URIs and Mappings
One feature that sets LinkML apart from frameworks such as JSON-Schema and UML is that fact that each element of your schema has a globally unique IRI/URI. This is somewhat hidden behind the scenes, so you can ignore this feature if you like, but it is also very easy to use this, which can provide benefits in terms of reusing and linking schemas, and working with the linked data stack.
background: URIs, IRIs, and CURIEs
URIs and IRIs are generalizations of URLs. URIs are used as identifiers in linked data standards and vocabularies.
URIs can be shortended as CURIEs (Compact URIs). Given a prefix declaration where we map
http://schema.org/, then we can use the CURIE
schema:Person to denote the person concept
A typical header for a linkml schema may look like this:
id: https://w3id.org/linkml/examples/personinfo name: personinfo default_curi_maps: - semweb_context prefixes: personinfo: https://w3id.org/linkml/examples/personinfo/ linkml: https://w3id.org/linkml/ schema: http://schema.org/ rdfs: http://www.w3.org/2000/01/rdf-schema# prov: http://www.w3.org/ns/prov# default_prefix: personinfo emit_prefixes: - rdf - rdfs - xsd - skos imports: - linkml:types
The prefixes section contains a list of prefix expansions that can be used to specify CURIEs. Additionally, prefixmaps can be imported from prefixcommons.
With the above prefixmap, the CURIE
schema:Person will expand to http://schema.org/Person
class uri and slot uri
The two slots
can be used to declare URIs for classes and slots respectively. These are typically specified as CURIEs
classes: Person: is_a: NamedThing description: >- A person (alive, dead, undead, or fictional). class_uri: schema:Person ... slots: id: identifier: true slot_uri: schema:identifier name: slot_uri: schema:name ...
When a JSON-LD context is generated for this schema, it will map json elements to their full linked data IRIs
If class and slot uris are omitted, then they are still generated behind the scenes, using the default_prefix slot at the schema level
For example, if Person did not declare a class_uri, then a CURIE
personinfo:Person would be used, which would expand to
You may wish to avoid committing to completely reusing a linked data concept, whilst wanting to retain a mapping. LinkML makes use of SKOS predicates as metamodel slots:
NamedThing: description: >- A generic grouping for any identifiable entity slots: - id - name - description - image close_mappings: - schema:Thing
The id_prefixes slot can be used to define a list of valid ID prefixes that instances of this class ought to have as part of their CURIE.
The order of the list matters since its a prioritized list with the ID prefix with the highest priority appearing at the top of the list.
For example, the biolink model defines a list of allowed id_prefixes for gene objects:
gene: slots: - id - name - symbol - description - synonym - xref exact_mappings: - SO:0000704 - SIO:010035 - WIKIDATA:Q7187 id_prefixes: - NCBIGene - ENSEMBL - HGNC - UniProtKB - MGI - ZFIN - dictyBase - WB - WormBase - FlyBase - FB - RGD - SGD - PomBase
Here we define the entity class
gene to have a list of ID prefixes with
NCBIGene having the highest priority.
this notebook demonstrates some potential pitfalls of JSON-LD 1.0 with some forms of CURIEs