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W
A
Acetylation (class in indra.statements)
Activation (class in indra.statements)
ActiveForm (class in indra.statements)
activities_by_target() (in module indra.databases.chembl_client)
ActivityCondition (class in indra.statements)
add_default_initial_conditions() (indra.assemblers.pysb.assembler.PysbAssembler method)
add_rule_to_model() (in module indra.assemblers.pysb.assembler)
add_statements() (indra.assemblers.cag.assembler.CAGAssembler method)
(indra.assemblers.cx.assembler.CxAssembler method)
(indra.assemblers.cyjs.assembler.CyJSAssembler method)
(indra.assemblers.english.assembler.EnglishAssembler method)
(indra.assemblers.graph.assembler.GraphAssembler method)
(indra.assemblers.index_card.assembler.IndexCardAssembler method)
(indra.assemblers.pysb.assembler.PysbAssembler method)
(indra.assemblers.sbgn.assembler.SBGNAssembler method)
(indra.explanation.model_checker.ModelChecker method)
(indra.mechlinker.MechLinker method)
(indra.preassembler.Preassembler method)
(indra.tools.incremental_model.IncrementalModel method)
AddModification (class in indra.statements)
Agent (class in indra.statements)
agent_from_entity() (indra.sources.medscan.processor.MedscanProcessor method)
agent_list() (indra.statements.Statement method)
agent_map (indra.preassembler.grounding_mapper.GroundingMapper attribute)
agent_set (indra.assemblers.pysb.assembler.PysbAssembler attribute)
AgentState (class in indra.mechlinker)
align_statements() (in module indra.tools.assemble_corpus)
all_direct_stmts (indra.sources.bel.rdf_processor.BelRdfProcessor attribute)
all_events (indra.sources.reach.processor.ReachProcessor attribute)
all_indirect_stmts (indra.sources.bel.rdf_processor.BelRdfProcessor attribute)
api_ruler (indra.sources.reach.reader.ReachReader attribute)
apply_to() (indra.mechlinker.AgentState method)
assembled_stmts (indra.tools.incremental_model.IncrementalModel attribute)
Association (class in indra.statements)
Autophosphorylation (class in indra.statements)
B
BaseAgent (class in indra.mechlinker)
BaseAgentSet (class in indra.mechlinker)
basename (indra.tools.gene_network.GeneNetwork attribute)
BeliefEngine (class in indra.belief)
BeliefScorer (class in indra.belief)
BelRdfProcessor (class in indra.sources.bel.rdf_processor)
BioContext (class in indra.statements)
BiogridProcessor (class in indra.sources.biogrid)
BiopaxProcessor (class in indra.sources.biopax.processor)
BMIModel (class in indra.assemblers.pysb.bmi_wrapper)
bound_conditions (indra.mechlinker.AgentState attribute)
BoundCondition (class in indra.statements)
build_transitive_closures() (indra.preassembler.hierarchy_manager.HierarchyManager method)
C
CAG (indra.assemblers.cag.assembler.CAGAssembler attribute)
CAGAssembler (class in indra.assemblers.cag.assembler)
CauseEffect (class in indra.sources.hume.processor)
check_entitlement() (in module indra.literature.elsevier_client)
check_model() (indra.explanation.model_checker.ModelChecker method)
check_prior_probs() (indra.belief.BeliefScorer method)
(indra.belief.SimpleScorer method)
check_statement() (indra.explanation.model_checker.ModelChecker method)
citation (indra.sources.reach.processor.ReachProcessor attribute)
combine_duplicate_stmts() (indra.preassembler.Preassembler static method)
combine_duplicates() (indra.preassembler.Preassembler method)
combine_related() (indra.preassembler.Preassembler method)
Complex (class in indra.statements)
complex_monomers_default() (in module indra.assemblers.pysb.assembler)
complex_monomers_one_step() (in module indra.assemblers.pysb.assembler)
Concept (class in indra.statements)
connected_subgraph() (indra.sources.tees.processor.TEESProcessor method)
Conversion (class in indra.statements)
converted_direct_stmts (indra.sources.bel.rdf_processor.BelRdfProcessor attribute)
converted_indirect_stmts (indra.sources.bel.rdf_processor.BelRdfProcessor attribute)
copy_default_config() (in module indra.tools.machine)
create_network() (in module indra.databases.ndex_client)
CWMSError
CWMSProcessor (class in indra.sources.cwms.processor)
CWMSRDFProcessor (class in indra.sources.cwms.rdf_processor)
cx (indra.assemblers.cx.assembler.CxAssembler attribute)
CxAssembler (class in indra.assemblers.cx.assembler)
CyJSAssembler (class in indra.assemblers.cyjs.assembler)
D
Deacetylation (class in indra.statements)
DecreaseAmount (class in indra.statements)
Defarnesylation (class in indra.statements)
default_mapper (in module indra.preassembler.sitemapper)
degenerate_stmts (indra.sources.bel.rdf_processor.BelRdfProcessor attribute)
Degeranylgeranylation (class in indra.statements)
Deglycosylation (class in indra.statements)
Dehydroxylation (class in indra.statements)
Demethylation (class in indra.statements)
Demyristoylation (class in indra.statements)
Depalmitoylation (class in indra.statements)
Dephosphorylation (class in indra.statements)
Deribosylation (class in indra.statements)
Desumoylation (class in indra.statements)
determine_reach_subtype() (in module indra.sources.reach.processor)
Deubiquitination (class in indra.statements)
directly_or_indirectly_related() (indra.preassembler.hierarchy_manager.HierarchyManager method)
doc_id (indra.sources.cwms.processor.CWMSProcessor attribute)
(indra.sources.trips.processor.TripsProcessor attribute)
doi_query() (in module indra.literature.crossref_client)
download_article() (in module indra.literature.elsevier_client)
download_article_from_ids() (in module indra.literature.elsevier_client)
download_from_search() (in module indra.literature.elsevier_client)
drum_system (indra.sources.trips.drum_reader.DrumReader attribute)
DrumReader (class in indra.sources.trips.drum_reader)
dump_statements() (in module indra.tools.assemble_corpus)
dump_stmt_strings() (in module indra.tools.assemble_corpus)
E
edge_properties (indra.assemblers.graph.assembler.GraphAssembler attribute)
eidos_reader (indra.sources.eidos.reader.EidosReader attribute)
EidosProcessor (class in indra.sources.eidos.processor)
EidosReader (class in indra.sources.eidos.reader)
EnglishAssembler (class in indra.assemblers.english.assembler)
entities (indra.sources.medscan.processor.MedscanRelation attribute)
entity_matches_key() (indra.statements.Agent method)
Evidence (class in indra.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)
expand_families() (in module indra.tools.assemble_corpus)
expand_pagination() (in module indra.literature.pubmed_client)
export_into_python() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
export_model() (indra.assemblers.pysb.assembler.PysbAssembler method)
export_sbgn() (in module indra.assemblers.pysb.assembler)
export_to_cytoscapejs() (indra.assemblers.cag.assembler.CAGAssembler method)
extend_with() (indra.preassembler.hierarchy_manager.HierarchyManager method)
extra_annotations (indra.sources.isi.processor.IsiProcessor attribute)
extract_and_process() (in module indra.sources.eidos.cli)
extract_from_directory() (in module indra.sources.eidos.cli)
extract_noun_relations() (indra.sources.cwms.processor.CWMSProcessor method)
extract_output() (in module indra.sources.tees.api)
extract_statement_from_query_result() (indra.sources.cwms.rdf_processor.CWMSRDFProcessor method)
extract_statements() (indra.sources.cwms.rdf_processor.CWMSRDFProcessor method)
extract_text() (in module indra.literature.elsevier_client)
extracted_events (indra.sources.trips.processor.TripsProcessor attribute)
extractions (indra.sources.trips.drum_reader.DrumReader attribute)
F
Farnesylation (class in indra.statements)
filename (in module indra.sources.medscan.api)
filter_belief() (in module indra.tools.assemble_corpus)
filter_by_db_refs() (in module indra.tools.assemble_corpus)
filter_by_type() (in module indra.tools.assemble_corpus)
filter_concept_names() (in module indra.tools.assemble_corpus)
filter_direct() (in module indra.tools.assemble_corpus)
filter_enzyme_kinase() (in module indra.tools.assemble_corpus)
filter_evidence_source() (in module indra.tools.assemble_corpus)
filter_gene_list() (in module indra.tools.assemble_corpus)
filter_genes_only() (in module indra.tools.assemble_corpus)
filter_grounded_only() (in module indra.tools.assemble_corpus)
filter_human_only() (in module indra.tools.assemble_corpus)
filter_inconsequential_acts() (in module indra.tools.assemble_corpus)
filter_inconsequential_mods() (in module indra.tools.assemble_corpus)
filter_mod_nokinase() (in module indra.tools.assemble_corpus)
filter_mutation_status() (in module indra.tools.assemble_corpus)
filter_no_hypothesis() (in module indra.tools.assemble_corpus)
filter_no_negated() (in module indra.tools.assemble_corpus)
filter_pmids() (in module indra.literature.pmc_client)
filter_top_level() (in module indra.tools.assemble_corpus)
filter_transcription_factor() (in module indra.tools.assemble_corpus)
filter_uuid_list() (in module indra.tools.assemble_corpus)
finalize() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
find_arg() (indra.sources.eidos.processor.EidosProcessor static method)
find_args() (indra.sources.eidos.processor.EidosProcessor static method)
find_contradicts() (indra.preassembler.Preassembler method)
find_entity (indra.preassembler.hierarchy_manager.HierarchyManager attribute)
find_event_parent_with_event_child() (indra.sources.tees.processor.TEESProcessor method)
find_event_with_outgoing_edges() (indra.sources.tees.processor.TEESProcessor method)
flatten_evidence() (in module indra.preassembler)
flatten_stmts() (in module indra.preassembler)
G
g (indra.sources.bel.rdf_processor.BelRdfProcessor attribute)
Gap (class in indra.statements)
gather_explicit_activities() (indra.mechlinker.MechLinker method)
gather_implicit_activities() (indra.mechlinker.MechLinker method)
Gef (class in indra.statements)
gene_list (indra.tools.gene_network.GeneNetwork attribute)
GeneNetwork (class in indra.tools.gene_network)
general_node_label() (indra.sources.tees.processor.TEESProcessor method)
generate_im() (indra.explanation.model_checker.ModelChecker method)
generate_jupyter_js() (indra.assemblers.cag.assembler.CAGAssembler method)
geneways_action_to_indra_statement_type() (in module indra.sources.geneways.processor)
GenewaysProcessor (class in indra.sources.geneways.processor)
Geranylgeranylation (class in indra.statements)
get_abstract() (in module indra.literature.elsevier_client)
(in module indra.literature.pubmed_client)
get_activating_mods() (indra.sources.bel.rdf_processor.BelRdfProcessor method)
get_activating_subs() (indra.sources.bel.rdf_processor.BelRdfProcessor method)
get_activation() (indra.sources.bel.rdf_processor.BelRdfProcessor method)
(indra.sources.reach.processor.ReachProcessor method)
get_activations() (indra.sources.trips.processor.TripsProcessor method)
get_activations_causal() (indra.sources.trips.processor.TripsProcessor method)
get_activations_stimulate() (indra.sources.trips.processor.TripsProcessor method)
get_active_forms() (indra.sources.trips.processor.TripsProcessor method)
get_active_forms_state() (indra.sources.trips.processor.TripsProcessor method)
get_activity_modification() (indra.sources.biopax.processor.BiopaxProcessor method)
get_agent_rule_str() (in module indra.assemblers.pysb.assembler)
get_agents() (indra.sources.ndex_cx.processor.NdexCxProcessor method)
(indra.sources.trips.processor.TripsProcessor method)
get_all_descendants() (in module indra.statements)
get_all_direct_statements() (indra.sources.bel.rdf_processor.BelRdfProcessor method)
get_all_events() (indra.sources.reach.processor.ReachProcessor method)
(indra.sources.trips.processor.TripsProcessor method)
get_all_indirect_statements() (indra.sources.bel.rdf_processor.BelRdfProcessor method)
get_annotation() (in module indra.assemblers.pysb.assembler)
get_api_ruler() (indra.sources.reach.reader.ReachReader method)
get_article() (in module indra.literature.elsevier_client)
get_article_xml (in module indra.literature.pubmed_client)
get_attribute() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
get_bel_stmts() (indra.tools.gene_network.GeneNetwork method)
get_binding_site_name() (in module indra.assemblers.pysb.assembler)
get_biopax_stmts() (indra.tools.gene_network.GeneNetwork method)
get_cancer_studies() (in module indra.databases.cbio_client)
get_cancer_types() (in module indra.databases.cbio_client)
get_case_lists() (in module indra.databases.cbio_client)
get_causal_relations() (indra.sources.eidos.processor.EidosProcessor method)
get_ccle_cna() (in module indra.databases.cbio_client)
get_ccle_lines_for_mutation() (in module indra.databases.cbio_client)
get_ccle_mrna() (in module indra.databases.cbio_client)
get_ccle_mutations() (in module indra.databases.cbio_client)
get_chebi_id_from_cas() (in module indra.databases.chebi_client)
get_chebi_id_from_pubchem() (in module indra.databases.chebi_client)
get_chembl_id() (in module indra.databases.chebi_client)
(in module indra.databases.chembl_client)
get_children() (indra.preassembler.hierarchy_manager.HierarchyManager method)
get_complexes() (indra.sources.bel.rdf_processor.BelRdfProcessor method)
(indra.sources.biopax.processor.BiopaxProcessor method)
(indra.sources.reach.processor.ReachProcessor method)
(indra.sources.trips.processor.TripsProcessor method)
get_concept() (indra.sources.eidos.processor.EidosProcessor static method)
get_conversions() (indra.sources.bel.rdf_processor.BelRdfProcessor method)
(indra.sources.biopax.processor.BiopaxProcessor method)
get_create_base_agent() (indra.mechlinker.BaseAgentSet method)
get_create_parameter() (in module indra.assemblers.pysb.assembler)
get_current_time() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
get_default_ndex_cred() (in module indra.databases.ndex_client)
get_degenerate_statements() (indra.sources.bel.rdf_processor.BelRdfProcessor method)
get_degradations() (indra.sources.trips.processor.TripsProcessor method)
get_documents() (indra.sources.hume.processor.HumeJsonLdProcessor method)
get_dois (in module indra.literature.elsevier_client)
get_drug_inhibition_stmts() (in module indra.databases.chembl_client)
get_entity_text_for_relation() (indra.sources.tees.processor.TEESProcessor method)
get_entrez_id() (in module indra.databases.hgnc_client)
get_evidence() (in module indra.databases.chembl_client)
(indra.sources.eidos.processor.EidosProcessor method)
get_family_members() (in module indra.databases.uniprot_client)
get_full_text() (in module indra.literature)
get_fulltext_links() (in module indra.literature.crossref_client)
get_gap() (indra.sources.biopax.processor.BiopaxProcessor method)
get_gef() (indra.sources.biopax.processor.BiopaxProcessor method)
get_gene_name() (in module indra.databases.uniprot_client)
get_gene_names() (indra.assemblers.cyjs.assembler.CyJSAssembler method)
get_gene_synonyms() (in module indra.databases.uniprot_client)
get_genetic_profiles() (in module indra.databases.cbio_client)
get_groundings() (indra.sources.eidos.processor.EidosProcessor static method)
get_hash() (indra.statements.Statement method)
get_heat_kernel() (in module indra.databases.relevance_client)
get_hedging() (indra.sources.eidos.processor.EidosProcessor static method)
get_hgnc_entry (in module indra.databases.hgnc_client)
get_hgnc_from_entrez() (in module indra.databases.hgnc_client)
get_hgnc_from_mouse() (in module indra.databases.hgnc_client)
get_hgnc_from_rat() (in module indra.databases.hgnc_client)
get_hgnc_id() (in module indra.databases.hgnc_client)
get_hgnc_name() (in module indra.databases.hgnc_client)
get_id_count() (in module indra.literature.pubmed_client)
get_id_from_mgi() (in module indra.databases.uniprot_client)
get_id_from_mnemonic() (in module indra.databases.uniprot_client)
get_id_from_rgd() (in module indra.databases.uniprot_client)
get_ids (in module indra.literature.pubmed_client)
get_ids_for_gene (in module indra.literature.pubmed_client)
get_im() (indra.explanation.model_checker.ModelChecker method)
get_input_var_names() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
get_issns_for_journal (in module indra.literature.pubmed_client)
get_kinetics() (in module indra.databases.chembl_client)
get_mesh_id() (in module indra.databases.chembl_client)
get_metadata (in module indra.literature.crossref_client)
get_metadata_for_ids() (in module indra.literature.pubmed_client)
get_metadata_from_xml_tree() (in module indra.literature.pubmed_client)
get_mgi_id() (in module indra.databases.uniprot_client)
get_mnemonic() (in module indra.databases.uniprot_client)
get_mod_site_name() (in module indra.assemblers.pysb.assembler)
get_model_agents() (indra.tools.incremental_model.IncrementalModel method)
get_modifications() (indra.sources.bel.rdf_processor.BelRdfProcessor method)
(indra.sources.biopax.processor.BiopaxProcessor method)
(indra.sources.reach.processor.ReachProcessor method)
(indra.sources.trips.processor.TripsProcessor method)
get_modifications_indirect() (indra.sources.trips.processor.TripsProcessor method)
get_monomer_pattern() (in module indra.assemblers.pysb.assembler)
get_mouse_id() (in module indra.databases.hgnc_client)
(in module indra.databases.uniprot_client)
get_mutations() (in module indra.databases.cbio_client)
(in module indra.databases.context_client)
get_negation() (indra.sources.eidos.processor.EidosProcessor static method)
get_node_names() (indra.sources.ndex_cx.processor.NdexCxProcessor method)
get_num_sequenced() (in module indra.databases.cbio_client)
get_output_var_names() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
get_parents() (indra.preassembler.hierarchy_manager.HierarchyManager method)
get_pcid() (in module indra.databases.chembl_client)
get_piis() (in module indra.literature.elsevier_client)
get_piis_for_date (in module indra.literature.elsevier_client)
get_pmid() (in module indra.databases.chembl_client)
get_pmids() (indra.sources.ndex_cx.processor.NdexCxProcessor method)
get_primary_id() (in module indra.databases.uniprot_client)
get_profile_data() (in module indra.databases.cbio_client)
get_protein_expression() (in module indra.databases.context_client)
get_protein_synonyms() (in module indra.databases.uniprot_client)
get_protein_targets_only() (in module indra.databases.chembl_client)
get_pubchem_id() (in module indra.databases.chebi_client)
get_publications() (in module indra.databases.biogrid_client)
get_rat_id() (in module indra.databases.hgnc_client)
(in module indra.databases.uniprot_client)
get_regulate_activities() (indra.sources.biopax.processor.BiopaxProcessor method)
get_regulate_amounts() (indra.sources.biopax.processor.BiopaxProcessor method)
(indra.sources.reach.processor.ReachProcessor method)
(indra.sources.trips.processor.TripsProcessor method)
get_related_node() (indra.sources.tees.processor.TEESProcessor method)
get_relevant_nodes() (in module indra.databases.relevance_client)
get_rgd_id() (in module indra.databases.uniprot_client)
get_site_pattern() (in module indra.assemblers.pysb.assembler)
get_sites() (indra.sources.medscan.processor.ProteinSiteInfo method)
get_start_time() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
get_statement_by_name() (in module indra.statements)
get_statements() (in module indra.sources.indra_db_rest.client_api)
(indra.sources.hume.processor.HumeProcessor method)
(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.client_api)
get_statements_for_paper() (in module indra.sources.indra_db_rest.client_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_string() (indra.assemblers.graph.assembler.GraphAssembler method)
get_subnetwork() (in module indra.tools.executable_subnetwork)
get_synonyms() (in module indra.databases.uniprot_client)
get_syntheses() (indra.sources.trips.processor.TripsProcessor method)
get_target_chemblid() (in module indra.databases.chembl_client)
get_time_step() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
get_time_units() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
get_title() (in module indra.literature.pubmed_client)
get_transcription() (indra.sources.bel.rdf_processor.BelRdfProcessor method)
get_translocation() (indra.sources.reach.processor.ReachProcessor method)
get_uncond_agent() (in module indra.assemblers.pysb.assembler)
get_uniprot_id() (in module indra.databases.hgnc_client)
get_unresolved_support_uuids() (in module indra.statements)
get_valid_location() (in module indra.statements)
,
[1]
get_valid_residue() (in module indra.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)
get_xml() (in module indra.sources.trips.client)
Glycosylation (class in indra.statements)
gm (indra.preassembler.grounding_mapper.GroundingMapper attribute)
graph (indra.assemblers.graph.assembler.GraphAssembler attribute)
(indra.assemblers.sif.assembler.SifAssembler attribute)
(indra.preassembler.hierarchy_manager.HierarchyManager attribute)
graph_properties (indra.assemblers.graph.assembler.GraphAssembler attribute)
graph_query() (in module indra.sources.biopax.pathway_commons_client)
GraphAssembler (class in indra.assemblers.graph.assembler)
grounded_monomer_patterns() (in module indra.assemblers.pysb.assembler)
GroundingMapper (class in indra.preassembler.grounding_mapper)
GtpActivation (class in indra.statements)
H
HasActivity (class in indra.statements)
hierarchies (indra.preassembler.Preassembler attribute)
HierarchyManager (class in indra.preassembler.hierarchy_manager)
HumeJsonLdProcessor (class in indra.sources.hume.processor)
HumeProcessor (class in indra.sources.hume.processor)
Hydroxylation (class in indra.statements)
I
id_lookup() (in module indra.literature)
(in module indra.literature.pmc_client)
IncreaseAmount (class in indra.statements)
IncrementalModel (class in indra.tools.incremental_model)
IndexCardAssembler (class in indra.assemblers.index_card.assembler)
indirect_stmts (indra.sources.bel.rdf_processor.BelRdfProcessor attribute)
indra.assemblers.cag.assembler (module)
indra.assemblers.cx.assembler (module)
indra.assemblers.cyjs.assembler (module)
indra.assemblers.english.assembler (module)
indra.assemblers.graph.assembler (module)
indra.assemblers.index_card.assembler (module)
indra.assemblers.pysb.assembler (module)
indra.assemblers.pysb.bmi_wrapper (module)
indra.assemblers.sbgn.assembler (module)
indra.assemblers.sif.assembler (module)
indra.assemblers.tsv.assembler (module)
indra.belief (module)
indra.databases.biogrid_client (module)
indra.databases.cbio_client (module)
indra.databases.chebi_client (module)
indra.databases.chembl_client (module)
indra.databases.context_client (module)
indra.databases.hgnc_client (module)
indra.databases.ndex_client (module)
indra.databases.relevance_client (module)
indra.databases.uniprot_client (module)
indra.explanation.model_checker (module)
indra.literature (module)
indra.literature.crossref_client (module)
indra.literature.elsevier_client (module)
indra.literature.newsapi_client (module)
indra.literature.pmc_client (module)
indra.literature.pubmed_client (module)
indra.mechlinker (module)
indra.preassembler (module)
indra.preassembler.grounding_mapper (module)
indra.preassembler.hierarchy_manager (module)
indra.preassembler.sitemapper (module)
indra.sources.bel.api (module)
indra.sources.bel.processor (module)
indra.sources.bel.rdf_processor (module)
indra.sources.biogrid (module)
indra.sources.biopax.api (module)
indra.sources.biopax.pathway_commons_client (module)
indra.sources.biopax.processor (module)
indra.sources.cwms (module)
indra.sources.cwms.api (module)
indra.sources.cwms.processor (module)
indra.sources.cwms.rdf_processor (module)
indra.sources.eidos (module)
indra.sources.eidos.api (module)
indra.sources.eidos.cli (module)
indra.sources.eidos.processor (module)
indra.sources.eidos.reader (module)
indra.sources.geneways.api (module)
indra.sources.geneways.processor (module)
indra.sources.hume (module)
indra.sources.hume.api (module)
indra.sources.hume.processor (module)
indra.sources.indra_db_rest (module)
indra.sources.indra_db_rest.client_api (module)
indra.sources.isi (module)
indra.sources.isi.api (module)
indra.sources.isi.processor (module)
indra.sources.lincs_drug (module)
indra.sources.lincs_drug.api (module)
indra.sources.lincs_drug.processor (module)
indra.sources.medscan (module)
indra.sources.medscan.api (module)
indra.sources.medscan.processor (module)
indra.sources.ndex_cx.api (module)
indra.sources.ndex_cx.processor (module)
indra.sources.reach.api (module)
indra.sources.reach.processor (module)
indra.sources.reach.reader (module)
indra.sources.signor (module)
indra.sources.sofia (module)
indra.sources.sofia.api (module)
indra.sources.sofia.processor (module)
indra.sources.sparser (module)
indra.sources.sparser.api (module)
indra.sources.tas (module)
indra.sources.tas.api (module)
indra.sources.tas.processor (module)
indra.sources.tees.api (module)
indra.sources.tees.processor (module)
indra.sources.trips.api (module)
indra.sources.trips.client (module)
indra.sources.trips.drum_reader (module)
indra.sources.trips.processor (module)
indra.statements (module)
indra.tools.assemble_corpus (module)
indra.tools.executable_subnetwork (module)
indra.tools.gene_network (module)
indra.tools.incremental_model (module)
indra.tools.machine (module)
IndraDBRestError
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)
Inhibition (class in indra.statements)
initialize() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
initialize_reader() (in module indra.sources.eidos.api)
InputError
InvalidLocationError
InvalidResidueError
is_human() (in module indra.databases.uniprot_client)
is_mouse() (in module indra.databases.uniprot_client)
is_opposite() (indra.preassembler.hierarchy_manager.HierarchyManager method)
is_rat() (in module indra.databases.uniprot_client)
is_secondary() (in module indra.databases.uniprot_client)
is_statement_in_list() (in module indra.sources.medscan.processor)
isa() (indra.preassembler.hierarchy_manager.HierarchyManager method)
isa_or_partof() (indra.preassembler.hierarchy_manager.HierarchyManager method)
IsiProcessor (class in indra.sources.isi.processor)
L
last_site_info_in_sentence (indra.sources.medscan.processor.MedscanProcessor attribute)
LincsProcessor (class in indra.sources.lincs_drug.processor)
LinkedStatement (class in indra.mechlinker)
load_prior() (indra.tools.incremental_model.IncrementalModel method)
load_site_map() (in module indra.preassembler.sitemapper)
load_statements() (in module indra.tools.assemble_corpus)
location (indra.mechlinker.AgentState attribute)
M
make_generic_copy() (indra.statements.Statement method)
make_model() (indra.assemblers.cag.assembler.CAGAssembler method)
(indra.assemblers.cx.assembler.CxAssembler method)
(indra.assemblers.cyjs.assembler.CyJSAssembler method)
(indra.assemblers.english.assembler.EnglishAssembler method)
(indra.assemblers.graph.assembler.GraphAssembler method)
(indra.assemblers.index_card.assembler.IndexCardAssembler method)
(indra.assemblers.pysb.assembler.PysbAssembler method)
(indra.assemblers.sbgn.assembler.SBGNAssembler method)
(indra.assemblers.sif.assembler.SifAssembler method)
(indra.assemblers.tsv.assembler.TsvAssembler method)
make_nxml_from_text() (in module indra.sources.sparser.api)
make_repository_component() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
make_statement() (indra.sources.geneways.processor.GenewaysProcessor method)
make_statement_camel() (in module indra.statements)
map_agent() (indra.preassembler.grounding_mapper.GroundingMapper method)
map_grounding() (in module indra.tools.assemble_corpus)
map_sequence() (in module indra.tools.assemble_corpus)
map_sites() (indra.preassembler.sitemapper.SiteMapper method)
MappedStatement (class in indra.preassembler.sitemapper)
matches_key() (indra.statements.Agent method)
max_path_length (indra.explanation.model_checker.PathResult attribute)
max_paths (indra.explanation.model_checker.PathResult attribute)
MechLinker (class in indra.mechlinker)
MedscanEntity (class in indra.sources.medscan.processor)
MedscanProcessor (class in indra.sources.medscan.processor)
MedscanProperty (class in indra.sources.medscan.processor)
MedscanRelation (class in indra.sources.medscan.processor)
Methylation (class in indra.statements)
ModCondition (class in indra.statements)
model (indra.assemblers.english.assembler.EnglishAssembler attribute)
(indra.assemblers.pysb.assembler.PysbAssembler attribute)
(indra.sources.biopax.processor.BiopaxProcessor attribute)
model_to_owl() (in module indra.sources.biopax.pathway_commons_client)
ModelChecker (class in indra.explanation.model_checker)
Modification (class in indra.statements)
mods (indra.mechlinker.AgentState attribute)
mutations (indra.mechlinker.AgentState attribute)
MutCondition (class in indra.statements)
Myristoylation (class in indra.statements)
N
name (indra.sources.medscan.processor.MedscanEntity attribute)
(indra.sources.medscan.processor.MedscanProperty attribute)
namespace_from_uri() (in module indra.sources.bel.rdf_processor)
NdexCxProcessor (class in indra.sources.ndex_cx.processor)
network_name (indra.assemblers.cx.assembler.CxAssembler attribute)
node_has_edge_with_label() (indra.sources.tees.processor.TEESProcessor method)
node_properties (indra.assemblers.graph.assembler.GraphAssembler attribute)
node_to_evidence() (indra.sources.tees.processor.TEESProcessor method)
normalize_medscan_name() (in module indra.sources.medscan.processor)
NotAStatementName
num_documents (in module indra.sources.medscan.api)
num_entities (indra.sources.medscan.processor.MedscanProcessor attribute)
num_entities_not_found (indra.sources.medscan.processor.MedscanProcessor attribute)
O
obj (indra.sources.medscan.processor.MedscanRelation attribute)
owl_str_to_model() (in module indra.sources.biopax.pathway_commons_client)
owl_to_model() (in module indra.sources.biopax.pathway_commons_client)
P
Palmitoylation (class in indra.statements)
par_to_sec (indra.sources.cwms.processor.CWMSProcessor attribute)
(indra.sources.trips.processor.TripsProcessor attribute)
paragraphs (indra.sources.cwms.processor.CWMSProcessor attribute)
(indra.sources.trips.processor.TripsProcessor attribute)
parse_identifiers_url() (in module indra.assemblers.pysb.assembler)
partof() (indra.preassembler.hierarchy_manager.HierarchyManager method)
path_found (indra.explanation.model_checker.PathResult attribute)
path_metrics (indra.explanation.model_checker.PathResult attribute)
PathMetric (class in indra.explanation.model_checker)
PathResult (class in indra.explanation.model_checker)
paths (indra.explanation.model_checker.PathResult attribute)
Phosphorylation (class in indra.statements)
physical_only (indra.sources.biogrid.BiogridProcessor attribute)
pmid (indra.sources.isi.processor.IsiProcessor attribute)
policies (indra.assemblers.pysb.assembler.PysbAssembler attribute)
position (indra.sources.reach.processor.Site attribute)
preassemble() (indra.tools.incremental_model.IncrementalModel method)
Preassembler (class in indra.preassembler)
print_boolean_net() (indra.assemblers.sif.assembler.SifAssembler method)
print_cx() (indra.assemblers.cx.assembler.CxAssembler method)
print_cyjs_context() (indra.assemblers.cyjs.assembler.CyJSAssembler method)
print_cyjs_graph() (indra.assemblers.cyjs.assembler.CyJSAssembler method)
print_event_statistics() (indra.sources.reach.processor.ReachProcessor method)
print_loopy() (indra.assemblers.sif.assembler.SifAssembler method)
print_model() (indra.assemblers.index_card.assembler.IndexCardAssembler method)
(indra.assemblers.pysb.assembler.PysbAssembler method)
(indra.assemblers.sbgn.assembler.SBGNAssembler method)
(indra.assemblers.sif.assembler.SifAssembler method)
print_parent_and_children_info() (indra.sources.tees.processor.TEESProcessor method)
print_statement_coverage() (indra.sources.bel.rdf_processor.BelRdfProcessor method)
print_statements() (indra.sources.bel.rdf_processor.BelRdfProcessor method)
(indra.sources.biopax.processor.BiopaxProcessor method)
process_belrdf() (in module indra.sources.bel.api)
process_belscript() (in module indra.sources.bel.api)
process_binding_statements() (indra.sources.tees.processor.TEESProcessor method)
process_csv() (in module indra.sources.tas.api)
process_csxml_from_file_handle() (indra.sources.medscan.processor.MedscanProcessor method)
process_cx() (in module indra.sources.ndex_cx.api)
process_cx_file() (in module indra.sources.ndex_cx.api)
process_decrease_expression_amount() (indra.sources.tees.processor.TEESProcessor method)
process_directory() (in module indra.sources.medscan.api)
process_directory_statements_sorted_by_pmid() (in module indra.sources.medscan.api)
process_ekb() (in module indra.sources.cwms.api)
process_file() (in module indra.sources.medscan.api)
process_file_sorted_by_pmid() (in module indra.sources.medscan.api)
process_from_web() (in module indra.sources.lincs_drug.api)
process_geneways_files() (in module indra.sources.geneways.api)
process_increase_expression_amount() (indra.sources.tees.processor.TEESProcessor method)
process_json() (in module indra.sources.eidos.api)
process_json_dict() (in module indra.sources.sparser.api)
process_json_file() (in module indra.sources.bel.api)
(in module indra.sources.eidos.api)
(in module indra.sources.isi.api)
(in module indra.sources.reach.api)
process_json_file_old() (in module indra.sources.hume.api)
process_json_ld() (in module indra.sources.eidos.api)
process_json_ld_file() (in module indra.sources.eidos.api)
process_json_ld_str() (in module indra.sources.eidos.api)
process_json_str() (in module indra.sources.eidos.api)
(in module indra.sources.reach.api)
process_jsonld_file() (in module indra.sources.hume.api)
process_model() (in module indra.sources.biopax.api)
process_ndex_neighborhood() (in module indra.sources.bel.api)
process_ndex_network() (in module indra.sources.ndex_cx.api)
process_nxml() (in module indra.sources.isi.api)
process_nxml_file() (in module indra.sources.reach.api)
(in module indra.sources.sparser.api)
process_nxml_str() (in module indra.sources.reach.api)
(in module indra.sources.sparser.api)
process_output_folder() (in module indra.sources.isi.api)
process_owl() (in module indra.sources.biopax.api)
process_pc_neighborhood() (in module indra.sources.biopax.api)
process_pc_pathsbetween() (in module indra.sources.biopax.api)
process_pc_pathsfromto() (in module indra.sources.biopax.api)
process_phosphorylation_statements() (indra.sources.tees.processor.TEESProcessor method)
process_pmc() (in module indra.sources.reach.api)
process_preprocessed() (in module indra.sources.isi.api)
process_pubmed_abstract() (in module indra.sources.reach.api)
process_pybel_graph (in module indra.sources.bel.api)
process_pybel_neighborhood() (in module indra.sources.bel.api)
process_rdf_file() (in module indra.sources.cwms.api)
process_relation() (indra.sources.medscan.processor.MedscanProcessor method)
process_sparser_output() (in module indra.sources.sparser.api)
process_table() (in module indra.sources.sofia.api)
process_text() (in module indra.sources.cwms.api)
(in module indra.sources.eidos.api)
(in module indra.sources.isi.api)
(in module indra.sources.reach.api)
(in module indra.sources.sparser.api)
(in module indra.sources.tees.api)
(in module indra.sources.trips.api)
(indra.sources.eidos.reader.EidosReader method)
process_xml() (in module indra.sources.sparser.api)
(in module indra.sources.trips.api)
properties (indra.sources.medscan.processor.MedscanEntity attribute)
protein_map_from_twg() (in module indra.preassembler.grounding_mapper)
ProteinSiteInfo (class in indra.sources.medscan.processor)
prune_influence_map() (indra.explanation.model_checker.ModelChecker method)
prune_influence_map_subj_obj() (indra.explanation.model_checker.ModelChecker method)
PybelProcessor (class in indra.sources.bel.processor)
PysbAssembler (class in indra.assemblers.pysb.assembler)
Q
query_protein (in module indra.databases.uniprot_client)
query_target() (in module indra.databases.chembl_client)
R
ReachProcessor (class in indra.sources.reach.processor)
ReachReader (class in indra.sources.reach.reader)
read_pmc() (indra.sources.trips.drum_reader.DrumReader method)
read_text() (indra.sources.trips.drum_reader.DrumReader method)
reader_output (indra.sources.isi.processor.IsiProcessor attribute)
receive_reply() (indra.sources.trips.drum_reader.DrumReader method)
reduce_activities() (in module indra.tools.assemble_corpus)
(indra.mechlinker.MechLinker method)
RefContext (class in indra.statements)
RegulateActivity (class in indra.statements)
RegulateAmount (class in indra.statements)
related_stmts (indra.preassembler.Preassembler attribute)
remove_im_params() (in module indra.explanation.model_checker)
RemoveModification (class in indra.statements)
rename_db_ref() (in module indra.tools.assemble_corpus)
render_stmt_graph() (in module indra.preassembler)
replace_activations() (indra.mechlinker.MechLinker method)
replace_complexes() (indra.mechlinker.MechLinker method)
require_active_forms() (indra.mechlinker.MechLinker method)
residue (indra.sources.reach.processor.Site attribute)
result_code (indra.explanation.model_checker.PathResult attribute)
results (indra.tools.gene_network.GeneNetwork attribute)
Ribosylation (class in indra.statements)
run_eidos() (in module indra.sources.eidos.cli)
run_on_text() (in module indra.sources.tees.api)
run_preassembly() (in module indra.tools.assemble_corpus)
(indra.tools.gene_network.GeneNetwork method)
run_preassembly_duplicate() (in module indra.tools.assemble_corpus)
run_preassembly_related() (in module indra.tools.assemble_corpus)
run_sparser() (in module indra.sources.sparser.api)
S
s2a() (in module indra.sources.tees.processor)
sample_statements() (in module indra.belief)
save() (indra.tools.incremental_model.IncrementalModel method)
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.index_card.assembler.IndexCardAssembler method)
(indra.assemblers.pysb.assembler.PysbAssembler method)
(indra.assemblers.sbgn.assembler.SBGNAssembler method)
(indra.assemblers.sif.assembler.SifAssembler method)
(indra.sources.biopax.processor.BiopaxProcessor method)
save_pdf() (indra.assemblers.graph.assembler.GraphAssembler method)
save_rst() (indra.assemblers.pysb.assembler.PysbAssembler method)
save_xml() (in module indra.sources.trips.client)
sbgn (indra.assemblers.sbgn.assembler.SBGNAssembler attribute)
SBGNAssembler (class in indra.assemblers.sbgn.assembler)
score_paths() (indra.explanation.model_checker.ModelChecker method)
score_statement() (indra.belief.BeliefScorer method)
(indra.belief.SimpleScorer method)
scorer (indra.belief.BeliefEngine attribute)
sec (indra.sources.medscan.processor.MedscanRelation attribute)
SelfModification (class in indra.statements)
send_query() (in module indra.databases.chembl_client)
(in module indra.sources.trips.client)
send_request (in module indra.databases.cbio_client)
send_request() (in module indra.databases.ndex_client)
(in module indra.literature.newsapi_client)
sentence_statements (indra.sources.medscan.processor.MedscanProcessor attribute)
sentences (indra.sources.cwms.processor.CWMSProcessor attribute)
(indra.sources.trips.processor.TripsProcessor attribute)
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_hierarchy_probs() (indra.belief.BeliefEngine method)
set_linked_probs() (indra.belief.BeliefEngine method)
set_prior_probs() (indra.belief.BeliefEngine method)
set_value() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
set_values() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
shorter_name() (in module indra.sources.hume.processor)
shortest_string_in_list() (in module indra.sources.hume.processor)
SifAssembler (class in indra.assemblers.sif.assembler)
SimpleScorer (class in indra.belief)
Site (class in indra.sources.reach.processor)
SiteMapper (class in indra.preassembler.sitemapper)
state_matches_key() (indra.statements.Agent method)
Statement (class in indra.statements)
statements (indra.assemblers.cag.assembler.CAGAssembler attribute)
(indra.assemblers.cx.assembler.CxAssembler attribute)
(indra.assemblers.cyjs.assembler.CyJSAssembler attribute)
(indra.assemblers.english.assembler.EnglishAssembler attribute)
(indra.assemblers.graph.assembler.GraphAssembler attribute)
(indra.assemblers.index_card.assembler.IndexCardAssembler attribute)
(indra.assemblers.pysb.assembler.PysbAssembler attribute)
(indra.assemblers.sbgn.assembler.SBGNAssembler attribute)
(indra.assemblers.tsv.assembler.TsvAssembler attribute)
(indra.sources.bel.processor.PybelProcessor attribute)
(indra.sources.bel.rdf_processor.BelRdfProcessor attribute)
(indra.sources.biogrid.BiogridProcessor attribute)
(indra.sources.biopax.processor.BiopaxProcessor attribute)
(indra.sources.cwms.processor.CWMSProcessor attribute)
(indra.sources.cwms.rdf_processor.CWMSRDFProcessor attribute)
(indra.sources.eidos.processor.EidosProcessor attribute)
(indra.sources.geneways.processor.GenewaysProcessor attribute)
(indra.sources.hume.processor.HumeJsonLdProcessor attribute)
(indra.sources.hume.processor.HumeProcessor attribute)
(indra.sources.isi.processor.IsiProcessor attribute)
(indra.sources.lincs_drug.processor.LincsProcessor attribute)
(indra.sources.medscan.processor.MedscanProcessor attribute)
(indra.sources.ndex_cx.processor.NdexCxProcessor attribute)
(indra.sources.reach.processor.ReachProcessor attribute)
(indra.sources.tees.processor.TEESProcessor attribute)
(indra.sources.trips.processor.TripsProcessor attribute)
stmt_from_rule() (in module indra.explanation.model_checker)
stmts (indra.preassembler.Preassembler attribute)
(indra.tools.incremental_model.IncrementalModel attribute)
stmts_from_json() (in module indra.statements)
stmts_to_json() (in module indra.statements)
strip_agent_context() (in module indra.tools.assemble_corpus)
subj (indra.sources.medscan.processor.MedscanRelation attribute)
Sumoylation (class in indra.statements)
svo_type (indra.sources.medscan.processor.MedscanRelation attribute)
T
tag_evidence_subtype() (in module indra.belief)
tagged_sentence (indra.sources.medscan.processor.MedscanRelation attribute)
TasProcessor (class in indra.sources.tas.processor)
TEESProcessor (class in indra.sources.tees.processor)
term_from_uri() (in module indra.sources.bel.rdf_processor)
time_context_from_dct() (indra.sources.eidos.processor.EidosProcessor static method)
time_context_from_ref() (indra.sources.eidos.processor.EidosProcessor method)
time_context_from_timex() (indra.sources.eidos.processor.EidosProcessor static method)
TimeContext (class in indra.statements)
to_graph() (indra.statements.Statement method)
to_json() (indra.statements.ActiveForm method)
(indra.statements.Complex method)
(indra.statements.Conversion method)
(indra.statements.Gap method)
(indra.statements.Gef method)
(indra.statements.Influence method)
(indra.statements.Modification method)
(indra.statements.RegulateActivity method)
(indra.statements.RegulateAmount method)
(indra.statements.SelfModification method)
(indra.statements.Statement method)
(indra.statements.Translocation method)
to_statement() (indra.sources.hume.processor.CauseEffect method)
Translocation (class in indra.statements)
Transphosphorylation (class in indra.statements)
tree (indra.sources.cwms.processor.CWMSProcessor attribute)
(indra.sources.eidos.processor.EidosProcessor attribute)
(indra.sources.hume.processor.HumeJsonLdProcessor attribute)
(indra.sources.reach.processor.ReachProcessor attribute)
(indra.sources.trips.processor.TripsProcessor attribute)
TripsProcessor (class in indra.sources.trips.processor)
TsvAssembler (class in indra.assemblers.tsv.assembler)
type (indra.sources.medscan.processor.MedscanEntity attribute)
(indra.sources.medscan.processor.MedscanProperty attribute)
U
Ubiquitination (class in indra.statements)
unique_stmts (indra.preassembler.Preassembler attribute)
UnknownNamespaceException
UnknownPolicyError
Unresolved (class in indra.statements)
UnresolvedUuidError
update() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
update_network() (in module indra.databases.ndex_client)
upload_model() (indra.assemblers.cx.assembler.CxAssembler method)
uri (indra.sources.medscan.processor.MedscanRelation attribute)
urn (indra.sources.medscan.processor.MedscanEntity attribute)
(indra.sources.medscan.processor.MedscanProperty attribute)
V
verb (indra.sources.medscan.processor.MedscanRelation attribute)
verbs (indra.sources.isi.processor.IsiProcessor attribute)
verify_location() (in module indra.databases.uniprot_client)
verify_modification() (in module indra.databases.uniprot_client)
W
WorldContext (class in indra.statements)
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