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W
A
Acetylation (class in indra.statements.statements)
AcsnProcessor (class in indra.sources.acsn.processor)
Activation (class in indra.statements.statements)
ActiveForm (class in indra.statements.statements)
activities_by_target() (in module indra.databases.chembl_client)
ActivityCondition (class in indra.statements.agent)
(class in indra.statements.statements)
add_activity_form() (indra.assemblers.pysb.base_agents.BaseAgent method)
add_activity_type() (indra.assemblers.pysb.base_agents.BaseAgent method)
add_agent() (indra.assemblers.kami.assembler.Nugget method)
add_default_initial_conditions() (indra.assemblers.pysb.assembler.PysbAssembler method)
add_edge() (indra.assemblers.cx.assembler.NiceCxAssembler method)
(indra.assemblers.kami.assembler.Nugget method)
add_edges_from() (indra.ontology.bio.BioOntology method)
(indra.ontology.bio.ontology.BioOntology method)
add_node() (indra.assemblers.cx.assembler.NiceCxAssembler method)
(indra.assemblers.kami.assembler.Nugget method)
add_nodes_from() (indra.ontology.bio.BioOntology method)
(indra.ontology.bio.ontology.BioOntology method)
add_reverse_effects() (indra.assemblers.pysb.preassembler.PysbPreassembler method)
add_rule_to_model() (in module indra.assemblers.pysb.assembler)
add_site_states() (indra.assemblers.pysb.base_agents.BaseAgent method)
add_statements() (indra.assemblers.cx.assembler.CxAssembler method)
(indra.assemblers.cyjs.assembler.CyJSAssembler method)
(indra.assemblers.english.assembler.EnglishAssembler method)
(indra.assemblers.graph.assembler.GraphAssembler method)
(indra.assemblers.html.assembler.HtmlAssembler method)
(indra.assemblers.index_card.assembler.IndexCardAssembler method)
(indra.assemblers.indranet.assembler.IndraNetAssembler method)
(indra.assemblers.pysb.assembler.PysbAssembler method)
(indra.assemblers.pysb.preassembler.PysbPreassembler method)
(indra.assemblers.sbgn.assembler.SBGNAssembler method)
(indra.explanation.model_checker.model_checker.ModelChecker method)
(indra.mechlinker.MechLinker method)
(indra.preassembler.Preassembler method)
(indra.tools.incremental_model.IncrementalModel method)
add_stats() (indra.util.statement_presentation.StmtGroup method)
add_typing() (indra.assemblers.kami.assembler.Nugget method)
AddModification (class in indra.statements.statements)
Agent (class in indra.statements.agent)
(class in indra.statements.statements)
agent_grounding_matches() (in module indra.preassembler.custom_preassembly)
agent_list() (indra.statements.statements.Association method)
(indra.statements.statements.Influence method)
(indra.statements.statements.Statement method)
agent_name_matches() (in module indra.preassembler.custom_preassembly)
agent_name_polarity_matches() (in module indra.preassembler.custom_preassembly)
agent_name_stmt_matches() (in module indra.preassembler.custom_preassembly)
agent_name_stmt_type_matches() (in module indra.preassembler.custom_preassembly)
agent_set (indra.assemblers.pysb.assembler.PysbAssembler attribute)
agent_texts() (in module indra.preassembler.grounding_mapper.analysis)
agent_texts_with_grounding() (in module indra.preassembler.grounding_mapper.analysis)
agents (indra.assemblers.english.assembler.SentenceBuilder attribute)
agents_stmt_type_matches() (in module indra.preassembler.custom_preassembly)
AgentState (class in indra.mechlinker)
AgentWithCoordinates (class in indra.assemblers.english.assembler)
AggregatorMeta (class in indra.util.statement_presentation)
align_statements() (in module indra.tools.assemble_corpus)
all_agents() (in module indra.preassembler.grounding_mapper.analysis)
all_events (indra.sources.reach.processor.ReachProcessor attribute)
all_nodes (indra.explanation.model_checker.model_checker.NodesContainer attribute)
all_sources (in module indra.util.statement_presentation)
And (class in indra.sources.indra_db_rest.query)
annotate_paper_from_db() (in module indra.tools.hypothesis_annotator)
api_ruler (indra.sources.reach.reader.ReachReader attribute)
append() (indra.assemblers.english.assembler.SentenceBuilder method)
(indra.pipeline.pipeline.AssemblyPipeline method)
append_as_list() (indra.assemblers.english.assembler.SentenceBuilder method)
append_as_sentence() (indra.assemblers.english.assembler.SentenceBuilder method)
append_warning() (indra.assemblers.html.assembler.HtmlAssembler method)
apply_to() (indra.mechlinker.AgentState method)
assembled_stmts (indra.tools.incremental_model.IncrementalModel attribute)
AssemblyPipeline (class in indra.pipeline.pipeline)
assert_no_cycle() (in module indra.belief)
assert_valid_agent() (in module indra.statements.validate)
assert_valid_bio_context() (in module indra.statements.validate)
assert_valid_context() (in module indra.statements.validate)
assert_valid_db_refs() (in module indra.statements.validate)
assert_valid_evidence() (in module indra.statements.validate)
assert_valid_id() (in module indra.statements.validate)
assert_valid_ns() (in module indra.statements.validate)
assert_valid_pmid_text_refs() (in module indra.statements.validate)
assert_valid_statement() (in module indra.statements.validate)
assert_valid_statement_semantics() (in module indra.statements.validate)
assert_valid_statements() (in module indra.statements.validate)
assert_valid_text_refs() (in module indra.statements.validate)
Association (class in indra.statements.statements)
Autophosphorylation (class in indra.statements.statements)
available_sources_src_counts() (in module indra.util.statement_presentation)
available_sources_stmts() (in module indra.util.statement_presentation)
AveAggregator (class in indra.util.statement_presentation)
B
BaseAgent (class in indra.assemblers.pysb.base_agents)
(class in indra.mechlinker)
BaseAgentSet (class in indra.assemblers.pysb.base_agents)
(class in indra.mechlinker)
basename (indra.tools.gene_network.GeneNetwork attribute)
BasicAggregator (class in indra.util.statement_presentation)
BayesianScorer (class in indra.belief)
BeliefEngine (class in indra.belief)
beliefs (indra.assemblers.html.assembler.HtmlAssembler attribute)
BeliefScorer (class in indra.belief)
bfs_search() (in module indra.explanation.pathfinding.pathfinding)
bfs_search_multiple_nodes() (in module indra.explanation.pathfinding.pathfinding)
BioContext (class in indra.statements.context)
(class in indra.statements.statements)
BioFactoidProcessor (class in indra.sources.biofactoid.processor)
BiogridProcessor (class in indra.sources.biogrid)
BioOntology (class in indra.ontology.bio)
(class in indra.ontology.bio.ontology)
BiopaxProcessor (class in indra.sources.biopax.processor)
BioregistryValidator (class in indra.statements.validate)
BMIModel (class in indra.assemblers.pysb.bmi_wrapper)
bound_conditions (indra.mechlinker.AgentState attribute)
BoundCondition (class in indra.statements.agent)
(class in indra.statements.statements)
build_refinements_graph() (in module indra.belief)
C
cancel() (indra.sources.indra_db_rest.processor.IndraDBQueryProcessor method)
check_entitlement() (in module indra.literature.elsevier_client)
check_extra_evidence() (in module indra.belief)
check_grounding_map() (indra.preassembler.grounding_mapper.mapper.GroundingMapper static method)
check_model() (indra.explanation.model_checker.model_checker.ModelChecker method)
check_prior_probs() (indra.belief.BeliefScorer method)
(indra.belief.SimpleScorer method)
(indra.belief.skl.HybridScorer method)
(indra.belief.skl.SklearnScorer method)
check_statement() (indra.explanation.model_checker.model_checker.ModelChecker method)
citation (indra.sources.reach.processor.ReachProcessor attribute)
cli() (indra.sources.utils.Processor class method)
cm_json_to_graph() (in module indra.assemblers.pysb.kappa_util)
cm_json_to_networkx() (in module indra.assemblers.pysb.kappa_util)
combine_duplicate_stmts() (indra.preassembler.Preassembler method)
combine_duplicates() (indra.preassembler.Preassembler method)
combine_related() (indra.preassembler.Preassembler method)
common_target (indra.explanation.model_checker.model_checker.NodesContainer attribute)
Complex (class in indra.statements.statements)
complex_monomers_default() (in module indra.assemblers.pysb.assembler)
complex_monomers_one_step() (in module indra.assemblers.pysb.assembler)
compositional_sort_key() (in module indra.statements.concept)
Concept (class in indra.statements.concept)
(class in indra.statements.statements)
concept (indra.statements.statements.Event attribute)
connected_subgraph() (indra.sources.tees.processor.TEESProcessor method)
Context (class in indra.statements.context)
(class in indra.statements.statements)
context (indra.statements.statements.Event attribute)
Conversion (class in indra.statements.statements)
convert_unit() (indra.statements.statements.QuantitativeState static method)
copy() (indra.sources.indra_db_rest.query.Query method)
copy_default_config() (in module indra.tools.machine)
correspondence_dict (indra.sources.acsn.processor.AcsnProcessor attribute)
CountsScorer (class in indra.belief.skl)
create_mod_site() (indra.assemblers.pysb.base_agents.BaseAgent method)
create_network() (in module indra.databases.ndex_client)
create_new_step() (indra.pipeline.pipeline.AssemblyPipeline method)
create_site() (indra.assemblers.pysb.base_agents.BaseAgent method)
CREEDSChemicalProcessor (class in indra.sources.creeds.processor)
CREEDSDiseaseProcessor (class in indra.sources.creeds.processor)
CREEDSGeneProcessor (class in indra.sources.creeds.processor)
CrogProcessor (class in indra.sources.crog.processor)
CTDChemicalDiseaseProcessor (class in indra.sources.ctd.processor)
CTDChemicalGeneProcessor (class in indra.sources.ctd.processor)
CTDGeneDiseaseProcessor (class in indra.sources.ctd.processor)
CTDProcessor (class in indra.sources.ctd.processor)
cx (indra.assemblers.cx.assembler.CxAssembler attribute)
CxAssembler (class in indra.assemblers.cx.assembler)
CyJSAssembler (class in indra.assemblers.cyjs.assembler)
D
db_rest_url (indra.assemblers.html.assembler.HtmlAssembler attribute)
db_sources (in module indra.util.statement_presentation)
DB_TEXT_COLOR (in module indra.assemblers.html.assembler)
DBQueryHashProcessor (class in indra.sources.indra_db_rest.processor)
DBQueryStatementProcessor (class in indra.sources.indra_db_rest.processor)
Deacetylation (class in indra.statements.statements)
DecreaseAmount (class in indra.statements.statements)
Defarnesylation (class in indra.statements.statements)
Degeranylgeranylation (class in indra.statements.statements)
Deglycosylation (class in indra.statements.statements)
Dehydroxylation (class in indra.statements.statements)
delta (indra.statements.statements.Event attribute)
Demethylation (class in indra.statements.statements)
Demyristoylation (class in indra.statements.statements)
Depalmitoylation (class in indra.statements.statements)
Dephosphorylation (class in indra.statements.statements)
Deribosylation (class in indra.statements.statements)
Desumoylation (class in indra.statements.statements)
determine_reach_subtype() (in module indra.sources.reach.processor)
Deubiquitination (class in indra.statements.statements)
df (indra.sources.trrust.processor.TrrustProcessor attribute)
(indra.sources.virhostnet.processor.VirhostnetProcessor attribute)
df_to_matrix() (indra.belief.skl.CountsScorer method)
(indra.belief.skl.SklearnScorer method)
DGIProcessor (class in indra.sources.dgi.processor)
digraph_from_df() (indra.assemblers.indranet.net.IndraNet class method)
DisambManager (class in indra.preassembler.grounding_mapper.disambiguate)
doc_id (indra.sources.trips.processor.TripsProcessor attribute)
doi_query() (in module indra.literature.crossref_client)
download_article() (in module indra.literature.elsevier_client)
download_article_from_ids() (in module indra.literature.elsevier_client)
download_from_search() (in module indra.literature.elsevier_client)
draw_im() (indra.explanation.model_checker.pysb.PysbModelChecker method)
draw_stmt_graph() (in module indra.statements.io)
(in module indra.statements.statements)
DrugbankProcessor (class in indra.sources.drugbank.processor)
drum_system (indra.sources.trips.drum_reader.DrumReader attribute)
DrumReader (class in indra.sources.trips.drum_reader)
dump() (indra.util.aws.JobLog method)
dump_logs() (in module indra.util.aws)
dump_statements() (in module indra.tools.assemble_corpus)
dump_stmt_strings() (in module indra.tools.assemble_corpus)
E
edge_properties (indra.assemblers.graph.assembler.GraphAssembler attribute)
eidos_reader (indra.sources.eidos.reader.EidosReader attribute)
EidosBioProcessor (class in indra.sources.eidos.bio_processor)
EidosProcessor (class in indra.sources.eidos.processor)
EidosReader (class in indra.sources.eidos.reader)
eliminate_exact_duplicates() (indra.sources.biopax.processor.BiopaxProcessor method)
EmptyQuery (class in indra.sources.indra_db_rest.query)
english_join() (in module indra.assemblers.english.assembler)
EnglishAssembler (class in indra.assemblers.english.assembler)
ensure_chebi_prefix() (in module indra.databases.identifiers)
ensure_chembl_prefix() (in module indra.databases.identifiers)
ensure_prefix() (in module indra.databases.identifiers)
ensure_prefix_if_needed() (in module indra.databases.bioregistry_client)
(in module indra.databases.identifiers)
entity_matches_key() (indra.statements.agent.Agent method)
(indra.statements.statements.Agent method)
entries_from_graph() (indra.databases.obo_client.OboClient static method)
entry_from_term() (indra.databases.owl_client.OwlClient static method)
ev_counts (indra.assemblers.html.assembler.HtmlAssembler attribute)
Event (class in indra.statements.statements)
Evidence (class in indra.statements.evidence)
(class in indra.statements.statements)
evidence_random_noise_prior() (in module indra.belief)
existing_edges (indra.assemblers.graph.assembler.GraphAssembler attribute)
existing_nodes (indra.assemblers.graph.assembler.GraphAssembler attribute)
ExistingFunctionError
expand_families() (in module indra.tools.assemble_corpus)
expand_pagination() (in module indra.literature.pubmed_client)
export_dict() (indra.util.nested_dict.NestedDict method)
export_into_python() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
export_model() (indra.assemblers.pysb.assembler.PysbAssembler method)
extend() (indra.preassembler.refinement.OntologyRefinementFilter method)
(indra.preassembler.refinement.RefinementFilter method)
extend_refinements_graph() (in module indra.belief)
extract_all_events() (indra.sources.eidos.processor.EidosProcessor method)
extract_and_process() (in module indra.sources.eidos.cli)
extract_causal_relations() (indra.sources.eidos.processor.EidosProcessor method)
extract_correlations() (indra.sources.eidos.processor.EidosProcessor method)
extract_events() (indra.sources.eidos.processor.EidosProcessor method)
extract_from_directory() (in module indra.sources.eidos.cli)
extract_groundings() (indra.sources.hypothesis.processor.HypothesisProcessor method)
extract_output() (in module indra.sources.tees.api)
extract_paragraphs() (in module indra.literature.elsevier_client)
(in module indra.literature.pmc_client)
extract_predication() (indra.sources.semrep.processor.SemRepXmlProcessor method)
extract_statements() (indra.sources.acsn.processor.AcsnProcessor method)
(indra.sources.crog.processor.CrogProcessor method)
(indra.sources.dgi.processor.DGIProcessor method)
(indra.sources.hypothesis.processor.HypothesisProcessor method)
(indra.sources.rlimsp.processor.RlimspProcessor method)
(indra.sources.trrust.processor.TrrustProcessor method)
(indra.sources.utils.Processor method)
(indra.sources.utils.RemoteProcessor method)
extract_stmts() (indra.sources.gnbr.processor.GnbrProcessor method)
extract_text() (in module indra.literature.elsevier_client)
(in module indra.literature.pmc_client)
extracted_events (indra.sources.trips.processor.TripsProcessor attribute)
extractions (indra.sources.trips.drum_reader.DrumReader attribute)
F
Farnesylation (class in indra.statements.statements)
feature_delta() (indra.sources.biopax.processor.BiopaxProcessor method)
fill_from_stmt_stats() (indra.util.statement_presentation.StmtGroup method)
filter_belief() (in module indra.tools.assemble_corpus)
filter_by_curation() (in module indra.tools.assemble_corpus)
filter_by_db_refs() (in module indra.tools.assemble_corpus)
filter_by_type() (in module indra.tools.assemble_corpus)
filter_complexes_by_size() (in module indra.tools.assemble_corpus)
filter_concept_names() (in module indra.tools.assemble_corpus)
filter_direct() (in module indra.tools.assemble_corpus)
filter_enzyme_kinase() (in module indra.tools.assemble_corpus)
filter_evidence_source() (in module indra.tools.assemble_corpus)
filter_gene_list() (in module indra.tools.assemble_corpus)
filter_genes_only() (in module indra.tools.assemble_corpus)
filter_grounded_only() (in module indra.tools.assemble_corpus)
filter_human_only() (in module indra.tools.assemble_corpus)
filter_inconsequential() (in module indra.tools.assemble_corpus)
filter_inconsequential_acts() (in module indra.tools.assemble_corpus)
filter_inconsequential_mods() (in module indra.tools.assemble_corpus)
filter_mod_nokinase() (in module indra.tools.assemble_corpus)
filter_mutation_status() (in module indra.tools.assemble_corpus)
filter_no_hypothesis() (in module indra.tools.assemble_corpus)
filter_no_negated() (in module indra.tools.assemble_corpus)
filter_paragraphs() (in module indra.literature.adeft_tools)
filter_pmids() (in module indra.literature.pmc_client)
filter_top_level() (in module indra.tools.assemble_corpus)
filter_transcription_factor() (in module indra.tools.assemble_corpus)
filter_uuid_list() (in module indra.tools.assemble_corpus)
finalize() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
find_arg() (in module indra.sources.eidos.processor)
find_args() (in module indra.sources.eidos.processor)
find_contradicts() (indra.preassembler.Preassembler method)
find_event_parent_with_event_child() (indra.sources.tees.processor.TEESProcessor method)
find_event_with_outgoing_edges() (indra.sources.tees.processor.TEESProcessor method)
find_matching_entities() (indra.sources.biopax.processor.BiopaxProcessor static method)
find_matching_left_right() (indra.sources.biopax.processor.BiopaxProcessor static method)
find_paths() (indra.explanation.model_checker.model_checker.ModelChecker method)
find_refinements_for_statement() (in module indra.preassembler)
find_sources() (in module indra.explanation.pathfinding.pathfinding)
finish() (indra.util.statement_presentation.StmtGroup method)
fit() (indra.belief.skl.SklearnScorer method)
fix_invalidities() (in module indra.tools.assemble_corpus)
(in module indra.tools.fix_invalidities)
fix_invalidities_agent() (in module indra.tools.fix_invalidities)
fix_invalidities_context() (in module indra.tools.fix_invalidities)
fix_invalidities_db_refs() (in module indra.tools.fix_invalidities)
fix_invalidities_evidence() (in module indra.tools.fix_invalidities)
fix_invalidities_stmt() (in module indra.tools.fix_invalidities)
flatten_evidence() (in module indra.preassembler)
flatten_stmts() (in module indra.preassembler)
flip_polarity() (indra.statements.statements.Association method)
(indra.statements.statements.Event method)
(indra.statements.statements.Influence method)
(indra.statements.statements.Statement method)
format_axis() (in module indra.util.plot_formatting)
from_df() (indra.assemblers.indranet.net.IndraNet class method)
from_dicts() (indra.util.statement_presentation.StmtGroup class method)
(indra.util.statement_presentation.StmtStat class method)
from_json_file() (indra.pipeline.pipeline.AssemblyPipeline class method)
from_seconds() (indra.statements.statements.QuantitativeState static method)
from_stmt_stats() (indra.util.statement_presentation.StmtGroup class method)
from_stmts() (indra.util.statement_presentation.StmtStat class method)
FromMeshIds (class in indra.sources.indra_db_rest.query)
FromPapers (class in indra.sources.indra_db_rest.query)
G
Gap (class in indra.statements.statements)
gather_explicit_activities() (indra.mechlinker.MechLinker method)
gather_implicit_activities() (indra.mechlinker.MechLinker method)
Gef (class in indra.statements.statements)
gene_list (indra.tools.gene_network.GeneNetwork attribute)
GeneNetwork (class in indra.tools.gene_network)
general_node_label() (indra.sources.tees.processor.TEESProcessor method)
generate_im() (indra.explanation.model_checker.pysb.PysbModelChecker method)
generate_source_css() (in module indra.assemblers.html.assembler)
geneways_action_to_indra_statement_type() (in module indra.sources.geneways.processor)
GenewaysProcessor (class in indra.sources.geneways.processor)
Geranylgeranylation (class in indra.statements.statements)
get() (indra.sources.indra_db_rest.query.Query method)
(indra.util.nested_dict.NestedDict method)
get_abstract() (in module indra.literature.elsevier_client)
(in module indra.literature.pubmed_client)
get_activation() (indra.sources.reach.processor.ReachProcessor method)
get_activations() (indra.sources.trips.processor.TripsProcessor method)
get_activations_causal() (indra.sources.trips.processor.TripsProcessor method)
get_activations_stimulate() (indra.sources.trips.processor.TripsProcessor method)
get_active_forms() (indra.sources.trips.processor.TripsProcessor method)
get_active_forms_state() (indra.sources.trips.processor.TripsProcessor method)
get_activity_modification() (indra.sources.biopax.processor.BiopaxProcessor method)
get_ag_ns_id() (in module indra.assemblers.indranet.assembler)
get_agent() (in module indra.sources.bel.processor)
(in module indra.sources.minerva.processor)
(indra.sources.acsn.processor.AcsnProcessor method)
get_agent_from_entity() (indra.sources.semrep.processor.SemRepXmlProcessor method)
get_agent_from_entity_info() (in module indra.sources.rlimsp.processor)
get_agent_from_grounding() (in module indra.sources.virhostnet.processor)
get_agent_from_refs() (in module indra.sources.minerva.processor)
get_agent_key() (in module indra.preassembler.refinement)
get_agent_rule_str() (in module indra.assemblers.pysb.assembler)
get_agents() (indra.sources.ndex_cx.processor.NdexCxProcessor method)
(indra.sources.trips.processor.TripsProcessor method)
get_agents_from_entities() (indra.sources.reach.processor.ReachProcessor method)
get_agents_with_name() (in module indra.preassembler.grounding_mapper.analysis)
get_all_descendants() (in module indra.statements.statements)
get_all_entities() (indra.sources.reach.processor.ReachProcessor method)
get_all_events() (indra.sources.eidos.processor.EidosProcessor method)
(indra.sources.reach.processor.ReachProcessor method)
(indra.sources.trips.processor.TripsProcessor method)
get_all_mps() (indra.explanation.model_checker.pysb.PysbModelChecker method)
get_all_nodes() (indra.explanation.model_checker.model_checker.NodesContainer method)
get_all_sources() (indra.belief.skl.CountsScorer static method)
get_annotation() (in module indra.assemblers.pysb.assembler)
get_annotations() (in module indra.sources.hypothesis.api)
get_api_ruler() (indra.sources.reach.reader.ReachReader method)
get_argument_value() (indra.pipeline.pipeline.AssemblyPipeline method)
get_article() (in module indra.literature.elsevier_client)
get_article_xml() (in module indra.literature.pubmed_client)
get_attribute() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
get_batch_command() (in module indra.util.aws)
get_bel_stmts() (indra.tools.gene_network.GeneNetwork method)
get_belief_score_by_hash() (indra.sources.indra_db_rest.processor.DBQueryStatementProcessor method)
get_belief_score_by_stmt() (indra.sources.indra_db_rest.processor.DBQueryStatementProcessor method)
get_belief_scores() (indra.sources.indra_db_rest.processor.IndraDBQueryProcessor method)
get_biopax_stmts() (indra.tools.gene_network.GeneNetwork method)
get_bioregistry_curie() (in module indra.databases.bioregistry_client)
get_bioregistry_prefix() (in module indra.databases.bioregistry_client)
get_bioregistry_url() (in module indra.databases.bioregistry_client)
get_cancer_studies() (in module indra.databases.cbio_client)
get_cancer_types() (in module indra.databases.cbio_client)
get_case_lists() (in module indra.databases.cbio_client)
get_causal_edge() (in module indra.assemblers.pybel.assembler)
get_ccle_cna() (in module indra.databases.cbio_client)
get_ccle_lines_for_mutation() (in module indra.databases.cbio_client)
get_ccle_mrna() (in module indra.databases.cbio_client)
get_ccle_mutations() (in module indra.databases.cbio_client)
get_chebi_entry_from_web() (in module indra.databases.chebi_client)
get_chebi_id() (in module indra.databases.drugbank_client)
get_chebi_id_from_cas() (in module indra.databases.chebi_client)
get_chebi_id_from_chembl() (in module indra.databases.chebi_client)
get_chebi_id_from_hmdb() (in module indra.databases.chebi_client)
get_chebi_id_from_name() (in module indra.databases.chebi_client)
get_chebi_id_from_pubchem() (in module indra.databases.chebi_client)
get_chebi_name_from_id() (in module indra.databases.chebi_client)
get_chebi_name_from_id_web() (in module indra.databases.chebi_client)
get_chembl_id() (in module indra.databases.chebi_client)
(in module indra.databases.chembl_client)
(in module indra.databases.drugbank_client)
get_chembl_name() (in module indra.databases.chembl_client)
get_children() (indra.ontology.ontology_graph.IndraOntology method)
get_citation_count_for_doi() (in module indra.literature.coci_client)
get_citation_count_for_pmid() (in module indra.literature.coci_client)
get_cli() (indra.sources.utils.Processor class method)
get_cm_cycles() (in module indra.assemblers.pysb.kappa_util)
get_collection_dois() (in module indra.literature.biorxiv_client)
get_collection_pubs() (in module indra.literature.biorxiv_client)
get_complexes() (indra.sources.hprd.processor.HprdProcessor method)
(indra.sources.reach.processor.ReachProcessor method)
(indra.sources.trips.processor.TripsProcessor method)
get_concept() (indra.sources.eidos.processor.EidosProcessor method)
get_content_from_pub_json() (in module indra.literature.biorxiv_client)
get_conversions() (indra.sources.biopax.processor.BiopaxProcessor method)
get_create_base_agent() (indra.assemblers.pysb.base_agents.BaseAgentSet method)
(indra.mechlinker.BaseAgentSet method)
get_create_parameter() (in module indra.assemblers.pysb.assembler)
get_curations() (in module indra.sources.indra_db_rest.api)
get_current_hgnc_id() (in module indra.databases.hgnc_client)
get_current_time() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
get_date_from_str() (in module indra.util.aws)
get_db_mapping() (in module indra.databases.drugbank_client)
(in module indra.databases.mesh_client)
get_default_ndex_cred() (in module indra.databases.ndex_client)
get_degradations() (indra.sources.trips.processor.TripsProcessor method)
get_dict() (indra.util.statement_presentation.AggregatorMeta method)
(indra.util.statement_presentation.BasicAggregator method)
(indra.util.statement_presentation.MultiAggregator method)
get_doid_id_from_doid_alt_id() (in module indra.databases.doid_client)
get_doid_id_from_doid_name() (in module indra.databases.doid_client)
get_doid_name_from_doid_id() (in module indra.databases.doid_client)
get_dois() (in module indra.literature.elsevier_client)
get_drug_inhibition_stmts() (in module indra.databases.chembl_client)
get_drug_target_data() (in module indra.databases.lincs_client)
get_drugbank_id_from_chebi_id() (in module indra.databases.drugbank_client)
get_drugbank_id_from_chembl_id() (in module indra.databases.drugbank_client)
get_drugbank_id_from_db_id() (in module indra.databases.drugbank_client)
get_drugbank_name() (in module indra.databases.drugbank_client)
get_efo_id_from_efo_name() (in module indra.databases.efo_client)
get_efo_name_from_efo_id() (in module indra.databases.efo_client)
get_ensembl_id() (in module indra.databases.hgnc_client)
get_entity_text_for_relation() (indra.sources.tees.processor.TEESProcessor method)
get_entrez_id() (in module indra.databases.hgnc_client)
get_enzymes() (in module indra.databases.hgnc_client)
get_ev_count() (indra.sources.indra_db_rest.processor.DBQueryStatementProcessor method)
get_ev_count_by_hash() (indra.sources.indra_db_rest.processor.DBQueryStatementProcessor method)
get_ev_counts() (indra.sources.indra_db_rest.processor.IndraDBQueryProcessor method)
get_ev_for_stmts_from_hashes() (in module indra.belief)
get_ev_for_stmts_from_supports() (in module indra.belief)
get_evidence() (in module indra.databases.chembl_client)
(in module indra.sources.gnbr.processor)
(indra.sources.eidos.processor.EidosProcessor method)
get_family() (in module indra.sources.minerva.processor)
get_formats() (in module indra.literature.biorxiv_client)
get_full_text() (in module indra.literature)
get_full_xml() (in module indra.literature.pubmed_client)
get_fulltext_links() (in module indra.literature.crossref_client)
get_function_from_name() (indra.pipeline.pipeline.AssemblyPipeline static method)
get_function_parameters() (indra.pipeline.pipeline.AssemblyPipeline static method)
get_gap_gef() (indra.sources.biopax.processor.BiopaxProcessor method)
get_gene_names() (indra.assemblers.cyjs.assembler.CyJSAssembler method)
get_gene_type() (in module indra.databases.hgnc_client)
get_genetic_profiles() (in module indra.databases.cbio_client)
get_gilda_models() (in module indra.preassembler.grounding_mapper.gilda)
get_git_info() (in module indra.util.get_version)
get_go_id() (in module indra.databases.mesh_client)
get_go_id_from_label() (in module indra.databases.go_client)
get_go_id_from_label_or_synonym() (in module indra.databases.go_client)
get_go_label() (in module indra.databases.go_client)
get_graph() (indra.explanation.model_checker.model_checker.ModelChecker method)
(indra.explanation.model_checker.pybel.PybelModelChecker method)
(indra.explanation.model_checker.pysb.PysbModelChecker method)
(indra.explanation.model_checker.signed_graph.SignedGraphModelChecker method)
(indra.explanation.model_checker.unsigned_graph.UnsignedGraphModelChecker method)
get_grounded_agent() (in module indra.sources.trrust.processor)
get_grounded_agents() (in module indra.assemblers.pysb.assembler)
get_grounding() (in module indra.preassembler.grounding_mapper.gilda)
(indra.statements.agent.Agent method)
(indra.statements.statements.Agent method)
get_groundings() (indra.sources.eidos.processor.EidosProcessor method)
get_hash() (indra.statements.statements.Statement method)
get_hash_statements_dict() (indra.sources.indra_db_rest.processor.DBQueryStatementProcessor method)
get_hedging() (indra.sources.eidos.processor.EidosProcessor static method)
get_hgnc_entry() (in module indra.databases.hgnc_client)
get_hgnc_from_ensembl() (in module indra.databases.hgnc_client)
get_hgnc_from_entrez() (in module indra.databases.hgnc_client)
get_hgnc_from_mouse() (in module indra.databases.hgnc_client)
get_hgnc_from_rat() (in module indra.databases.hgnc_client)
get_hgnc_id() (in module indra.databases.hgnc_client)
get_hgnc_id_from_mgi_name() (in module indra.databases.hgnc_client)
get_hgnc_id_from_mirbase_id() (in module indra.databases.mirbase_client)
get_hgnc_name() (in module indra.databases.hgnc_client)
get_hgnc_name_from_mgi_name() (in module indra.databases.hgnc_client)
get_hgncs_from_enzyme() (in module indra.databases.hgnc_client)
get_hierarchy_probs() (indra.belief.BeliefEngine method)
get_hierarchy_probs_from_hashes() (indra.belief.BeliefEngine method)
get_hp_id_from_hp_name() (in module indra.databases.hp_client)
get_hp_name_from_hp_id() (in module indra.databases.hp_client)
get_id() (indra.ontology.ontology_graph.IndraOntology static method)
get_id_count() (in module indra.literature.pubmed_client)
get_id_from_alt_id() (in module indra.databases.mondo_client)
(indra.databases.obo_client.OntologyClient method)
get_id_from_name() (in module indra.databases.ec_client)
(in module indra.databases.mgi_client)
(in module indra.databases.mondo_client)
(indra.databases.obo_client.OntologyClient method)
(indra.ontology.ontology_graph.IndraOntology method)
(indra.ontology.virtual.ontology.VirtualOntology method)
get_id_from_name_or_synonym() (indra.databases.obo_client.OntologyClient method)
get_id_from_name_synonym() (in module indra.databases.mgi_client)
get_identifiers_ns() (in module indra.databases.identifiers)
get_identifiers_url() (in module indra.databases.identifiers)
get_ido_id_from_ido_name() (in module indra.databases.ido_client)
get_ido_name_from_ido_id() (in module indra.databases.ido_client)
get_ids() (in module indra.literature.pubmed_client)
get_ids_for_gene() (in module indra.literature.pubmed_client)
get_ids_for_mesh() (in module indra.literature.pubmed_client)
get_im() (indra.explanation.model_checker.pysb.PysbModelChecker method)
get_inchi_key() (in module indra.databases.chebi_client)
(in module indra.databases.pubchem_client)
get_input_var_names() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
get_issns_for_journal() (in module indra.literature.pubmed_client)
get_jobs() (in module indra.util.aws)
get_json_record() (in module indra.databases.pubchem_client)
get_kinetics() (in module indra.databases.chembl_client)
get_leaves() (indra.util.nested_dict.NestedDict method)
get_less_specifics() (indra.preassembler.refinement.RefinementFilter method)
get_mappings() (indra.ontology.ontology_graph.IndraOntology method)
get_mesh_annotations() (in module indra.literature.pubmed_client)
get_mesh_id() (in module indra.databases.chembl_client)
(in module indra.databases.pubchem_client)
get_mesh_id_from_db_id() (in module indra.databases.mesh_client)
get_mesh_id_from_go_id() (in module indra.databases.mesh_client)
get_mesh_id_name() (in module indra.databases.mesh_client)
get_mesh_id_name_from_web() (in module indra.databases.mesh_client)
get_mesh_name() (in module indra.databases.mesh_client)
get_mesh_name_from_web() (in module indra.databases.mesh_client)
get_mesh_tree_numbers() (in module indra.databases.mesh_client)
get_mesh_tree_numbers_from_web() (in module indra.databases.mesh_client)
get_metadata() (in module indra.literature.crossref_client)
get_metadata_for_ids() (in module indra.literature.pubmed_client)
get_metadata_from_xml_tree() (in module indra.literature.pubmed_client)
get_mirbase_id_from_hgnc_id() (in module indra.databases.mirbase_client)
get_mirbase_id_from_hgnc_symbol() (in module indra.databases.mirbase_client)
get_mirbase_id_from_mirbase_name() (in module indra.databases.mirbase_client)
get_mirbase_name_from_mirbase_id() (in module indra.databases.mirbase_client)
get_model_agents() (indra.tools.incremental_model.IncrementalModel method)
get_modifications() (indra.sources.biopax.processor.BiopaxProcessor method)
(indra.sources.reach.processor.ReachProcessor method)
(indra.sources.trips.processor.TripsProcessor method)
get_modifications_indirect() (indra.sources.trips.processor.TripsProcessor method)
get_monomer_pattern() (in module indra.assemblers.pysb.assembler)
get_more_specifics() (indra.preassembler.refinement.RefinementFilter method)
get_mouse_id() (in module indra.databases.hgnc_client)
get_mutations() (in module indra.databases.cbio_client)
(in module indra.databases.context_client)
get_name() (in module indra.databases.biolookup_client)
(indra.ontology.ontology_graph.IndraOntology method)
get_name_from_id() (in module indra.databases.ec_client)
(in module indra.databases.mgi_client)
(in module indra.databases.mondo_client)
(indra.databases.obo_client.OntologyClient method)
get_namespace() (in module indra.databases.go_client)
get_negation() (indra.sources.eidos.processor.EidosProcessor static method)
get_new_instance() (indra.util.statement_presentation.StmtGroup method)
get_node_names() (indra.sources.ndex_cx.processor.NdexCxProcessor method)
get_node_property() (indra.ontology.ontology_graph.IndraOntology method)
(indra.ontology.virtual.ontology.VirtualOntology method)
get_nodes() (indra.explanation.model_checker.pybel.PybelModelChecker method)
(indra.explanation.model_checker.signed_graph.SignedGraphModelChecker method)
(indra.explanation.model_checker.unsigned_graph.UnsignedGraphModelChecker method)
get_nodes_to_agents() (indra.explanation.model_checker.model_checker.ModelChecker method)
(indra.explanation.model_checker.pybel.PybelModelChecker method)
(indra.explanation.model_checker.pysb.PysbModelChecker method)
(indra.explanation.model_checker.signed_graph.SignedGraphModelChecker method)
(indra.explanation.model_checker.unsigned_graph.UnsignedGraphModelChecker method)
get_ns() (indra.ontology.ontology_graph.IndraOntology static method)
get_ns_from_bioregistry() (in module indra.databases.bioregistry_client)
get_ns_from_identifiers() (in module indra.databases.identifiers)
get_ns_id() (indra.ontology.ontology_graph.IndraOntology static method)
get_ns_id_from_bioregistry() (in module indra.databases.bioregistry_client)
get_ns_id_from_bioregistry_curie() (in module indra.databases.bioregistry_client)
get_ns_id_from_identifiers() (in module indra.databases.identifiers)
get_nugget_dict() (indra.assemblers.kami.assembler.Nugget method)
get_num_sequenced() (in module indra.databases.cbio_client)
get_output_var_names() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
get_parents() (indra.databases.obo_client.OntologyClient method)
(indra.ontology.ontology_graph.IndraOntology method)
get_path() (indra.util.nested_dict.NestedDict method)
get_path_iter() (in module indra.explanation.pathfinding.pathfinding)
get_paths() (indra.util.nested_dict.NestedDict method)
get_pcid() (in module indra.databases.chembl_client)
get_pdf_xml_url_base() (in module indra.literature.biorxiv_client)
get_piis() (in module indra.literature.elsevier_client)
get_piis_for_date() (in module indra.literature.elsevier_client)
get_pmid() (in module indra.databases.chembl_client)
get_pmids() (in module indra.databases.pubchem_client)
(indra.sources.ndex_cx.processor.NdexCxProcessor method)
get_polarity() (indra.ontology.ontology_graph.IndraOntology method)
get_ppis() (indra.sources.hprd.processor.HprdProcessor method)
get_preferred_compound_ids() (in module indra.databases.pubchem_client)
get_primary_id() (in module indra.databases.chebi_client)
(in module indra.databases.go_client)
get_primary_mappings() (in module indra.databases.mesh_client)
get_profile_data() (in module indra.databases.cbio_client)
get_protein_expression() (in module indra.databases.context_client)
get_protein_refs() (indra.databases.lincs_client.LincsClient method)
get_protein_targets_only() (in module indra.databases.chembl_client)
get_ptms() (indra.sources.hprd.processor.HprdProcessor method)
get_pubchem_id() (in module indra.databases.chebi_client)
get_query_english() (indra.sources.indra_db_rest.query.Query method)
get_query_json() (indra.sources.indra_db_rest.query.Query method)
get_ranked_stmts() (in module indra.belief)
get_rat_id() (in module indra.databases.hgnc_client)
get_ref() (indra.explanation.model_checker.model_checker.ModelChecker method)
get_refinements() (indra.explanation.model_checker.pysb.PysbModelChecker method)
get_regulate_activities() (indra.sources.biopax.processor.BiopaxProcessor method)
get_regulate_amounts() (indra.sources.biopax.processor.BiopaxProcessor method)
(indra.sources.reach.processor.ReachProcessor method)
(indra.sources.trips.processor.TripsProcessor method)
get_related() (indra.preassembler.refinement.OntologyRefinementFilter method)
(indra.preassembler.refinement.RefinementConfirmationFilter method)
(indra.preassembler.refinement.RefinementFilter method)
(indra.preassembler.refinement.SplitGroupFilter method)
get_related_node() (indra.sources.tees.processor.TEESProcessor method)
get_relation() (indra.databases.obo_client.OntologyClient method)
get_relations() (indra.databases.obo_client.OntologyClient method)
get_relevant_keys() (in module indra.preassembler.refinement)
get_replacement() (indra.ontology.ontology_graph.IndraOntology method)
get_resource_path() (in module indra.resources)
get_s3_client() (in module indra.util.aws)
get_s3_file_tree() (in module indra.util.aws)
get_sentences_for_agent() (in module indra.preassembler.grounding_mapper.analysis)
get_site_pattern() (in module indra.assemblers.pysb.assembler)
get_small_molecule_name() (indra.databases.lincs_client.LincsClient method)
get_small_molecule_refs() (indra.databases.lincs_client.LincsClient method)
get_sorted_compositional_groundings() (in module indra.statements.concept)
get_sorted_neighbors() (in module indra.explanation.pathfinding.util)
get_source_count() (indra.sources.indra_db_rest.processor.DBQueryStatementProcessor method)
get_source_count_by_hash() (indra.sources.indra_db_rest.processor.DBQueryStatementProcessor method)
get_source_counts() (indra.sources.indra_db_rest.processor.IndraDBQueryProcessor method)
get_source_hash() (indra.statements.evidence.Evidence method)
(indra.statements.statements.Evidence method)
get_specific_id() (in module indra.databases.chebi_client)
get_standard_agent() (in module indra.ontology.standardize)
get_standard_name() (in module indra.ontology.standardize)
get_start_time() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
get_statement_by_name() (in module indra.statements.statements)
get_statements() (in module indra.sources.indra_db_rest.api)
(indra.sources.isi.processor.IsiProcessor method)
(indra.sources.ndex_cx.processor.NdexCxProcessor method)
(indra.tools.gene_network.GeneNetwork method)
(indra.tools.incremental_model.IncrementalModel method)
get_statements_by_hash() (in module indra.sources.indra_db_rest.api)
get_statements_for_papers() (in module indra.sources.indra_db_rest.api)
get_statements_from_query() (in module indra.sources.indra_db_rest.api)
get_statements_noprior() (indra.tools.incremental_model.IncrementalModel method)
get_statements_prior() (indra.tools.incremental_model.IncrementalModel method)
get_status() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
get_std_chemical() (in module indra.sources.gnbr.processor)
get_std_disease() (in module indra.sources.gnbr.processor)
get_std_gene() (in module indra.sources.gnbr.processor)
get_stmt_evidence() (in module indra.belief)
get_stmt_type() (in module indra.sources.acsn.processor)
get_string() (indra.assemblers.graph.assembler.GraphAssembler method)
get_subgraph() (in module indra.explanation.pathfinding.util)
get_subnetwork() (in module indra.tools.executable_subnetwork)
get_substance_annotations() (in module indra.literature.pubmed_client)
get_synonyms() (in module indra.databases.mgi_client)
get_syntheses() (indra.sources.trips.processor.TripsProcessor method)
get_target_chemblid() (in module indra.databases.chembl_client)
get_taxonomy_id() (in module indra.databases.taxonomy_client)
get_term_agents() (indra.sources.trips.processor.TripsProcessor method)
get_text_content_for_gene() (in module indra.literature.adeft_tools)
get_text_content_for_pmids() (in module indra.literature.adeft_tools)
get_text_from_rxiv_text() (in module indra.literature.biorxiv_client)
get_text_from_rxiv_xml() (in module indra.literature.biorxiv_client)
get_text_refs() (in module indra.sources.hypothesis.processor)
get_text_url_base() (in module indra.literature.biorxiv_client)
get_time_step() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
get_time_units() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
get_title() (in module indra.literature.pubmed_client)
get_top_compositional_grounding() (in module indra.statements.concept)
get_top_level_parents() (indra.ontology.ontology_graph.IndraOntology method)
get_total_nodes() (indra.explanation.model_checker.model_checker.NodesContainer method)
get_translocation() (indra.sources.reach.processor.ReachProcessor method)
get_type() (indra.ontology.ontology_graph.IndraOntology method)
get_typing_dict() (indra.assemblers.kami.assembler.Nugget method)
get_uncond_agent() (in module indra.assemblers.pysb.assembler)
get_uniprot_id() (in module indra.databases.hgnc_client)
get_unresolved_support_uuids() (in module indra.statements.statements)
get_url_prefix() (in module indra.databases.identifiers)
get_valid_location() (in module indra.databases.go_client)
get_valid_residue() (in module indra.statements.resources)
(in module indra.statements.statements)
get_value() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
get_values() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
get_var_name() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
get_var_rank() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
get_var_type() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
get_var_units() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
get_version() (in module indra.sources.sparser.api)
(in module indra.util.get_version)
get_version_df() (in module indra.sources.dgi.api)
get_xml() (in module indra.literature.pmc_client)
(in module indra.sources.trips.client)
gets() (indra.util.nested_dict.NestedDict method)
Glycosylation (class in indra.statements.statements)
GnbrProcessor (class in indra.sources.gnbr.processor)
graph (indra.assemblers.graph.assembler.GraphAssembler attribute)
(indra.assemblers.sif.assembler.SifAssembler attribute)
(indra.explanation.model_checker.model_checker.ModelChecker attribute)
(indra.explanation.model_checker.pybel.PybelModelChecker attribute)
(indra.explanation.model_checker.pysb.PysbModelChecker attribute)
(indra.explanation.model_checker.signed_graph.SignedGraphModelChecker attribute)
(indra.explanation.model_checker.unsigned_graph.UnsignedGraphModelChecker attribute)
graph_properties (indra.assemblers.graph.assembler.GraphAssembler attribute)
GraphAssembler (class in indra.assemblers.graph.assembler)
ground_agent() (in module indra.preassembler.grounding_mapper.gilda)
ground_statement() (in module indra.preassembler.grounding_mapper.gilda)
ground_statements() (in module indra.preassembler.grounding_mapper.gilda)
grounded_monomer_patterns() (in module indra.assemblers.pysb.assembler)
GroundingMapper (class in indra.preassembler.grounding_mapper.mapper)
groundings (indra.sources.hypothesis.processor.HypothesisProcessor attribute)
groundings_from_annotation() (indra.sources.hypothesis.processor.HypothesisProcessor static method)
group_and_sort_statements() (in module indra.util.statement_presentation)
GtpActivation (class in indra.statements.statements)
H
has_tree_prefix() (in module indra.databases.mesh_client)
HasActivity (class in indra.statements.statements)
HasAgent (class in indra.sources.indra_db_rest.query)
HasDatabases (class in indra.sources.indra_db_rest.query)
HasEvidenceBound (class in indra.sources.indra_db_rest.query)
HasHash (class in indra.sources.indra_db_rest.query)
HasNumAgents (class in indra.sources.indra_db_rest.query)
HasNumEvidence (class in indra.sources.indra_db_rest.query)
HasOnlySource (class in indra.sources.indra_db_rest.query)
HasReadings (class in indra.sources.indra_db_rest.query)
HasSources (class in indra.sources.indra_db_rest.query)
HasType (class in indra.sources.indra_db_rest.query)
HprdProcessor (class in indra.sources.hprd.processor)
HtmlAssembler (class in indra.assemblers.html.assembler)
HybridScorer (class in indra.belief.skl)
Hydroxylation (class in indra.statements.statements)
HypothesisProcessor (class in indra.sources.hypothesis.processor)
I
id_df (indra.sources.hprd.processor.HprdProcessor attribute)
id_lookup() (in module indra.literature)
(in module indra.literature.pmc_client)
IdentifiersValidator (class in indra.statements.validate)
im_json_to_graph() (in module indra.assemblers.pysb.kappa_util)
include() (indra.util.statement_presentation.AggregatorMeta method)
(indra.util.statement_presentation.BasicAggregator method)
(indra.util.statement_presentation.MultiAggregator method)
IncreaseAmount (class in indra.statements.statements)
IncrementalModel (class in indra.tools.incremental_model)
IndexCardAssembler (class in indra.assemblers.index_card.assembler)
indra.assemblers.cx.assembler
module
indra.assemblers.cyjs.assembler
module
indra.assemblers.english.assembler
module
indra.assemblers.graph.assembler
module
indra.assemblers.html.assembler
module
indra.assemblers.index_card.assembler
module
indra.assemblers.indranet
module
indra.assemblers.indranet.assembler
module
indra.assemblers.indranet.net
module
indra.assemblers.kami.assembler
module
indra.assemblers.pybel.assembler
module
indra.assemblers.pysb.assembler
module
indra.assemblers.pysb.base_agents
module
indra.assemblers.pysb.bmi_wrapper
module
indra.assemblers.pysb.kappa_util
module
indra.assemblers.pysb.preassembler
module
indra.assemblers.sbgn.assembler
module
indra.assemblers.sif.assembler
module
indra.assemblers.tsv.assembler
module
indra.belief
module
indra.belief.skl
module
indra.databases
module
indra.databases.biolookup_client
module
indra.databases.bioregistry_client
module
indra.databases.cbio_client
module
indra.databases.chebi_client
module
indra.databases.chembl_client
module
indra.databases.context_client
module
indra.databases.doid_client
module
indra.databases.drugbank_client
module
indra.databases.ec_client
module
indra.databases.efo_client
module
indra.databases.go_client
module
indra.databases.hgnc_client
module
indra.databases.hp_client
module
indra.databases.identifiers
module
indra.databases.ido_client
module
indra.databases.lincs_client
module
indra.databases.mesh_client
module
indra.databases.mgi_client
module
indra.databases.mirbase_client
module
indra.databases.mondo_client
module
indra.databases.ndex_client
module
indra.databases.obo_client
module
indra.databases.owl_client
module
indra.databases.pubchem_client
module
indra.databases.taxonomy_client
module
indra.databases.uniprot_client
module
indra.explanation.model_checker.model_checker
module
indra.explanation.model_checker.pybel
module
indra.explanation.model_checker.pysb
module
indra.explanation.model_checker.signed_graph
module
indra.explanation.model_checker.unsigned_graph
module
indra.explanation.pathfinding.pathfinding
module
indra.explanation.pathfinding.util
module
indra.explanation.reporting
module
indra.literature
module
indra.literature.adeft_tools
module
indra.literature.biorxiv_client
module
indra.literature.coci_client
module
indra.literature.crossref_client
module
indra.literature.elsevier_client
module
indra.literature.newsapi_client
module
indra.literature.pmc_client
module
indra.literature.pubmed_client
module
indra.mechlinker
module
indra.ontology
module
indra.ontology.app
module
indra.ontology.bio
module
indra.ontology.bio.__main__
module
indra.ontology.bio.ontology
module
indra.ontology.ontology_graph
module
indra.ontology.standardize
module
indra.ontology.virtual
module
indra.ontology.virtual.ontology
module
indra.pipeline
module
indra.pipeline.decorators
module
indra.pipeline.pipeline
module
indra.preassembler
module
indra.preassembler.custom_preassembly
module
indra.preassembler.grounding_mapper
module
indra.preassembler.grounding_mapper.analysis
module
indra.preassembler.grounding_mapper.disambiguate
module
indra.preassembler.grounding_mapper.gilda
module
indra.preassembler.grounding_mapper.mapper
module
indra.preassembler.refinement
module
indra.preassembler.sitemapper
module
indra.resources
module
indra.sources.acsn
module
indra.sources.acsn.api
module
indra.sources.acsn.processor
module
indra.sources.bel.api
module
indra.sources.bel.processor
module
indra.sources.biofactoid
module
indra.sources.biofactoid.api
module
indra.sources.biofactoid.processor
module
indra.sources.biogrid
module
indra.sources.biopax
module
indra.sources.biopax.api
module
indra.sources.biopax.processor
module
indra.sources.creeds
module
indra.sources.creeds.api
module
indra.sources.creeds.processor
module
indra.sources.crog
module
indra.sources.crog.api
module
indra.sources.crog.processor
module
indra.sources.ctd
module
indra.sources.ctd.api
module
indra.sources.ctd.processor
module
indra.sources.dgi
module
indra.sources.dgi.api
module
indra.sources.dgi.processor
module
indra.sources.drugbank
module
indra.sources.drugbank.api
module
indra.sources.drugbank.processor
module
indra.sources.eidos
module
indra.sources.eidos.api
module
indra.sources.eidos.bio_processor
module
indra.sources.eidos.cli
module
indra.sources.eidos.client
module
indra.sources.eidos.processor
module
indra.sources.eidos.reader
module
indra.sources.eidos.server
module
indra.sources.geneways.api
module
indra.sources.geneways.processor
module
indra.sources.gnbr
module
indra.sources.gnbr.api
module
indra.sources.gnbr.processor
module
indra.sources.hprd
module
indra.sources.hprd.api
module
indra.sources.hprd.processor
module
indra.sources.hypothesis
module
indra.sources.hypothesis.api
module
indra.sources.hypothesis.processor
module
indra.sources.indra_db_rest
module
indra.sources.indra_db_rest.api
module
indra.sources.indra_db_rest.processor
module
indra.sources.indra_db_rest.query
module
indra.sources.isi
module
indra.sources.isi.api
module
indra.sources.isi.processor
module
indra.sources.minerva
module
indra.sources.minerva.api
module
indra.sources.minerva.processor
module
indra.sources.ndex_cx.api
module
indra.sources.ndex_cx.processor
module
indra.sources.omnipath
module
indra.sources.omnipath.api
module
indra.sources.omnipath.processor
module
indra.sources.phosphoelm
module
indra.sources.phosphoelm.api
module
indra.sources.phosphoelm.processor
module
indra.sources.reach
module
indra.sources.reach.api
module
indra.sources.reach.processor
module
indra.sources.reach.reader
module
indra.sources.rlimsp
module
indra.sources.rlimsp.api
module
indra.sources.rlimsp.processor
module
indra.sources.semrep
module
indra.sources.semrep.api
module
indra.sources.semrep.processor
module
indra.sources.signor.api
module
indra.sources.signor.processor
module
indra.sources.sparser
module
indra.sources.sparser.api
module
indra.sources.tas
module
indra.sources.tas.api
module
indra.sources.tas.processor
module
indra.sources.tees.api
module
indra.sources.tees.processor
module
indra.sources.trips.api
module
indra.sources.trips.client
module
indra.sources.trips.drum_reader
module
indra.sources.trips.processor
module
indra.sources.trrust
module
indra.sources.trrust.api
module
indra.sources.trrust.processor
module
indra.sources.ubibrowser
module
indra.sources.ubibrowser.api
module
indra.sources.ubibrowser.processor
module
indra.sources.utils
module
indra.sources.virhostnet
module
indra.sources.virhostnet.api
module
indra.sources.virhostnet.processor
module
indra.statements.agent
module
indra.statements.concept
module
indra.statements.context
module
indra.statements.evidence
module
indra.statements.io
module
indra.statements.resources
module
indra.statements.statements
module
indra.statements.util
module
indra.statements.validate
module
indra.tools.analyze_ontology
module
indra.tools.assemble_corpus
module
indra.tools.executable_subnetwork
module
indra.tools.fix_invalidities
module
indra.tools.gene_network
module
indra.tools.hypothesis_annotator
module
indra.tools.incremental_model
module
indra.tools.machine
module
indra.util.aws
module
indra.util.get_version
module
indra.util.nested_dict
module
indra.util.plot_formatting
module
indra.util.statement_presentation
module
IndraDBQueryProcessor (class in indra.sources.indra_db_rest.processor)
IndraNet (class in indra.assemblers.indranet.net)
IndraNetAssembler (class in indra.assemblers.indranet.assembler)
IndraOntology (class in indra.ontology.ontology_graph)
infer_activations() (indra.mechlinker.MechLinker static method)
infer_active_forms() (indra.mechlinker.MechLinker static method)
infer_complexes() (indra.mechlinker.MechLinker static method)
infer_modifications() (indra.mechlinker.MechLinker static method)
Influence (class in indra.statements.statements)
Inhibition (class in indra.statements.statements)
initialize() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
(indra.ontology.bio.BioOntology method)
(indra.ontology.bio.ontology.BioOntology method)
(indra.ontology.ontology_graph.IndraOntology method)
(indra.ontology.virtual.ontology.VirtualOntology method)
(indra.preassembler.refinement.OntologyRefinementFilter method)
(indra.preassembler.refinement.RefinementFilter method)
initialize_reader() (in module indra.sources.eidos.api)
(indra.sources.eidos.reader.EidosReader method)
InputError
,
[1]
insert() (indra.pipeline.pipeline.AssemblyPipeline method)
internal_source_mappings (in module indra.util.statement_presentation)
invalid_site_pos (indra.sources.hprd.processor.HprdProcessor attribute)
InvalidAgent
InvalidContext
InvalidIdentifier
InvalidLocationError
,
[1]
InvalidResidueError
,
[1]
InvalidStatement
InvalidTextRefs
is_disease() (in module indra.databases.mesh_client)
is_enzyme() (in module indra.databases.mesh_client)
is_function() (indra.pipeline.pipeline.AssemblyPipeline static method)
is_kinase() (in module indra.databases.hgnc_client)
is_molecular() (in module indra.databases.mesh_client)
is_opposite() (indra.ontology.ontology_graph.IndraOntology method)
is_phosphatase() (in module indra.databases.hgnc_client)
is_protein() (in module indra.databases.mesh_client)
is_ref() (indra.explanation.model_checker.model_checker.NodesContainer method)
is_transcription_factor() (in module indra.databases.hgnc_client)
is_working() (indra.sources.indra_db_rest.processor.IndraDBQueryProcessor method)
isa() (indra.ontology.ontology_graph.IndraOntology method)
isa_or_partof() (indra.ontology.ontology_graph.IndraOntology method)
IsiProcessor (class in indra.sources.isi.processor)
isrel() (indra.ontology.ontology_graph.IndraOntology method)
items() (indra.assemblers.pysb.base_agents.BaseAgentSet method)
iter_s3_keys() (in module indra.util.aws)
J
JobLog (class in indra.util.aws)
jsonify_arg_input() (in module indra.pipeline.pipeline)
K
KamiAssembler (class in indra.assemblers.kami.assembler)
kill_all() (in module indra.util.aws)
L
label() (indra.ontology.ontology_graph.IndraOntology static method)
length (indra.explanation.model_checker.model_checker.PathMetric attribute)
LincsClient (class in indra.databases.lincs_client)
LinkedStatement (class in indra.mechlinker)
load() (indra.util.aws.JobLog method)
load_grounding_map() (in module indra.preassembler.grounding_mapper.mapper)
load_lincs_csv() (in module indra.databases.lincs_client)
load_prior() (indra.tools.incremental_model.IncrementalModel method)
load_resource_json() (in module indra.resources)
load_statements() (in module indra.tools.assemble_corpus)
location (indra.mechlinker.AgentState attribute)
lookup() (in module indra.databases.biolookup_client)
lookup_curie() (in module indra.databases.biolookup_client)
M
main_interm (indra.explanation.model_checker.model_checker.NodesContainer attribute)
main_nodes (indra.explanation.model_checker.model_checker.NodesContainer attribute)
make_df() (indra.assemblers.indranet.assembler.IndraNetAssembler method)
make_generic_copy() (indra.statements.statements.Statement method)
make_hash() (in module indra.statements.statements)
(in module indra.statements.util)
make_json_model() (indra.assemblers.html.assembler.HtmlAssembler method)
make_model() (indra.assemblers.cx.assembler.CxAssembler method)
(indra.assemblers.cx.assembler.NiceCxAssembler method)
(indra.assemblers.cyjs.assembler.CyJSAssembler method)
(indra.assemblers.english.assembler.EnglishAssembler method)
(indra.assemblers.graph.assembler.GraphAssembler method)
(indra.assemblers.html.assembler.HtmlAssembler method)
(indra.assemblers.index_card.assembler.IndexCardAssembler method)
(indra.assemblers.indranet.assembler.IndraNetAssembler method)
(indra.assemblers.kami.assembler.KamiAssembler method)
(indra.assemblers.pysb.assembler.PysbAssembler method)
(indra.assemblers.sbgn.assembler.SBGNAssembler method)
(indra.assemblers.sif.assembler.SifAssembler method)
(indra.assemblers.tsv.assembler.TsvAssembler method)
make_model_by_preassembly() (indra.assemblers.indranet.assembler.IndraNetAssembler method)
make_model_from_df() (indra.assemblers.indranet.assembler.IndraNetAssembler method)
make_nxml_from_text() (in module indra.sources.sparser.api)
make_repository_component() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
make_sentence() (indra.assemblers.english.assembler.SentenceBuilder method)
make_standard_stats() (in module indra.util.statement_presentation)
make_statement() (indra.sources.geneways.processor.GenewaysProcessor method)
make_statement_camel() (in module indra.statements.statements)
make_stmt() (in module indra.sources.trrust.processor)
make_stmt_from_relation_key() (in module indra.util.statement_presentation)
make_string_from_relation_key() (in module indra.util.statement_presentation)
make_top_level_label_from_names_key() (in module indra.util.statement_presentation)
many_ups_for_refseq (indra.sources.hprd.processor.HprdProcessor attribute)
map_agent() (indra.preassembler.grounding_mapper.mapper.GroundingMapper method)
map_agents_for_stmt() (indra.preassembler.grounding_mapper.mapper.GroundingMapper method)
map_db_refs() (in module indra.tools.assemble_corpus)
map_grounding() (in module indra.tools.assemble_corpus)
map_sequence() (in module indra.tools.assemble_corpus)
map_sites() (indra.preassembler.sitemapper.SiteMapper method)
map_stmts() (indra.preassembler.grounding_mapper.mapper.GroundingMapper method)
map_to() (indra.ontology.ontology_graph.IndraOntology method)
MappedStatement (class in indra.preassembler.sitemapper)
maps_to() (indra.ontology.ontology_graph.IndraOntology method)
matches_key() (indra.statements.agent.Agent method)
(indra.statements.statements.Agent method)
max_path_length (indra.explanation.model_checker.model_checker.PathResult attribute)
max_paths (indra.explanation.model_checker.model_checker.PathResult attribute)
MaxAggregator (class in indra.util.statement_presentation)
MechLinker (class in indra.mechlinker)
merge_groundings() (in module indra.tools.assemble_corpus)
merge_results() (indra.sources.indra_db_rest.processor.DBQueryStatementProcessor method)
metadata (indra.assemblers.html.assembler.HtmlAssembler attribute)
Methylation (class in indra.statements.statements)
Migration (class in indra.statements.statements)
MissingIdentifier
mk_str() (in module indra.statements.statements)
mod_condition_from_mod_feature() (indra.sources.biopax.processor.BiopaxProcessor static method)
ModCondition (class in indra.statements.agent)
(class in indra.statements.statements)
model (indra.assemblers.english.assembler.EnglishAssembler attribute)
(indra.assemblers.html.assembler.HtmlAssembler attribute)
(indra.assemblers.indranet.assembler.IndraNetAssembler attribute)
(indra.assemblers.pysb.assembler.PysbAssembler attribute)
(indra.sources.biopax.processor.BiopaxProcessor attribute)
ModelChecker (class in indra.explanation.model_checker.model_checker)
Modification (class in indra.statements.statements)
mods (indra.mechlinker.AgentState attribute)
module
indra.assemblers.cx.assembler
indra.assemblers.cyjs.assembler
indra.assemblers.english.assembler
indra.assemblers.graph.assembler
indra.assemblers.html.assembler
indra.assemblers.index_card.assembler
indra.assemblers.indranet
indra.assemblers.indranet.assembler
indra.assemblers.indranet.net
indra.assemblers.kami.assembler
indra.assemblers.pybel.assembler
indra.assemblers.pysb.assembler
indra.assemblers.pysb.base_agents
indra.assemblers.pysb.bmi_wrapper
indra.assemblers.pysb.kappa_util
indra.assemblers.pysb.preassembler
indra.assemblers.sbgn.assembler
indra.assemblers.sif.assembler
indra.assemblers.tsv.assembler
indra.belief
indra.belief.skl
indra.databases
indra.databases.biolookup_client
indra.databases.bioregistry_client
indra.databases.cbio_client
indra.databases.chebi_client
indra.databases.chembl_client
indra.databases.context_client
indra.databases.doid_client
indra.databases.drugbank_client
indra.databases.ec_client
indra.databases.efo_client
indra.databases.go_client
indra.databases.hgnc_client
indra.databases.hp_client
indra.databases.identifiers
indra.databases.ido_client
indra.databases.lincs_client
indra.databases.mesh_client
indra.databases.mgi_client
indra.databases.mirbase_client
indra.databases.mondo_client
indra.databases.ndex_client
indra.databases.obo_client
indra.databases.owl_client
indra.databases.pubchem_client
indra.databases.taxonomy_client
indra.databases.uniprot_client
indra.explanation.model_checker.model_checker
indra.explanation.model_checker.pybel
indra.explanation.model_checker.pysb
indra.explanation.model_checker.signed_graph
indra.explanation.model_checker.unsigned_graph
indra.explanation.pathfinding.pathfinding
indra.explanation.pathfinding.util
indra.explanation.reporting
indra.literature
indra.literature.adeft_tools
indra.literature.biorxiv_client
indra.literature.coci_client
indra.literature.crossref_client
indra.literature.elsevier_client
indra.literature.newsapi_client
indra.literature.pmc_client
indra.literature.pubmed_client
indra.mechlinker
indra.ontology
indra.ontology.app
indra.ontology.bio
indra.ontology.bio.__main__
indra.ontology.bio.ontology
indra.ontology.ontology_graph
indra.ontology.standardize
indra.ontology.virtual
indra.ontology.virtual.ontology
indra.pipeline
indra.pipeline.decorators
indra.pipeline.pipeline
indra.preassembler
indra.preassembler.custom_preassembly
indra.preassembler.grounding_mapper
indra.preassembler.grounding_mapper.analysis
indra.preassembler.grounding_mapper.disambiguate
indra.preassembler.grounding_mapper.gilda
indra.preassembler.grounding_mapper.mapper
indra.preassembler.refinement
indra.preassembler.sitemapper
indra.resources
indra.sources.acsn
indra.sources.acsn.api
indra.sources.acsn.processor
indra.sources.bel.api
indra.sources.bel.processor
indra.sources.biofactoid
indra.sources.biofactoid.api
indra.sources.biofactoid.processor
indra.sources.biogrid
indra.sources.biopax
indra.sources.biopax.api
indra.sources.biopax.processor
indra.sources.creeds
indra.sources.creeds.api
indra.sources.creeds.processor
indra.sources.crog
indra.sources.crog.api
indra.sources.crog.processor
indra.sources.ctd
indra.sources.ctd.api
indra.sources.ctd.processor
indra.sources.dgi
indra.sources.dgi.api
indra.sources.dgi.processor
indra.sources.drugbank
indra.sources.drugbank.api
indra.sources.drugbank.processor
indra.sources.eidos
indra.sources.eidos.api
indra.sources.eidos.bio_processor
indra.sources.eidos.cli
indra.sources.eidos.client
indra.sources.eidos.processor
indra.sources.eidos.reader
indra.sources.eidos.server
indra.sources.geneways.api
indra.sources.geneways.processor
indra.sources.gnbr
indra.sources.gnbr.api
indra.sources.gnbr.processor
indra.sources.hprd
indra.sources.hprd.api
indra.sources.hprd.processor
indra.sources.hypothesis
indra.sources.hypothesis.api
indra.sources.hypothesis.processor
indra.sources.indra_db_rest
indra.sources.indra_db_rest.api
indra.sources.indra_db_rest.processor
indra.sources.indra_db_rest.query
indra.sources.isi
indra.sources.isi.api
indra.sources.isi.processor
indra.sources.minerva
indra.sources.minerva.api
indra.sources.minerva.processor
indra.sources.ndex_cx.api
indra.sources.ndex_cx.processor
indra.sources.omnipath
indra.sources.omnipath.api
indra.sources.omnipath.processor
indra.sources.phosphoelm
indra.sources.phosphoelm.api
indra.sources.phosphoelm.processor
indra.sources.reach
indra.sources.reach.api
indra.sources.reach.processor
indra.sources.reach.reader
indra.sources.rlimsp
indra.sources.rlimsp.api
indra.sources.rlimsp.processor
indra.sources.semrep
indra.sources.semrep.api
indra.sources.semrep.processor
indra.sources.signor.api
indra.sources.signor.processor
indra.sources.sparser
indra.sources.sparser.api
indra.sources.tas
indra.sources.tas.api
indra.sources.tas.processor
indra.sources.tees.api
indra.sources.tees.processor
indra.sources.trips.api
indra.sources.trips.client
indra.sources.trips.drum_reader
indra.sources.trips.processor
indra.sources.trrust
indra.sources.trrust.api
indra.sources.trrust.processor
indra.sources.ubibrowser
indra.sources.ubibrowser.api
indra.sources.ubibrowser.processor
indra.sources.utils
indra.sources.virhostnet
indra.sources.virhostnet.api
indra.sources.virhostnet.processor
indra.statements.agent
indra.statements.concept
indra.statements.context
indra.statements.evidence
indra.statements.io
indra.statements.resources
indra.statements.statements
indra.statements.util
indra.statements.validate
indra.tools.analyze_ontology
indra.tools.assemble_corpus
indra.tools.executable_subnetwork
indra.tools.fix_invalidities
indra.tools.gene_network
indra.tools.hypothesis_annotator
indra.tools.incremental_model
indra.tools.machine
indra.util.aws
indra.util.get_version
indra.util.nested_dict
indra.util.plot_formatting
indra.util.statement_presentation
motif_window (indra.sources.hprd.processor.HprdProcessor attribute)
MovementContext (class in indra.statements.context)
(class in indra.statements.statements)
MultiAggregator (class in indra.util.statement_presentation)
mutations (indra.mechlinker.AgentState attribute)
MutCondition (class in indra.statements.agent)
(class in indra.statements.statements)
Myristoylation (class in indra.statements.statements)
N
name (indra.assemblers.pysb.assembler.Param attribute)
(indra.assemblers.pysb.assembler.Policy attribute)
(indra.ontology.ontology_graph.IndraOntology attribute)
,
[1]
namespace_embedded() (in module indra.databases.identifiers)
NdexCxProcessor (class in indra.sources.ndex_cx.processor)
NestedDict (class in indra.util.nested_dict)
network (indra.assemblers.cx.assembler.NiceCxAssembler attribute)
network_name (indra.assemblers.cx.assembler.CxAssembler attribute)
NiceCxAssembler (class in indra.assemblers.cx.assembler)
no_hgnc_for_egid (indra.sources.hprd.processor.HprdProcessor attribute)
no_mech_ctr (indra.sources.signor.processor.SignorProcessor attribute)
no_mech_rows (indra.sources.signor.processor.SignorProcessor attribute)
no_up_for_hgnc (indra.sources.hprd.processor.HprdProcessor attribute)
no_up_for_refseq (indra.sources.hprd.processor.HprdProcessor attribute)
node_has_edge_with_label() (indra.sources.tees.processor.TEESProcessor method)
node_properties (indra.assemblers.graph.assembler.GraphAssembler attribute)
node_to_evidence() (indra.sources.tees.processor.TEESProcessor method)
nodes_from_suffix() (indra.ontology.ontology_graph.IndraOntology method)
NodesContainer (class in indra.explanation.model_checker.model_checker)
normalize_active_forms() (in module indra.tools.assemble_corpus)
normalize_equivalences() (indra.preassembler.Preassembler method)
normalize_opposites() (indra.preassembler.Preassembler method)
NotAStatementName
NotRegisteredFunctionError
Nugget (class in indra.assemblers.kami.assembler)
O
OboClient (class in indra.databases.obo_client)
off_by_one (indra.sources.hprd.processor.HprdProcessor attribute)
OmniPathProcessor (class in indra.sources.omnipath.processor)
ontology (indra.preassembler.Preassembler attribute)
OntologyClient (class in indra.databases.obo_client)
OntologyRefinementFilter (class in indra.preassembler.refinement)
open_dijkstra_search() (in module indra.explanation.pathfinding.pathfinding)
open_resource_file() (in module indra.resources)
Or (class in indra.sources.indra_db_rest.query)
organism_priority (indra.sources.reach.processor.ReachProcessor attribute)
OwlClient (class in indra.databases.owl_client)
P
Palmitoylation (class in indra.statements.statements)
par_to_sec (indra.sources.trips.processor.TripsProcessor attribute)
paragraphs (indra.sources.trips.processor.TripsProcessor attribute)
Param (class in indra.assemblers.pysb.assembler)
parameters (indra.assemblers.pysb.assembler.Policy attribute)
parse_context_entry() (in module indra.sources.hypothesis.processor)
parse_grounding_entry() (in module indra.sources.hypothesis.processor)
parse_identifiers_url() (in module indra.assemblers.pysb.assembler)
(in module indra.databases.identifiers)
parse_psi_mi() (in module indra.sources.virhostnet.processor)
parse_source_ids() (in module indra.sources.virhostnet.processor)
parse_text_refs() (in module indra.sources.virhostnet.processor)
partof() (indra.ontology.ontology_graph.IndraOntology method)
path_found (indra.explanation.model_checker.model_checker.PathResult attribute)
path_metrics (indra.explanation.model_checker.model_checker.PathResult attribute)
path_sign_to_signed_nodes() (in module indra.explanation.pathfinding.util)
PathMetric (class in indra.explanation.model_checker.model_checker)
PathResult (class in indra.explanation.model_checker.model_checker)
paths (indra.explanation.model_checker.model_checker.PathResult attribute)
PhosphoElmProcessor (class in indra.sources.phosphoelm.processor)
Phosphorylation (class in indra.statements.statements)
physical_only (indra.sources.biogrid.BiogridProcessor attribute)
policies (indra.assemblers.pysb.assembler.PysbAssembler attribute)
Policy (class in indra.assemblers.pysb.assembler)
position (indra.sources.reach.processor.Site property)
preassemble() (indra.tools.incremental_model.IncrementalModel method)
Preassembler (class in indra.preassembler)
predict() (indra.belief.skl.SklearnScorer method)
predict_log_proba() (indra.belief.skl.SklearnScorer method)
predict_proba() (indra.belief.skl.SklearnScorer method)
prepend() (indra.assemblers.english.assembler.SentenceBuilder method)
pretty_print_stmts() (in module indra.statements.io)
(in module indra.statements.statements)
print_boolean_net() (indra.assemblers.sif.assembler.SifAssembler method)
print_cx() (indra.assemblers.cx.assembler.CxAssembler method)
print_cyjs_context() (indra.assemblers.cyjs.assembler.CyJSAssembler method)
print_cyjs_graph() (indra.assemblers.cyjs.assembler.CyJSAssembler method)
print_event_statistics() (indra.sources.reach.processor.ReachProcessor method)
print_loopy() (indra.assemblers.sif.assembler.SifAssembler method)
print_model() (indra.assemblers.cx.assembler.NiceCxAssembler method)
(indra.assemblers.index_card.assembler.IndexCardAssembler method)
(indra.assemblers.pysb.assembler.PysbAssembler method)
(indra.assemblers.sbgn.assembler.SBGNAssembler method)
(indra.assemblers.sif.assembler.SifAssembler method)
print_parent_and_children_info() (indra.sources.tees.processor.TEESProcessor method)
print_quiet_logs() (indra.sources.indra_db_rest.processor.IndraDBQueryProcessor static method)
print_stmt_summary() (in module indra.statements.io)
(in module indra.statements.statements)
print_summary() (indra.sources.utils.RemoteProcessor method)
print_validation_report() (in module indra.statements.validate)
prioritize_organism_grounding() (in module indra.sources.reach.processor)
process_agents_from_entities() (in module indra.sources.reach.api)
process_annotations() (in module indra.sources.hypothesis.api)
process_archive() (in module indra.sources.hprd.api)
process_bel_stmt() (in module indra.sources.bel.api)
process_belscript() (in module indra.sources.bel.api)
process_binding_statements() (indra.sources.tees.processor.TEESProcessor method)
process_cbn_jgif_file() (in module indra.sources.bel.api)
process_chemical_disease() (in module indra.sources.gnbr.api)
process_chemical_disease_from_web() (in module indra.sources.gnbr.api)
process_chemical_gene() (in module indra.sources.gnbr.api)
process_chemical_gene_from_web() (in module indra.sources.gnbr.api)
process_csv() (in module indra.sources.tas.api)
process_cx() (in module indra.sources.ndex_cx.api)
process_cx_file() (in module indra.sources.ndex_cx.api)
process_dataframe() (in module indra.sources.ctd.api)
process_decrease_expression_amount() (indra.sources.tees.processor.TEESProcessor method)
process_df() (in module indra.sources.acsn.api)
(in module indra.sources.dgi.api)
(in module indra.sources.ubibrowser.api)
(in module indra.sources.virhostnet.api)
process_element_tree() (in module indra.sources.drugbank.api)
process_file() (in module indra.sources.minerva.api)
(in module indra.sources.ubibrowser.api)
process_files() (in module indra.sources.acsn.api)
(in module indra.sources.minerva.api)
process_flat_files() (in module indra.sources.hprd.api)
process_fries_json_group() (in module indra.sources.reach.api)
process_from_dump() (in module indra.sources.phosphoelm.api)
process_from_file() (in module indra.sources.creeds.api)
(in module indra.sources.signor.api)
process_from_files() (in module indra.sources.gnbr.api)
process_from_json_file() (in module indra.sources.rlimsp.api)
process_from_jsonish_str() (in module indra.sources.rlimsp.api)
process_from_web() (in module indra.sources.acsn.api)
(in module indra.sources.biofactoid.api)
(in module indra.sources.creeds.api)
(in module indra.sources.crog.api)
(in module indra.sources.ctd.api)
(in module indra.sources.drugbank.api)
(in module indra.sources.gnbr.api)
(in module indra.sources.minerva.api)
(in module indra.sources.omnipath.api)
(in module indra.sources.tas.api)
(in module indra.sources.trrust.api)
(in module indra.sources.ubibrowser.api)
(in module indra.sources.virhostnet.api)
process_from_webservice() (in module indra.sources.rlimsp.api)
process_gene_disease() (in module indra.sources.gnbr.api)
process_gene_disease_from_web() (in module indra.sources.gnbr.api)
process_gene_gene() (in module indra.sources.gnbr.api)
process_gene_gene_from_web() (in module indra.sources.gnbr.api)
process_geneways_files() (in module indra.sources.geneways.api)
process_increase_expression_amount() (indra.sources.tees.processor.TEESProcessor method)
process_json() (in module indra.sources.biofactoid.api)
process_json_bio() (in module indra.sources.eidos.api)
process_json_bio_entities() (in module indra.sources.eidos.api)
process_json_dict() (in module indra.sources.sparser.api)
process_json_file() (in module indra.sources.bel.api)
(in module indra.sources.isi.api)
(in module indra.sources.reach.api)
process_json_str() (in module indra.sources.reach.api)
process_jsonl_file() (in module indra.sources.rlimsp.api)
process_jsonl_str() (in module indra.sources.rlimsp.api)
process_large_corpus() (in module indra.sources.bel.api)
process_ligrec_interactions() (indra.sources.omnipath.processor.OmniPathProcessor method)
process_model() (in module indra.sources.biopax.api)
process_ndex_network() (in module indra.sources.ndex_cx.api)
process_nxml() (in module indra.sources.isi.api)
process_nxml_file() (in module indra.sources.reach.api)
(in module indra.sources.sparser.api)
process_nxml_str() (in module indra.sources.reach.api)
(in module indra.sources.sparser.api)
process_output_folder() (in module indra.sources.isi.api)
process_owl() (in module indra.sources.biopax.api)
process_owl_gz() (in module indra.sources.biopax.api)
process_owl_str() (in module indra.sources.biopax.api)
process_pc_neighborhood() (in module indra.sources.biopax.api)
process_pc_pathsbetween() (in module indra.sources.biopax.api)
process_pc_pathsfromto() (in module indra.sources.biopax.api)
process_phosphorylation_statements() (indra.sources.tees.processor.TEESProcessor method)
process_phosphorylations() (indra.sources.phosphoelm.processor.PhosphoElmProcessor method)
process_pmc() (in module indra.sources.reach.api)
process_preprocessed() (in module indra.sources.isi.api)
process_ptm_mods() (indra.sources.omnipath.processor.OmniPathProcessor method)
process_pubmed_abstract() (in module indra.sources.reach.api)
process_pybel_graph() (in module indra.sources.bel.api)
process_pybel_neighborhood() (in module indra.sources.bel.api)
process_pybel_network() (in module indra.sources.bel.api)
process_row() (in module indra.sources.virhostnet.processor)
process_small_corpus() (in module indra.sources.bel.api)
process_sparser_output() (in module indra.sources.sparser.api)
process_statement() (indra.explanation.model_checker.model_checker.ModelChecker method)
(indra.explanation.model_checker.pybel.PybelModelChecker method)
(indra.explanation.model_checker.pysb.PysbModelChecker method)
(indra.explanation.model_checker.signed_graph.SignedGraphModelChecker method)
(indra.explanation.model_checker.unsigned_graph.UnsignedGraphModelChecker method)
process_statements() (indra.sources.semrep.processor.SemRepXmlProcessor method)
process_subject() (indra.explanation.model_checker.model_checker.ModelChecker method)
(indra.explanation.model_checker.pysb.PysbModelChecker method)
process_text() (in module indra.sources.eidos.client)
(in module indra.sources.isi.api)
(in module indra.sources.reach.api)
(in module indra.sources.sparser.api)
(in module indra.sources.tees.api)
(in module indra.sources.trips.api)
(indra.sources.eidos.reader.EidosReader method)
process_text_bio() (in module indra.sources.eidos.api)
process_text_bio_entities() (in module indra.sources.eidos.api)
process_tsv() (in module indra.sources.ctd.api)
(in module indra.sources.virhostnet.api)
process_version() (in module indra.sources.dgi.api)
process_xml() (in module indra.sources.drugbank.api)
(in module indra.sources.sparser.api)
(in module indra.sources.trips.api)
process_xml_file() (in module indra.sources.semrep.api)
(in module indra.sources.trips.api)
Processor (class in indra.sources.utils)
protein_map_from_twg() (in module indra.preassembler.grounding_mapper.analysis)
prune_influence_map() (indra.explanation.model_checker.pysb.PysbModelChecker method)
prune_influence_map_degrade_bind_positive() (indra.explanation.model_checker.pysb.PysbModelChecker method)
prune_influence_map_subj_obj() (indra.explanation.model_checker.pysb.PysbModelChecker method)
prune_signed_nodes() (in module indra.explanation.model_checker.model_checker)
PybelAssembler (class in indra.assemblers.pybel.assembler)
PybelEdge (class in indra.explanation.reporting)
PybelModelChecker (class in indra.explanation.model_checker.pybel)
PybelProcessor (class in indra.sources.bel.processor)
PyOboClient (class in indra.databases.obo_client)
PysbAssembler (class in indra.assemblers.pysb.assembler)
PysbModelChecker (class in indra.explanation.model_checker.pysb)
PysbPreassembler (class in indra.assemblers.pysb.preassembler)
Q
QualitativeDelta (class in indra.statements.statements)
QuantitativeState (class in indra.statements.statements)
Query (class in indra.sources.indra_db_rest.query)
query_target() (in module indra.databases.chembl_client)
R
ReachOfflineReadingError
ReachProcessor (class in indra.sources.reach.processor)
ReachReader (class in indra.sources.reach.reader)
read_and_annotate() (in module indra.tools.hypothesis_annotator)
read_pmc() (indra.sources.trips.drum_reader.DrumReader method)
read_text() (indra.sources.trips.drum_reader.DrumReader method)
reader_sources (in module indra.util.statement_presentation)
READER_TEXT_COLOR (in module indra.assemblers.html.assembler)
real_agent_list() (indra.statements.statements.Statement method)
receive_reply() (indra.sources.trips.drum_reader.DrumReader method)
reduce_activities() (in module indra.tools.assemble_corpus)
(indra.mechlinker.MechLinker method)
ref_interm (indra.explanation.model_checker.model_checker.NodesContainer attribute)
ref_nodes (indra.explanation.model_checker.model_checker.NodesContainer attribute)
RefContext (class in indra.statements.context)
(class in indra.statements.statements)
RefEdge (class in indra.explanation.reporting)
RefinementConfirmationFilter (class in indra.preassembler.refinement)
RefinementFilter (class in indra.preassembler.refinement)
register_pipeline() (in module indra.pipeline.decorators)
RegulateActivity (class in indra.statements.statements)
RegulateAmount (class in indra.statements.statements)
related_stmts (indra.preassembler.Preassembler attribute)
relation (indra.explanation.reporting.PybelEdge property)
relations_df (indra.sources.acsn.processor.AcsnProcessor attribute)
RemoteProcessor (class in indra.sources.utils)
remove_im_params() (in module indra.explanation.model_checker.pysb)
RemoveModification (class in indra.statements.statements)
rename_agents() (indra.preassembler.grounding_mapper.mapper.GroundingMapper static method)
rename_db_ref() (in module indra.tools.assemble_corpus)
rename_s3_prefix() (in module indra.util.aws)
render_stmt_graph() (in module indra.preassembler)
replace_activations() (indra.mechlinker.MechLinker method)
replace_activities() (indra.assemblers.pysb.preassembler.PysbPreassembler method)
replace_complexes() (indra.mechlinker.MechLinker method)
require_active_forms() (indra.mechlinker.MechLinker method)
residue (indra.sources.reach.processor.Site property)
result_code (indra.explanation.model_checker.model_checker.PathResult attribute)
results (indra.tools.gene_network.GeneNetwork attribute)
retain_molecular_complexes() (indra.sources.isi.processor.IsiProcessor method)
reverse (indra.explanation.reporting.PybelEdge property)
reverse_label() (indra.ontology.ontology_graph.IndraOntology static method)
reverse_source_mappings (in module indra.util.statement_presentation)
Ribosylation (class in indra.statements.statements)
RlimspParagraph (class in indra.sources.rlimsp.processor)
RlimspProcessor (class in indra.sources.rlimsp.processor)
row_set() (indra.util.statement_presentation.StmtGroup method)
row_to_statements() (indra.sources.dgi.processor.DGIProcessor method)
run() (indra.pipeline.pipeline.AssemblyPipeline method)
run_adeft_disambiguation() (indra.preassembler.grounding_mapper.disambiguate.DisambManager method)
run_eidos() (in module indra.sources.eidos.cli)
run_function() (indra.pipeline.pipeline.AssemblyPipeline method)
run_gilda_disambiguation() (indra.preassembler.grounding_mapper.disambiguate.DisambManager method)
run_mechlinker() (in module indra.tools.assemble_corpus)
run_on_text() (in module indra.sources.tees.api)
run_preassembly() (in module indra.tools.assemble_corpus)
(indra.tools.gene_network.GeneNetwork method)
run_preassembly_duplicate() (in module indra.tools.assemble_corpus)
run_preassembly_related() (in module indra.tools.assemble_corpus)
run_simple_function() (indra.pipeline.pipeline.AssemblyPipeline static method)
run_sparser() (in module indra.sources.sparser.api)
RunnableArgument (class in indra.pipeline.pipeline)
S
s2a() (in module indra.sources.tees.processor)
sample_statements() (in module indra.belief)
save() (indra.tools.incremental_model.IncrementalModel method)
save_base_map() (in module indra.preassembler.grounding_mapper.analysis)
save_dot() (indra.assemblers.graph.assembler.GraphAssembler method)
save_json() (indra.assemblers.cyjs.assembler.CyJSAssembler method)
save_model() (indra.assemblers.cx.assembler.CxAssembler method)
(indra.assemblers.cyjs.assembler.CyJSAssembler method)
(indra.assemblers.html.assembler.HtmlAssembler method)
(indra.assemblers.index_card.assembler.IndexCardAssembler method)
(indra.assemblers.pybel.assembler.PybelAssembler method)
(indra.assemblers.pysb.assembler.PysbAssembler method)
(indra.assemblers.sbgn.assembler.SBGNAssembler method)
(indra.assemblers.sif.assembler.SifAssembler method)
(indra.sources.biopax.processor.BiopaxProcessor method)
save_pdf() (indra.assemblers.graph.assembler.GraphAssembler method)
save_rst() (indra.assemblers.pysb.assembler.PysbAssembler method)
save_sentences() (in module indra.preassembler.grounding_mapper.analysis)
save_xml() (in module indra.sources.trips.client)
sbgn (indra.assemblers.sbgn.assembler.SBGNAssembler attribute)
SBGNAssembler (class in indra.assemblers.sbgn.assembler)
score_evidence_list() (indra.belief.SimpleScorer method)
score_paths() (indra.explanation.model_checker.pysb.PysbModelChecker method)
score_statement() (indra.belief.BeliefScorer method)
score_statements() (indra.belief.BeliefScorer method)
(indra.belief.SimpleScorer method)
(indra.belief.skl.HybridScorer method)
(indra.belief.skl.SklearnScorer method)
search_science_direct() (in module indra.literature.elsevier_client)
SelfModification (class in indra.statements.statements)
SemRepXmlProcessor (class in indra.sources.semrep.processor)
send_query() (in module indra.databases.chembl_client)
(in module indra.sources.trips.client)
send_request() (in module indra.databases.cbio_client)
(in module indra.databases.ndex_client)
(in module indra.literature.newsapi_client)
sentence (indra.assemblers.english.assembler.SentenceBuilder attribute)
SentenceBuilder (class in indra.assemblers.english.assembler)
sentences (indra.sources.trips.processor.TripsProcessor attribute)
seq_dict (indra.sources.hprd.processor.HprdProcessor attribute)
set_base_initial_condition() (in module indra.assemblers.pysb.assembler)
set_CCLE_context() (indra.assemblers.cyjs.assembler.CyJSAssembler method)
set_context() (indra.assemblers.cx.assembler.CxAssembler method)
(indra.assemblers.pysb.assembler.PysbAssembler method)
set_expression() (indra.assemblers.pysb.assembler.PysbAssembler method)
set_extended_initial_condition() (in module indra.assemblers.pysb.assembler)
set_fig_params() (in module indra.util.plot_formatting)
set_hierarchy_probs() (indra.belief.BeliefEngine method)
set_linked_probs() (indra.belief.BeliefEngine method)
set_pretty_print_max_width() (in module indra.statements.io)
(in module indra.statements.statements)
set_prior_probs() (indra.belief.BeliefEngine method)
set_style() (in module indra.databases.ndex_client)
set_value() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
set_values() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
shortest_simple_paths() (in module indra.explanation.pathfinding.pathfinding)
SifAssembler (class in indra.assemblers.sif.assembler)
SifProcessor (class in indra.sources.minerva.processor)
signed_edges_to_signed_nodes() (in module indra.explanation.model_checker.model_checker)
signed_from_df() (indra.assemblers.indranet.net.IndraNet class method)
signed_nodes_to_signed_edge() (in module indra.explanation.pathfinding.util)
SignedGraphModelChecker (class in indra.explanation.model_checker.signed_graph)
SignorProcessor (class in indra.sources.signor.processor)
SimpleScorer (class in indra.belief)
Site (class in indra.sources.reach.processor)
SiteMapper (class in indra.preassembler.sitemapper)
sites (indra.assemblers.pysb.assembler.Policy attribute)
SklearnScorer (class in indra.belief.skl)
source (indra.explanation.reporting.PybelEdge property)
source_node (indra.explanation.model_checker.model_checker.PathMetric attribute)
SplitGroupFilter (class in indra.preassembler.refinement)
src_url() (in module indra.assemblers.html.assembler)
standardize_agent_name() (in module indra.ontology.standardize)
(indra.preassembler.grounding_mapper.mapper.GroundingMapper static method)
standardize_counts() (in module indra.util.statement_presentation)
standardize_db_refs() (in module indra.ontology.standardize)
(indra.preassembler.grounding_mapper.mapper.GroundingMapper static method)
standardize_name_db_refs() (in module indra.ontology.standardize)
standardize_names_groundings() (in module indra.tools.assemble_corpus)
start() (indra.util.statement_presentation.StmtGroup method)
state_matches_key() (indra.statements.agent.Agent method)
(indra.statements.statements.Agent method)
Statement (class in indra.statements.statements)
statement_base_verb() (in module indra.assemblers.english.assembler)
statement_passive_verb() (in module indra.assemblers.english.assembler)
statement_present_verb() (in module indra.assemblers.english.assembler)
statements (indra.assemblers.cx.assembler.CxAssembler attribute)
(indra.assemblers.cyjs.assembler.CyJSAssembler attribute)
(indra.assemblers.english.assembler.EnglishAssembler attribute)
(indra.assemblers.graph.assembler.GraphAssembler attribute)
(indra.assemblers.html.assembler.HtmlAssembler attribute)
(indra.assemblers.index_card.assembler.IndexCardAssembler attribute)
(indra.assemblers.pysb.assembler.PysbAssembler attribute)
(indra.assemblers.sbgn.assembler.SBGNAssembler attribute)
(indra.assemblers.tsv.assembler.TsvAssembler attribute)
(indra.sources.bel.processor.PybelProcessor attribute)
(indra.sources.biofactoid.processor.BioFactoidProcessor attribute)
(indra.sources.biogrid.BiogridProcessor attribute)
(indra.sources.biopax.processor.BiopaxProcessor attribute)
(indra.sources.creeds.processor.CREEDSChemicalProcessor attribute)
(indra.sources.creeds.processor.CREEDSDiseaseProcessor attribute)
(indra.sources.creeds.processor.CREEDSGeneProcessor attribute)
(indra.sources.dgi.processor.DGIProcessor attribute)
(indra.sources.drugbank.processor.DrugbankProcessor attribute)
(indra.sources.eidos.processor.EidosProcessor attribute)
(indra.sources.geneways.processor.GenewaysProcessor attribute)
(indra.sources.hprd.processor.HprdProcessor attribute)
(indra.sources.hypothesis.processor.HypothesisProcessor attribute)
(indra.sources.isi.processor.IsiProcessor attribute)
(indra.sources.minerva.processor.SifProcessor attribute)
(indra.sources.ndex_cx.processor.NdexCxProcessor attribute)
(indra.sources.phosphoelm.processor.PhosphoElmProcessor attribute)
(indra.sources.reach.processor.ReachProcessor attribute)
(indra.sources.signor.processor.SignorProcessor attribute)
(indra.sources.tees.processor.TEESProcessor attribute)
(indra.sources.trips.processor.TripsProcessor attribute)
(indra.sources.trrust.processor.TrrustProcessor attribute)
(indra.sources.utils.RemoteProcessor property)
(indra.sources.virhostnet.processor.VirhostnetProcessor attribute)
stmt_agents (indra.assemblers.english.assembler.EnglishAssembler attribute)
stmt_from_json() (in module indra.statements.io)
(in module indra.statements.statements)
stmt_from_json_str() (in module indra.statements.io)
(in module indra.statements.statements)
stmt_from_rule() (in module indra.explanation.reporting)
stmt_to_english() (in module indra.util.statement_presentation)
stmt_type() (in module indra.statements.statements)
StmtGroup (class in indra.util.statement_presentation)
stmts (indra.preassembler.Preassembler attribute)
(indra.tools.incremental_model.IncrementalModel attribute)
stmts_from_annotation() (indra.sources.hypothesis.processor.HypothesisProcessor method)
stmts_from_indranet_path() (in module indra.explanation.reporting)
stmts_from_json() (in module indra.statements.io)
(in module indra.statements.statements)
stmts_from_json_file() (in module indra.statements.io)
(in module indra.statements.statements)
stmts_from_pybel_path() (in module indra.explanation.reporting)
stmts_from_pysb_path() (in module indra.explanation.reporting)
stmts_to_json() (in module indra.statements.io)
(in module indra.statements.statements)
stmts_to_json_file() (in module indra.statements.io)
(in module indra.statements.statements)
stmts_to_matrix() (indra.belief.skl.CountsScorer method)
(indra.belief.skl.SklearnScorer method)
StmtStat (class in indra.util.statement_presentation)
strip_agent_context() (in module indra.tools.assemble_corpus)
strip_supports() (in module indra.tools.assemble_corpus)
submit_curation() (in module indra.sources.indra_db_rest.api)
SumAggregator (class in indra.util.statement_presentation)
Sumoylation (class in indra.statements.statements)
T
tag_evidence_subtype() (in module indra.belief)
tag_instance() (in module indra.util.aws)
tag_myself() (in module indra.util.aws)
tag_text() (in module indra.assemblers.html.assembler)
target (indra.explanation.reporting.PybelEdge property)
target_node (indra.explanation.model_checker.model_checker.PathMetric attribute)
TasProcessor (class in indra.sources.tas.processor)
TEESProcessor (class in indra.sources.tees.processor)
TimeContext (class in indra.statements.context)
(class in indra.statements.statements)
timed_out() (indra.sources.indra_db_rest.processor.IndraDBQueryProcessor method)
to_database() (indra.assemblers.pybel.assembler.PybelAssembler method)
to_digraph() (indra.assemblers.indranet.net.IndraNet method)
to_graph() (indra.statements.statements.Statement method)
to_json() (indra.pipeline.pipeline.RunnableArgument method)
(indra.statements.evidence.Evidence method)
(indra.statements.statements.ActiveForm method)
(indra.statements.statements.Association method)
(indra.statements.statements.Complex method)
(indra.statements.statements.Conversion method)
(indra.statements.statements.Event method)
(indra.statements.statements.Evidence method)
(indra.statements.statements.Gap method)
(indra.statements.statements.Gef method)
(indra.statements.statements.Influence method)
(indra.statements.statements.Modification method)
(indra.statements.statements.RegulateActivity method)
(indra.statements.statements.RegulateAmount method)
(indra.statements.statements.SelfModification method)
(indra.statements.statements.Statement method)
(indra.statements.statements.Translocation method)
to_json_file() (indra.pipeline.pipeline.AssemblyPipeline method)
to_matrix() (indra.belief.skl.SklearnScorer method)
to_signed_graph() (indra.assemblers.indranet.net.IndraNet method)
to_simple_json() (indra.sources.indra_db_rest.query.Query method)
to_web() (indra.assemblers.pybel.assembler.PybelAssembler method)
Translocation (class in indra.statements.statements)
Transphosphorylation (class in indra.statements.statements)
tree (indra.sources.reach.processor.ReachProcessor attribute)
(indra.sources.trips.processor.TripsProcessor attribute)
TripsProcessor (class in indra.sources.trips.processor)
TrrustProcessor (class in indra.sources.trrust.processor)
TsvAssembler (class in indra.assemblers.tsv.assembler)
U
UbiBrowserProcessor (class in indra.sources.ubibrowser.processor)
Ubiquitination (class in indra.statements.statements)
ungrounded_texts() (in module indra.preassembler.grounding_mapper.analysis)
unique (indra.assemblers.pysb.assembler.Param attribute)
unique_stmts (indra.preassembler.Preassembler attribute)
universal_extract_paragraphs() (in module indra.literature.adeft_tools)
universal_extract_text() (in module indra.literature.adeft_tools)
UnknownIdentifier
UnknownNamespace
UnknownPolicyError
Unresolved (class in indra.statements.statements)
UnresolvedUuidError
,
[1]
UnsignedGraphModelChecker (class in indra.explanation.model_checker.unsigned_graph)
update() (indra.assemblers.pysb.bmi_wrapper.BMIModel method)
update_agent_db_refs() (indra.preassembler.grounding_mapper.mapper.GroundingMapper method)
update_by_prefix() (indra.databases.obo_client.PyOboClient class method)
update_coords() (indra.assemblers.english.assembler.AgentWithCoordinates method)
update_counts() (indra.belief.BayesianScorer method)
update_filter_func() (indra.explanation.model_checker.model_checker.ModelChecker method)
update_network() (in module indra.databases.ndex_client)
update_probs() (indra.belief.BayesianScorer method)
(indra.belief.SimpleScorer method)
update_resource() (indra.databases.obo_client.OboClient class method)
upload_annotation() (in module indra.sources.hypothesis.api)
upload_model() (indra.assemblers.cx.assembler.CxAssembler method)
upload_statement_annotation() (in module indra.sources.hypothesis.api)
url (indra.sources.crog.processor.CrogProcessor attribute)
(indra.sources.utils.RemoteProcessor attribute)
V
validate_agent() (in module indra.statements.validate)
validate_db_refs() (in module indra.statements.validate)
validate_evidence() (in module indra.statements.validate)
validate_id() (in module indra.statements.validate)
validate_ns() (in module indra.statements.validate)
validate_statement() (in module indra.statements.validate)
validate_text_refs() (in module indra.statements.validate)
value (indra.assemblers.pysb.assembler.Param attribute)
value_per_second() (indra.statements.statements.QuantitativeState static method)
verbs (indra.sources.isi.processor.IsiProcessor attribute)
version (indra.ontology.ontology_graph.IndraOntology attribute)
VirhostnetProcessor (class in indra.sources.virhostnet.processor)
VirtualOntology (class in indra.ontology.virtual.ontology)
W
wait_until_done() (indra.sources.indra_db_rest.processor.IndraDBQueryProcessor method)
WorldContext (class in indra.statements.context)
(class in indra.statements.statements)
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