncrementalModel (class in indra.tools.incremental_model) IndexCardAssembler (class in indra.assemblers.index_card.assembler) 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.belief.skl module indra.databases module indra.databases.biolookup_client module indra.databases.bioregistry_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.drugbank_client module indra.databases.ec_client module indra.databases.efo_client module indra.databases.go_client module indra.databases.hgnc_client module indra.databases.hp_client module indra.databases.identifiers module indra.databases.ido_client module indra.databases.lincs_client module indra.databases.mesh_client module indra.databases.mgi_client module indra.databases.mirbase_client module indra.databases.mondo_client module indra.databases.ndex_client module indra.databases.obo_client module indra.databases.owl_client module indra.databases.pubchem_client module indra.databases.taxonomy_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.explanation.pathfinding.pathfinding module indra.explanation.pathfinding.util module indra.explanation.reporting module indra.literature module indra.literature.adeft_tools module indra.literature.biorxiv_client module indra.literature.coci_client 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.ontology module indra.ontology.app module indra.ontology.bio module indra.ontology.bio.__main__ module indra.ontology.bio.ontology module indra.ontology.ontology_graph module indra.ontology.standardize module indra.ontology.virtual module indra.ontology.virtual.ontology module indra.pipeline module indra.pipeline.decorators module indra.pipeline.pipeline module indra.preassembler module indra.preassembler.custom_preassembly module indra.preassembler.grounding_mapper module indra.preassembler.grounding_mapper.analysis module indra.preassembler.grounding_mapper.disambiguate module indra.preassembler.grounding_mapper.gilda module indra.preassembler.grounding_mapper.mapper module indra.preassembler.refinement module indra.preassembler.sitemapper module indra.resources module indra.sources.acsn module indra.sources.acsn.api module indra.sources.acsn.processor module indra.sources.bel.api module indra.sources.bel.processor module indra.sources.biofactoid module indra.sources.biofactoid.api module indra.sources.biofactoid.processor module indra.sources.biogrid module indra.sources.biopax module indra.sources.biopax.api module indra.sources.biopax.processor module indra.sources.creeds module indra.sources.creeds.api module indra.sources.creeds.processor module indra.sources.crog module indra.sources.crog.api module indra.sources.crog.processor module indra.sources.ctd module indra.sources.ctd.api module indra.sources.ctd.processor module indra.sources.dgi module indra.sources.dgi.api module indra.sources.dgi.processor module indra.sources.drugbank module

indra.sources.drugbank.api module indra.sources.drugbank.processor module indra.sources.eidos module indra.sources.eidos.api module indra.sources.eidos.bio_processor module indra.sources.eidos.cli module indra.sources.eidos.client 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.gnbr module indra.sources.gnbr.api module indra.sources.gnbr.processor module indra.sources.hprd module indra.sources.hprd.api module indra.sources.hprd.processor module indra.sources.hypothesis module indra.sources.hypothesis.api module indra.sources.hypothesis.processor module indra.sources.indra_db_rest module indra.sources.indra_db_rest.api module indra.sources.indra_db_rest.processor module indra.sources.indra_db_rest.query module indra.sources.isi module indra.sources.isi.api module indra.sources.isi.processor module indra.sources.minerva module indra.sources.minerva.api module indra.sources.minerva.processor module indra.sources.ndex_cx.api module indra.sources.ndex_cx.processor module indra.sources.omnipath module indra.sources.omnipath.api module indra.sources.omnipath.processor module indra.sources.phosphoelm module indra.sources.phosphoelm.api module indra.sources.phosphoelm.processor module indra.sources.reach 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.semrep module indra.sources.semrep.api module indra.sources.semrep.processor module indra.sources.signor.api module indra.sources.signor.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.sources.ubibrowser module indra.sources.ubibrowser.api module indra.sources.ubibrowser.processor module indra.sources.utils module indra.sources.virhostnet module indra.sources.virhostnet.api module indra.sources.virhostnet.processor module indra.statements.agent module indra.statements.concept module indra.statements.context module indra.statements.evidence module indra.statements.io module indra.statements.resources module indra.statements.statements module indra.statements.util module indra.statements.validate module indra.tools.analyze_ontology module indra.tools.assemble_corpus module indra.tools.executable_subnetwork module indra.tools.fix_invalidities module indra.tools.gene_network module indra.tools.hypothesis_annotator module indra.tools.incremental_model module indra.tools.machine module indra.util.aws module indra.util.get_version module indra.util.nested_dict module indra.util.plot_formatting module indra.util.statement_presentation module IndraDBQueryProcessor (class in indra.sources.indra_db_rest.processor) IndraNet (class in indra.assemblers.indranet.net) IndraNetAssembler (class in indra.assemblers.indranet.assembler) IndraOntology (class in indra.ontology.ontology_graph) 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) (indra.ontology.bio.BioOntology method) (indra.ontology.bio.ontology.BioOntology method) (indra.ontology.ontology_graph.IndraOntology method) (indra.ontology.virtual.ontology.VirtualOntology method) (indra.preassembler.refinement.OntologyRefinementFilter method) (indra.preassembler.refinement.RefinementFilter method) initialize_reader() (in module indra.sources.eidos.api) (indra.sources.eidos.reader.EidosReader method) InputError, [1] insert() (indra.pipeline.pipeline.AssemblyPipeline method) internal_source_mappings (in module indra.util.statement_presentation) invalid_site_pos (indra.sources.hprd.processor.HprdProcessor attribute) InvalidAgent InvalidContext InvalidIdentifier InvalidLocationError, [1] InvalidResidueError, [1] InvalidStatement InvalidTextRefs is_disease() (in module indra.databases.mesh_client) is_enzyme() (in module indra.databases.mesh_client) is_function() (indra.pipeline.pipeline.AssemblyPipeline static method) is_kinase() (in module indra.databases.hgnc_client) is_molecular() (in module indra.databases.mesh_client) is_opposite() (indra.ontology.ontology_graph.IndraOntology method) is_phosphatase() (in module indra.databases.hgnc_client) is_protein() (in module indra.databases.mesh_client) is_ref() (indra.explanation.model_checker.model_checker.NodesContainer method) is_transcription_factor() (in module indra.databases.hgnc_client) is_working() (indra.sources.indra_db_rest.processor.IndraDBQueryProcessor method) isa() (indra.ontology.ontology_graph.IndraOntology method) isa_or_partof() (indra.ontology.ontology_graph.IndraOntology method) IsiProcessor (class in indra.sources.isi.processor) isrel() (indra.ontology.ontology_graph.IndraOntology method) items() (indra.assemblers.pysb.base_agents.BaseAgentSet method) iter_s3_keys() (in module indra.util.aws)

J

JobLog (class in indra.util.aws)

jsonify_arg_input() (in module indra.pipeline.pipeline)

K

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

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

L

label() (indra.ontology.ontology_graph.IndraOntology static method) length (indra.explanation.model_checker.model_checker.PathMetric attribute) LincsClient (class in indra.databases.lincs_client) LinkedStatement (class in indra.mechlinker) load() (indra.util.aws.JobLog method) 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_resource_json() (in module indra.resources) load_statements() (in module indra.tools.assemble_corpus) location (indra.mechlinker.AgentState attribute) lookup() (in module indra.databases.biolookup_client) lookup_curie() (in module indra.databases.biolookup_client)

M

main_interm (indra.explanation.model_checker.model_checker.NodesContainer attribute) main_nodes (indra.explanation.model_checker.model_checker.NodesContainer attribute) make_df() (indra.assemblers.indranet.assembler.IndraNetAssembler method) make_generic_copy() (indra.statements.statements.Statement method) make_hash() (in module indra.statements.statements) (in module indra.statements.util) make_json_model() (indra.assemblers.html.assembler.HtmlAssembler method) make_model() (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_model_by_preassembly() (indra.assemblers.indranet.assembler.IndraNetAssembler method) make_model_from_df() (indra.assemblers.indranet.assembler.IndraNetAssembler method) make_nxml_from_text() (in module indra.sources.sparser.api) make_repository_component() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) make_sentence() (indra.assemblers.english.assembler.SentenceBuilder method) make_standard_stats() (in module indra.util.statement_presentation) make_statement() (indra.sources.geneways.processor.GenewaysProcessor method) make_statement_camel() (in module indra.statements.statements) make_stmt() (in module indra.sources.trrust.processor) make_stmt_from_relation_key() (in module indra.util.statement_presentation) make_string_from_relation_key() (in module indra.util.statement_presentation) make_top_level_label_from_names_key() (in module indra.util.statement_presentation) 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_db_refs() (in module indra.tools.assemble_corpus) map_grounding() (in module indra.tools.assemble_corpus) map_sequence() (in module indra.tools.assemble_corpus) map_sites() (indra.preassembler.sitemapper.SiteMapper method) map_stmts() (indra.preassembler.grounding_mapper.mapper.GroundingMapper method) map_to() (indra.ontology.ontology_graph.IndraOntology method) MappedStatement (class in indra.preassembler.sitemapper) maps_to() (indra.ontology.ontology_graph.IndraOntology method) matches_key() (indra.statements.agent.Agent method) (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) MaxAggregator (class in indra.util.statement_presentation) MechLinker (class in indra.mechlinker) merge_groundings() (in module indra.tools.assemble_corpus) merge_results() (indra.sources.indra_db_rest.processor.DBQueryStatementProcessor method) metadata (indra.assemblers.html.assembler.HtmlAssembler attribute) Methylation (class in indra.statements.statements) Migration (class in indra.statements.statements) MissingIdentifier mk_str() (in module indra.statements.statements) mod_condition_from_mod_feature() (indra.sources.biopax.processor.BiopaxProcessor static method) ModCondition (class in indra.statements.agent) (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) ModelChecker (class in indra.explanation.model_checker.model_checker) Modification (class in indra.statements.statements) mods (indra.mechlinker.AgentState attribute) module indra.assemblers.cx.assembler indra.assemblers.cyjs.assembler indra.assemblers.english.assembler indra.assemblers.graph.assembler indra.assemblers.html.assembler indra.assemblers.index_card.assembler indra.assemblers.indranet indra.assemblers.indranet.assembler indra.assemblers.indranet.net indra.assemblers.kami.assembler indra.assemblers.pybel.assembler indra.assemblers.pysb.assembler indra.assemblers.pysb.base_agents indra.assemblers.pysb.bmi_wrapper indra.assemblers.pysb.kappa_util indra.assemblers.pysb.preassembler indra.assemblers.sbgn.assembler indra.assemblers.sif.assembler indra.assemblers.tsv.assembler indra.belief indra.belief.skl indra.databases indra.databases.biolookup_client indra.databases.bioregistry_client indra.databases.cbio_client indra.databases.chebi_client indra.databases.chembl_client indra.databases.context_client indra.databases.doid_client indra.databases.drugbank_client indra.databases.ec_client indra.databases.efo_client indra.databases.go_client indra.databases.hgnc_client indra.databases.hp_client indra.databases.identifiers indra.databases.ido_client indra.databases.lincs_client indra.databases.mesh_client indra.databases.mgi_client indra.databases.mirbase_client indra.databases.mondo_client indra.databases.ndex_client indra.databases.obo_client indra.databases.owl_client indra.databases.pubchem_client indra.databases.taxonomy_client indra.databases.uniprot_client indra.explanation.model_checker.model_checker indra.explanation.model_checker.pybel indra.explanation.model_checker.pysb indra.explanation.model_checker.signed_graph indra.explanation.model_checker.unsigned_graph indra.explanation.pathfinding.pathfinding indra.explanation.pathfinding.util indra.explanation.reporting indra.literature indra.literature.adeft_tools indra.literature.biorxiv_client indra.literature.coci_client indra.literature.crossref_client indra.literature.elsevier_client indra.literature.newsapi_client indra.literature.pmc_client indra.literature.pubmed_client indra.mechlinker indra.ontology indra.ontology.app indra.ontology.bio indra.ontology.bio.__main__ indra.ontology.bio.ontology indra.ontology.ontology_graph indra.ontology.standardize indra.ontology.virtual indra.ontology.virtual.ontology indra.pipeline indra.pipeline.decorators indra.pipeline.pipeline indra.preassembler indra.preassembler.custom_preassembly indra.preassembler.grounding_mapper indra.preassembler.grounding_mapper.analysis indra.preassembler.grounding_mapper.disambiguate indra.preassembler.grounding_mapper.gilda indra.preassembler.grounding_mapper.mapper indra.preassembler.refinement indra.preassembler.sitemapper indra.resources indra.sources.acsn indra.sources.acsn.api indra.sources.acsn.processor indra.sources.bel.api indra.sources.bel.processor indra.sources.biofactoid indra.sources.biofactoid.api indra.sources.biofactoid.processor indra.sources.biogrid indra.sources.biopax indra.sources.biopax.api indra.sources.biopax.processor indra.sources.creeds indra.sources.creeds.api indra.sources.creeds.processor indra.sources.crog indra.sources.crog.api indra.sources.crog.processor indra.sources.ctd indra.sources.ctd.api indra.sources.ctd.processor indra.sources.dgi indra.sources.dgi.api indra.sources.dgi.processor indra.sources.drugbank indra.sources.drugbank.api indra.sources.drugbank.processor indra.sources.eidos indra.sources.eidos.api indra.sources.eidos.bio_processor indra.sources.eidos.cli indra.sources.eidos.client indra.sources.eidos.processor indra.sources.eidos.reader indra.sources.eidos.server indra.sources.geneways.api indra.sources.geneways.processor indra.sources.gnbr indra.sources.gnbr.api indra.sources.gnbr.processor indra.sources.hprd indra.sources.hprd.api indra.sources.hprd.processor indra.sources.hypothesis indra.sources.hypothesis.api indra.sources.hypothesis.processor indra.sources.indra_db_rest indra.sources.indra_db_rest.api indra.sources.indra_db_rest.processor indra.sources.indra_db_rest.query indra.sources.isi indra.sources.isi.api indra.sources.isi.processor indra.sources.minerva indra.sources.minerva.api indra.sources.minerva.processor indra.sources.ndex_cx.api indra.sources.ndex_cx.processor indra.sources.omnipath indra.sources.omnipath.api indra.sources.omnipath.processor indra.sources.phosphoelm indra.sources.phosphoelm.api indra.sources.phosphoelm.processor indra.sources.reach indra.sources.reach.api indra.sources.reach.processor indra.sources.reach.reader indra.sources.rlimsp indra.sources.rlimsp.api indra.sources.rlimsp.processor indra.sources.semrep indra.sources.semrep.api indra.sources.semrep.processor indra.sources.signor.api indra.sources.signor.processor indra.sources.sparser indra.sources.sparser.api indra.sources.tas indra.sources.tas.api indra.sources.tas.processor indra.sources.tees.api indra.sources.tees.processor indra.sources.trips.api indra.sources.trips.client indra.sources.trips.drum_reader indra.sources.trips.processor indra.sources.trrust indra.sources.trrust.api indra.sources.trrust.processor indra.sources.ubibrowser indra.sources.ubibrowser.api indra.sources.ubibrowser.processor indra.sources.utils indra.sources.virhostnet indra.sources.virhostnet.api indra.sources.virhostnet.processor indra.statements.agent indra.statements.concept indra.statements.context indra.statements.evidence indra.statements.io indra.statements.resources indra.statements.statements indra.statements.util indra.statements.validate indra.tools.analyze_ontology indra.tools.assemble_corpus indra.tools.executable_subnetwork indra.tools.fix_invalidities indra.tools.gene_network indra.tools.hypothesis_annotator indra.tools.incremental_model indra.tools.machine indra.util.aws indra.util.get_version indra.util.nested_dict indra.util.plot_formatting indra.util.statement_presentation

motif_window (indra.sources.hprd.processor.HprdProcessor attribute) MovementContext (class in indra.statements.context) (class in indra.statements.statements) MultiAggregator (class in indra.util.statement_presentation) mutations (indra.mechlinker.AgentState attribute) MutCondition (class in indra.statements.agent) (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.ontology.ontology_graph.IndraOntology attribute), [1] namespace_embedded() (in module indra.databases.identifiers) 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_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) nodes_from_suffix() (indra.ontology.ontology_graph.IndraOntology method) NodesContainer (class in indra.explanation.model_checker.model_checker) normalize_active_forms() (in module indra.tools.assemble_corpus) normalize_equivalences() (indra.preassembler.Preassembler method) normalize_opposites() (indra.preassembler.Preassembler method) NotAStatementName NotRegisteredFunctionError Nugget (class in indra.assemblers.kami.assembler)

O

OboClient (class in indra.databases.obo_client) off_by_one (indra.sources.hprd.processor.HprdProcessor attribute) OmniPathProcessor (class in indra.sources.omnipath.processor) ontology (indra.preassembler.Preassembler attribute) OntologyClient (class in indra.databases.obo_client)

OntologyRefinementFilter (class in indra.preassembler.refinement) open_dijkstra_search() (in module indra.explanation.pathfinding.pathfinding) open_resource_file() (in module indra.resources) Or (class in indra.sources.indra_db_rest.query) organism_priority (indra.sources.reach.processor.ReachProcessor attribute) OwlClient (class in indra.databases.owl_client)

P

Palmitoylation (class in indra.statements.statements) par_to_sec (indra.sources.trips.processor.TripsProcessor attribute) paragraphs (indra.sources.trips.processor.TripsProcessor attribute) Param (class in indra.assemblers.pysb.assembler) parameters (indra.assemblers.pysb.assembler.Policy attribute) parse_context_entry() (in module indra.sources.hypothesis.processor) parse_grounding_entry() (in module indra.sources.hypothesis.processor) parse_identifiers_url() (in module indra.assemblers.pysb.assembler) (in module indra.databases.identifiers) parse_psi_mi() (in module indra.sources.virhostnet.processor) parse_source_ids() (in module indra.sources.virhostnet.processor) parse_text_refs() (in module indra.sources.virhostnet.processor) partof() (indra.ontology.ontology_graph.IndraOntology method) path_found (indra.explanation.model_checker.model_checker.PathResult attribute) path_metrics (indra.explanation.model_checker.model_checker.PathResult attribute) path_sign_to_signed_nodes() (in module indra.explanation.pathfinding.util) 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) PhosphoElmProcessor (class in indra.sources.phosphoelm.processor) Phosphorylation (class in indra.statements.statements) physical_only (indra.sources.biogrid.BiogridProcessor attribute) policies (indra.assemblers.pysb.assembler.PysbAssembler attribute) Policy (class in indra.assemblers.pysb.assembler) position (indra.sources.reach.processor.Site property) preassemble() (indra.tools.incremental_model.IncrementalModel method) Preassembler (class in indra.preassembler) predict() (indra.belief.skl.SklearnScorer method) predict_log_proba() (indra.belief.skl.SklearnScorer method) predict_proba() (indra.belief.skl.SklearnScorer method) prepend() (indra.assemblers.english.assembler.SentenceBuilder method) pretty_print_stmts() (in module indra.statements.io) (in module indra.statements.statements) 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_quiet_logs() (indra.sources.indra_db_rest.processor.IndraDBQueryProcessor static method) print_stmt_summary() (in module indra.statements.io) (in module indra.statements.statements) print_summary() (indra.sources.utils.RemoteProcessor method) print_validation_report() (in module indra.statements.validate) prioritize_organism_grounding() (in module indra.sources.reach.processor) process_agents_from_entities() (in module indra.sources.reach.api) process_annotations() (in module indra.sources.hypothesis.api) process_archive() (in module indra.sources.hprd.api) process_bel_stmt() (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_chemical_disease() (in module indra.sources.gnbr.api) process_chemical_disease_from_web() (in module indra.sources.gnbr.api) process_chemical_gene() (in module indra.sources.gnbr.api) process_chemical_gene_from_web() (in module indra.sources.gnbr.api) process_csv() (in module indra.sources.tas.api) process_cx() (in module indra.sources.ndex_cx.api) process_cx_file() (in module indra.sources.ndex_cx.api) process_dataframe() (in module indra.sources.ctd.api) process_decrease_expression_amount() (indra.sources.tees.processor.TEESProcessor method) process_df() (in module indra.sources.acsn.api) (in module indra.sources.dgi.api) (in module indra.sources.ubibrowser.api) (in module indra.sources.virhostnet.api) process_element_tree() (in module indra.sources.drugbank.api) process_file() (in module indra.sources.minerva.api) (in module indra.sources.ubibrowser.api) process_files() (in module indra.sources.acsn.api) (in module indra.sources.minerva.api) process_flat_files() (in module indra.sources.hprd.api) process_fries_json_group() (in module indra.sources.reach.api) process_from_dump() (in module indra.sources.phosphoelm.api) process_from_file() (in module indra.sources.creeds.api) (in module indra.sources.signor.api) process_from_files() (in module indra.sources.gnbr.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.acsn.api) (in module indra.sources.biofactoid.api) (in module indra.sources.creeds.api) (in module indra.sources.crog.api) (in module indra.sources.ctd.api) (in module indra.sources.drugbank.api) (in module indra.sources.gnbr.api) (in module indra.sources.minerva.api) (in module indra.sources.omnipath.api) (in module indra.sources.signor.api) (in module indra.sources.tas.api) (in module indra.sources.trrust.api) (in module indra.sources.ubibrowser.api) (in module indra.sources.virhostnet.api)

process_from_webservice() (in module indra.sources.rlimsp.api) process_gene_disease() (in module indra.sources.gnbr.api) process_gene_disease_from_web() (in module indra.sources.gnbr.api) process_gene_gene() (in module indra.sources.gnbr.api) process_gene_gene_from_web() (in module indra.sources.gnbr.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.biofactoid.api) process_json_bio() (in module indra.sources.eidos.api) process_json_bio_entities() (in module indra.sources.eidos.api) process_json_dict() (in module indra.sources.sparser.api) process_json_file() (in module indra.sources.bel.api) (in module indra.sources.isi.api) (in module indra.sources.reach.api) process_json_str() (in module indra.sources.reach.api) process_jsonl_file() (in module indra.sources.rlimsp.api) process_jsonl_str() (in module indra.sources.rlimsp.api) process_large_corpus() (in module indra.sources.bel.api) process_ligrec_interactions() (indra.sources.omnipath.processor.OmniPathProcessor method) 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_gz() (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_phosphorylations() (indra.sources.phosphoelm.processor.PhosphoElmProcessor method) process_pmc() (in module indra.sources.reach.api) process_preprocessed() (in module indra.sources.isi.api) process_ptm_mods() (indra.sources.omnipath.processor.OmniPathProcessor method) 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_row() (in module indra.sources.virhostnet.processor) 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_statements() (indra.sources.semrep.processor.SemRepXmlProcessor method) process_subject() (indra.explanation.model_checker.model_checker.ModelChecker method) (indra.explanation.model_checker.pysb.PysbModelChecker method) process_text() (in module indra.sources.eidos.client) (in module indra.sources.isi.api) (in module indra.sources.reach.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_text_bio() (in module indra.sources.eidos.api) process_text_bio_entities() (in module indra.sources.eidos.api) process_tsv() (in module indra.sources.ctd.api) (in module indra.sources.virhostnet.api) process_uniprot_entry() (in module indra.sources.signor.processor) process_version() (in module indra.sources.dgi.api) process_xml() (in module indra.sources.drugbank.api) (in module indra.sources.sparser.api) (in module indra.sources.trips.api) process_xml_file() (in module indra.sources.semrep.api) (in module indra.sources.trips.api) Processor (class in indra.sources.utils) protein_map_from_twg() (in module indra.preassembler.grounding_mapper.analysis) 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_signed_nodes() (in module indra.explanation.model_checker.model_checker) PybelAssembler (class in indra.assemblers.pybel.assembler) PybelEdge (class in indra.explanation.reporting) PybelModelChecker (class in indra.explanation.model_checker.pybel) PybelProcessor (class in indra.sources.bel.processor) PyOboClient (class in indra.databases.obo_client) 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 (class in indra.sources.indra_db_rest.query) query_target() (in module indra.databases.chembl_client)

R

ReachOfflineReadingError ReachProcessor (class in indra.sources.reach.processor) ReachReader (class in indra.sources.reach.reader) read_and_annotate() (in module indra.tools.hypothesis_annotator) read_pmc() (indra.sources.trips.drum_reader.DrumReader method) read_text() (indra.sources.trips.drum_reader.DrumReader method) reader_sources (in module indra.util.statement_presentation) READER_TEXT_COLOR (in module indra.assemblers.html.assembler) real_agent_list() (indra.statements.statements.Statement method) receive_reply() (indra.sources.trips.drum_reader.DrumReader method) reduce_activities() (in module indra.tools.assemble_corpus) (indra.mechlinker.MechLinker method) ref_interm (indra.explanation.model_checker.model_checker.NodesContainer attribute) ref_nodes (indra.explanation.model_checker.model_checker.NodesContainer attribute) RefContext (class in indra.statements.context) (class in indra.statements.statements) RefEdge (class in indra.explanation.reporting) RefinementConfirmationFilter (class in indra.preassembler.refinement) RefinementFilter (class in indra.preassembler.refinement) register_pipeline() (in module indra.pipeline.decorators) RegulateActivity (class in indra.statements.statements) RegulateAmount (class in indra.statements.statements) related_stmts (indra.preassembler.Preassembler attribute) relation (indra.explanation.reporting.PybelEdge property) relations_df (indra.sources.acsn.processor.AcsnProcessor attribute) RemoteProcessor (class in indra.sources.utils) 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) rename_s3_prefix() (in module indra.util.aws)

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) require_active_forms() (indra.mechlinker.MechLinker method) residue (indra.sources.reach.processor.Site property) result_code (indra.explanation.model_checker.model_checker.PathResult attribute) results (indra.tools.gene_network.GeneNetwork attribute) retain_molecular_complexes() (indra.sources.isi.processor.IsiProcessor method) reverse (indra.explanation.reporting.PybelEdge property) reverse_label() (indra.ontology.ontology_graph.IndraOntology static method) reverse_source_mappings (in module indra.util.statement_presentation) Ribosylation (class in indra.statements.statements) RlimspParagraph (class in indra.sources.rlimsp.processor) RlimspProcessor (class in indra.sources.rlimsp.processor) row_set() (indra.util.statement_presentation.StmtGroup method) row_to_statements() (indra.sources.dgi.processor.DGIProcessor method) run() (indra.pipeline.pipeline.AssemblyPipeline method) run_adeft_disambiguation() (indra.preassembler.grounding_mapper.disambiguate.DisambManager method) run_eidos() (in module indra.sources.eidos.cli) run_function() (indra.pipeline.pipeline.AssemblyPipeline method) run_gilda_disambiguation() (indra.preassembler.grounding_mapper.disambiguate.DisambManager method) run_mechlinker() (in module indra.tools.assemble_corpus) 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_simple_function() (indra.pipeline.pipeline.AssemblyPipeline static method) run_sparser() (in module indra.sources.sparser.api) RunnableArgument (class in indra.pipeline.pipeline)

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.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) score_statements() (indra.belief.BeliefScorer method) (indra.belief.SimpleScorer method) (indra.belief.skl.HybridScorer method) (indra.belief.skl.SklearnScorer method) search_science_direct() (in module indra.literature.elsevier_client) SelfModification (class in indra.statements.statements) SemRepXmlProcessor (class in indra.sources.semrep.processor) send_query() (in module indra.databases.chembl_client) (in module indra.sources.trips.client) send_request() (in module indra.databases.cbio_client) (in module indra.databases.ndex_client) (in module indra.literature.newsapi_client) sentence (indra.assemblers.english.assembler.SentenceBuilder attribute) SentenceBuilder (class in indra.assemblers.english.assembler) sentences (indra.sources.trips.processor.TripsProcessor attribute) 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_pretty_print_max_width() (in module indra.statements.io) (in module indra.statements.statements) set_prior_probs() (indra.belief.BeliefEngine method) set_style() (in module indra.databases.ndex_client) set_value() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) set_values() (indra.assemblers.pysb.bmi_wrapper.BMIModel method) shortest_simple_paths() (in module indra.explanation.pathfinding.pathfinding) SifAssembler (class in indra.assemblers.sif.assembler) SifProcessor (class in indra.sources.minerva.processor) signed_edges_to_signed_nodes() (in module indra.explanation.model_checker.model_checker) signed_from_df() (indra.assemblers.indranet.net.IndraNet class method) signed_nodes_to_signed_edge() (in module indra.explanation.pathfinding.util) 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) SklearnScorer (class in indra.belief.skl) source (indra.explanation.reporting.PybelEdge property) source_node (indra.explanation.model_checker.model_checker.PathMetric attribute) SplitGroupFilter (class in indra.preassembler.refinement) src_url() (in module indra.assemblers.html.assembler) standardize_agent_name() (in module indra.ontology.standardize) (indra.preassembler.grounding_mapper.mapper.GroundingMapper static method) standardize_counts() (in module indra.util.statement_presentation)

standardize_db_refs() (in module indra.ontology.standardize) (indra.preassembler.grounding_mapper.mapper.GroundingMapper static method) standardize_name_db_refs() (in module indra.ontology.standardize) standardize_names_groundings() (in module indra.tools.assemble_corpus) start() (indra.util.statement_presentation.StmtGroup method) state_matches_key() (indra.statements.agent.Agent method) (indra.statements.statements.Agent method) Statement (class in indra.statements.statements) statement_base_verb() (in module indra.assemblers.english.assembler) statement_passive_verb() (in module indra.assemblers.english.assembler) statement_present_verb() (in module indra.assemblers.english.assembler) statements (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.biofactoid.processor.BioFactoidProcessor attribute) (indra.sources.biogrid.BiogridProcessor attribute) (indra.sources.biopax.processor.BiopaxProcessor attribute) (indra.sources.creeds.processor.CREEDSChemicalProcessor attribute) (indra.sources.creeds.processor.CREEDSDiseaseProcessor attribute) (indra.sources.creeds.processor.CREEDSGeneProcessor attribute) (indra.sources.dgi.processor.DGIProcessor attribute) (indra.sources.drugbank.processor.DrugbankProcessor attribute) (indra.sources.eidos.processor.EidosProcessor attribute) (indra.sources.geneways.processor.GenewaysProcessor attribute) (indra.sources.hprd.processor.HprdProcessor attribute) (indra.sources.hypothesis.processor.HypothesisProcessor attribute) (indra.sources.isi.processor.IsiProcessor attribute) (indra.sources.minerva.processor.SifProcessor attribute) (indra.sources.ndex_cx.processor.NdexCxProcessor attribute) (indra.sources.phosphoelm.processor.PhosphoElmProcessor 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.sources.utils.RemoteProcessor property) (indra.sources.virhostnet.processor.VirhostnetProcessor attribute) stats (indra.sources.signor.processor.SignorProcessor attribute) stmt_agents (indra.assemblers.english.assembler.EnglishAssembler attribute) stmt_from_json() (in module indra.statements.io) (in module indra.statements.statements) stmt_from_json_str() (in module indra.statements.io) (in module indra.statements.statements) stmt_from_rule() (in module indra.explanation.reporting) stmt_to_english() (in module indra.util.statement_presentation) stmt_type() (in module indra.statements.statements) StmtGroup (class in indra.util.statement_presentation) stmts (indra.preassembler.Preassembler attribute) (indra.tools.incremental_model.IncrementalModel attribute) stmts_from_annotation() (indra.sources.hypothesis.processor.HypothesisProcessor method) stmts_from_indranet_path() (in module indra.explanation.reporting) stmts_from_json() (in module indra.statements.io) (in module indra.statements.statements) stmts_from_json_file() (in module indra.statements.io) (in module indra.statements.statements) stmts_from_pybel_path() (in module indra.explanation.reporting) stmts_from_pysb_path() (in module indra.explanation.reporting) stmts_to_json() (in module indra.statements.io) (in module indra.statements.statements) stmts_to_json_file() (in module indra.statements.io) (in module indra.statements.statements) stmts_to_matrix() (indra.belief.skl.CountsScorer method) (indra.belief.skl.SklearnScorer method) StmtStat (class in indra.util.statement_presentation) strip_agent_context() (in module indra.tools.assemble_corpus) strip_supports() (in module indra.tools.assemble_corpus) submit_curation() (in module indra.sources.indra_db_rest.api) SumAggregator (class in indra.util.statement_presentation) Sumoylation (class in indra.statements.statements)

T

tag_evidence_subtype() (in module indra.belief) tag_instance() (in module indra.util.aws) tag_myself() (in module indra.util.aws) tag_text() (in module indra.assemblers.html.assembler) target (indra.explanation.reporting.PybelEdge property) target_node (indra.explanation.model_checker.model_checker.PathMetric attribute) TasProcessor (class in indra.sources.tas.processor) TEESProcessor (class in indra.sources.tees.processor) TimeContext (class in indra.statements.context) (class in indra.statements.statements) timed_out() (indra.sources.indra_db_rest.processor.IndraDBQueryProcessor method) to_database() (indra.assemblers.pybel.assembler.PybelAssembler method) to_digraph() (indra.assemblers.indranet.net.IndraNet method) to_graph() (indra.statements.statements.Statement method) to_json() (indra.pipeline.pipeline.RunnableArgument method) (indra.statements.evidence.Evidence method) (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_json_file() (indra.pipeline.pipeline.AssemblyPipeline method) to_matrix() (indra.belief.skl.SklearnScorer method) to_signed_graph() (indra.assemblers.indranet.net.IndraNet method) to_simple_json() (indra.sources.indra_db_rest.query.Query method) to_web() (indra.assemblers.pybel.assembler.PybelAssembler method) Translocation (class in indra.statements.statements) Transphosphorylation (class in indra.statements.statements) tree (indra.sources.reach.processor.ReachProcessor attribute) (indra.sources.trips.processor.TripsProcessor attribute) TripsProcessor (class in indra.sources.trips.processor) TrrustProcessor (class in indra.sources.trrust.processor) TsvAssembler (class in indra.assemblers.tsv.assembler)

U

UbiBrowserProcessor (class in indra.sources.ubibrowser.processor) 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) UnknownIdentifier UnknownNamespace UnknownPolicyError Unresolved (class in indra.statements.statements) UnresolvedUuidError, [1] 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_by_prefix() (indra.databases.obo_client.PyOboClient class method) update_coords() (indra.assemblers.english.assembler.AgentWithCoordinates method) update_counts() (indra.belief.BayesianScorer method) update_filter_func() (indra.explanation.model_checker.model_checker.ModelChecker method) update_network() (in module indra.databases.ndex_client) update_probs() (indra.belief.BayesianScorer method) (indra.belief.SimpleScorer method) update_resource() (indra.databases.obo_client.OboClient class method) upload_annotation() (in module indra.sources.hypothesis.api) upload_model() (indra.assemblers.cx.assembler.CxAssembler method) upload_statement_annotation() (in module indra.sources.hypothesis.api) url (indra.sources.crog.processor.CrogProcessor attribute) (indra.sources.utils.RemoteProcessor attribute)

V

validate_agent() (in module indra.statements.validate) validate_db_refs() (in module indra.statements.validate) validate_evidence() (in module indra.statements.validate) validate_id() (in module indra.statements.validate) validate_ns() (in module indra.statements.validate) validate_statement() (in module indra.statements.validate)

validate_text_refs() (in module indra.statements.validate) value (indra.assemblers.pysb.assembler.Param attribute) value_per_second() (indra.statements.statements.QuantitativeState static method) verbs (indra.sources.isi.processor.IsiProcessor attribute) version (indra.ontology.ontology_graph.IndraOntology attribute) VirhostnetProcessor (class in indra.sources.virhostnet.processor) VirtualOntology (class in indra.ontology.virtual.ontology)

W

wait_until_done() (indra.sources.indra_db_rest.processor.IndraDBQueryProcessor method)

WorldContext (class in indra.statements.context) (class in indra.statements.statements)