Adapt a vocabulary

lokf adapt copies a published LinkML vocabulary into a LOKF domain schema. The copy imports lokf.yaml, shares no element name with it, and its classes descend from Concept. Pass it as --schema, or import it from a schema of your own when you add to it.

lokf adapt biolink_model.yaml                       # -> biolink_model_lokf.yaml beside it
lokf adapt biolink_model.yaml -o schema/biolink_lokf.yaml --lokf schema/lokf.yaml

It needs only the core install. Validating or projecting a bundle under the result needs lokf[build], as --schema always does.

What it changes

Move	What	Why
fold imports	The vocabulary’s own imports are merged into the one file; the copy imports linkml:types and lokf.	Imports resolve beside the file that names them; the copy must stand alone.
drop for LOKF’s	The vocabulary’s identifier slot and its rdf:type slot are deleted; what listed them now lists LOKF’s id and type.	A class carries one identifier and one type designator, and LOKF’s are those.
detach, demote	A slot that inherited from a dropped one loses its is_a; every other designates_type is stripped.	Biolink’s category: is_a: type would otherwise inherit LOKF’s designator; type is the one.
rename, IRIs kept	Every name lokf.yaml also defines, in any section, is renamed (name → biolink_name, agent → BiolinkAgent) with its slot_uri/class_uri pinned and the old name in aliases.	The name is local to the schema; the IRI carries the meaning. A type and a slot called unit is an overlap LinkML warns about.
fold into LOKF’s	A slot or class attribute that means what a Concept slot means is deleted, not renamed. Every class that used it uses LOKF’s slot instead, with the deleted slot’s constraints copied into a slot_usage. It matches by slot_uri or an exact_mappings entry (schema:name is title, over http or https), or by --fold; --keep holds it back. The fold is refused when two Concept slots share the IRI, until --fold picks one, and when the shape differs: multivalued against single, or a class or a number against a string.	One fact, one key, one IRI: a concept writes title, not title and slsa_name.
re-root	Every rootless, non-mixin class that carries the identifier gets is_a: Concept; tree_root comes off.	One line puts the whole vocabulary in the concept union; KnowledgeBundle is the document root.
one canonical form	Two names that would canonicalise to one (biolink’s KnowledgeGraph and knowledge graph) are both kept: the canonical spelling keeps its name, the other is renamed as a shared name is.	The rewrite would otherwise keep one definition and lose the other.
canonical names	Class names CamelCased, slot names underscored.	type, frontmatter keys and the JSON-LD context all use these forms; derived IRIs do not change.
verify	The copy is loaded beside lokf.yaml with SchemaView: every reference resolves, no name is shared, every re-rooted class reaches Concept.	A copy that fails is not written.

The report names each move’s targets, and the copy’s schema-level notes record them for anyone who opens the file.

Options

Option	Meaning
-o, --output PATH	Where to write the copy: a file, or a directory that gets <stem>_lokf.yaml, with a trailing slash for a new one (default: beside the input).
--root CLASS	A class to re-root on Concept, as the vocabulary names it; repeatable, replaces detection. A vocabulary with no identifier slot (gist’s shape) has no root to detect; name each top class.
--lokf PATH	The lokf.yaml to share no name with (default: a local checkout, else the copy packaged with lokf).
--prefix P	Prefix for renamed elements (default: the vocabulary’s default_prefix).
--fold V=L	Fold the vocabulary’s slot V, or attribute Class.attr, into LOKF’s slot L, for one that declares no mapping; repeatable. A name missing on either side is refused, and so is a shape that differs from L’s.
--keep V	Leave slot V, or attribute Class.attr, out of the fold by IRI; repeatable. It is renamed or kept as it would be without the mapping, and the copy’s notes record it.
--dry-run	Print the report and verify the copy; write nothing.
--check	Write nothing; exit 1 unless --output already holds exactly this copy and it verifies.

In CI

The copy depends on two moving inputs, the vocabulary’s release and lokf.yaml. Keep it fresh with one step:

lokf adapt upstream/biolink_model.yaml -o schema/biolink_lokf.yaml --lokf schema/lokf.yaml --check

The lokf repository’s just biolink is the worked case: it fetches biolink-model at a pinned tag, checks its sha256, adapts it, and validates and projects examples/biolink/.

Limits

• A slot ranged over uriorcurie projects as an xsd:anyURI literal, a class-ranged one as an IRI; that is the vocabulary’s choice, kept.
• An unranged slot takes the vocabulary’s default_range, usually string, so an object property the vocabulary left unranged projects as a literal.
• Comments in the source YAML are not carried over; the copy is generated, not edited.