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INDRA v1.14.1

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@bgyori bgyori released this 23 Sep 18:35
1.14.1
cbce65d

Representation

  • New MovementContext class to represent movement time/places for Events
  • New QuantitativeState class to represent specific quantities associated with Events

Input sources

  • Support for extracting Migration statements from CWMS in indra.sources.cwms
  • Adaptation to changes in Eidos API and output format in indra.sources.eidos
  • Adaptation to changes in Hume API and output format in indra.sources.hume
  • Custom processor for migration tables in indra.sources.eidos.migration_table_processor
  • Support for representing source counts in INDRA DB REST in indra.sources.indra_db_res

Internal assembly

  • Significantly improved and generalized DB refs name standardization, and preassembly matching/refinement for all entities including chemicals and biological processes
  • New custom matches/refinement function feature in Preassembler in indra.preassembler and BeliefEngine in indra.belief
  • Support for new World Modelers ontology
  • Grounding mapper refactored with new misgrounding map functionality in indra.preassembler.grounding_mapper

Model assemblers

  • New IndraNet assembler to assemble custom networks for path finding in indra.assemblers.indranet
  • New NiceCxAssembler for streamlined CX network assembly in indra.assemblers.cx
  • Significantly improved HTML assembler with source count badges and support for templates indra.assemblers.html
  • Refactored index card assembler with extended metadata support in indra.assemblers.index_card

Database/literature clients

  • New PubChem client in indra.databases.pubchem_client
  • New miRBase client in indra.databases.mirbase_client
  • New Experimental Factor Ontology (EFO) client in indra.databases.efo_client
  • New Phenotype Ontology (HP) client in indra.databases.hp_client
  • New Disease Ontology (DOID) client in indra.databases.doid_client
  • New mapping functionalities in HGNC, MeSH and ChEBI clients
  • ScienceDirect search feature added in Elsevier client in indra.literature.elsevier_client
  • Additional article info extraction and support for getting MeSH annotations in PubMed client in indra.literature.pubmed_client.

Model analysis

  • Refactored ModelChecker with four new subclasses for analysis of specific model/network types in indra.explanation

Tools

  • S3 corpus upload feature in LiveCuration tool in indra.tools.live_curation
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