INDRA
1.6
License and funding
Installation
Getting started with INDRA
INDRA modules reference
Tutorials
REST API
INDRA
Docs
»
Index
Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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.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)
add_to_review() (indra.db.content_manager.ContentManager method)
AddModification (class in indra.statements)
Agent (class in indra.statements)
agent_map (indra.preassembler.grounding_mapper.GroundingMapper attribute)
agent_set (indra.assemblers.pysb_assembler.PysbAssembler attribute)
AgentState (class in indra.mechlinker)
all_direct_stmts (indra.sources.bel.belrdf_processor.BelRdfProcessor attribute)
all_events (indra.sources.reach.processor.ReachProcessor attribute)
all_indirect_stmts (indra.sources.bel.belrdf_processor.BelRdfProcessor attribute)
api_ruler (indra.sources.reach.reach_reader.ReachReader attribute)
apply_to() (indra.mechlinker.AgentState method)
assembled_stmts (indra.tools.incremental_model.IncrementalModel attribute)
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)
BelRdfProcessor (class in indra.sources.bel.belrdf_processor)
BiopaxProcessor (class in indra.sources.biopax.processor)
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)
check_model() (indra.explanation.model_checker.ModelChecker 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)
commit() (indra.db.database_manager.DatabaseManager 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)
connected_subgraph() (indra.sources.tees.processor.TEESProcessor method)
ContentManager (class in indra.db.content_manager)
Conversion (class in indra.statements)
converted_direct_stmts (indra.sources.bel.belrdf_processor.BelRdfProcessor attribute)
converted_indirect_stmts (indra.sources.bel.belrdf_processor.BelRdfProcessor attribute)
copy() (indra.db.database_manager.DatabaseManager method)
copy_default_config() (in module indra.tools.machine)
copy_into_db() (indra.db.content_manager.ContentManager method)
create_network() (in module indra.databases.ndex_client)
create_tables() (indra.db.database_manager.DatabaseManager method)
cx (indra.assemblers.cx_assembler.CxAssembler attribute)
CxAssembler (class in indra.assemblers.cx_assembler)
D
DatabaseError (class in indra.db.content_manager)
DatabaseManager (class in indra.db.database_manager)
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.belrdf_processor.BelRdfProcessor attribute)
Degeranylgeranylation (class in indra.statements)
Deglycosylation (class in indra.statements)
Dehydroxylation (class in indra.statements)
delete_all() (indra.db.database_manager.DatabaseManager method)
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)
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_file() (indra.db.content_manager.NihFtpClient method)
drop_tables() (indra.db.database_manager.DatabaseManager method)
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.eidos_reader.EidosReader attribute)
EidosJsonLdProcessor (class in indra.sources.eidos.processor)
EidosJsonProcessor (class in indra.sources.eidos.processor)
EidosReader (class in indra.sources.eidos.eidos_reader)
EnglishAssembler (class in indra.assemblers.english_assembler)
enrich_textrefs() (indra.db.content_manager.Manuscripts 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_model() (indra.assemblers.pysb_assembler.PysbAssembler method)
export_sbgn() (in module indra.assemblers.pysb_assembler)
export_to_cytoscapejs() (indra.assemblers.cag_assembler.CAGAssembler method)
extracted_events (indra.sources.trips.processor.TripsProcessor attribute)
F
Farnesylation (class in indra.statements)
filter_belief() (in module indra.tools.assemble_corpus)
filter_by_type() (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_pmids() (in module indra.literature.pmc_client)
filter_query() (indra.db.database_manager.DatabaseManager method)
filter_text_content() (indra.db.content_manager.PmcManager method)
filter_text_refs() (indra.db.content_manager.ContentManager method)
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)
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)
fix_doi() (indra.db.content_manager.Pubmed method)
flatten_evidence() (in module indra.preassembler)
flatten_stmts() (in module indra.preassembler)
ftp_ls() (indra.db.content_manager.NihFtpClient method)
ftp_ls_timestamped() (indra.db.content_manager.NihFtpClient method)
G
g (indra.sources.bel.belrdf_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)
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_abstracts_by_pmids() (in module indra.db.util)
get_activating_mods() (indra.sources.bel.belrdf_processor.BelRdfProcessor method)
get_activating_subs() (indra.sources.bel.belrdf_processor.BelRdfProcessor method)
get_activation() (indra.sources.bel.belrdf_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_active_tables() (indra.db.database_manager.DatabaseManager 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.belrdf_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.belrdf_processor.BelRdfProcessor method)
get_annotation() (in module indra.assemblers.pysb_assembler)
get_api_ruler() (indra.sources.reach.reach_reader.ReachReader method)
get_article() (in module indra.literature.elsevier_client)
get_article_xml (in module indra.literature.pubmed_client)
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_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_column_names() (indra.db.database_manager.DatabaseManager method)
get_column_objects() (indra.db.database_manager.DatabaseManager method)
get_complexes() (indra.sources.bel.belrdf_processor.BelRdfProcessor method)
(indra.sources.biopax.processor.BiopaxProcessor method)
(indra.sources.reach.processor.ReachProcessor method)
(indra.sources.trips.processor.TripsProcessor method)
get_composite_activating_mods() (indra.sources.bel.belrdf_processor.BelRdfProcessor method)
get_conversions() (indra.sources.bel.belrdf_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_csv_as_dict() (indra.db.content_manager.NihFtpClient method)
get_data_from_xml_str() (indra.db.content_manager.PmcManager method)
get_default_ndex_cred() (in module indra.databases.ndex_client)
get_defaults() (in module indra.db.util)
get_degenerate_statements() (indra.sources.bel.belrdf_processor.BelRdfProcessor method)
get_degradations() (indra.sources.trips.processor.TripsProcessor 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)
get_family_members() (in module indra.databases.uniprot_client)
get_file() (indra.db.content_manager.NihFtpClient method)
get_full_text() (in module indra.literature)
get_fulltext_links() (in module indra.literature.crossref_client)
get_gap() (indra.sources.biopax.processor.BiopaxProcessor method)
get_gef() (indra.sources.biopax.processor.BiopaxProcessor method)
get_gene_name() (in module indra.databases.uniprot_client)
get_genetic_profiles() (in module indra.databases.cbio_client)
get_heat_kernel() (in module indra.databases.relevance_client)
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_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_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_missing_pmids() (indra.db.content_manager.PmcManager method)
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.belrdf_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_node_names() (indra.sources.ndex_cx.processor.NdexCxProcessor method)
get_num_sequenced() (in module indra.databases.cbio_client)
get_parents() (indra.preassembler.hierarchy_manager.HierarchyManager method)
get_pcid() (in module indra.databases.chembl_client)
get_pmid() (in module indra.databases.chembl_client)
get_pmids() (indra.sources.ndex_cx.processor.NdexCxProcessor method)
get_primary_db() (in module indra.db.util)
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_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_statements() (in module indra.db.util)
(indra.sources.ndex_cx.processor.NdexCxProcessor method)
(indra.tools.gene_network.GeneNetwork method)
(indra.tools.incremental_model.IncrementalModel method)
get_statements_by_gene_role_type() (in module indra.db.util)
get_statements_noprior() (indra.tools.incremental_model.IncrementalModel method)
get_statements_prior() (indra.tools.incremental_model.IncrementalModel method)
get_string() (indra.assemblers.graph_assembler.GraphAssembler method)
get_subnetwork() (in module indra.tools.executable_subnetwork)
get_syntheses() (indra.sources.trips.processor.TripsProcessor method)
get_tables() (indra.db.database_manager.DatabaseManager method)
get_target_chemblid() (in module indra.databases.chembl_client)
get_tarname_from_filename() (indra.db.content_manager.Manuscripts method)
get_title() (in module indra.literature.pubmed_client)
get_transcription() (indra.sources.bel.belrdf_processor.BelRdfProcessor method)
get_translocation() (indra.sources.reach.processor.ReachProcessor method)
get_uncompressed_bytes() (indra.db.content_manager.NihFtpClient 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)
get_valid_residue() (in module indra.statements)
get_values() (indra.db.database_manager.DatabaseManager method)
get_xml() (in module indra.sources.trips.trips_client)
get_xml_file() (indra.db.content_manager.NihFtpClient method)
Glycosylation (class in indra.statements)
gm (indra.preassembler.grounding_mapper.GroundingMapper attribute)
grab_session() (indra.db.database_manager.DatabaseManager method)
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
has_entry() (indra.db.database_manager.DatabaseManager method)
HasActivity (class in indra.statements)
hierarchies (indra.preassembler.Preassembler attribute)
HierarchyManager (class in indra.preassembler.hierarchy_manager)
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.belrdf_processor.BelRdfProcessor attribute)
indra.assemblers.cag_assembler (module)
indra.assemblers.cx_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.sbgn_assembler (module)
indra.assemblers.sif_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.db (module)
indra.db.content_manager (module)
indra.db.database_manager (module)
indra.db.util (module)
indra.explanation.model_checker (module)
indra.literature (module)
indra.literature.crossref_client (module)
indra.literature.elsevier_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.bel_api (module)
indra.sources.bel.belrdf_processor (module)
indra.sources.bel.pybel_processor (module)
indra.sources.biopax.biopax_api (module)
indra.sources.biopax.pathway_commons_client (module)
indra.sources.biopax.processor (module)
indra.sources.eidos.eidos_api (module)
indra.sources.eidos.eidos_reader (module)
indra.sources.eidos.processor (module)
indra.sources.geneways.geneways_api (module)
indra.sources.geneways.processor (module)
indra.sources.ndex_cx.ndex_cx_api (module)
indra.sources.ndex_cx.processor (module)
indra.sources.reach.processor (module)
indra.sources.reach.reach_api (module)
indra.sources.reach.reach_reader (module)
indra.sources.tees.processor (module)
indra.sources.tees.tees_api (module)
indra.sources.trips.processor (module)
indra.sources.trips.trips_api (module)
indra.sources.trips.trips_client (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)
IndraDatabaseError
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)
InputError
insert() (indra.db.database_manager.DatabaseManager method)
insert_agents() (in module indra.db.util)
insert_db_stmts() (in module indra.db.util)
insert_many() (indra.db.database_manager.DatabaseManager method)
InvalidLocationError
InvalidResidueError
is_human() (in module indra.databases.uniprot_client)
is_mouse() (in module indra.databases.uniprot_client)
is_rat() (in module indra.databases.uniprot_client)
is_secondary() (in module indra.databases.uniprot_client)
isa() (indra.preassembler.hierarchy_manager.HierarchyManager method)
L
LinkedStatement (class in indra.mechlinker)
load_files() (indra.db.content_manager.Pubmed method)
load_prior() (indra.tools.incremental_model.IncrementalModel method)
load_site_map() (in module indra.preassembler.sitemapper)
load_statements() (in module indra.tools.assemble_corpus)
load_text_refs() (indra.db.content_manager.Pubmed method)
location (indra.mechlinker.AgentState attribute)
M
make_model() (indra.assemblers.cag_assembler.CAGAssembler method)
(indra.assemblers.cx_assembler.CxAssembler 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)
make_statement() (indra.sources.geneways.processor.GenewaysProcessor method)
make_statement_camel() (in module indra.statements)
make_text_ref_str() (indra.db.content_manager.ContentManager method)
Manuscripts (class in indra.db.content_manager)
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)
max_path_length (indra.explanation.model_checker.PathResult attribute)
max_paths (indra.explanation.model_checker.PathResult attribute)
MechLinker (class in indra.mechlinker)
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
namespace_from_uri() (in module indra.sources.bel.belrdf_processor)
NdexCxProcessor (class in indra.sources.ndex_cx.processor)
network_name (indra.assemblers.cx_assembler.CxAssembler attribute)
NihFtpClient (class in indra.db.content_manager)
NihManager (class in indra.db.content_manager)
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)
NotAStatementName
O
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.trips.processor.TripsProcessor attribute)
paragraphs (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)
PmcManager (class in indra.db.content_manager)
PmcOA (class in indra.db.content_manager)
policies (indra.assemblers.pysb_assembler.PysbAssembler attribute)
populate() (indra.db.content_manager.ContentManager method)
(indra.db.content_manager.PmcManager method)
(indra.db.content_manager.Pubmed method)
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_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.belrdf_processor.BelRdfProcessor method)
print_statements() (indra.sources.bel.belrdf_processor.BelRdfProcessor method)
(indra.sources.biopax.processor.BiopaxProcessor method)
prior_probs (indra.belief.BeliefEngine attribute)
process_archive() (indra.db.content_manager.PmcManager method)
process_belrdf() (in module indra.sources.bel.bel_api)
process_belscript() (in module indra.sources.bel.bel_api)
process_binding_statements() (indra.sources.tees.processor.TEESProcessor method)
process_cx() (in module indra.sources.ndex_cx.ndex_cx_api)
process_cx_file() (in module indra.sources.ndex_cx.ndex_cx_api)
process_decrease_expression_amount() (indra.sources.tees.processor.TEESProcessor method)
process_geneways_files() (in module indra.sources.geneways.geneways_api)
process_increase_expression_amount() (indra.sources.tees.processor.TEESProcessor method)
process_json() (in module indra.sources.eidos.eidos_api)
process_json_file() (in module indra.sources.bel.bel_api)
(in module indra.sources.eidos.eidos_api)
(in module indra.sources.reach.reach_api)
process_json_ld() (in module indra.sources.eidos.eidos_api)
process_json_ld_file() (in module indra.sources.eidos.eidos_api)
process_json_ld_str() (in module indra.sources.eidos.eidos_api)
process_json_str() (in module indra.sources.eidos.eidos_api)
(in module indra.sources.reach.reach_api)
process_model() (in module indra.sources.biopax.biopax_api)
process_ndex_neighborhood() (in module indra.sources.bel.bel_api)
process_ndex_network() (in module indra.sources.ndex_cx.ndex_cx_api)
process_nxml_file() (in module indra.sources.reach.reach_api)
process_nxml_str() (in module indra.sources.reach.reach_api)
process_owl() (in module indra.sources.biopax.biopax_api)
process_pc_neighborhood() (in module indra.sources.biopax.biopax_api)
process_pc_pathsbetween() (in module indra.sources.biopax.biopax_api)
process_pc_pathsfromto() (in module indra.sources.biopax.biopax_api)
process_phosphorylation_statements() (indra.sources.tees.processor.TEESProcessor method)
process_pmc() (in module indra.sources.reach.reach_api)
process_pubmed_abstract() (in module indra.sources.reach.reach_api)
process_pybel_graph() (in module indra.sources.bel.bel_api)
process_text() (in module indra.sources.eidos.eidos_api)
(in module indra.sources.reach.reach_api)
(in module indra.sources.tees.tees_api)
(in module indra.sources.trips.trips_api)
(indra.sources.eidos.eidos_reader.EidosReader method)
process_xml() (in module indra.sources.trips.trips_api)
protein_map_from_twg() (in module indra.preassembler.grounding_mapper)
prune_influence_map() (indra.explanation.model_checker.ModelChecker method)
Pubmed (class in indra.db.content_manager)
PybelProcessor (class in indra.sources.bel.pybel_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.reach_reader)
reduce_activities() (in module indra.tools.assemble_corpus)
(indra.mechlinker.MechLinker method)
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)
result_code (indra.explanation.model_checker.PathResult attribute)
results (indra.tools.gene_network.GeneNetwork attribute)
ret_file() (indra.db.content_manager.NihFtpClient method)
Ribosylation (class in indra.statements)
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)
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_model() (indra.assemblers.cx_assembler.CxAssembler 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.trips_client)
sbgn (indra.assemblers.sbgn_assembler.SBGNAssembler attribute)
SBGNAssembler (class in indra.assemblers.sbgn_assembler)
score_paths() (indra.explanation.model_checker.ModelChecker method)
select_all() (indra.db.database_manager.DatabaseManager method)
select_one() (indra.db.database_manager.DatabaseManager method)
SelfModification (class in indra.statements)
send_query() (in module indra.databases.chembl_client)
(in module indra.sources.trips.trips_client)
send_request (in module indra.databases.cbio_client)
send_request() (in module indra.databases.ndex_client)
sentences (indra.sources.trips.processor.TripsProcessor attribute)
set_base_initial_condition() (in module indra.assemblers.pysb_assembler)
set_context() (indra.assemblers.cx_assembler.CxAssembler method)
(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)
show_tables() (indra.db.database_manager.DatabaseManager method)
SifAssembler (class in indra.assemblers.sif_assembler)
SiteMapper (class in indra.preassembler.sitemapper)
Statement (class in indra.statements)
statements (indra.assemblers.cag_assembler.CAGAssembler attribute)
(indra.assemblers.cx_assembler.CxAssembler 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.sources.bel.belrdf_processor.BelRdfProcessor attribute)
(indra.sources.bel.pybel_processor.PybelProcessor attribute)
(indra.sources.biopax.processor.BiopaxProcessor attribute)
(indra.sources.eidos.processor.EidosJsonLdProcessor attribute)
(indra.sources.eidos.processor.EidosJsonProcessor attribute)
(indra.sources.geneways.processor.GenewaysProcessor 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)
strip_agent_context() (in module indra.tools.assemble_corpus)
subtype_probs (indra.belief.BeliefEngine attribute)
Sumoylation (class in indra.statements)
T
tag_evidence_subtype() (in module indra.belief)
TEESProcessor (class in indra.sources.tees.processor)
term_from_uri() (in module indra.sources.bel.belrdf_processor)
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)
Translocation (class in indra.statements)
Transphosphorylation (class in indra.statements)
tree (indra.sources.eidos.processor.EidosJsonLdProcessor attribute)
(indra.sources.eidos.processor.EidosJsonProcessor attribute)
(indra.sources.reach.processor.ReachProcessor attribute)
(indra.sources.trips.processor.TripsProcessor attribute)
TripsProcessor (class in indra.sources.trips.processor)
U
Ubiquitination (class in indra.statements)
unique_stmts (indra.preassembler.Preassembler attribute)
UnknownPolicyError
unpack_archive_path() (indra.db.content_manager.PmcManager method)
Unresolved (class in indra.statements)
UnresolvedUuidError
update() (indra.db.content_manager.ContentManager method)
(indra.db.content_manager.Manuscripts method)
(indra.db.content_manager.PmcOA method)
(indra.db.content_manager.Pubmed method)
update_network() (in module indra.databases.ndex_client)
upload_archives() (indra.db.content_manager.PmcManager method)
upload_article() (indra.db.content_manager.Pubmed method)
upload_batch() (indra.db.content_manager.PmcManager method)
upload_model() (indra.assemblers.cx_assembler.CxAssembler method)
UploadError
V
verify_location() (in module indra.databases.uniprot_client)
verify_modification() (in module indra.databases.uniprot_client)