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INDRA v1.6.0

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@bgyori bgyori released this 20 Mar 03:41
1.6.0
e2027fa

Representation:

  • New Influence Statement to represent causal influence between a subject
    and an object, and optionally the polarity and magnitude of change in
    subject and object

Input processors

  • TEES: new API in indra.sources.tees to read with the
    Turku Event Extraction System
    (https://github.com/jbjorne/TEES) and instantiate INDRA Statements
  • PyBEL: new API in indra.sources.bel that allows processing PyBEL graphs
    (https://github.com/pybel/pybel) as an input to INDRA
  • NDEx CX: new API in indra.sources.ndex_cx to process networks on NDEx
    (http://ndexbio.org) and extract INDRA Statements
  • Signor: new API in indra.sources.signor to read the content of the
    Signor signaling network database (https://signor.uniroma2.it/) as
    INDRA Statements
  • Geneways: new API in indra.sources.geneways to read the output generated
    by the Genewayes reading system
    (https://www.ncbi.nlm.nih.gov/pubmed/15016385)
  • Eidos: new API in indra.sources.eidos to read text using the Eidos reading
    system (https://github.com/clulab/eidos/) and process its output of
    causal interactions into INDRA Statements
  • BBN: new API in indra.sources.bbn to process causal interactions extracted
    by BBN's world modelers reading system

Core assembly modules

  • Flexible parameterization of the BeliefEngine in indra.belief, and support for prior
    belief assignment based on more granular attributes of a Statement's evidence

Output assemblers

  • Causal Analysis Graphs: new assembler in indra.assemblers.cag_assembler
    to assemble into "Causal Analysis Graphs", and display with the Delphi package
    (https://github.com/ml4ai/delphi)
  • PyBEL: new assembler in indra.assemblers.pybel_assembler to assemble into
    a PyBEL graph and allow analysis on PyBEL web
    (https://pybel.scai.fraunhofer.de/)

Model analysis

  • Integration with kappy to facilitate Kappa model analysis and simulation
  • Several new, optimized graph data structures in indra.explanation

Tools

  • The "machine" (basis of The RAS Machine) has been moved
    to indra.tools.machine.

Database clients and resources

  • FamPlex (renamed from Bioentities) is no longer a submodule, it is available
    directly under indra.resources.famplex
  • New ChEBML client in indra.databases.chembl_client
  • New functionalities in cBio portal and ChEBI clients

High-throughput reading and database

  • Various high-througput reading modules refactored into four submodules based
    on use case in indra.tools.reading
  • New database module in indra.db to cache INDRA Statements from
    reading at scale
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