INDRA CoGEx modules reference

• INDRA CoGEx Knowledge Assembly (indra_cogex.assembly)
  • NodeAssembler
    • NodeAssembler.add_nodes()
    • NodeAssembler.assemble_nodes()
    • NodeAssembler.get_aggregate_node()
• INDRA CoGEx Client
  • Enrichment Analysis (indra_cogex.client.enrichment)
    • Continuous Gene Enrichment Analysis (indra_cogex.client.enrichment.continuous)
    • Discrete Gene Enrichment Analysis (indra_cogex.client.enrichment.discrete)
      • EXAMPLE_GENE_IDS
      • go_ora()
      • indra_downstream_ora()
      • indra_upstream_ora()
      • phenotype_ora()
      • reactome_ora()
      • wikipathways_ora()
    • Signed Gene Enrichment Analysis (indra_cogex.client.enrichment.signed)
      • main()
      • reverse_causal_reasoning()
    • Gene Enrichment Analysis Utilities (indra_cogex.client.enrichment.utils)
      • collect_gene_sets()
      • get_entity_to_regulators()
      • get_entity_to_targets()
      • get_go()
      • get_phenotype_gene_sets()
      • get_reactome()
      • get_wikipathways()
  • Neo4j Client (indra_cogex.client.neo4j_client)
    • Neo4jClient
      • Neo4jClient.add_node()
      • Neo4jClient.add_nodes()
      • Neo4jClient.add_relations()
      • Neo4jClient.close_session()
      • Neo4jClient.create_nodes()
      • Neo4jClient.create_single_property_node_index()
      • Neo4jClient.create_single_property_relationship_index()
      • Neo4jClient.create_tx()
      • Neo4jClient.delete_all()
      • Neo4jClient.get_all_relations()
      • Neo4jClient.get_common_sources()
      • Neo4jClient.get_common_targets()
      • Neo4jClient.get_predecessors()
      • Neo4jClient.get_property_from_relations()
      • Neo4jClient.get_relations()
      • Neo4jClient.get_session()
      • Neo4jClient.get_source_agents()
      • Neo4jClient.get_source_relations()
      • Neo4jClient.get_sources()
      • Neo4jClient.get_successors()
      • Neo4jClient.get_target_agents()
      • Neo4jClient.get_target_relations()
      • Neo4jClient.get_targets()
      • Neo4jClient.has_relation()
      • Neo4jClient.neo4j_to_node()
      • Neo4jClient.neo4j_to_relation()
      • Neo4jClient.neo4j_to_relations()
      • Neo4jClient.node_to_agent()
      • Neo4jClient.ping()
      • Neo4jClient.query_dict()
      • Neo4jClient.query_dict_value_json()
      • Neo4jClient.query_nodes()
      • Neo4jClient.query_relations()
      • Neo4jClient.query_tx()
      • Neo4jClient.session
    • autoclient()
    • process_identifier()
  • The INDRA CoGEx Neo4j Client (indra_cogex.client.queries)
    • drug_has_indication()
    • gene_has_codependency()
    • gene_has_domain()
    • get_cell_lines_with_cna()
    • get_cell_lines_with_mutation()
    • get_cell_types_for_marker()
    • get_clinical_trials_for_project()
    • get_cna_genes_in_cell_line()
    • get_codependents_for_gene()
    • get_diseases_for_gene()
    • get_diseases_for_phenotype()
    • get_diseases_for_trial()
    • get_diseases_for_variant()
    • get_domains_for_gene()
    • get_drugs_for_indication()
    • get_drugs_for_sensitive_cell_line()
    • get_drugs_for_side_effect()
    • get_drugs_for_target()
    • get_drugs_for_targets()
    • get_drugs_for_trial()
    • get_edge_counter()
    • get_enzyme_activities_for_gene()
    • get_evidences_for_mesh()
    • get_evidences_for_stmt_hash()
    • get_evidences_for_stmt_hashes()
    • get_genes_for_disease()
    • get_genes_for_domain()
    • get_genes_for_enzyme_activity()
    • get_genes_for_go_term()
    • get_genes_for_pathway()
    • get_genes_for_phenotype()
    • get_genes_for_variant()
    • get_genes_in_tissue()
    • get_go_terms_for_gene()
    • get_indications_for_drug()
    • get_journal_for_publication()
    • get_journals_for_publisher()
    • get_markers_for_cell_type()
    • get_mesh_ids_for_pmid()
    • get_mesh_ids_for_pmids()
    • get_mutated_genes_in_cell_line()
    • get_node_counter()
    • get_ontology_child_terms()
    • get_ontology_parent_terms()
    • get_patents_for_project()
    • get_pathways_for_gene()
    • get_phenotypes_for_disease()
    • get_phenotypes_for_gene()
    • get_phenotypes_for_variant_gwas()
    • get_pmids_for_mesh()
    • get_projects_for_clinical_trial()
    • get_projects_for_patent()
    • get_projects_for_publication()
    • get_publications_for_journal()
    • get_publications_for_project()
    • get_publisher_for_journal()
    • get_schema_graph()
    • get_sensitive_cell_lines_for_drug()
    • get_shared_pathways_for_genes()
    • get_side_effects_for_drug()
    • get_statements()
    • get_stmts_for_mesh()
    • get_stmts_for_paper()
    • get_stmts_for_pmids()
    • get_stmts_for_stmt_hashes()
    • get_stmts_meta_for_stmt_hashes()
    • get_targets_for_drug()
    • get_targets_for_drugs()
    • get_tissues_for_gene()
    • get_trials_for_disease()
    • get_trials_for_drug()
    • get_variants_for_disease()
    • get_variants_for_gene()
    • get_variants_for_phenotype_gwas()
    • has_cna_in_cell_line()
    • has_enzyme_activity()
    • has_gene_disease_association()
    • has_phenotype()
    • has_phenotype_gene()
    • has_variant_disease_association()
    • has_variant_gene_association()
    • has_variant_phenotype_association()
    • is_cell_line_sensitive_to_drug()
    • is_drug_target()
    • is_gene_in_pathway()
    • is_gene_in_tissue()
    • is_gene_mutated_in_cell_line()
    • is_go_term_for_gene()
    • is_journal_published_by()
    • is_marker_for_cell_type()
    • is_published_in_journal()
    • is_side_effect_for_drug()
    • isa_or_partof()
  • Subnetwork Client (indra_cogex.client.subnetwork)
    • indra_mediated_subnetwork()
    • indra_subnetwork()
    • indra_subnetwork_go()
    • indra_subnetwork_relations()
    • indra_subnetwork_tissue()
• Indexing of The Database
  • Indexing The Database (indra_cogex.indexing)
    • index_evidence_on_stmt_hash()
    • index_indra_rel_on_stmt_hash()
    • index_nodes_on_id()
  • Indexing CLI (indra_cogex.indexing.cli)
    • indra_cogex indexing
• INDRA CoGEx Sources
  • Source CLI (indra_cogex.sources.cli)
  • INDRA CoGEx Sources Processor (indra_cogex.sources.processor)
    • Processor
      • Processor.cli()
      • Processor.dump()
      • Processor.get_cli()
      • Processor.get_nodes()
      • Processor.get_relations()
  • Data Validation (indra_cogex.sources.processor_util)
    • DataTypeError
    • UnknownTypeError
    • data_validator()
  • Bgee Processor (indra_cogex.sources.bgee)
    • BgeeProcessor
      • BgeeProcessor.get_nodes()
      • BgeeProcessor.get_relations()
  • cBioPortal Processor (indra_cogex.sources.cbioportal)
  • CellMarker Processor (indra_cogex.sources.cellmarker)
  • chembl Processor (indra_cogex.sources.chembl)
  • clinicaltrials Processor (indra_cogex.sources.clinicaltrials)
  • DisGeNet Processor (indra_cogex.sources.disgenet)
  • HGNCEnzyme Processor (indra_cogex.sources.ec)
  • goa Processor (indra_cogex.sources.goa)
  • GWAS Processor (indra_cogex.sources.gwas)
  • HPOA Processor (indra_cogex.sources.hpoa)
  • INDRA DB Processor (indra_cogex.sources.indra_db)
  • INDRA Ontology Processor (indra_cogex.sources.indra_ontology)
  • InterPro Processor (indra_cogex.sources.interpro)
  • NIH RePORTER Processor (indra_cogex.sources.nih_reporter)
  • Odinson Processor (indra_cogex.sources.odinson)
    • Odinson Client (indra_cogex.sources.odinson.client)
    • Odinson Document (indra_cogex.sources.odinson.document)
    • Odinson Grammar (indra_cogex.sources.odinson.grammars)
  • Pathways Processor (indra_cogex.sources.pathways)
  • PubMed Processor (indra_cogex.sources.pubmed)
  • Sider Processor (indra_cogex.sources.sider)
  • WikiData Processor (indra_cogex.sources.wikidata)
• INDRA CoGEx Representation (indra_cogex.representation)
  • Node
    • Node.grounding()
    • Node.standardized()
    • Node.to_json()
  • Relation
    • Relation.to_json()
  • generate_paper_clause()
  • indra_stmts_from_relations()
  • norm_id()