INDRA modules reference
- INDRA Statements (
indra.statements)- General information and statement types
- Grounding and DB references
- JSON serialization of INDRA Statements
AcetylationActivationActiveFormActivityConditionAddModificationAgentAssociationAutophosphorylationBioContextBoundConditionComplexConceptContextConversionDeacetylationDecreaseAmountDefarnesylationDegeranylgeranylationDeglycosylationDehydroxylationDemethylationDemyristoylationDepalmitoylationDephosphorylationDeribosylationDesumoylationDeubiquitinationEventEvidenceFarnesylationGapGefGeranylgeranylationGlycosylationGtpActivationHasActivityHydroxylationIncreaseAmountInfluenceInhibitionInputErrorInvalidLocationErrorInvalidResidueErrorMethylationMigrationModConditionModificationMovementContextMutConditionMyristoylationNotAStatementNamePalmitoylationPhosphorylationQualitativeDeltaQuantitativeStateRefContextRegulateActivityRegulateAmountRemoveModificationRibosylationSelfModificationStatementSumoylationTimeContextTranslocationTransphosphorylationUbiquitinationUnresolvedUnresolvedUuidErrorWorldContextdraw_stmt_graph()get_all_descendants()get_statement_by_name()get_unresolved_support_uuids()get_valid_residue()make_hash()make_statement_camel()mk_str()pretty_print_stmts()print_stmt_summary()set_pretty_print_max_width()stmt_from_json()stmt_from_json_str()stmt_type()stmts_from_json()stmts_from_json_file()stmts_to_json()stmts_to_json_file()
- Agents (
indra.statements.agent) - Concepts (
indra.statements.concept) - Evidence (
indra.statements.evidence) - Context (
indra.statements.context) - Input/output, serialization (
indra.statements.io) - Validation (
indra.statements.validate)BioregistryValidatorIdentifiersValidatorInvalidAgentInvalidContextInvalidIdentifierInvalidStatementInvalidTextRefsMissingIdentifierUnknownIdentifierUnknownNamespaceassert_valid_agent()assert_valid_bio_context()assert_valid_context()assert_valid_db_refs()assert_valid_evidence()assert_valid_id()assert_valid_ns()assert_valid_pmid_text_refs()assert_valid_statement()assert_valid_statement_semantics()assert_valid_statements()assert_valid_text_refs()print_validation_report()validate_agent()validate_db_refs()validate_evidence()validate_id()validate_ns()validate_statement()validate_text_refs()
- Resource access (
indra.statements.resources) - Utils (
indra.statements.util)
- General information and statement types
- Processors for knowledge input (
indra.sources)- Reading Systems
- REACH (
indra.sources.reach)- 1. INDRA communicating with a locally running REACH Server (
indra.sources.reach.api) - 2. INDRA communicating with the UA REACH Server (
indra.sources.reach.api) - 3. INDRA using a REACH JAR through a Python-Java bridge (
indra.sources.reach.reader) - 4. Use REACH separately to produce output files and then process those with INDRA
- REACH API (
indra.sources.reach.api) - REACH Processor (
indra.sources.reach.processor) - REACH reader (
indra.sources.reach.reader)
- 1. INDRA communicating with a locally running REACH Server (
- TRIPS (
indra.sources.trips) - Sparser (
indra.sources.sparser) - MedScan (
indra.sources.medscan) - TEES (
indra.sources.tees) - ISI (
indra.sources.isi) - Geneways (
indra.sources.geneways) - RLIMS-P (
indra.sources.rlimsp) - Eidos (
indra.sources.eidos)- 1. INDRA communicating with a separately running Eidos webapp (
indra.sources.eidos.client) - 2. INDRA using an Eidos JAR directly through a Python-Java bridge (
indra.sources.eidos.reader) - 3. INDRA using a Flask sever wrapping an Eidos JAR in a separate process (
indra.sources.eidos.server) - 4. INDRA calling the Eidos CLI using java through the command line (
indra.sources.eidos.cli) - 5. Use Eidos separately to produce output files and then process those with INDRA
- Eidos API (
indra.sources.eidos.api) - Eidos Processor (
indra.sources.eidos.processor) - Eidos Bio Processor (
indra.sources.eidos.bio_processor) - Eidos Client (
indra.sources.eidos.client) - Eidos Reader (
indra.sources.eidos.reader) - Eidos Webserver (
indra.sources.eidos.server) - Eidos CLI (
indra.sources.eidos.cli)
- 1. INDRA communicating with a separately running Eidos webapp (
- GNBR (
indra.sources.gnbr) - SemRep (
indra.sources.semrep)
- REACH (
- Molecular Pathway Databases
- BEL (
indra.sources.bel) - BioPAX (
indra.sources.biopax) - SIGNOR (
indra.sources.signor) - BioGrid (
indra.sources.biogrid) - Human Protein Reference Database (
indra.sources.hprd) - TRRUST Database (
indra.sources.trrust) - Phospho.ELM (
indra.sources.phosphoelm) - VirHostNet (
indra.sources.virhostnet) - OmniPath (
indra.sources.omnipath) - UbiBrowser Database (
indra.sources.ubibrowser) - ACSN Database (
indra.sources.acsn)
- BEL (
- Chemical Information Databases
- Custom Knowledge Bases
- Utilities
- Reading Systems
- Database clients (
indra.databases)- identifiers.org mappings and URLs (
indra.databases.identifiers) - Bioregistry mappings and URLs (
indra.databases.bioregistry_client) - HGNC client (
indra.databases.hgnc_client)get_current_hgnc_id()get_ensembl_id()get_entrez_id()get_enzymes()get_gene_type()get_hgnc_entry()get_hgnc_from_ensembl()get_hgnc_from_entrez()get_hgnc_from_mouse()get_hgnc_from_rat()get_hgnc_id()get_hgnc_id_from_mgi_name()get_hgnc_name()get_hgnc_name_from_mgi_name()get_hgncs_from_enzyme()get_mouse_id()get_rat_id()get_uniprot_id()is_kinase()is_phosphatase()is_transcription_factor()
- UniProt client (
indra.databases.uniprot_client) - ChEBI client (
indra.databases.chebi_client) - Cell type context client (
indra.databases.context_client) - NDEx client (
indra.databases.ndex_client) - cBio portal client (
indra.databases.cbio_client) - ChEMBL client (
indra.databases.chembl_client) - LINCS client (
indra.databases.lincs_client) - MeSH client (
indra.databases.mesh_client)get_db_mapping()get_go_id()get_mesh_id_from_db_id()get_mesh_id_from_go_id()get_mesh_id_name()get_mesh_id_name_from_web()get_mesh_name()get_mesh_name_from_web()get_mesh_tree_numbers()get_mesh_tree_numbers_from_web()get_primary_mappings()has_tree_prefix()is_disease()is_enzyme()is_molecular()is_protein()
- GO client (
indra.databases.go_client) - PubChem client (
indra.databases.pubchem_client) - miRBase client (
indra.databases.mirbase_client) - Experimental Factor Ontology (EFO) client (
indra.databases.efo_client) - Human Phenotype Ontology (HP) client (
indra.databases.hp_client) - Disease Ontology (DOID) client (
indra.databases.doid_client) - Infectious Disease Ontology client (
indra.databases.ido_client) - Taxonomy client (
indra.databases.taxonomy_client) - DrugBank client (
indra.databases.drugbank_client) - Enyzme Class client (
indra.databases.ec_client) - OBO client (
indra.databases.obo_client) - OWL client (
indra.databases.owl_client) - Biolookup client (
indra.databases.biolookup_client) - MONDO client (
indra.databases.mondo_client) - MGI client (
indra.databases.mgi_client) - RGD client (
indra.databases.rgd_client)
- identifiers.org mappings and URLs (
- Literature clients (
indra.literature)get_full_text()id_lookup()- Pubmed client (
indra.literature.pubmed_client)ensure_xml_files()expand_pagination()generate_retractions_file()get_abstract()get_all_ids()get_article_xml()get_full_xml()get_id_count()get_ids()get_ids_for_gene()get_ids_for_mesh()get_issn_info()get_issns_for_journal()get_mesh_annotations()get_metadata_for_all_ids()get_metadata_for_ids()get_metadata_from_xml_tree()get_publication_types()get_substance_annotations()get_title()is_retracted()
- Pubmed Central client (
indra.literature.pmc_client) - bioRxiv client (
indra.literature.biorxiv_client) - CrossRef client (
indra.literature.crossref_client) - COCI client (
indra.literature.coci_client) - Elsevier client (
indra.literature.elsevier_client) - NewsAPI client (
indra.literature.newsapi_client) - Adeft Tools (
indra.literature.adeft_tools)
- INDRA Ontologies (
indra.ontology)- IndraOntology (
indra.ontology)IndraOntologyIndraOntology.nameIndraOntology.versionIndraOntology.get_children()IndraOntology.get_id()IndraOntology.get_id_from_name()IndraOntology.get_mappings()IndraOntology.get_name()IndraOntology.get_node_property()IndraOntology.get_ns()IndraOntology.get_ns_id()IndraOntology.get_parents()IndraOntology.get_polarity()IndraOntology.get_replacement()IndraOntology.get_top_level_parents()IndraOntology.get_type()IndraOntology.initialize()IndraOntology.is_opposite()IndraOntology.isa()IndraOntology.isa_or_partof()IndraOntology.isrel()IndraOntology.label()IndraOntology.map_to()IndraOntology.maps_to()IndraOntology.nameIndraOntology.nodes_from_suffix()IndraOntology.partof()IndraOntology.reverse_label()
- Grounding and name standardization (
indra.ontology.standardize) - INDRA BioOntology (
indra.ontology.bio_ontology) - Virtual Ontology (
indra.ontology.virtual_ontology) - Ontology web service (
indra.ontology.app)
- IndraOntology (
- Preassembly (
indra.preassembler)- Preassembler (
indra.preassembler)PreassemblerPreassembler.stmtsPreassembler.unique_stmtsPreassembler.related_stmtsPreassembler.ontologyPreassembler.add_statements()Preassembler.combine_duplicate_stmts()Preassembler.combine_duplicates()Preassembler.combine_related()Preassembler.find_contradicts()Preassembler.normalize_equivalences()Preassembler.normalize_opposites()
find_refinements_for_statement()flatten_evidence()flatten_stmts()render_stmt_graph()
- Refinement filter classes and functions (
indra.preassembler.refinement) - Custom preassembly functions (
indra.preassembler.custom_preassembly) - Entity grounding mapping and standardization (
indra.preassembler.grounding_mapper) - Site curation and mapping (
indra.preassembler.sitemapper)
- Preassembler (
- Belief prediction (
indra.belief)- Belief Engine API (
indra.belief)BayesianScorerBeliefEngineBeliefScorerSimpleScorerassert_no_cycle()build_refinements_graph()check_extra_evidence()evidence_random_noise_prior()extend_refinements_graph()get_ev_for_stmts_from_hashes()get_ev_for_stmts_from_supports()get_ranked_stmts()get_stmt_evidence()sample_statements()tag_evidence_subtype()
- Belief prediction with sklearn models (
indra.belief.skl)
- Belief Engine API (
- Mechanism Linker (
indra.mechlinker)AgentStateBaseAgentBaseAgentSetLinkedStatementMechLinkerMechLinker.add_statements()MechLinker.gather_explicit_activities()MechLinker.gather_implicit_activities()MechLinker.infer_activations()MechLinker.infer_active_forms()MechLinker.infer_complexes()MechLinker.infer_modifications()MechLinker.reduce_activities()MechLinker.replace_activations()MechLinker.replace_complexes()MechLinker.require_active_forms()
- Assemblers of model output (
indra.assemblers)- Executable PySB models (
indra.assemblers.pysb.assembler)- PySB Assembler (
indra.assemblers.pysb.assembler)ParamPolicyPysbAssemblerUnknownPolicyErroradd_rule_to_model()complex_monomers_default()complex_monomers_one_step()get_agent_rule_str()get_annotation()get_create_parameter()get_grounded_agents()get_monomer_pattern()get_site_pattern()get_uncond_agent()grounded_monomer_patterns()parse_identifiers_url()set_base_initial_condition()set_extended_initial_condition()
- PySB PreAssembler (
indra.assemblers.pysb.preassembler) - Base Agents (
indra.assemblers.pysb.base_agents) - A utility to get graphs from kappa (
indra.assemblers.pysb.kappa_util)
- PySB Assembler (
- Cytoscape networks (
indra.assemblers.cx.assembler) - Natural language (
indra.assemblers.english.assembler) - Node-edge graphs (
indra.assemblers.graph.assembler)GraphAssemblerGraphAssembler.statementsGraphAssembler.graphGraphAssembler.existing_nodesGraphAssembler.existing_edgesGraphAssembler.graph_propertiesGraphAssembler.node_propertiesGraphAssembler.edge_propertiesGraphAssembler.add_statements()GraphAssembler.get_string()GraphAssembler.make_model()GraphAssembler.save_dot()GraphAssembler.save_pdf()
- SIF / Boolean networks (
indra.assemblers.sif.assembler) - MITRE “index cards” (
indra.assemblers.index_card.assembler) - SBGN output (
indra.assemblers.sbgn.assembler) - Cytoscape JS networks (
indra.assemblers.cyjs.assembler) - Tabular output (
indra.assemblers.tsv.assembler) - HTML browsing and curation (
indra.assemblers.html.assembler) - BMI wrapper for PySB-assembled models (
indra.assemblers.pysb.bmi_wrapper)BMIModelBMIModel.export_into_python()BMIModel.finalize()BMIModel.get_attribute()BMIModel.get_current_time()BMIModel.get_input_var_names()BMIModel.get_output_var_names()BMIModel.get_start_time()BMIModel.get_status()BMIModel.get_time_step()BMIModel.get_time_units()BMIModel.get_value()BMIModel.get_values()BMIModel.get_var_name()BMIModel.get_var_rank()BMIModel.get_var_type()BMIModel.get_var_units()BMIModel.initialize()BMIModel.make_repository_component()BMIModel.set_value()BMIModel.set_values()BMIModel.update()
- PyBEL graphs (
indra.assemblers.pybel.assembler) - Kami models (
indra.assemblers.kami.assembler) - IndraNet Graphs (
indra.assemblers.indranet)
- Executable PySB models (
- Explanation (
indra.explanation)- Check whether a model satisfies a property (
indra.explanation.model_checker)- Shared Model Checking Functionality (
indra.explanation.model_checker.model_checker) - Checking PySB model (
indra.explanation.model_checker.pysb) - Checking Signed Graph (
indra.explanation.model_checker.signed_graph) - Checking Unsigned Graph (
indra.explanation.model_checker.unsigned_graph) - Checking PyBEL Graph (
indra.explanation.model_checker.pybel)
- Shared Model Checking Functionality (
- Path finding algorithms for explanation (
indra.explanation.pathfinding) - Reporting explanations (
indra.explanation.reporting)
- Check whether a model satisfies a property (
- Assembly Pipeline (
indra.pipeline)AssemblyPipelineAssemblyPipeline.append()AssemblyPipeline.create_new_step()AssemblyPipeline.from_json_file()AssemblyPipeline.get_argument_value()AssemblyPipeline.get_function_from_name()AssemblyPipeline.get_function_parameters()AssemblyPipeline.insert()AssemblyPipeline.is_function()AssemblyPipeline.run()AssemblyPipeline.run_function()AssemblyPipeline.run_simple_function()AssemblyPipeline.to_json_file()
NotRegisteredFunctionErrorRunnableArgumentjsonify_arg_input()ExistingFunctionErrorregister_pipeline()
- Tools (
indra.tools)- Run assembly components in a pipeline (
indra.tools.assemble_corpus)align_statements()dump_statements()dump_stmt_strings()expand_families()filter_belief()filter_by_curation()filter_by_db_refs()filter_by_type()filter_complexes_by_size()filter_concept_names()filter_direct()filter_enzyme_kinase()filter_evidence_source()filter_gene_list()filter_genes_only()filter_grounded_only()filter_human_only()filter_inconsequential()filter_inconsequential_acts()filter_inconsequential_mods()filter_mod_nokinase()filter_mutation_status()filter_no_hypothesis()filter_no_negated()filter_retracted_sources()filter_top_level()filter_transcription_factor()filter_uuid_list()fix_invalidities()load_statements()map_db_refs()map_grounding()map_sequence()merge_groundings()normalize_active_forms()reduce_activities()rename_db_ref()run_mechlinker()run_preassembly()run_preassembly_duplicate()run_preassembly_related()standardize_names_groundings()strip_agent_context()strip_supports()
- Fix common invalidities in Statements (
indra.tools.fix_invalidities) - Analyze ontology graph for issues (
indra.tools.analyze_ontology) - Annotate websites with INDRA through hypothes.is (
indra.tools.hypothesis_annotator) - Build a network from a gene list (
indra.tools.gene_network) - Build an executable model from a fragment of a large network (
indra.tools.executable_subnetwork) - Build a model incrementally over time (
indra.tools.incremental_model)IncrementalModelIncrementalModel.stmtsIncrementalModel.assembled_stmtsIncrementalModel.add_statements()IncrementalModel.get_model_agents()IncrementalModel.get_statements()IncrementalModel.get_statements_noprior()IncrementalModel.get_statements_prior()IncrementalModel.load_prior()IncrementalModel.preassemble()IncrementalModel.save()
- The RAS Machine (
indra.tools.machine)
- Run assembly components in a pipeline (
- Resource files
- Util (
indra.util)- Statement presentation (
indra.util.statement_presentation)- Vocabulary
- Simple Example
- Advanced Example
- Class Overview
AggregatorMetaAveAggregatorBasicAggregatorMaxAggregatorMultiAggregatorStmtGroupStmtStatSumAggregatorall_sourcesavailable_sources_src_counts()available_sources_stmts()db_sourcesgroup_and_sort_statements()internal_source_mappingsmake_standard_stats()make_stmt_from_relation_key()make_string_from_relation_key()make_top_level_label_from_names_key()reader_sourcesreverse_source_mappingsstandardize_counts()stmt_to_english()
- Utilities for using AWS (
indra.util.aws) - A utility to get the INDRA version (
indra.util.get_version) - Define NestedDict (
indra.util.nested_dict) - Shorthands for plot formatting (
indra.util.plot_formatting)
- Statement presentation (