INDRA v1.21.0

Package structure and dependencies

• Multiple modules for the world modeling use case separated out into the INDRA World package (https://github.com/indralab/indra_world). For the specific modules affected, see #1278 and #1283.
• rdflib is no longer a requirement.
• Increased protmapper version (0.0.22) with updated protein resources.

Core assembly modules

• Multiple updates to the INDRA BioOntology (version incremented from 1.12 to 1.18) including adding entity types for nodes, UniProt-Entrez mappings for non-human proteins, chemical family relations from LSPCI in indra.ontology.bio.
• Belief engine significantly refactored to allow more flexibility in statement scoring in indra.belief.
• New belief scorer module added which learns and applies scorers using sklearn models based on curation data in indra.belief.skl.

Statement representation

• Improved statement validation checking and exception messages in indra.statements.validate.

Knowledge sources

• New input API and processor for the GNBR reading system in indra.sources.gnbr.
• INDRA DB client module in indra.sources.indra_db_rest significantly refactored with changes to the API, improved control over e.g., limits and logging, and a new query module in indra.sources.indra_db_rest.query to allow complex query construction.
• Improved evidence extraction for CrOG in indra.sources.crog.
• Improved processing of statement polarities from CTD in indra.sources.ctd.

Model assemblers

• Improved hub layout generation for CX networks in indra.assemblers.cx.
• HtmlAssembler extended to generate links out for database sources, display belief badges, and improve knowledge source badges in indra.assemblers.html.
• IndraNet assembler extended to provide better aggregation logic for
  Statements into network edges in indra.assemblers.indranet.
• PyBEL assembler extended to include additional annotations on edges in indra.assemblers.pybel.

Tools

• Assemble corpus extended with mechanism linking functions in indra.tools.assemble_corpus.
• Validity fixing tools indra.tools.fix_invalidities.

Resources and database clients

• Expose GO namespaces for terms in indra.databases.go_client.
• Expose locus types in HGNC client in indra.databases.hgnc_client.
• Improved prefix/id format handling in identifiers.org client indra.databases.identifiers.
• New Infectious Disease Ontology client in indra.databases.ido_client.
• MeSH client extended to provide supplementary concept mappings to primary terms and tree numbers for supplementary concepts in indra.databases.mesh_client.
• New client for ingesting OWL ontologies in indra.databases.owl_client and corresponding refactoring OBO client in indra.databases.obo_client.
• Resource file content updates for FamPlex, HGNC and MeSH.