Merge pull request #92 from psychoinformatics-de/reorg

Establish schema object hierarchy; removed unnecessary class

src/linkml/ontology/datalad.yaml

@@ -28,7 +28,7 @@ classes:
       - has_annex_remote
     slot_usage:
       distribution:
-        range: FilesystemDirectory
+        range: FileContainer
         equals_expression: "{tree}"
       is_version_of:
         range: DataladDataset

src/linkml/ontology/datasets.yaml

@@ -347,31 +347,28 @@ classes:
     broad_mappings:
       - foaf:Document
 
-  FilesystemDirectory:
-    class_uri: dlco:FilesystemDirectory
+  FileContainer:
+    class_uri: dlco:FileContainer
     mixin: true
     is_a: Distribution
     description: >-
-       Filesystem structure which contains references to files,
-       or other directories.
+       Container that holds references to files, or other containers.
     slots:
       - qualified_part
     slot_usage:
       qualified_part:
-        range: FilesystemDirectoryItem
-    exact_mappings:
+        range: FileContainerItem
+    close_mappings:
       - ncit:NCIT_C62486
     broad_mappings:
       - ncit:NCIT_C49057
-    narrow_mappings:
-      - ncit:NCIT_C172256
 
-  FilesystemDirectoryItem:
-    class_uri: dlco:FilesystemDirectoryItem
+  FileContainerItem:
+    class_uri: dlco:FileContainerItem
     mixin: true
     is_a: QualifiedPart
     description: >-
-       Named reference of a content item in the context of a `FilesystemDirectory`
+       Named reference of a content item in the context of a `FileContainer`
 
   DataService:
     class_uri: dlco:DataService

src/linkml/ontology/git.yaml

@@ -99,7 +99,7 @@ classes:
 
   GitTree:
     mixin: true
-    is_a: FilesystemDirectory
+    is_a: FileContainer
     mixins:
       - GitShaIDed
     description: >-

src/linkml/ontology/schema_objects.yaml

@@ -41,6 +41,23 @@ classes:
       - HasRequiredMetaTypeDesignator
     description: >-
       Base class for any recognized metadata object type.
+      This class should never be used directly, only its subclasses.
+
+  DistributionObject:
+    class_uri: dlco:DistributionObject
+    is_a: TypedObject
+    description: >-
+      Metadata object for a [Distribution](https://concepts.datalad.org/ontology/Distribution).
+    mixins:
+      - Distribution
+    slots:
+      - meta_code
+    slot_usage:
+      has_part:
+        multivalued: true
+        range: DistributionObject
+      license:
+        range: LicenseDocumentObject
 
   GUIDedTypedObject:
     class_uri: dlco:GUIDedTypedObject
@@ -155,15 +172,15 @@ classes:
     slot_usage:
       qualified_part:
         multivalued: true
-        range: FilesystemDirectoryItemObject
+        range: FileContainerItemObject
 
-  FilesystemDirectoryItemObject:
-    class_uri: dlco:FilesystemDirectoryItemObject
+  FileContainerItemObject:
+    class_uri: dlco:FileContainerItemObject
     is_a: MetadataObject
     mixins:
-      - FilesystemDirectoryItem
+      - FileContainerItem
     description: >-
-      Metadata object for a [FilesystemDirectoryItem](https://concepts.datalad.org/ontology/FilesystemDirectoryItem).
+      Metadata object for a [FileContainerItem](https://concepts.datalad.org/ontology/FileContainerItem).
     slots:
       - relation
     slot_usage:
@@ -172,6 +189,7 @@ classes:
         #any_of:
         #  - range: GitShaIDedObject
         #  - range: StableAnnexKeyObject
+        # TODO try making range `DistributionObject`
         range: GUIDedTypedObject
     todos:
       - figure out why a union range specification is not working
@@ -246,3 +264,39 @@ classes:
       qualified_access:
         multivalued: true
         range: AnnexAccessObject
+
+  EntityObject:
+    class_uri: dlco:EntityObject
+    is_a: MetadataObject
+    mixins:
+      - Entity
+    slots:
+      - meta_type
+    description: >-
+      Metadata object for a [Entity](https://concepts.datalad.org/ontology/Entity).
+
+  GrantObject:
+    class_uri: dlco:GrantObject
+    is_a: EntityObject
+    mixins:
+      - Grant
+    description: >-
+      Metadata object for a [Grant](https://concepts.datalad.org/ontology/Grant).
+
+  LicenseDocumentObject:
+    class_uri: dlco:LicenseDocumentObject
+    is_a: MetadataObject
+    mixins:
+      - LicenseDocument
+    description: >-
+      Metadata object for a [LicenseDocument](https://concepts.datalad.org/ontology/LicenseDocument).
+    slots:
+      - meta_id
+
+  PublicationObject:
+    class_uri: dlco:PublicationObject
+    is_a: EntityObject
+    mixins:
+      - Publication
+    description: >-
+      Metadata object for a [Publication](https://concepts.datalad.org/ontology/Publication).

src/linkml/schemas/datalad-dataset-components.yaml

@@ -198,15 +198,15 @@ classes:
         inlined: true
         inlined_as_list: true
         multivalued: true
-        range: FilesystemDirectoryItemObject
+        range: FileContainerItemObject
 
-  FilesystemDirectoryItemObject:
-    class_uri: dlco:FilesystemDirectoryItemObject
+  FileContainerItemObject:
+    class_uri: dlco:FileContainerItemObject
     is_a: MetadataObject
     mixins:
-      - FilesystemDirectoryItem
+      - FileContainerItem
     description: >-
-      Metadata object for a `FilesystemDirectoryItem`.
+      Metadata object for a `FileContainerItem`.
     slots:
       - relation
     slot_usage:

src/linkml/schemas/dataset-version.yaml

@@ -48,23 +48,13 @@ classes:
     mixins:
       - HasRequiredMetaTypeDesignator
     description: >-
-      Base class for any object with a type designator slot. This class
-      should never be used directly, only its subclasses.
-
-  DUIDedTypedObject:
-    class_uri: dlco:DUIDedTypedObject
-    is_a: TypedObject
-    description: >-
-      Metadata object that is uniquely identified within a
-      metadata document by some code.
-    slots:
-      - meta_code
+      Schema-specific implementation of [TypedObject](https://concepts.datalad.org/ontology/TypedObject).
 
   DistributionObject:
     class_uri: dlco:DistributionObject
     is_a: TypedObject
     description: >-
-      TODO
+      Schema-specific implementation of [Object](https://concepts.datalad.org/ontology/Object).
     mixins:
       - Distribution
     slots:
@@ -83,10 +73,9 @@ classes:
     class_uri: dlco:FileContainerObject
     is_a: DistributionObject
     mixins:
-      # this should be FileContainer and a FilesystemDirectory a subclass of it
-      - FilesystemDirectory
+      - FileContainer
     description: >-
-      TODO
+      Schema-specific implementation of [FileContainerObject](https://concepts.datalad.org/ontology/FileContainerObject).
     slot_usage:
       qualified_part:
         multivalued: true
@@ -96,36 +85,35 @@ classes:
 
   FileContainerItemObject:
     class_uri: dlco:FileContainerItemObject
+    is_a: MetadataObject
     mixins:
-      - QualifiedPart
+      - FileContainerItem
     description: >-
-      Metadata object for a `QualifiedPart`, where the part is
-      a `DistributionObject`.
+      Schema-specific implementation of [FileContainerItemObject](https://concepts.datalad.org/ontology/FileContainerItemObject).
     slot_usage:
       relation:
         inlined: false
         range: DistributionObject
 
-
   DigitalDocumentObject:
     class_uri: dlco:DigitalDocumentObject
     is_a: DistributionObject
     mixins:
       - DigitalDocument
     description: >-
-      TODO
+      Schema-specific implementation of [DigitalDocumentObject](https://concepts.datalad.org/ontology/DigitalDocumentObject).
     slot_usage:
       license:
         inlined: false
         range: LicenseDocumentObject
 
-
   DatasetVersionObject:
     class_uri: dlco:DatasetVersionObject
+    is_a: MetadataObject
     mixins:
       - Dataset
     description: >-
-      TODO
+      Schema-specific implementation of [DatasetVersionObject](https://concepts.datalad.org/ontology/DatasetVersionObject).
     attributes:
       custom_licenses:
         multivalued: true
@@ -171,28 +159,29 @@ classes:
 
   AgentObject:
     class_uri: dlco:AgentObject
+    is_a: MetadataObject
     mixins:
       - Agent
+    description: >-
+      Schema-specific implementation of [AgentObject](https://concepts.datalad.org/ontology/AgentObject).
     slots:
       - meta_type
-    description: >-
-      TODO
 
   PersonObject:
     class_uri: dlco:PersonObject
     is_a: AgentObject
     mixins:
       - Person
     description: >-
-      TODO
+      Schema-specific implementation of [PersonObject](https://concepts.datalad.org/ontology/PersonObject).
 
   ResearchContributorObject:
     class_uri: dlco:ResearchContributorObject
     is_a: PersonObject
     mixins:
       - ResearchContributor
     description: >-
-      TODO
+      Schema-specific implementation of [ResearchContributorObject](https://concepts.datalad.org/ontology/ResearchContributorObject).
     slot_usage:
       affiliation:
         range: OrganizationObject
@@ -202,27 +191,28 @@ classes:
     is_a: AgentObject
     mixins:
       - Organization
+    description: >-
+      Schema-specific implementation of [OrganizationObject](https://concepts.datalad.org/ontology/OrganizationObject).
     slots:
       - meta_code
 
-    description: >-
-      TODO
-
   EntityObject:
     class_uri: dlco:EntityObject
+    is_a: MetadataObject
     mixins:
       - Entity
     slots:
       - meta_type
     description: >-
-      TODO
+      Schema-specific implementation of [EntityObject](https://concepts.datalad.org/ontology/EntityObject).
 
   AgentRoleObject:
     class_uri: dlco:AgentRoleObject
+    is_a: MetadataObject
     mixins:
       - Role
     description: >-
-      TODO
+      Schema-specific implementation of [AgentRoleObject](https://concepts.datalad.org/ontology/AgentRoleObject).
     slots:
       - meta_id
     id_prefixes:
@@ -239,10 +229,11 @@ classes:
 
   AgentInfluenceObject:
     class_uri: dlco:AgentInfluenceObject
+    is_a: MetadataObject
     mixins:
       - AgentInfluence
     description: >-
-      TODO
+      Schema-specific implementation of [AgentInfluenceObject](https://concepts.datalad.org/ontology/AgentInfluenceObject).
     slot_usage:
       agent:
         inlined: true
@@ -253,10 +244,11 @@ classes:
 
   EntityInfluenceObject:
     class_uri: dlco:EntityInfluenceObject
+    is_a: MetadataObject
     mixins:
       - EntityInfluence
     description: >-
-      TODO
+      Schema-specific implementation of [EntityInfluenceObject](https://concepts.datalad.org/ontology/EntityInfluenceObject).
     slot_usage:
       entity:
         inlined: true
@@ -267,10 +259,11 @@ classes:
 
   EntityRoleObject:
     class_uri: dlco:EntityRoleObject
+    is_a: MetadataObject
     mixins:
       - Role
     description: >-
-      TODO
+      Schema-specific implementation of [EntityRoleObject](https://concepts.datalad.org/ontology/EntityRoleObject).
     slots:
       - meta_id
     id_prefixes:
@@ -288,14 +281,15 @@ classes:
     mixins:
       - Grant
     description: >-
-      TODO
+      Schema-specific implementation of [GrantObject](https://concepts.datalad.org/ontology/GrantObject).
 
   LicenseDocumentObject:
     class_uri: dlco:LicenseDocumentObject
+    is_a: MetadataObject
     mixins:
       - LicenseDocument
     description: >-
-      TODO
+      Schema-specific implementation of [LicenseDocumentObject](https://concepts.datalad.org/ontology/LicenseDocumentObject).
     slots:
       - meta_id
 
@@ -305,4 +299,4 @@ classes:
     mixins:
       - Publication
     description: >-
-      TODO
+      Schema-specific implementation of [PublicationObject](https://concepts.datalad.org/ontology/PublicationObject).