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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)
ActivityCondition (class in indra.statements)
add_statements() (indra.assemblers.english_assembler.EnglishAssembler method)
(indra.assemblers.graph_assembler.GraphAssembler method)
(indra.mechlinker.MechLinker method)
(indra.preassembler.Preassembler method)
(indra.tools.incremental_model.IncrementalModel method)
Agent (class in indra.statements)
AgentState (class in indra.mechlinker)
all_direct_stmts (indra.sources.bel.processor.BelProcessor attribute)
all_events (indra.sources.reach.processor.ReachProcessor attribute)
all_indirect_stmts (indra.sources.bel.processor.BelProcessor 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)
BelProcessor (class in indra.sources.bel.processor)
BiopaxProcessor (class in indra.sources.biopax.processor)
BoundCondition (class in indra.statements)
build_transitive_closures() (indra.preassembler.hierarchy_manager.HierarchyManager method)
C
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)
Conversion (class in indra.statements)
converted_direct_stmts (indra.sources.bel.processor.BelProcessor attribute)
converted_indirect_stmts (indra.sources.bel.processor.BelProcessor attribute)
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.processor.BelProcessor 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)
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)
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)
EnglishAssembler (class in indra.assemblers.english_assembler)
Evidence (class in indra.statements)
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)
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_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)
flatten_evidence() (in module indra.preassembler)
flatten_stmts() (in module indra.preassembler)
G
g (indra.sources.bel.processor.BelProcessor 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)
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.processor.BelProcessor method)
get_activating_subs() (indra.sources.bel.processor.BelProcessor method)
get_activation() (indra.sources.bel.processor.BelProcessor 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_all_direct_statements() (indra.sources.bel.processor.BelProcessor method)
get_all_events() (indra.sources.reach.processor.ReachProcessor method)
(indra.sources.trips.processor.TripsProcessor method)
get_all_indirect_statements() (indra.sources.bel.processor.BelProcessor method)
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_biopax_stmts() (indra.tools.gene_network.GeneNetwork method)
get_chebi_id_from_pubchem() (in module indra.databases.chebi_client)
get_children() (indra.preassembler.hierarchy_manager.HierarchyManager method)
get_complexes() (indra.sources.bel.processor.BelProcessor 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.processor.BelProcessor method)
get_conversions() (indra.sources.bel.processor.BelProcessor method)
(indra.sources.biopax.processor.BiopaxProcessor method)
get_create_base_agent() (indra.mechlinker.BaseAgentSet method)
get_degenerate_statements() (indra.sources.bel.processor.BelProcessor method)
get_degradations() (indra.sources.trips.processor.TripsProcessor method)
get_dois (in module indra.literature.elsevier_client)
get_entrez_id() (in module indra.databases.hgnc_client)
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_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_is_direct() (in module indra.assemblers.index_card_assembler)
get_issns_for_journal (in module indra.literature.pubmed_client)
get_metadata (in module indra.literature.crossref_client)
get_metadata_for_ids() (in module indra.literature.pubmed_client)
get_mgi_id() (in module indra.databases.uniprot_client)
get_mnemonic() (in module indra.databases.uniprot_client)
get_model_agents() (indra.tools.incremental_model.IncrementalModel method)
get_modifications() (indra.sources.bel.processor.BelProcessor method)
(indra.sources.biopax.processor.BiopaxProcessor method)
(indra.sources.reach.processor.ReachProcessor method)
(indra.sources.trips.processor.TripsProcessor method)
get_mouse_id() (in module indra.databases.hgnc_client)
(in module indra.databases.uniprot_client)
get_parents() (indra.preassembler.hierarchy_manager.HierarchyManager method)
get_primary_id() (in module indra.databases.uniprot_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_relevant_nodes() (in module indra.databases.relevance_client)
get_rgd_id() (in module indra.databases.uniprot_client)
get_statements() (indra.tools.gene_network.GeneNetwork method)
(indra.tools.incremental_model.IncrementalModel method)
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_syntheses() (indra.sources.trips.processor.TripsProcessor method)
get_title() (in module indra.literature.pubmed_client)
get_transcription() (indra.sources.bel.processor.BelProcessor method)
get_translocation() (indra.sources.reach.processor.ReachProcessor method)
get_uniprot_id() (in module indra.databases.hgnc_client)
get_valid_location() (in module indra.statements)
get_valid_residue() (in module indra.statements)
get_xml() (in module indra.sources.trips.trips_client)
Glycosylation (class in indra.statements)
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)
H
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)
indirect_stmts (indra.sources.bel.processor.BelProcessor attribute)
indra.assemblers.english_assembler (module)
indra.assemblers.graph_assembler (module)
indra.assemblers.index_card_assembler (module)
indra.assemblers.sif_assembler (module)
indra.belief (module)
indra.databases.biogrid_client (module)
indra.databases.chebi_client (module)
indra.databases.hgnc_client (module)
indra.databases.ndex_client (module)
indra.databases.relevance_client (module)
indra.databases.uniprot_client (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.processor (module)
indra.sources.biopax.biopax_api (module)
indra.sources.biopax.pathway_commons_client (module)
indra.sources.biopax.processor (module)
indra.sources.reach.processor (module)
indra.sources.reach.reach_api (module)
indra.sources.reach.reach_reader (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.gene_network (module)
indra.tools.incremental_model (module)
indra.tools.mechlinker_queries (module)
indra.tools.reading (module)
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)
Inhibition (class in indra.statements)
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_prior() (indra.tools.incremental_model.IncrementalModel method)
load_site_map() (in module indra.preassembler.sitemapper)
load_statements() (in module indra.tools.assemble_corpus)
M
make_model() (indra.assemblers.english_assembler.EnglishAssembler method)
(indra.assemblers.graph_assembler.GraphAssembler method)
(indra.assemblers.sif_assembler.SifAssembler 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)
MechLinker (class in indra.mechlinker)
Methylation (class in indra.statements)
ModCondition (class in indra.statements)
model (indra.assemblers.english_assembler.EnglishAssembler attribute)
(indra.sources.biopax.processor.BiopaxProcessor attribute)
model_to_owl() (in module indra.sources.biopax.pathway_commons_client)
Modification (class in indra.statements)
MutCondition (class in indra.statements)
Myristoylation (class in indra.statements)
N
namespace_from_uri() (in module indra.sources.bel.processor)
node_properties (indra.assemblers.graph_assembler.GraphAssembler attribute)
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)
partof() (indra.preassembler.hierarchy_manager.HierarchyManager method)
Phosphorylation (class in indra.statements)
preassemble() (indra.tools.incremental_model.IncrementalModel method)
Preassembler (class in indra.preassembler)
print_boolean_net() (indra.assemblers.sif_assembler.SifAssembler method)
print_event_statistics() (indra.sources.reach.processor.ReachProcessor method)
print_loopy() (indra.assemblers.sif_assembler.SifAssembler method)
print_model() (indra.assemblers.sif_assembler.SifAssembler method)
print_statement_coverage() (indra.sources.bel.processor.BelProcessor method)
print_statements() (indra.sources.bel.processor.BelProcessor method)
(indra.sources.biopax.processor.BiopaxProcessor method)
prior_probs (indra.belief.BeliefEngine attribute)
process_belrdf() (in module indra.sources.bel.bel_api)
process_json_file() (in module indra.sources.reach.reach_api)
process_json_str() (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_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_pmc() (in module indra.sources.reach.reach_api)
process_pubmed_abstract() (in module indra.sources.reach.reach_api)
process_text() (in module indra.sources.reach.reach_api)
(in module indra.sources.trips.trips_api)
process_xml() (in module indra.sources.trips.trips_api)
protein_map_from_twg() (in module indra.preassembler.grounding_mapper)
Q
query_protein (in module indra.databases.uniprot_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)
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)
results (indra.tools.gene_network.GeneNetwork attribute)
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
save() (indra.tools.incremental_model.IncrementalModel method)
save_dot() (indra.assemblers.graph_assembler.GraphAssembler method)
save_model() (indra.assemblers.sif_assembler.SifAssembler method)
(indra.sources.biopax.processor.BiopaxProcessor method)
save_pdf() (indra.assemblers.graph_assembler.GraphAssembler method)
save_xml() (in module indra.sources.trips.trips_client)
SelfModification (class in indra.statements)
send_query() (in module indra.sources.trips.trips_client)
send_request() (in module indra.databases.ndex_client)
sentences (indra.sources.trips.processor.TripsProcessor attribute)
set_hierarchy_probs() (indra.belief.BeliefEngine method)
set_linked_probs() (indra.belief.BeliefEngine method)
set_prior_probs() (indra.belief.BeliefEngine method)
SifAssembler (class in indra.assemblers.sif_assembler)
SiteMapper (class in indra.preassembler.sitemapper)
Statement (class in indra.statements)
statements (indra.assemblers.english_assembler.EnglishAssembler attribute)
(indra.assemblers.graph_assembler.GraphAssembler attribute)
(indra.sources.bel.processor.BelProcessor attribute)
(indra.sources.biopax.processor.BiopaxProcessor attribute)
(indra.sources.reach.processor.ReachProcessor attribute)
(indra.sources.trips.processor.TripsProcessor attribute)
stmts (indra.preassembler.Preassembler attribute)
(indra.tools.incremental_model.IncrementalModel attribute)
strip_agent_context() (in module indra.tools.assemble_corpus)
Sumoylation (class in indra.statements)
T
term_from_uri() (in module indra.sources.bel.processor)
to_graph() (indra.statements.Statement method)
to_json() (indra.statements.Statement method)
Translocation (class in indra.statements)
Transphosphorylation (class in indra.statements)
tree (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)
V
verify_location() (in module indra.databases.uniprot_client)
verify_modification() (in module indra.databases.uniprot_client)
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