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INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

Domains

biomedical, systems biology

Infores ID

Unknown

FAIRsharing ID

Unknown

Product Summary

Contacts

Sorger Lab, Harvard Medical School

Github: sorgerlab

URL: https://indra.readthedocs.io/en/latest/

Gyori Lab, Northeastern University

URL: https://gyorilab.github.io/

Products

From this Resource

ID	Name	URL	Category	Format	Description
indra.discovery	INDRA Biomedical Discovery Engine	discovery.indra.bio	GraphicalInterface	http	Web interface for the INDRA Biomedica...
indra.api.cogex	INDRA CoGEx Query API	apidocs	ProgrammingInterface	http	REST API for INDRA CoGEx queries
indra.python	INDRA Python Library	indra	ProcessProduct	python	Python library for automated model as...
indra.cogex.code	INDRA CoGEx Build Code	indra_cogex	ProcessProduct	❔	INDRA CoGEx is a graph database integ...

Details

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system that interfaces with natural language processing systems and structured databases to collect mechanistic and causal assertions. It represents them in a standardized form (INDRA Statements) and assembles them into various modeling formalisms including causal graphs and dynamical models.

Key Features

Knowledge Integration: Aggregates mechanistic information from multiple sources including pathway databases, literature extraction via NLP, and curated databases
Standardized Representation: Converts diverse knowledge into uniform INDRA Statements format
Assembly Procedures: Applies knowledge-level assembly to correct systematic errors, resolve redundancies, and assess reliability
Multiple Output Formats: Generates causal graphs, rule-based models (PySB), and network models

Data Sources

INDRA integrates knowledge from numerous biomedical resources including:

Pathway Databases

BioPAX format databases
SIGNOR
BioGRID
Human Protein Reference Database (HPRD)
Phospho.ELM
OmniPath

Chemical Information

DrugBank
ChEMBL
Comparative Toxicogenomics Database (CTD)

Literature Mining

Multiple NLP systems (REACH, TRIPS, Sparser, etc.)
PubMed abstracts and full-text articles

Applications

Pathway analysis and modeling
Drug discovery and mechanism elucidation
Systems biology model construction
Biomedical hypothesis generation
Network-based discovery

Access

INDRA is available as:

Open-source Python library
Web-based discovery interface
REST API for programmatic access
Docker containers for deployment