INDRA

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INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system, originally developed for molecular systems biology and then generalized to other domains (see INDRA World). INDRA draws on natural language processing systems and structured databases to collect mechanistic and causal assertions, represents them in a standardized form (INDRA Statements), and assembles them into various modeling formalisms including causal graphs and dynamical models.

At the core of INDRA are its knowledge-level assembly procedures, allowing sources to be assembled into coherent models, a process that involves correcting systematic input errors, finding and resolving redundancies, inferring missing information, filtering to a relevant scope and assessing the reliability of causal information.

The detailed INDRA documentation is available at http://indra.readthedocs.io.

Contents

• INDRA Modules
  • Knowledge sources
  • Output model assemblers
  • Internal knowledge assembly
  • Other modules
• Citation
• Installation
• INDRA REST API
• INDRA Docker
• Using INDRA
• Funding

INDRA Modules

Knowledge sources

INDRA is currently integrated with the following natural language processing systems and structured databases. These input modules (available in indra.sources) all produce INDRA Statements.

Reading systems:

| Reader | Module | Reference | |------------|--------------------------------------------------------------------------------------------------------|-------------------------------------------------| | TRIPS/DRUM | indra.sources.trips | http://trips.ihmc.us/parser/cgi/drum | | REACH | indra.sources.reach | https://github.com/clulab/reach | | Sparser | indra.sources.sparser | https://github.com/ddmcdonald/sparser | | Eidos | indra.sources.eidos | https://github.com/clulab/eidos | | TEES | indra.sources.tees | https://github.com/jbjorne/TEES | | MedScan | indra.sources.medscan | https://doi.org/10.1093/bioinformatics/btg207 | | RLIMS-P | indra.sources.rlimsp | https://research.bioinformatics.udel.edu/rlimsp | | ISI/AMR | indra.sources.isi | https://github.com/sgarg87/big_mech_isi_gg | | Geneways | indra.sources.geneways | https://www.ncbi.nlm.nih.gov/pubmed/15016385 | | GNBR | indra.sources.gnbr | https://zenodo.org/record/3459420 | | SemRep | indra.sources.semrep | https://github.com/lhncbc/SemRep | | textToKnowledgeGraph | indra.sources.tkg | https://github.com/ndexbio/llm-text-to-knowledge-graph |

Biological pathway databases:

| Database / Exchange format | Module | Reference | |----------------------------|----------------------------|-----------------------------------------------------------------| | PathwayCommons / BioPax | indra.sources.biopax | http://pathwaycommons.org/ <br/> http://www.biopax.org/ | | Large Corpus / BEL | indra.sources.bel | https://github.com/pybel/pybel <br/> https://github.com/OpenBEL | | Signor | indra.sources.signor | https://signor.uniroma2.it/ | | BioGRID | indra.sources.biogrid | https://thebiogrid.org/ | | Target Affinity Spectrum | indra.sources.tas | https://doi.org/10.1101/358978 | | HPRD | indra.sources.hprd | http://www.hprd.org | | | TRRUST | indra.sources.trrust | https://www.grnpedia.org/trrust/ | | | Phospho.ELM | indra.sources.phosphoelm | http://phospho.elm.eu.org/ | | VirHostNet | indra.sources.virhostnet | http://virhostnet.prabi.fr/ | | CTD | indra.sources.ctd | http://ctdbase.org | | DrugBank | indra.sources.drugbank | https://www.drugbank.ca/ | | OmniPath | indra.sources.omnipath | https://omnipathdb.org/ | | DGI | indra.sources.dgi | https://www.dgidb.org/ | | CRoG | indra.sources.crog | https://github.com/chemical-roles/chemical-roles | | CREEDS | indra.sources.creeds | https://maayanlab.cloud/CREEDS/ | | UbiBrowser | indra.sources.ubibrowser | http://ubibrowser.ncpsb.org.cn/ | | ACSN | indra.sources.acsn | https://acsn.curie.fr/ACSN2/ACSN2.html | | WormBase | indra.sources.wormbase | https://www.wormbase.org |

Custom knowledge bases:

| Database / Exchange format | Module | Reference | |----------------------------|-------------------------------|--------------------------------------| | NDEx / CX | indra.sources.ndex_cx | http://ndexbio.org | | INDRA DB / INDRA Statements| indra.sources.indra_db_rest | https://github.com/indralab/indra_db | | Hypothes.is | indra.sources.hypothesis | https://hypothes.is | | Biofactoid | indra.sources.biofactoid | https://biofactoid.org/ | | MINERVA | indra.sources.minerva | https://covid19map.elixir-luxembourg.org/minerva/ |

Output model assemblers

INDRA also provides several model output assemblers that take INDRA Statements as input. The most sophisticated model assembler is the PySB Assembler, which implements a policy-guided automated assembly procedure of a rule-based executable model