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INDRA v1.8.0

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@bgyori bgyori released this 28 Aug 17:41
1.8.0
393958b

Setup and dependencies:

  • INDRA now supports networkx 2.x
  • The Cython version restriction is now removed, and the recommended installation method for pyjnius is through Github
  • Extra dependencies for various modules are now given explicitly in setup.py
  • Separate configuration module (indra.config) to manage config.ini and db_config.ini files
  • Contribution guidelines added

Representation:

  • Extensions to keys and hashes used to identify related Statements (indra.statements)
  • Statements now implement a contradicts method to find contradictions

Input processors:

  • Major improvements and adaptation to changes in Eidos (indra.sources.eidos), Hume (indra.sources.hume), CWMS (indra.sources.cwms), and SOFIA (indra.sources.sofia) reader inputs
  • BBN reader renamed to Hume (indra.sources.hume)
  • Ontologies for the Eidos, Hume, and CWMS readers are integrated, and grounding information from these sources is represented
  • New ISI reader API and processor added (indra.sources.isi)
  • New Medscan reader API and processor added (indra.sources.medscan)
  • Generalized and refactored SIGNOR input API and processor added (indra.sources.signor)
  • BEL resources are now PyBEL compatible and processing defaults to PyBEL, rather than BEL/RDF (indra.sources.bel)
  • Imrpoved modification and mutation site extraction, and handling of complex controllers in REACH input processor (indra.sources.reach)
  • Bug fixes and improvements in TEES (indra.sources.tees) and Sparser (indra.sources.sparser) inputs
  • Broader set of Increase/DecreaseAmount Statements extracted from TRIPS (indra.sources.trips)
  • Added robust DRUM reader to use TRIPS/DRUM locally (indra.sources.trips.drum_reader)

Core assembly modules

  • Contradiction finding in Preassembler (indra.preassembler)
  • Handling of new is_opposite relationship in Statements, HierarchyManager and Preassembler
  • Generalized reasoning across isa/partof paths in HierarchyManager (indra.preassembler.hierarchy_manager)
  • New Ontology Mapper added (indra.preassembler.ontology_mapper)
  • SiteMapper uses cache to speed up sequence access (indra.preassembler.site_mapper)
  • Assembly filters now extend across BoundConditions (indra.tools.assemble_corpus)

Output assemblers

  • BMI wrapper implemented for PySB models for integrated simulation in workflows (indra.assemblers.bmi_wrapper)
  • CAG Assembler can produce Jupyter-embeddable graphs and TSVs (indra.assemblers.cag_assembler)
  • Many generalizations and improvements in PyBEL assembler (indra.assemblers.pybel_assembler)
  • Bug fixes and improvements in PySB, SIF, Graph, English, IndexCard and CX assemblers

Literature and database clients:

  • NewsAPI client added (indra.literature.news_api)
  • Many new functionalities to access content in Elsevier client (indra.literature.elsevier)
  • UniProt client (indra.databases.uniprot_client) extended with protein synonyms; optimizations in resource loading result in faster import times

Resources

  • Many resource files updated, including FamPlex (indra.resources.famplex)
  • New INDRA JSON schema and documentation added (indra/resources/statements_schema.json)

Analysis and explanation

High-throughput reading and database

  • REST API updates and extensions (db_rest_api and rest_api)
  • Separate client and config modules for DB (indra.db.client and indra.db.config)
  • New reading and preassembly managers for DB (indra.db.reading_manager, indra.db.preassembly_manager)
  • New statistics module for DB (indra.db.stats)
  • New reporting and log analysis functionalities for AWS-based reading (indra.tools.reading and indra.tools.reading.db_reading)
  • Extensive improvements to running and managing AWS-based reading jobs (indra.tools.reading)
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