INDRA Documentation INDRA Documentation, Release 1.15.2 INDRA (the Integrated Network and Dynamical...

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Transcript of INDRA Documentation INDRA Documentation, Release 1.15.2 INDRA (the Integrated Network and Dynamical...

  • INDRA Documentation Release 1.16.0

    B. M. Gyori, J. A. Bachman

    Feb 13, 2020

  • Contents

    1 License and funding 3

    2 Installation 5 2.1 Installing Python . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 2.2 Installing INDRA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

    2.2.1 Installing via Github . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 2.2.2 Cloning the source code from Github . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 2.2.3 Installing releases with pip . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

    2.3 INDRA dependencies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 2.3.1 PySB and BioNetGen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 2.3.2 Pyjnius . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 2.3.3 Graphviz . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 2.3.4 Matplotlib . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 2.3.5 Optional additional dependencies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

    2.4 Configuring INDRA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

    3 Getting started with INDRA 9 3.1 Importing INDRA and its modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 3.2 Basic usage examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

    3.2.1 Reading a sentence with TRIPS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 3.2.2 Reading a PubMed Central article with REACH . . . . . . . . . . . . . . . . . . . . . . . . 10 3.2.3 Getting the neighborhood of proteins from the BEL Large Corpus . . . . . . . . . . . . . . 10 3.2.4 Getting paths between two proteins from PathwayCommons (BioPAX) . . . . . . . . . . . . 10 3.2.5 Constructing INDRA Statements manually . . . . . . . . . . . . . . . . . . . . . . . . . . 10 3.2.6 Assembling a PySB model and exporting to SBML . . . . . . . . . . . . . . . . . . . . . . 11

    4 INDRA modules reference 13 4.1 INDRA Statements (indra.statements) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

    4.1.1 JSON serialization of INDRA Statements . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 4.2 Processors for knowledge input (indra.sources) . . . . . . . . . . . . . . . . . . . . . . . . . . 36

    4.2.1 Biology-oriented Reading Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36 4.2.2 General Purpose Reading Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 4.2.3 Standard Molecular Pathway Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70 4.2.4 Custom Knowledge Bases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86

    4.3 Database clients (indra.databases) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94 4.3.1 HGNC client (indra.hgnc_client) . . . . . . . . . . . . . . . . . . . . . . . . . . . 94 4.3.2 Uniprot client (indra.databases.uniprot_client) . . . . . . . . . . . . . . . . . 97

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  • 4.3.3 ChEBI client (indra.databases.chebi_client) . . . . . . . . . . . . . . . . . . . 97 4.3.4 BioGRID client (indra.databases.biogrid_client) . . . . . . . . . . . . . . . . 98 4.3.5 Cell type context client (indra.databases.context_client) . . . . . . . . . . . . 99 4.3.6 Network relevance client (indra.databases.relevance_client) . . . . . . . . . 99 4.3.7 NDEx client (indra.databases.ndex_client) . . . . . . . . . . . . . . . . . . . . 100 4.3.8 cBio portal client (indra.databases.cbio_client) . . . . . . . . . . . . . . . . . 101 4.3.9 ChEMBL client (indra.databases.chembl_client) . . . . . . . . . . . . . . . . 104 4.3.10 LINCS client (indra.databases.lincs_client) . . . . . . . . . . . . . . . . . . . 106 4.3.11 MeSH client (indra.databases.mesh_client) . . . . . . . . . . . . . . . . . . . . 106 4.3.12 GO client (indra.databases.go_client) . . . . . . . . . . . . . . . . . . . . . . . 107 4.3.13 PubChem client (indra.databases.pubchem_client) . . . . . . . . . . . . . . . . 108 4.3.14 miRBase client (indra.databases.mirbase_client) . . . . . . . . . . . . . . . . 108 4.3.15 Experimental Factor Ontology (EFO) client (indra.databases.efo_client) . . . . 109 4.3.16 Human Phenotype Ontology (HP) client (indra.databases.hp_client) . . . . . . . 109 4.3.17 Disease Ontology (DOID) client (indra.databases.doid_client) . . . . . . . . . 110

    4.4 Literature clients (indra.literature) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110 4.4.1 Pubmed client (indra.literature.pubmed_client) . . . . . . . . . . . . . . . . 111 4.4.2 Pubmed Central client (indra.literature.pmc_client) . . . . . . . . . . . . . . . 113 4.4.3 CrossRef client (indra.literature.crossref_client) . . . . . . . . . . . . . . 114 4.4.4 Elsevier client (indra.literature.elsevier_client) . . . . . . . . . . . . . . . 114 4.4.5 NewsAPI client (indra.literature.newsapi_client) . . . . . . . . . . . . . . . 116 4.4.6 Deft Tools (indra.literature.adeft_tools) . . . . . . . . . . . . . . . . . . . . 117

    4.5 Preassembly (indra.preassembler) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118 4.5.1 Preassembler (indra.preassembler) . . . . . . . . . . . . . . . . . . . . . . . . . . . 118 4.5.2 Hierarchy manager (indra.preassembler.hierarchy_manager) . . . . . . . . . 124 4.5.3 Entity grounding mapping and standardization (indra.preassembler.

    grounding_mapper) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127 4.5.4 Site curation and mapping (indra.preassembler.sitemapper) . . . . . . . . . . . 135 4.5.5 Ontology mapping (indra.preassembler.ontology_mapper) . . . . . . . . . . . 137

    4.6 Belief Engine (indra.belief) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137 4.7 Mechanism Linker (indra.mechlinker) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140 4.8 Assemblers of model output (indra.assemblers) . . . . . . . . . . . . . . . . . . . . . . . . . 144

    4.8.1 Executable PySB models (indra.assemblers.pysb.assembler) . . . . . . . . . . 144 4.8.2 Cytoscape networks (indra.assemblers.cx.assembler) . . . . . . . . . . . . . . 149 4.8.3 Natural language (indra.assemblers.english.assembler) . . . . . . . . . . . . 151 4.8.4 Node-edge graphs (indra.assemblers.graph.assembler) . . . . . . . . . . . . . 152 4.8.5 SIF / Boolean networks (indra.assemblers.sif.assembler) . . . . . . . . . . . . 154 4.8.6 MITRE “index cards” (indra.assemblers.index_card.assembler) . . . . . . . 155 4.8.7 SBGN output (indra.assemblers.sbgn.assembler) . . . . . . . . . . . . . . . . 155 4.8.8 Cytoscape JS networks (indra.assemblers.cyjs.assembler) . . . . . . . . . . . 156 4.8.9 Causal analysis graphs (indra.assemblers.cag.assembler) . . . . . . . . . . . . 157 4.8.10 Tabular output (indra.assemblers.tsv.assembler) . . . . . . . . . . . . . . . . 158 4.8.11 HTML browsing and curation (indra.assemblers.html.assembler) . . . . . . . 160 4.8.12 BMI wrapper for PySB-assembled models (indra.assemblers.pysb.bmi_wrapper) 162 4.8.13 PyBEL graphs (indra.assemblers.pybel.assembler) . . . . . . . . . . . . . . . 165 4.8.14 Kami models (indra.assemblers.kami.assembler) . . . . . . . . . . . . . . . . 166 4.8.15 IndraNet Graphs (indra.assemblers.indranet) . . . . . . . . . . . . . . . . . . . 167

    4.9 Explanation (indra.explanation) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170 4.9.1 Check whether a model satisfies a property (indra.explanation.model_checker) 170

    4.10 Tools (indra.tools) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178 4.10.1 Run assembly components in a pipeline (indra.tools.assemble_corpus) . . . . . 178 4.10.2 Real-time feedback for assembly (indra.tools.live_curation) . . . . . . . . . . . 189 4.10.3 Build a network from a gene list (indra.tools.gene_network) . . . . . . . . . . . . 192

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  • 4.10.4 Build an executable model from a fragment of a large network (indra.tools. executable_subnetwork) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194

    4.10.5 Build a model incrementally over time (indra.tools.incremental_model) . . . . 194 4.10.6 The RAS Machine (indra.tools.machine) . . . . . . . . . . . . . . . . . . . . . . . 196

    4.11 Util (indra.util) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197 4.11.1 Utilities for using AWS (indra.util.aws) . . . . . . . . . . . . . . . . . . . . . . . . 197 4.11.2 A utility to get the INDRA version (indra.util.get_version) . . . . . . . . . . . . 200 4.11.3 Define NestedDict (indra.util.nested_dict) . . . . . . . . . . . . . . . . . . . . . 200 4.11.4 Some shorthands for plot formatting (indra.util.plot_formatting) . . . . . . . . 200

    5 Tutorials 203 5.1 Using natural language to build models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203

    5.1.1 Read INDRA Statements from a natural language string . . . . . . . . . . . . . . . . . . . 203 5.1.2 Assemble the INDRA Statements into a rule-based executable model . . . . . . . . . . . . . 204 5.1.3 Exporting the model into other common formats . . . . . . . . . . . . . . . . . . . . . . . . 205

    5.2 The Statement curation interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206 5.2.1 Curating a Statement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206 5.2.2