Index

Symbols

--all indra_cogex-indexing command line option --exist-ok indra_cogex-indexing command line option --index-evidence-nodes indra_cogex-indexing command line option

--index-indra-relations indra_cogex-indexing command line option --index-nodes indra_cogex-indexing command line option

A

add_node() (Neo4jClient method) add_nodes() (Neo4jClient method) (NodeAssembler method)

add_relations() (Neo4jClient method) assemble_nodes() (NodeAssembler method) autoclient() (in module indra_cogex.client.neo4j_client)

B

BgeeProcessor (class in indra_cogex.sources.bgee)

C

cli() (Processor class method) close_session() (Neo4jClient method) collect_gene_sets() (in module indra_cogex.client.enrichment.utils)

create_nodes() (Neo4jClient method) create_single_property_node_index() (Neo4jClient method) create_single_property_relationship_index() (Neo4jClient method) create_tx() (Neo4jClient method)

D

data_validator() (in module indra_cogex.sources.processor_util) DataTypeError

delete_all() (Neo4jClient method) drug_has_indication() (in module indra_cogex.client.queries) dump() (Processor method)

E

EXAMPLE_GENE_IDS (in module indra_cogex.client.enrichment.discrete)

G

gene_has_codependency() (in module indra_cogex.client.queries) gene_has_domain() (in module indra_cogex.client.queries) generate_paper_clause() (in module indra_cogex.representation) get_aggregate_node() (NodeAssembler method) get_all_relations() (Neo4jClient method) get_cell_lines_with_cna() (in module indra_cogex.client.queries) get_cell_lines_with_mutation() (in module indra_cogex.client.queries) get_cell_types_for_marker() (in module indra_cogex.client.queries) get_cli() (Processor class method) get_clinical_trials_for_project() (in module indra_cogex.client.queries) get_cna_genes_in_cell_line() (in module indra_cogex.client.queries) get_codependents_for_gene() (in module indra_cogex.client.queries) get_common_sources() (Neo4jClient method) get_common_targets() (Neo4jClient method) get_diseases_for_gene() (in module indra_cogex.client.queries) get_diseases_for_phenotype() (in module indra_cogex.client.queries) get_diseases_for_trial() (in module indra_cogex.client.queries) get_diseases_for_variant() (in module indra_cogex.client.queries) get_domains_for_gene() (in module indra_cogex.client.queries) get_drugs_for_indication() (in module indra_cogex.client.queries) get_drugs_for_sensitive_cell_line() (in module indra_cogex.client.queries) get_drugs_for_side_effect() (in module indra_cogex.client.queries) get_drugs_for_target() (in module indra_cogex.client.queries) get_drugs_for_targets() (in module indra_cogex.client.queries) get_drugs_for_trial() (in module indra_cogex.client.queries) get_edge_counter() (in module indra_cogex.client.queries) get_entity_to_regulators() (in module indra_cogex.client.enrichment.utils) get_entity_to_targets() (in module indra_cogex.client.enrichment.utils) get_enzyme_activities_for_gene() (in module indra_cogex.client.queries) get_evidences_for_mesh() (in module indra_cogex.client.queries) get_evidences_for_stmt_hash() (in module indra_cogex.client.queries) get_evidences_for_stmt_hashes() (in module indra_cogex.client.queries) get_genes_for_disease() (in module indra_cogex.client.queries) get_genes_for_domain() (in module indra_cogex.client.queries) get_genes_for_enzyme_activity() (in module indra_cogex.client.queries) get_genes_for_go_term() (in module indra_cogex.client.queries) get_genes_for_pathway() (in module indra_cogex.client.queries) get_genes_for_phenotype() (in module indra_cogex.client.queries) get_genes_for_variant() (in module indra_cogex.client.queries) get_genes_in_tissue() (in module indra_cogex.client.queries) get_go() (in module indra_cogex.client.enrichment.utils) get_go_terms_for_gene() (in module indra_cogex.client.queries) get_indications_for_drug() (in module indra_cogex.client.queries) get_journal_for_publication() (in module indra_cogex.client.queries) get_journals_for_publisher() (in module indra_cogex.client.queries) get_markers_for_cell_type() (in module indra_cogex.client.queries) get_mesh_ids_for_pmid() (in module indra_cogex.client.queries) get_mesh_ids_for_pmids() (in module indra_cogex.client.queries) get_mutated_genes_in_cell_line() (in module indra_cogex.client.queries) get_node_counter() (in module indra_cogex.client.queries) get_nodes() (BgeeProcessor method) (Processor method)

get_ontology_child_terms() (in module indra_cogex.client.queries) get_ontology_parent_terms() (in module indra_cogex.client.queries) get_patents_for_project() (in module indra_cogex.client.queries) get_pathways_for_gene() (in module indra_cogex.client.queries) get_phenotype_gene_sets() (in module indra_cogex.client.enrichment.utils) get_phenotypes_for_disease() (in module indra_cogex.client.queries) get_phenotypes_for_gene() (in module indra_cogex.client.queries) get_phenotypes_for_variant_gwas() (in module indra_cogex.client.queries) get_pmids_for_mesh() (in module indra_cogex.client.queries) get_predecessors() (Neo4jClient method) get_projects_for_clinical_trial() (in module indra_cogex.client.queries) get_projects_for_patent() (in module indra_cogex.client.queries) get_projects_for_publication() (in module indra_cogex.client.queries) get_property_from_relations() (Neo4jClient static method) get_publications_for_journal() (in module indra_cogex.client.queries) get_publications_for_project() (in module indra_cogex.client.queries) get_publisher_for_journal() (in module indra_cogex.client.queries) get_reactome() (in module indra_cogex.client.enrichment.utils) get_relations() (BgeeProcessor method) (Neo4jClient method) (Processor method) get_schema_graph() (in module indra_cogex.client.queries) get_sensitive_cell_lines_for_drug() (in module indra_cogex.client.queries) get_session() (Neo4jClient method) get_shared_pathways_for_genes() (in module indra_cogex.client.queries) get_side_effects_for_drug() (in module indra_cogex.client.queries) get_source_agents() (Neo4jClient method) get_source_relations() (Neo4jClient method) get_sources() (Neo4jClient method) get_statements() (in module indra_cogex.client.queries) get_stmts_for_mesh() (in module indra_cogex.client.queries) get_stmts_for_paper() (in module indra_cogex.client.queries) get_stmts_for_pmids() (in module indra_cogex.client.queries) get_stmts_for_stmt_hashes() (in module indra_cogex.client.queries) get_stmts_meta_for_stmt_hashes() (in module indra_cogex.client.queries) get_successors() (Neo4jClient method) get_target_agents() (Neo4jClient method) get_target_relations() (Neo4jClient method) get_targets() (Neo4jClient method) get_targets_for_drug() (in module indra_cogex.client.queries) get_targets_for_drugs() (in module indra_cogex.client.queries) get_tissues_for_gene() (in module indra_cogex.client.queries) get_trials_for_disease() (in module indra_cogex.client.queries) get_trials_for_drug() (in module indra_cogex.client.queries) get_variants_for_disease() (in module indra_cogex.client.queries) get_variants_for_gene() (in module indra_cogex.client.queries) get_variants_for_phenotype_gwas() (in module indra_cogex.client.queries) get_wikipathways() (in module indra_cogex.client.enrichment.utils) go_ora() (in module indra_cogex.client.enrichment.discrete) grounding() (Node method)

H

has_cna_in_cell_line() (in module indra_cogex.client.queries) has_enzyme_activity() (in module indra_cogex.client.queries) has_gene_disease_association() (in module indra_cogex.client.queries) has_phenotype() (in module indra_cogex.client.queries)

has_phenotype_gene() (in module indra_cogex.client.queries) has_relation() (Neo4jClient method) has_variant_disease_association() (in module indra_cogex.client.queries) has_variant_gene_association() (in module indra_cogex.client.queries) has_variant_phenotype_association() (in module indra_cogex.client.queries)

I

index_evidence_on_stmt_hash() (in module indra_cogex.indexing) index_indra_rel_on_stmt_hash() (in module indra_cogex.indexing) index_nodes_on_id() (in module indra_cogex.indexing) indra_cogex-indexing command line option --all --exist-ok --index-evidence-nodes --index-indra-relations --index-nodes indra_cogex.assembly module indra_cogex.client.enrichment.discrete module indra_cogex.client.enrichment.signed module indra_cogex.client.enrichment.utils module indra_cogex.client.neo4j_client module indra_cogex.client.queries module indra_cogex.client.subnetwork module indra_cogex.indexing module indra_cogex.representation module

indra_cogex.sources.bgee module indra_cogex.sources.processor module indra_cogex.sources.processor_util module indra_downstream_ora() (in module indra_cogex.client.enrichment.discrete) indra_mediated_subnetwork() (in module indra_cogex.client.subnetwork) indra_stmts_from_relations() (in module indra_cogex.representation) indra_subnetwork() (in module indra_cogex.client.subnetwork) indra_subnetwork_go() (in module indra_cogex.client.subnetwork) indra_subnetwork_relations() (in module indra_cogex.client.subnetwork) indra_subnetwork_tissue() (in module indra_cogex.client.subnetwork) indra_upstream_ora() (in module indra_cogex.client.enrichment.discrete) is_cell_line_sensitive_to_drug() (in module indra_cogex.client.queries) is_drug_target() (in module indra_cogex.client.queries) is_gene_in_pathway() (in module indra_cogex.client.queries) is_gene_in_tissue() (in module indra_cogex.client.queries) is_gene_mutated_in_cell_line() (in module indra_cogex.client.queries) is_go_term_for_gene() (in module indra_cogex.client.queries) is_journal_published_by() (in module indra_cogex.client.queries) is_marker_for_cell_type() (in module indra_cogex.client.queries) is_published_in_journal() (in module indra_cogex.client.queries) is_side_effect_for_drug() (in module indra_cogex.client.queries) isa_or_partof() (in module indra_cogex.client.queries)

M

main() (in module indra_cogex.client.enrichment.signed) module indra_cogex.assembly indra_cogex.client.enrichment.discrete indra_cogex.client.enrichment.signed indra_cogex.client.enrichment.utils indra_cogex.client.neo4j_client indra_cogex.client.queries indra_cogex.client.subnetwork indra_cogex.indexing indra_cogex.representation indra_cogex.sources.bgee indra_cogex.sources.processor indra_cogex.sources.processor_util

N

neo4j_to_node() (Neo4jClient static method) neo4j_to_relation() (Neo4jClient class method) neo4j_to_relations() (Neo4jClient static method) Neo4jClient (class in indra_cogex.client.neo4j_client)

Node (class in indra_cogex.representation) node_to_agent() (Neo4jClient static method) NodeAssembler (class in indra_cogex.assembly) norm_id() (in module indra_cogex.representation)

P

phenotype_ora() (in module indra_cogex.client.enrichment.discrete) ping() (Neo4jClient method)

process_identifier() (in module indra_cogex.client.neo4j_client) Processor (class in indra_cogex.sources.processor)

Q

query_dict() (Neo4jClient method) query_dict_value_json() (Neo4jClient method)

query_nodes() (Neo4jClient method) query_relations() (Neo4jClient method) query_tx() (Neo4jClient method)

R

reactome_ora() (in module indra_cogex.client.enrichment.discrete)

Relation (class in indra_cogex.representation) reverse_causal_reasoning() (in module indra_cogex.client.enrichment.signed)

S

session (Neo4jClient attribute)

standardized() (Node class method)

T

to_json() (Node method) (Relation method)

U

UnknownTypeError

W

wikipathways_ora() (in module indra_cogex.client.enrichment.discrete)