id: https://concepts.datalad.org/s/things/v1 name: things-schema # only the major version is reflected in the identifier, but this is the full version version: 1.0.0 status: eunal:concept-status/CURRENT title: Generic schema for an arbitrarily detailed description of "things" description: | This schema provides a generic [`Thing`](Thing) concept as a basic building block. Key concepts of this schema are that any `Thing` - has a unique identifier ([`pid`](pid)) - can be mapped to arbitrary external schemas and terminologies to maximize semantic alignment with existing metadata ecosystems (see [`mappings`](mappings)) - can be further described by attributes ([`attributes`](attributes)) and qualified relations to other "things" ([`characterized_by`](characterized_by)), without prescribing a particular vocabulary - can be associated with a specialized schema class for enabling detailed validation and precise data transformations ([`schema_type`](schema_type)) without limiting the general expressiveness to a fixed set of classes available this foundational schema. More information on this schema is available on a [dedicated page](about). Each class comes with dedicated examples that exemplify its use. A good starting point are the [examples of the `Thing` class](Thing#examples). Although this generic schema could be used directly, it is meant to be used as a foundational building block for more targeted schemas. Therefore, the schema does not define common slots like `name`, or `description`, and leaves this to more targeted schemas to decide if such slots are needed, and how they should be defined. The envisioned use and reuse of this schema is to import it and built targeted derivatives of `Thing` and other classes provided here. See the [PROV schema](/s/prov) for an example that is built on this schema. This schema also incorporates the schema(s) - [`types`](https://concepts.datalad.org/s/types/v1) The schema definition is available as - [JSON-LD context](../v1.context.jsonld) - [LinkML YAML](../v1.yaml) - [LinkML YAML (static/resolved)](../v1.static.yaml) - [OWL TTL](../v1.owl.ttl) - [SHACL TTL](../v1.shacl.ttl) Upcoming changes to this schema may be available in an [(unreleased) development version](../../things/unreleased). license: MIT prefixes: # here for alignment of `pid` ADMS: http://www.w3.org/ns/adms# # SHACL annotations dash: http://datashapes.org/dash# # primarily for the examples, but also a foundational vocab bibo: http://purl.org/ontology/bibo/ # here for alignment of `relations` dcat: http://www.w3.org/ns/dcat# # foundational dcterms: http://purl.org/dc/terms/ # self-reference dlschemas: https://concepts.datalad.org/s/ dlthings: https://concepts.datalad.org/s/things/v1/ dltypes: https://concepts.datalad.org/s/types/v1/ # here is a large, versatile source of controlled vocabularies/codes eunal: http://publications.europa.eu/resource/authority/ ex: http://example.org/ # here as a technical necessity linkml: https://w3id.org/linkml/ # here as a large ecosystem for alignment and annotation obo: http://purl.obolibrary.org/obo/ # foundational owl: http://www.w3.org/2002/07/owl# rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# rdfs: http://www.w3.org/2000/01/rdf-schema# # Required for `Thing`-definition schema: http://schema.org/ # form annotations sh: http://www.w3.org/ns/shacl# # here for alignment of `attributes` sio: http://semanticscience.org/resource/ # foundational skos: http://www.w3.org/2004/02/skos/core# xsd: http://www.w3.org/2001/XMLSchema# # Example convenience namespace that makes it possible to not think about # a dedicated distribution/dataset/dataset-version-unqiue namespace. # The prefix can be materialized ala # linkml-convert -s ... -t rdf -P exthisns=http://example.org/ --infer ... # # The following prefix is an example, a use case specific derived # schema needs to define its own, differently named and defined namespace(s). # # A custom umbrella namespace (e.g. for a project, a consortium, a domain) # to keep vocabulary and entities local to this scope exthisns: https://example.org/ns/ default_prefix: dlthings # list of Curie prefixes that are used in the representation of instances of # the model. All prefixes in this list are added to the prefix sections of # the target models. emit_prefixes: - dlthings - dltypes - rdf - rdfs - skos - xsd imports: - dlschemas:types/v1 - linkml:types slots: broad_mappings: slot_uri: skos:broadMatch is_a: mappings title: Broad mappings description: >- A list of terms from different schemas or terminology systems that have broader meaning. range: uriorcurie multivalued: true close_mappings: slot_uri: skos:closeMatch is_a: mappings title: Close mappings description: >- A list of terms from different schemas or terminology systems that have close meaning. range: uriorcurie multivalued: true description: slot_uri: dlthings:description title: Description description: A free-text account of the subject. range: string exact_mappings: - dcterms:description - rdfs:comment broad_mappings: - obo:IAO_0000300 annotations: dash:singleLine: false exact_mappings: slot_uri: skos:exactMatch is_a: mappings title: Exact mappings description: >- A list of terms from different schemas or terminology systems that have identical meaning. range: uriorcurie multivalued: true attributes: slot_uri: dlthings:attributes title: Attributes description: >- Declares a relation that associates a `Thing` (or another attribute) with an attribute, where an attribute is an intrinsic characteristic, such as a quality, capability, disposition, function, or is an externally derived attribute determined from some descriptor (e.g. a quantity, position, label/identifier). Technically, this declaration is done via an `AttributeSpecification` that combines a `predicate` with a value declaration and the attribute-related slots of a `Thing`. Importantly, such attributes are declared inline, because they do not have a unique identifier. If an identifier is available, a `Thing` declaration (see `relation`), and a qualification of that relationship via a `Statement` (see `characterized_by`) should be preferred. range: AttributeSpecification inlined: true inlined_as_list: true multivalued: true exact_mappings: - sio:SIO_000008 pid: slot_uri: dlthings:pid identifier: true title: Persistent identifier description: >- Persistent and globally unique identifier of a `Thing`. range: uriorcurie exact_mappings: - dcterms:identifier - schema:identifier - ADMS:identifier characterized_by: slot_uri: dlthings:characterized_by title: Is characterized by description: >- Qualifies relationships between a subject `Thing` and an object `Thing` with a `Statement` declaring a `predicate` on the nature of the relationship. range: Statement inlined: true inlined_as_list: true multivalued: true exact_mappings: - obo:RO_0000053 mappings: slot_uri: skos:mappingRelation description: >- A list of terms from different schemas or terminology systems that have comparable meaning. These may include terms that are precisely equivalent, broader or narrower in meaning, or otherwise semantically related but not equivalent from a strict ontological perspective. range: uriorcurie multivalued: true annotations: slot_uri: dlthings:annotations title: Annotations description: >- A record of properties of the metadata record on a subject, a collection of tag/text tuples with the semantics of OWL Annotation. range: Annotation inlined: true multivalued: true exact_mappings: - obo:NCIT_C44272 annotation_tag: description: A tag identifying an annotation. range: Thing annotation_value: description: The actual annotation. range: string narrow_mappings: slot_uri: skos:narrowMatch is_a: mappings title: Narrow mappings description: >- A list of terms from different schemas or terminology systems that have narrower meaning. range: uriorcurie multivalued: true object: slot_uri: rdf:object description: >- Reference to a `Thing` within a `Statement`. inlined: false multivalued: false # TODO really could/should have a range defined #range: Thing relational_role: OBJECT exact_mappings: - rdf:object notes: - We do not declare a range here to be able to tighten the range in subclasses of class that need a particular range. This appears to be working around a linkml limitation. predicate: slot_uri: rdf:predicate description: >- Reference to a `Property` within a `Statement`. range: Property inlined: false multivalued: false relational_role: PREDICATE exact_mappings: - rdf:predicate range: slot_uri: rdfs:range description: >- Declares that the value of a `Thing` or `AttributeSpecification` are instances of a particular class. range: uriorcurie exact_mappings: - rdfs:range related_mappings: slot_uri: skos:relatedMatch is_a: mappings title: Related mappings description: >- A list of terms from different schemas or terminology systems that have related meaning. range: uriorcurie multivalued: true relations: slot_uri: dlthings:relation title: Relations description: >- Declares an unqualified relation of the subject `Thing` to another `Thing`. This schema slot is used to define related things inline. If such a definition is not needed. A qualified relationship can be declared directly using the `characterized_by` slot. domain: Thing inlined: true inlined_as_list: false multivalued: true range: Thing relational_role: OBJECT symmetric: true exact_mappings: - dcat:relation - dcterms:relation value: slot_uri: rdf:value description: >- Value that is a direct representation of a thing. relational_role: OBJECT range: string exact_mappings: - rdf:value classes: ThingMixin: mixin: true description: >- Mix-in with the common interface of `Thing` and `AttributeSpecification`. This interface enables type specifications (`rdf:type`) for things and attributes via a `type` designator slot to indicate specialized schema classes for validation where a slot's `range` is too generic. A thing or attribute can be further describe with statements on qualified relations to other things (`characterized_by`), or inline attributes (`attributes`). A set of `mappings` slots enables the alignment for arbitrary external schemas and terminologies. slots: - annotations - broad_mappings - close_mappings - description - exact_mappings - attributes - characterized_by - narrow_mappings - related_mappings - schema_type ValueSpecificationMixin: mixin: true description: >- Mix-in for a (structured) value specification. Two slots are provided to define a (literal) value (`value`) and its type (`range`). slots: - range - value AttributeSpecification: mixins: - ThingMixin - ValueSpecificationMixin slots: - predicate slot_usage: predicate: required: true description: >- An attribute is conceptually a thing, but it requires no dedicated identifier (`pid`). Instead, it is linked to a `Thing` via its `attributes` slot and declares a `predicate` on the nature of the relationship. exact_mappings: - sio:SIO_000614 close_mappings: - dlthings:Thing Property: class_uri: dlthings:Property is_a: Thing description: >- An RDF property, a `Thing` used to define a `predicate`, for example in a `Statement`. exact_mappings: - rdf:Property Statement: class_uri: dlthings:Statement description: >- An RDF statement that links a `predicate` (a `Property`) with an `object` (a `Thing`) to the subject to form a triple. A `Statement` is used to qualify a relation to a `Thing` referenced by its identifier. For specifying a qualified relation to an attribute that has no dedicated identifier, use an `AttributeSpecification`. slots: - object - predicate slot_usage: object: required: true range: Thing predicate: required: true exact_mappings: - rdf:Statement Thing: class_uri: dlthings:Thing mixins: - ThingMixin description: >- The most basic, identifiable item. In addition to the slots that are common between a `Thing` and an `AttributeSpecification` (see `ThingMixin`), two additional slots are provided. The `pid` slot takes the required identifier for a `Thing`. The `relation` slot allows for the inline specification of other `Thing` instances. Such a relation is unqualified (and symmetric), and should be further characterized via a `Statement` (see `characterized_by`). From a schema perspective, the `relation` slots allows for building self-contained, structured documents (e.g., a JSON object) with arbitrarily complex information on a `Thing`. slots: - pid - relations slot_usage: pid: annotations: sh:order: 1 characterized_by: annotations: sh:order: 2 attributes: annotations: sh:order: 3 description: annotations: sh:order: 4 # reannotate to work around linkml issue # https://hub.psychoinformatics.de/inm7/annotate.inm7.de-data/issues/2#issuecomment-4113 dash:singleLine: false annotations: annotations: sh:order: 5 relations: annotations: sh:order: 6 exact_mappings: annotations: sh:order: 7 close_mappings: annotations: sh:order: 8 broad_mappings: annotations: sh:order: 9 narrow_mappings: annotations: sh:order: 10 related_mappings: annotations: sh:order: 11 exact_mappings: - schema:Thing ValueSpecification: is_a: Thing mixins: - ValueSpecificationMixin description: >- A `Thing` that is a value of some kind. This class can be used to describe an outcome of a measurement, a factual value or constant, or other qualitative or quantitative information with an associated identifier. If no identifier is available, an `AttributeSpecification` can be used within the context of an associated `Thing` (`attributes`). slot_usage: value: required: true notes: - >- It is required, because when it is not needed, `Thing` should be used as a type. Its absence is therefore likely a sign of an error. exact_mappings: - obo:OBI_0001933 Annotation: description: >- A tag/value pair with the semantics of OWL Annotation. slots: - annotation_tag - annotation_value slot_usage: annotation_tag: key: true