INDRA v1.22.0

Package structure and dependencies

• Protmapper and Gilda version requirements increased, PySB dependency restriction relaxed

Core assembly modules

• Ontology graph represents obsolete ID replacements in indra.ontology
• Improved BioOntology graph which now includes MONDO, ECCODE, and improves OBO hierarchy import to avoid cycles indra.ontology.bio
• Identifier standardization now applies replaced IDs in indra.ontology.standardize
• Refactor preassembler refinement finding to expose more endpoints in indra.preassembler.refinement
• Refinement finding optimized when split index isn used in indra.preassembler.refinement
• Grounding mapping disambiguation additional back-end options in indra.preassembler.grounding_mapper
• Ontology analysis extends to finding cycles indra.tools.analyze_ontology

Statement representation

• Additional functions for JSON (de)serialization of single Statements in indra.statements
• Validation: multiple validators supported, refactored to use classes indra.statements.validate

Knowledge sources

• New API and processor for running the SemRep reading system and processing its outputs indra.sources.semrep
• New API and processor for CREEDS data in indra.sources.creeds
• New API and processor for UbiBrowser in indra.sources.ubibrowser
• New API and processor for the ACSN database in indra.sources.acsn
• BEL processor now uses Selventa IDs instead of names in indra.sources.bel
• Improved identifier extraction from BioPAX in indra.sources.biopax
• Eidos reader/CLI updated to work with the latest Eidos version in indra.sources.eidos
• Improved HPRD API with option to process compressed archive directly in indra.sources.hprd
• MINERVA client improved to process latest project automatically in indra.sources.minerva
• Improved OmniPath processing to decouple evidences among Statements in indra.sources.omnipath
• Streamlined RLIMS-P API with improved identifier extraction in indra.sources.rlimsp
• SIGNOR processor is now compatible with latest data format indra.sources.signor

Model assemblers

• Refactored (more options, better consistency) styling for the HTML Assembler in indra.assemblers.html
• New option in IndraNetAssembler to represent self loops indra.assemblers.indranet

Model analysis

• Additional options added to ModelChecker to control explanation paths indra.explanation.model_checker

Tools

• Additional cases handled in validity fixing of identifiers indra.tools.fix_invalidities

Resources and database clients

• New client to access Bioregistry content in indra.databases.bioregistry_client
• New client to access the Expasy enzyme (EC code) database in indra.databases.ec_client
• New client to interact with the Biolookup web service in indra.databases.biolookup_client
• Extended HGNC client to provide enzyme code mappings for genes in indra.databases.hgnc_client
• Extended MeSH client to access CAS mappings for compounds indra.databases.mesh_client
• New client to interact with MONDO diseases indra.databases.mondo_client
• Extended OBO client allowing access to more ontologies indra.databases.obo_client
• Extended PubChem client with additional functionalities indra.databases.pubchem_client
• Multiple resource files updated including for Biomappings, ChEBI, FamPlex, HGNC,
  identifiers.org, MeSH, and Selventa entries

Literature clients

• PubMed client extended to provide substance-specific publications indra.literature.pubmed_client
• New client to access COCI data from OpenCitations in indra.literature.coci_client