Merge pull request #76 from psychoinformatics-de/simplify

Further adopt externally defined classes

src/linkml/ontology/checksumming.yaml

@@ -36,23 +36,27 @@ enums:
 
 slots:
   checksum:
-    slot_uri: spdx:checksum
+    slot_uri: dlco:checksum
     description: >-
       The checksum property provides a mechanism that can be used to verify
       that the contents of a file or package have not changed.
     range: Checksum
+    exact_mappings:
+      - spdx:checksum
 
   digest:
-    slot_uri: spdx:checksumValue
+    slot_uri: dlco:checksumValue
     description: >-
       Lower case hexadecimal encoded checksum digest value produced using a
       specific algorithm.
     range: HexBinary
+    exact_mappings:
+      - spdx:checksumValue
 
 
 classes:
   Checksum:
-    class_uri: spdx:Checksum
+    class_uri: dlco:Checksum
     description: >-
       A Checksum is a value that allows to check the integrity of the contents
       of a file. Even small changes to the content of the file will change its
@@ -66,3 +70,5 @@ classes:
         slot_uri: spdx:algorithm
         description: >-
           Identifies the algorithm used to produce the subject `Checksum`.
+    exact_mappings:
+      - spdx:Checksum

src/linkml/ontology/properties.yaml

@@ -43,10 +43,13 @@ slots:
     range: EmailAddress
 
   has_part:
-    slot_uri: dcterms:hasPart
+    slot_uri: dlco:hasPart
     description: >-
       A related resource that is included either physically
       or logically in the described resource.
+    exact_mappings:
+      - dcterms:hasPart
+
 
   name:
     slot_uri: dlco:name
@@ -57,12 +60,15 @@ slots:
     range: string
 
   relation:
-    slot_uri: dcterms:relation
+    slot_uri: dlco:relation
     description: >-
       The resource related to the source resource.
     relational_role: OBJECT
+    exact_mappings:
+      - dcterms:relation
 
   uuid:
+    slot_uri: dlco:uuid
     description: >-
       Associated UUID identifier.
     range: UUID

src/linkml/ontology/provenance.yaml

@@ -17,54 +17,64 @@ default_prefix: dlco
 slots:
   # Commit was_generated_by CommitActivity
   was_generated_by:
-    slot_uri: prov:wasGeneratedBy
+    slot_uri: dlco:wasGeneratedBy
     description: >-
       A generation is the completion of production of a new entity by an
       activity. This entity did not exist before generation and becomes
       available for usage after this generation.
     domain: Entity
     range: Activity
+    exact_mappings:
+      - prov:wasGeneratedBy
 
   # Commit was_derived_from Commit
   was_derived_from:
-    slot_uri: prov:wasDerivedFrom
+    slot_uri: dlco:wasDerivedFrom
     description: >-
       A derivation is a transformation of an entity into another, an update
       of an entity resulting in a new one, or the construction of a new
       entity based on a pre-existing entity.
     domain: Entity
     range: Entity
+    exact_mappings:
+      - prov:wasDerivedFrom
 
   # Commit was_attributed_to Author
   was_attributed_to:
-    slot_uri: prov:wasAttributedTo
+    slot_uri: dlco:wasAttributedTo
     description: >-
       Attribution is the ascribing of an entity to an agent.
     domain: Entity
     range: Agent
+    exact_mappings:
+      - prov:wasAttributedTo
 
   # Commit was_associated_with Committer
   was_associated_with:
-    slot_uri: prov:wasAssociatedWith
+    slot_uri: dlco:wasAssociatedWith
     description: >-
       An activity association is an assignment of responsibility to an agent
       for an activity, indicating that the agent had a role in the activity.
       It further allows for a plan to be specified, which is the plan intended
       by the agent to achieve some goals in the context of this activity.
     domain: Activity
     range: Agent
+    exact_mappings:
+      - prov:wasAssociatedWith
 
   was_informed_by:
-    slot_uri: prov:wasInformedBy
+    slot_uri: dlco:wasInformedBy
     description: >-
       Communication is the exchange of an entity by two activities, one activity
       using the entity generated by the other.
     domain: Activity
     range: Activity
+    exact_mappings:
+      - prov:wasInformedBy
 
   # CommitActivity ended_at DateTime
   ended_at:
-    slot_uri: prov:endedAtTime
+    slot_uri: dlco:endedAtTime
     description: >-
       End is when an activity is deemed to have been ended by an entity,
       known as trigger. The activity no longer exists after its end.
@@ -73,89 +83,109 @@ slots:
     domain: Activity
     #range: datetime
     range: string
+    exact_mappings:
+      - prov:endedAtTime
     notes:
       - successful validation with `datetime` as a range and linkml-jsonschema-validate` depends on a patched linkml, see https://github.com/linkml/linkml/issues/1806
       - a related problem also exists for `linkml-validate`, we cannot have a more specific range right now
 
   # Commit generated_at DateTime (committer time)
   generated_at:
-    slot_uri: prov:generatedAtTime
+    slot_uri: dlco:generatedAtTime
     description: >-
       (Date and) time at which the generation of an entity took place or was
       completed.
     domain: Entity
     range: datetime
+    exact_mappings:
+      - prov:generatedAtTime
 
   # Commit was_revision_of Dataset(unversioned concept)
   was_revision_of:
-    slot_uri: prov:wasRevisionOf 
+    slot_uri: dlco:wasRevisionOf
     description: >-
       A revision is a derivation for which the resulting entity is a revised
       version of some original. The implication here is that the resulting
       entity contains substantial content from the original. Revision is a
       particular case of derivation.
     domain: Entity
     range: Entity
+    exact_mappings:
+      - prov:wasRevisionOf
 
   # DataladRun acted_on_behalf_of Author
   acted_on_behalf_of:
-    slot_uri: prov:actedOnBehalfOf
+    slot_uri: dlco:actedOnBehalfOf
     description: >-
       Delegation is the assignment of authority and responsibility to an
       agent (by itself or by another agent) to carry out a specific activity
       as a delegate or representative, while the agent it acts on behalf of
       retains some responsibility for the outcome of the delegated work.
     domain: Agent
     range: Agent
+    exact_mappings:
+      - prov:actedOnBehalfOf
 
   at_location:
-    slot_uri: prov:atLocation
+    slot_uri: dlco:atLocation
     description: >-
       A location can be an identifiable geographic place (ISO 19112),
       but it can also be a non-geographic place such as a directory,
       row, or column. As such, there are numerous ways in which
       location can be expressed, such as by a coordinate, address,
       landmark, and so forth.
     range: Location
+    exact_mappings:
+      - prov:atLocation
 
 
 classes:
   Entity:
     mixin: true
-    class_uri: prov:Entity
+    class_uri: dlco:Entity
     description: >-
       A physical, digital, conceptual, or other kind of thing with some
       fixed aspects; entities may be real or imaginary.
+    exact_mappings:
+      - prov:Entity
 
   Activity:
     mixin: true
-    class_uri: prov:Activity
+    class_uri: dlco:Activity
     description: >-
       An activity is something that occurs over a period of time and acts
       upon or with entities; it may include consuming, processing,
       transforming, modifying, relocating, using, or generating entities.
+    exact_mappings:
+      - prov:Activity
 
   Agent:
     mixin: true
-    class_uri: prov:Agent
+    class_uri: dlco:Agent
     description: >-
       Something that bears some form of responsibility for an activity
       taking place, for the existence of an entity, or for another
       agent's activity.
+    exact_mappings:
+      - prov:Agent
 
   SoftwareAgent:
     mixin: true
     is_a: Agent
-    class_uri: prov:SoftwareAgent
+    class_uri: dlco:SoftwareAgent
     description: >-
       Running software.
+    exact_mappings:
+      - prov:SoftwareAgent
 
   Location:
     mixin: true
-    class_uri: prov:Location
+    class_uri: dlco:Location
     description: >-
       A location can be an identifiable geographic place (ISO 19112),
       but it can also be a non-geographic place such as a directory,
       row, or column. As such, there are numerous ways in which location
       can be expressed, such as by a coordinate, address, landmark, and
       so forth.
+    exact_mappings:
+      - prov:Location