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INDRA v1.9.0

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@bgyori bgyori released this 24 Oct 14:13
1.9.0
bb11e72

Package structure

  • The DB is no longer part of the INDRA package, and indra_db_rest, indra.db and indra.tools.reading.db_reading have been moved to https://github.com/indralab/indra_db
  • Most of the models and applications in the models folder have been moved to https://github.com/sorgerlab/indra_apps with just some core examples and models remaining
  • Files in the submodules in indra.sources are now following a standardized naming of api.py and processor.py. The corresponding APIs haven't changed.
  • The indra.assemblers module is now divided into further submodules, one for each output assembler, e.g. indra.assemblers.pysb. This changes the way these modules need to be imported to e.g. from indra.assemblers.pysb import PysbAssembler.

Representation

  • Object model for Context added, including BioContext and WorldContext and further classes. Evidence now has a context attribute to carry this information (which previously appeared in annotations).
  • New Association Statement class to represent non-causal and non-directional relationships
  • SBO annotations in JSON serialization are now obtional and off by default

Input processors

  • New input processor and API for LINCS drug-target relationships (indra.sources.lincs_drug)
  • New input processor and API for Target Affinity Spectrum data for drug-target relationships (indra.sources.tas)
  • The Eidos input processor has numerous improvements and extenstions including producing WorldContext for each Evidence, carrying negation and hedging, and picking up more meta-information and annotations (indra.sources.eidos.processor)
  • The Eidos reader has been updated to work with Eidos version 0.2.2 (indra.sources.eidos.reader)
  • The BEL input processor now produces BioContext for each Evidence (indra.sources.bel.processor)
  • Many new features in the INDRA DB REST client (indra.sources.indra_db_rest) including ordering, timeouts, various size limits, retries, etc.
  • REACH input processor now produces BioContext for each Evidence (indra.sources.reach.processor)
  • SIGNOR input processor now produces BioContext for each Evidence (indra.sources.signor.processor)
  • SOFIA input processor now produces WorldContext for each Evidence (indra.sources.sofia.processor)
  • TEES API and processor refactored to support batch reading (indra.sources.tees)

Core assembly modules

  • The BeliefEngine in indra.belief has been refactored to allow subclassing the BeliefScorer to implement custom scoring approaches. The default scores have been moved to a resource file in indra.resources.
  • The BeliefEngine can now handle negative as well as positive evidence for a given Statement.
  • The Preassembler now adds annotations for raw texts corresponding to Agents that would otherwise be lost upon duplicate resolution.

Output assemblers

  • New hub layout generator for CX networks in indra.assemblers.cx
  • Improvements and extensions to English assembler in indra.assemblers.english

Literature and database client

  • New client to the MeSH database to allow name lookup and standardization in indra.databases.mesh_client
  • New client to the LINCS small molecule and protein tables in indra.databases.lincs_client
  • NDEx client can now be used without explicitly passing credentials in indra.databases.ndex_client
  • Improvements to Elsevier client to be able to extract text from a wider range of XML formats in indra.literature.elsevier_client

Resources

  • Resource files for new sources and database clients added
  • Statements JSON schema updated with Context object model
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