gist LinkML schema

gist LinkML schema

src/gist/schema/ holds six LinkML modules. gist.yaml is the entry point that the generators, the tests and the documentation site read. Its id is https://w3id.org/lmodel/gist. The two supplementary modules, gist_rdfs_annotations.yaml and gist_sub_class_assertions.yaml, are not imported by gist.yaml. They exist for annotation enrichment and OWL RL reasoner support.

The prefix gist: binds to Semantic Arts’ namespace https://w3id.org/semanticarts/ns/ontology/gist/, so every class_uri and slot_uri names gist’s own term. Every module’s default prefix is gist_linkml: (https://w3id.org/lmodel/gist/), which holds only what the rendering adds: the GistThing mixin, the types for the datatypes linkml:types lacks, the enums and the subsets (gist namespace policy).

The modules are generated, not hand-written. The gist-to-LinkML transform rewrites them from the upstream Turtle, and the SSSOM overlay then merges the three curated mapping sets into their *_mappings slots. just gen-project runs both first, so an edit made directly in src/gist/schema/ is lost on the next build. The copier-template README still says to edit this folder: change the transform script or a mapping TSV instead (Regenerate the schema).

Each class carries the slot of every property whose rdfs:domain names it or one of its superclasses. Through the GistThing mixin, it also carries the 89 slots of the properties gist declares without a domain. docs/about.md says where the schema checks data more strictly than gist’s OWL.

just lint checks the modules with LinkML’s recommended rules, less one. .linkmllint.yaml turns off no_xsd_int_type, because gist allows xsd:int literals, and a type with that IRI keeps them valid in the SHACL shapes.