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INDRA v1.10.0

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@bgyori bgyori released this 27 Nov 14:03
1.10.0
da0fd12

This is the last release of INDRA that is compatible with both Python 2.7 and Python 3.5+. The next release will drop Python 2 compatibility and maintain compatibility with Python 3.5+ only.

Package structure, dependencies

  • INDRA is now compatible with ndex2 version >= 2.0

Representation

  • New text_refs attribute in Evidence which allows representing text
    references other than PMID, e.g. DOI, URL, etc.
  • Evidence str/repr display improved and extended to support pretty printing
    large Evidence objects

Input processors

  • Geographical location context extracted from Eidos in indra.sources.eidos
  • EKB file-based processing added to TRIPS and CWMS APIs in
    indra.sources.trips and indra.sources.cwms
  • REACH processor now extracts and propagate entity coordinates from
    REACH output in indra.sources.reach
  • Sparser API has more robust timeout and failure handling, and multiple
    improvements in the processor in indra.sources.sparser
  • New function to submit curation via INDRA DB REST API in
    indra.sources.indra_db_rest
  • Improvements and extensions in INDRA DB REST API including the ability
    to limit number of returned Statements in indra.sources.indra_db_rest
  • Bug fixes in MedScan processor in indra.sources.medscan

Core assembly modules

  • Belief engine refactored to pass evidences instead of scores when propagating
    evidence on the refinements graph in indra.belief
  • The assembly of large Complexes and Associations has been significantly
    optimized in indra.statements and indra.preassembler

Output assemblers

  • New HTML Statement browser and curation interface added in
    indra.assemblers.html
  • English assembler extended to handle Influence, Association, and Conversion
    Statements in indra.assemblers.english
  • Bug fixes in CX assembly and hub layout in indra.assemblers.cx

Literature and database clients

  • New GO client added in indra.databases.go_client which allows normalizing
    biological processes and cellular components to standardized names
  • UniProt client can now retreive descriptions of proteins in
    indra.databases.uniprot_client

Resources

  • All resource files updated to latest version as of 10/30/2018
  • Ontologies for SOFIA, Eidos and Hume, and mapping between them updated
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