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