INDRA v1.13.0

Representation

• INDRA Events introduced as arguments of Influences or as standalone statements
• Influence statements are no longer derived from IncreaseAmount
• New object model for representing Delta/QualitativeDelta in Events

Input processors

• Support for standalone Events and Migration events extracted from CWMS in indra.sources.cwms
• Support for extracting standalone Events from Eidos in indra.sources.eidos
• Support for extracting standalone Events from Hume in indra.sources.hume
• Support for extracting standalone Events from Sofia in indra.sources.sofia

Database/Literature clients

• Support for determining type of gene in indra.databases.hgnc_client
• Support for mapping outdated gene names to current ones in indra.databases.hgnc_client
• Improved extraction of text from Elsevier XMLs in indra.literature.elsevier_client
• Additional annotations and metadata extraction support in indra.literature.pubmed_client

Dependencies

• Use Open JDK instead of Oracle JDK with pyjnius
• deft renamed to adeft

Assemblers

• All relevant assemblers adapted to new Influence/Event/Concept representation
• Support for generating Kappa influence and contact maps in PySB assembler in indra.assemblers.pysb
• Support for Influence statements in CX assembler in indra.assemblers.cx

Model analysis

• Additional logic in ModelChecker for Kappa influence map pruning in indra.explanation.model_checker

Reading tools

• Refactoring of AWS-based reading tools