INDRA v1.5.0

Package structure

• All knowledge sources have been moved to the indra.sources submodule

Representation:

• New Conversion Statement type for representing metabolic conversions
• RasGap/RasGef/RasGtpActivation renamed to the more general Gap/Gef/GtpActivation
• Improved JSON serialization with SBO mappings for INDRA Statements
• New graph visualization for Statements

Input processors:

• New input processor for NDEx CX networks in indra.sources.ndex_cx
• New API and input processor for Sparser (https://github.com/ddmcdonald/sparser)
• Better grounding prioritization and new extraction patterns in TRIPS processor

Core assembly modules:

• Better linking of modifications in MechLinker in indra.mechlinker
• More advanced automated SiteMapper mapping logic in indra.preassembler.site_mapper

Output assemblers

• Major improvements in PySB Assembler including
  • new assembly policies (e.g. for Conversion)
  • new rate laws (Michaelis-Menten and Hill function)
  • better handing of grounded monomers
  • extended semantic annotations referring to provenance and the role of
    monomers in rules
• Assembler into KAMI in indra.assemblers.kami_assembler. KAMI is a knowledge
  representation and meta-model for Kappa: https://github.com/Kappa-Dev/KAMI.
• Full reimplementation of SBGN assembler to follow reaction network-based assembly
• SifAssembler extended with new Loopy (http://ncase.me/loopy/) output mode
• Various improvements and extensions in CyJSAssembler and CxAssembler

Model Analysis

• New explanation module in indra.explanation to check INDRA-assembled PySB
  models against a set of INDRA Statements

Tools

• New large-scale reading pipeline implemented for Amazon Batch
• New Amazon-based processing for the RAS Machine

Databases and Resources

• New client to cBio Portal web API for accessing patient and cell line data
• New client to PhosphoSite web API for accessing phosphosite locations and
  mapping between organisms
• Extension of the Bioentities submodule with more extensive grounding entries
  and references
• Mapping between human, rat and mouse proteins and genes in UniProt and HGNC clients
• Updates to all other database resource files

Other

• Extended REST API which can be run locally to interact with INDRA.
  New API documentation are in the rest_api folder.
• New model projects and evaluations in models
• Extended documentation in doc