INDRA v1.16.0

Input processors

• New PhosphoELM API and processor in indra.sources.phosphoelm.
• PyBEL API and processor updated for PyBEL 0.14 compatibility in indra.sources.bel.
• Improvements in regrounding approach with Eidos in indra.sources.eidos.
• Bug fixes to offline reading via the REACH API in indra.sources.reach.
• Refactor ISI reader API and processor for containerization in indra.sources.isi.

Core assembly modules

• Full integration of Gilda disambiguation with grounding mapper both as
  a package and a web service in indra.preassembler.grounding_mapper.
• Refactor grounding mapper module to separate out standardization functions
  in indra.preassembler.grounding_mapper.standardize.

Output assemblers

• Many improvements to the HTML assembler including refactoring,
  improved grouping and heading generation, and support Influences in
  indra.assemblers.html.
• Improvements to grounding and introduction of part_of relations in
  PyBEL assembler in indra.assemblers.pybel.

Resources

• Integrate a set of known MeSH to GO mappings.

Explanation

• Improvements to reporting paths in the explanation module in
  indra.explanation.

Tools

• Many new features in the Live curation, including actively loading
  and saving corpora on S3 in indra.tools.live_curation.
• Add new high-throughput reader management for ISI and TRIPS readers
  in indra.tools.reading
• Significant refactoring of indra.tools.reading to separate reader
  classes and improve containerization.