INDRA modules reference

• INDRA Statements (indra.statements)
  • General information and statement types
    • Grounding and DB references
    • JSON serialization of INDRA Statements
  • 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)
  • Resource access (indra.statements.resources)
  • Utils (indra.statements.util)
• 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)
    • TRIPS (indra.sources.trips)
      • TRIPS API (indra.sources.trips.api)
      • TRIPS Processor (indra.sources.trips.processor)
      • TRIPS Web-service Client (indra.sources.trips.client)
      • TRIPS/DRUM Local Reader (indra.sources.trips.drum_reader)
    • Sparser (indra.sources.sparser)
      • Sparser API (indra.sources.sparser.api)
    • MedScan (indra.sources.medscan)
      • MedScan API (indra.sources.medscan.api)
      • MedScan Processor (indra.sources.medscan.processor)
    • TEES (indra.sources.tees)
      • TEES API (indra.sources.tees.api)
      • TEES Processor (indra.sources.tees.processor)
    • ISI (indra.sources.isi)
      • ISI API (indra.sources.isi.api)
      • ISI Processor (indra.sources.isi.processor)
    • Geneways (indra.sources.geneways)
      • Geneways API (indra.sources.geneways.api)
      • Geneways Processor (indra.sources.geneways.processor)
    • RLIMS-P (indra.sources.rlimsp)
      • RLIMS-P API (indra.sources.rlimsp.api)
      • RLIMSP-P Processor (indra.sources.rlimsp.processor)
    • 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)
    • GNBR (indra.sources.gnbr)
      • GNBR API (indra.sources.gnbr.api)
      • GNBR Processor (indra.sources.gnbr.processor)
  • Molecular Pathway Databases
    • BEL (indra.sources.bel)
      • BEL API (indra.sources.bel.api)
      • PyBEL Processor (indra.sources.bel.processor)
    • BioPAX (indra.sources.biopax)
      • BioPAX API (indra.sources.biopax.api)
      • BioPAX Processor (indra.sources.biopax.processor)
    • SIGNOR (indra.sources.signor)
      • SIGNOR API (indra.sources.signor.api)
      • SIGNOR Processor (indra.sources.signor.processor)
    • BioGrid (indra.sources.biogrid)
    • Human Protein Reference Database (indra.sources.hprd)
      • HPRD API (indra.sources.hprd.api)
      • HPRD Processor (indra.sources.hprd.processor)
    • TRRUST Database (indra.sources.trrust)
      • TRRUST API (indra.sources.trrust.api)
      • TRRUST Processor (indra.sources.trrust.processor)
    • Phospho.ELM (indra.sources.phosphoelm)
      • Phospho.ELM API (indra.sources.phosphoelm.api)
      • Phospho.ELM Processor (indra.sources.phosphoelm.processor)
    • VirHostNet (indra.sources.virhostnet)
      • VirHostNet API (indra.sources.virhostnet.api)
      • VirHostNet Processor (indra.sources.virhostnet.processor)
    • OmniPath (indra.sources.omnipath)
      • OmniPath API (indra.sources.omnipath.api)
      • OmniPath Processor (indra.sources.omnipath.processor)
    • UbiBrowser Database (indra.sources.ubibrowser)
      • UbiBrowser API (indra.sources.ubibrowser.api)
      • UbiBrowser Processor (indra.sources.ubibrowser.processor)
    • ACSN Database (indra.sources.acsn)
      • ACSN API (indra.sources.acsn.api)
      • ACSN Processor (indra.sources.acsn.processor)
  • Chemical Information Databases
    • CTD (indra.sources.ctd)
      • CTD API (indra.sources.ctd.api)
      • CTD Processor (indra.sources.ctd.processor)
    • DrugBank (indra.sources.drugbank)
      • DrugBank API (indra.sources.drugbank.api)
      • DrugBank Processor (indra.sources.drugbank.processor)
    • Drug Gene Interaction (DGI) Database (indra.sources.dgi)
      • DGI API (indra.sources.dgi.api)
      • DGI Processor (indra.sources.dgi.processor)
    • Target Affinity Spectrum (indra.sources.tas)
      • TAS API (indra.sources.tas.api)
      • TAS Processor (indra.sources.tas.processor)
    • CRoG (indra.sources.crog)
      • CRoG API (indra.sources.crog.api)
      • CRoG Processor (indra.sources.crog.processor)
    • CREEDS (indra.sources.creeds)
      • CREEDS API (indra.sources.creeds.api)
      • CREEDS Processor (indra.sources.creeds.processor)
  • Custom Knowledge Bases
    • NDEx CX API (indra.sources.ndex_cx.api)
      • NDEx CX Processor (indra.sources.ndex_cx.processor)
    • INDRA Database REST Client (indra.sources.indra_db_rest)
      • API to the INDRA Database REST Service (indra.sources.indra_db_rest.api)
      • Advanced Query Construction (indra.sources.indra_db_rest.query)
      • INDRA Database REST Processor (indra.sources.indra_db_rest.processor)
    • Hypothes.is (indra.sources.hypothesis)
      • Curation tutorial
      • Hypothes.is API (indra.sources.hypothesis.api)
      • Hypothes.is Processor (indra.sources.hypothesis.processor)
    • Biofactoid (indra.sources.biofactoid)
      • Biofactoid API (indra.sources.biofactoid.api)
      • Biofactoid Processor (indra.sources.biofactoid.processor)
    • MINERVA (indra.sources.minerva)
      • MINERVA Source API (indra.sources.minerva.api)
      • MINERVA SIF Processor (indra.sources.minerva.processor)
  • Utilities
• Database clients (indra.databases)
  • identifiers.org mappings and URLs (indra.databases.identifiers)
  • HGNC client (indra.databases.hgnc_client)
  • 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)
  • 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)
  • OBO client (indra.databases.obo_client)
  • OWL client (indra.databases.owl_client)
  • Biolookup client (indra.databases.biolookup_client)
• Literature clients (indra.literature)
  • Pubmed client (indra.literature.pubmed_client)
  • 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)
  • Grounding and name standardization (indra.ontology.standardize)
  • INDRA BioOntology (indra.ontology.bio_ontology)
    • Generating and caching the BioOntology
  • Virtual Ontology (indra.ontology.virtual_ontology)
  • Ontology web service (indra.ontology.app)
• Preassembly (indra.preassembler)
  • Preassembler (indra.preassembler)
  • Refinement filter classes and functions (indra.preassembler.refinement)
  • Custom preassembly functions (indra.preassembler.custom_preassembly)
  • Entity grounding mapping and standardization (indra.preassembler.grounding_mapper)
    • Grounding mapping
    • Disambiguation with machine-learned models
    • Gilda grounding functions
    • Analysis scripts for grounding
  • Site curation and mapping (indra.preassembler.sitemapper)
• Belief prediction (indra.belief)
  • Belief Engine API (indra.belief)
  • Belief prediction with sklearn models (indra.belief.skl)
• Mechanism Linker (indra.mechlinker)
• Assemblers of model output (indra.assemblers)
  • Executable PySB models (indra.assemblers.pysb.assembler)
    • PySB Assembler (indra.assemblers.pysb.assembler)
    • 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)
  • Cytoscape networks (indra.assemblers.cx.assembler)
  • Natural language (indra.assemblers.english.assembler)
  • Node-edge graphs (indra.assemblers.graph.assembler)
  • 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)
  • PyBEL graphs (indra.assemblers.pybel.assembler)
  • Kami models (indra.assemblers.kami.assembler)
  • IndraNet Graphs (indra.assemblers.indranet)
• 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)
  • Path finding algorithms for explanation (indra.explanation.pathfinding)
    • Path finding functions (indra.explanation.pathfinding.pathfinding)
    • Path finding utilities (indra.explanation.pathfinding.util)
  • Reporting explanations (indra.explanation.reporting)
• Assembly Pipeline (indra.pipeline)
• Tools (indra.tools)
  • Run assembly components in a pipeline (indra.tools.assemble_corpus)
  • Fix common invalidities in Statements (indra.tools.fix_invalidities)
  • 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)
  • The RAS Machine (indra.tools.machine)
    • Prerequisites
    • Starting a New Model
    • Setting Up Search Terms
    • Extending a Model
• Resource files
• Util (indra.util)
  • Statement presentation (indra.util.statement_presentation)
    • Vocabulary
    • Simple Example
    • Advanced Example
    • Class Overview
  • 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)