SSSOM overlay

SSSOM overlay

just apply-sssom-overlay runs scripts/apply_sssom_overlay.py --schema-dir src/gist/schema --mappings-dir src/gist/mappings after just gen-linkml. It reads the rows of the three mapping sets (CDM, DPV, ISO/IEC 22989). It expands each row’s subject with its TSV’s curie_map and matches it to the element with that IRI: its class_uri, slot_uri, enum_uri or permissible-value meaning, else default_prefix:name. For every class, slot, enum, type or permissible value so matched, it merges the object CURIE into the matching exact_mappings, close_mappings, broad_mappings, narrow_mappings or related_mappings slot of the gist LinkML schema. It also declares any new object-side prefix from the TSV’s curie_map. It keeps existing entries, drops duplicates, rewrites the YAML with ruamel.yaml in round-trip mode, and is idempotent. Matching by IRI keeps a row on the right element where a gist term such as gist:hasParty is rendered as the snake_case slot has_party. The script is schema-independent: --schema lets it target another lmodel schema.