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INDRA v1.11.0

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@bgyori bgyori released this 05 Mar 01:37
1.11.0
1c35b16

Python compatibility

  • This release of INDRA is compatible with Python 3.5+ only and 2.x is not supported anymore.

Package structure, dependencies

  • The protmapper package is a new dependency which takes over interfacing with UniProt (including file-based access and web service access). Consequently, almost all functionalities of indra.databases.uniprot_client and indra.databases.phosphosite_client, as well as the core of indra.preassembler.site_mapper are now provided by protmapper. The overall API of these INDRA modules has not changed, however.
  • INDRA is now also available as a Docker image on Dockerhub under
    labsyspharm/indra, further instructions in the README
  • Installation instructions for the Python-Java bridge pyjnius have been updated,
    INDRA's Java/Scala based dependencies can now work with versions of Java up to 11.
  • The statements.py file has been refactored into its own module in
    indra.statements, the overall API has not changed.
  • INDRA's logging is now fully hierarchical and follows the submodule
    structure.

Input processors

  • CWMS processor in indra.sources.cwms can extract temporal and geo-spatial
    context.
  • Major overhaul of Hume processor in indra.sources.hume, supporting latest
    JSON-LD format and extracting temporal and geo-spatial context
  • An additional JSON-based API and processor is now available for SOFIA in
    indra.sources.sofia, supporting text reading.
  • New input processor for the RLIMS-P reading system in indra.sources.rlimsp.
  • The INDRA DB REST source in indra.sources.indra_db_rest has been refactored
    into multiple files and now provides a Processor class-based interface similar
    to other input sources.
  • More robust handling of invalid identifiers in PyBEL inputs in
    indra.sources.bel.
  • BioPAX input processor in indra.sources.biopax now eliminates spurious
    duplicate extractions by patterns
  • New analysis script is available in indra.sources.trips for TRIPS/CWMS
    extractions.

Core assembly modules

  • Belief engine makes a new Bayesian scorer class available in indra.belief
    which allows integrating curation directly into belief scores.
  • Preassembler in indra.preassembler preserves original grounding in addition
    to the original entity texts upon Statement deduplication.
  • The SiteMapper has been substantially refactored to take its core functionality from the protmapper package (https://github.com/indralab/protmapper).
  • A new disambiguation tool, DEFT (https://github.com/indralab/deft) is now
    integrated into the grounding mapping process in
    indra.preassembler.grounding_mapper.
  • Bug fixes and performance improvements in HierarchyManager in
    indra.preassembler.hierarchy_manager.
  • Bug fixes and performance improvements in OntologyMapper in
    indra.preassembler.ontology_mapper.
  • Assembly pipeline in indra.tools.assemble_corpus now supports merging
    grounding from multiple evidences at the Statement level, as well as additional
    preasssembly functionalities such as evidence flattening.

Tools

  • New web service added for real-time curation of Statements with belief
    updates, ontology extension, and re-grounding/re-assembly in
    indra.tools.live_curation.

Output assemblers

  • Major overhaul of the PySB Assembler in indra.assemblers.pysb to refactor
    into multiple files, support individual statement-level policies, and passing
    in parameterization from outside.
  • CX assembler in indra.assemblers.cx supports setting custom network visual
    styles.
  • Major improvements and many new features in the HTML assembler for curation in
    indra.assemblers.html, including grouping and ranking of Statements
  • Fixes to the SBGN assembly format in indra.assemblers.sbgn.

Literature and database clients

  • PMC client in indra.literature.pmc now supports getting text from NXML
  • Protein lengths now available via the UniProt client in
    indra.databases.uniprot_client

Resources

  • All resource files updated to latest version as of 12/1/2018
  • New ontology mapping resources for Hume and CWMS

REST API

  • Multiple new input and assembly endpoints added to the REST API for Eidos,
    CWMS, Sofia, and Hume, ontology mapping, and belief filtering.
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