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 adds a new module for Bioregistry under indra.databases which allows converting back and forth between prefixes and IDs used in Bioregistry and namespaces and IDs used in INDRA. It also generalizes the indra.statements.validate module to be able to use Bioregistry (instead of identifiers.org) as a validator for namespaces and identifiers.
The broader validation offered by the new module highlighted some issues related to sources that are also modified in this PR:
For RLIMS-P, the CTD namespace is replaced by MESH and some further corner cases are handled.
For BEL, a new resource file for 4 Selventa namespaces is introduced and used to look up IDs and cross-references from names. The proper IDs replace the previous names in db_refs.
This PR adds a new module for Bioregistry under
indra.databaseswhich allows converting back and forth between prefixes and IDs used in Bioregistry and namespaces and IDs used in INDRA. It also generalizes theindra.statements.validatemodule to be able to use Bioregistry (instead of identifiers.org) as a validator for namespaces and identifiers.The broader validation offered by the new module highlighted some issues related to sources that are also modified in this PR: