INDRA v 1.7.0

Configuration:

• INDRA now comes with a dedicated configuration file (created when
  first importing indra) at ~/.config/indra/config.ini in which paths to various
  resources and access keys can be configured

Representation:

• New Concept parent class for Agent. Concepts allow representing entities
  of interest without the assumption of molecular state that Agents have.

Input processors

• BioGRID: new dedicated input processor for interactions from BioGRID
  in indra.sources.biogrid. This is preferable to the BioGRID content
  coming from Pathway Commons (via indra.sources.biopax), in some cases.
• CWMS: new API and processor for the TRIPS/CWMS reading system
  (http://trips.ihmc.us/parser/cgi/cwmsreader) in indra.sources.cwms
• SOFIA: initial implementation for input processor for reading output from
  the SOFIA reading system added in indra.sources.sofia
• Grounding information from Eidos, BBN and CWMS systems now represented and
  used in assembly

Core assembly modules

• All core assembly procedures now extend to BoundConditions of Agents
• HierarchyManager generalized to allow merging multiple hierarchies
  into a single manager
• New isa hierarchies added for non-biology use cases that now work with
  HierarchyManager / Preassembler
• Custom grounding map can now be propagated into assembly from
  indra.tools.machine and also via indra.tools.assemble_corpus

Output assemblers

• TSV Assembler: new assembler in indra.assemblers.tsv_assembler to
  output knowledge in a tabular format, suitable for human curation

High-throughput reading and database

• REST API for database module to query INDRA Statement content from local or
  remote database
• Various improvements and extensions of high-throughput reading framework
  and database utilities