INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
This PR works through updating various interlinked resource files along with the ontology graph. It also fixes some corner cases and makes improvements necessary for changes in conventions/assumptions in inputs being processed. Some specific changes:
UniProt resources coming from the protmapper are updated with the requirement protmapper>=0.0.29
HGNC and MGI gene resources updated
Ontologies GO, EFO, DOID, HP and MONDO updated
Identifiers registry info derived from Bioregistry and identifiers.org updated
Chemical info from CHEBI and various associated mappings updated
FamPlex changes propagated and grounding map updated
The BioOntology version is updated from 1.32 to 1.33.
This PR works through updating various interlinked resource files along with the ontology graph. It also fixes some corner cases and makes improvements necessary for changes in conventions/assumptions in inputs being processed. Some specific changes:
protmapper>=0.0.29The BioOntology version is updated from 1.32 to 1.33.