INDRA modules reference¶
- INDRA Statements (
indra.statements
)- General information and statement types
- 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
)
- 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
)
- 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
) - 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
)
- identifiers.org mappings and URLs (
- 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
)
- Pubmed client (
- INDRA Ontologies (
indra.ontology
) - 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
) - Site curation and mapping (
indra.preassembler.sitemapper
)
- Preassembler (
- Belief prediction (
indra.belief
) - Mechanism Linker (
indra.mechlinker
) - Assemblers of model output (
indra.assemblers
)- Executable PySB models (
indra.assemblers.pysb.assembler
) - 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
)
- 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
) - 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
)
- Run assembly components in a pipeline (
- Resource files
- Util (
indra.util
)