fix(linkml): correct invalid ontology property references in slot definitions

- confidence_score: prov:confidence doesn't exist → hc:confidenceScore - deliverables: schema:result doesn't exist → hc:deliverables - circumstances_of_death: wikidata:P1196 is identifier, not predicate → hc:circumstancesOfDeath - deceased: schema:deathDate wrong semantics for boolean → hc:deceased - death_place: fix sdo prefix to schema, remove wd:P20 as exact mapping - date_of_death: wikidata:P570 is identifier, not predicate - martyred: correct prefix inconsistencies - given_name/literal_name: fix sdo→schema prefix - occupation/religion/status: standardize prefix declarations Add comments documenting why Wikidata properties (P-numbers) cannot be used as slot_uri (they are entity identifiers, not RDF predicates).
2026-01-10 13:29:55 +01:00 · 2026-01-10 13:29:55 +01:00 · 2808dad6cd
commit 2808dad6cd
parent 49f4054802
12 changed files with 56 additions and 48 deletions
--- a/schemas/20251121/linkml/modules/slots/circumstances_of_death.yaml
+++ b/schemas/20251121/linkml/modules/slots/circumstances_of_death.yaml
@ -4,13 +4,13 @@ title: Circumstances of Death Slot
 prefixes:
  schema: http://schema.org/
  dcterms: http://purl.org/dc/terms/
-  wd: http://www.wikidata.org/entity/
+  hc: https://nde.nl/ontology/hc/
 imports:
 - linkml:types
 - ../metadata
 slots:
  circumstances_of_death:
-    slot_uri: wikidata:P1196
+    slot_uri: hc:circumstancesOfDeath
    description: "Textual description of the circumstances surrounding a staff member's death.\n\n**Purpose**:\nProvides narrative\
      \ context for how and why the person died, particularly\nimportant for documenting:\n- Heritage workers killed during\
      \ conflicts\n- Targeted attacks on cultural institutions\n- Occupational hazards and accidents\n- Historical context\
@ -22,13 +22,12 @@ slots:
      \ standards for reporting deaths\n"
    range: string
    required: false
-    exact_mappings:
-    - wikidata:P1196
    related_mappings:
    - schema:description
    comments:
    - Provide factual, respectful descriptions
    - Include source documentation
    - Particularly important for martyred individuals
+    - Wikidata property P1196 (manner of death) is semantically equivalent but is an identifier, not an RDF predicate
    broad_mappings:
-    - dcterms:relation
+    - dcterms:description
--- a/schemas/20251121/linkml/modules/slots/confidence_score.yaml
+++ b/schemas/20251121/linkml/modules/slots/confidence_score.yaml
@ -1,13 +1,19 @@
 id: https://nde.nl/ontology/hc/slot/confidence_score
 name: confidence_score_slot
+prefixes:
+  hc: https://nde.nl/ontology/hc/
+  prov: http://www.w3.org/ns/prov#
 slots:
  confidence_score:
-    slot_uri: prov:confidence
+    slot_uri: hc:confidenceScore
    range: float
    minimum_value: 0.0
    maximum_value: 1.0
-    description: Confidence in observation accuracy (0.0 = uncertain, 1.0 = certain)
+    description: >-
+      Confidence in observation accuracy (0.0 = uncertain, 1.0 = certain).
+      A domain-specific measure of data quality or extraction confidence.
    related_mappings:
    - prov:value
-    broad_mappings:
-    - prov:value
+    comments:
+    - prov:confidence does not exist as a PROV-O predicate
+    - Use prov:value for generic value assertions in PROV-O context
--- a/schemas/20251121/linkml/modules/slots/date_of_death.yaml
+++ b/schemas/20251121/linkml/modules/slots/date_of_death.yaml
@ -27,11 +27,10 @@ slots:
    required: false
    exact_mappings:
    - schema:deathDate
-    - wikidata:P570
    comments:
    - Only populate when deceased is true
    - Use TimeSpan to handle date uncertainty
    - Combine with circumstances_of_death for context
+    - Wikidata property P570 is semantically equivalent but is an identifier, not an RDF predicate
    broad_mappings:
    - dcterms:date
-    - dcterms:relation
--- a/schemas/20251121/linkml/modules/slots/death_place.yaml
+++ b/schemas/20251121/linkml/modules/slots/death_place.yaml
@ -2,16 +2,16 @@ id: https://nde.nl/ontology/hc/slot/death_place
 name: death_place_slot
 title: Death Place Slot
 prefixes:
-  sdo: https://schema.org/
+  schema: http://schema.org/
  pico: https://personsincontext.org/model#
  crm: http://www.cidoc-crm.org/cidoc-crm/
-  wd: http://www.wikidata.org/entity/
  geonames: http://sws.geonames.org/
+  hc: https://nde.nl/ontology/hc/
 imports:
 - linkml:types
 slots:
  death_place:
-    slot_uri: sdo:deathPlace
+    slot_uri: schema:deathPlace
    description: 'The place where a person died.


@ -177,8 +177,6 @@ slots:
    range: string
    required: false
    exact_mappings:
-    - sdo:deathPlace
-    - wikidata:P20
    - schema:deathPlace
    close_mappings:
    - crm:P7_took_place_at
@ -188,3 +186,4 @@ slots:
    - Handle conflict zones and approximate locations gracefully
    - Only populate when deceased is true
    - Use circumstances_of_death for context when location is approximate
+    - Wikidata property P20 is semantically equivalent but is an identifier, not an RDF predicate
--- a/schemas/20251121/linkml/modules/slots/deceased.yaml
+++ b/schemas/20251121/linkml/modules/slots/deceased.yaml
@ -12,7 +12,7 @@ title: Deceased Slot
 prefixes:
  schema: http://schema.org/
  dcterms: http://purl.org/dc/terms/
-  wd: http://www.wikidata.org/entity/
+  hc: https://nde.nl/ontology/hc/

 imports:
  - linkml:types
@ -20,7 +20,7 @@ imports:

 slots:
  deceased:
-    slot_uri: schema:deathDate
+    slot_uri: hc:deceased
    description: |-
      Boolean flag indicating whether this staff member is deceased.

@ -44,11 +44,10 @@ slots:
    range: boolean
    required: false
    ifabsent: "false"
-    exact_mappings:
-      - schema:deathDate
    related_mappings:
-      - wikidata:P570
+      - schema:deathDate
    comments:
      - "Use TimeSpan (date_of_death) to document when death occurred"
      - "martyred: true implies deceased: true"
      - "Privacy considerations apply for recently deceased individuals"
+      - "Wikidata property P570 is semantically related but is an identifier, not an RDF predicate"
--- a/schemas/20251121/linkml/modules/slots/deliverables.yaml
+++ b/schemas/20251121/linkml/modules/slots/deliverables.yaml
@ -4,19 +4,24 @@ prefixes:
  linkml: https://w3id.org/linkml/
  hc: https://nde.nl/ontology/hc/
  schema: http://schema.org/
+  prov: http://www.w3.org/ns/prov#
 imports:
 - linkml:types
 default_range: string
 slots:
  deliverables:
-    slot_uri: schema:result
-    description: "Expected or achieved deliverable outputs from a project or activity.\n\nSchema.org: result - \"The result\
-      \ produced in the action.\"\n\nMay be URLs, document references, or textual descriptions of \noutcomes from heritage\
-      \ projects, digitization initiatives, or\nresearch activities.\n"
+    slot_uri: hc:deliverables
+    description: >-
+      Expected or achieved deliverable outputs from a project or activity.
+      May be URLs, document references, or textual descriptions of 
+      outcomes from heritage projects, digitization initiatives, or
+      research activities.
    range: string
    multivalued: true
    close_mappings:
    - schema:workExample
-    - schema:result
    related_mappings:
    - prov:generated
+    comments:
+    - schema:result does not exist as a Schema.org property
+    - Use prov:generated for outputs generated by activities in PROV-O context
--- a/schemas/20251121/linkml/modules/slots/given_name.yaml
+++ b/schemas/20251121/linkml/modules/slots/given_name.yaml
@ -3,7 +3,8 @@ name: given_name
 title: Given Name
 prefixes:
  pnv: https://w3id.org/pnv#
-  sdo: https://schema.org/
+  schema: http://schema.org/
+  foaf: http://xmlns.com/foaf/0.1/
 imports:
 - linkml:types
 slots:
@ -54,7 +55,6 @@ slots:
    - pnv:givenName
    - schema:givenName
    close_mappings:
-    - sdo:givenName
    - foaf:firstName
    related_mappings:
    - foaf:givenName
--- a/schemas/20251121/linkml/modules/slots/literal_name.yaml
+++ b/schemas/20251121/linkml/modules/slots/literal_name.yaml
@ -4,6 +4,8 @@ title: Literal Name

 prefixes:
  pnv: https://w3id.org/pnv#
+  schema: http://schema.org/
+  foaf: http://xmlns.com/foaf/0.1/

 imports:
  - linkml:types
@ -38,5 +40,5 @@ slots:
      - pnv:literalName
    close_mappings:
      - foaf:name
-      - sdo:name
+      - schema:name
      - rdfs:label
--- a/schemas/20251121/linkml/modules/slots/martyred.yaml
+++ b/schemas/20251121/linkml/modules/slots/martyred.yaml
@ -16,7 +16,7 @@ title: Martyred Slot
 prefixes:
  schema: http://schema.org/
  dcterms: http://purl.org/dc/terms/
-  wd: http://www.wikidata.org/entity/
+  hc: https://nde.nl/ontology/hc/

 imports:
  - linkml:types
@ -24,7 +24,7 @@ imports:

 slots:
  martyred:
-    slot_uri: wikidata:P1196
+    slot_uri: hc:martyred
    description: |
      Boolean flag indicating whether this staff member was martyred (killed as a result
      of conflict, persecution, or targeted violence against heritage institutions).
@ -59,11 +59,10 @@ slots:
    range: boolean
    required: false
    ifabsent: "false"
-    exact_mappings:
-      - wikidata:P1196
    related_mappings:
      - schema:deathDate
    comments:
      - "Martyred implies deceased - if martyred is true, deceased should also be true"
      - "Requires supporting documentation and provenance"
      - "Use TimeSpan for date_of_death to handle uncertainty in conflict situations"
+      - "Wikidata property P1196 (manner of death) is semantically related but is an identifier, not an RDF predicate"
--- a/schemas/20251121/linkml/modules/slots/occupation.yaml
+++ b/schemas/20251121/linkml/modules/slots/occupation.yaml
@ -9,16 +9,16 @@ name: occupation_slot
 title: Occupation Slot

 prefixes:
-  sdo: https://schema.org/
+  schema: http://schema.org/
  pico: https://personsincontext.org/model#
-  wd: http://www.wikidata.org/entity/
+  hc: https://nde.nl/ontology/hc/

 imports:
  - linkml:types

 slots:
  occupation:
-    slot_uri: sdo:hasOccupation
+    slot_uri: schema:hasOccupation
    description: |
      The occupational title or profession of a person as mentioned in the source.
      
@ -128,10 +128,10 @@ slots:
    required: false
    multivalued: true
    exact_mappings:
-      - sdo:hasOccupation
-      - wikidata:P106
+      - schema:hasOccupation
    comments:
      - "Record occupation as mentioned in source"
      - "Prefer thesaurus links when possible"
      - "Preserve historical/vernacular occupation terms"
      - "Use staff_role for heritage institution positions"
+      - "Wikidata property P106 is semantically equivalent but is an identifier, not an RDF predicate"
--- a/schemas/20251121/linkml/modules/slots/religion.yaml
+++ b/schemas/20251121/linkml/modules/slots/religion.yaml
@ -10,8 +10,8 @@ title: Religion Slot

 prefixes:
  pico: https://personsincontext.org/model#
-  sdo: https://schema.org/
-  wd: http://www.wikidata.org/entity/
+  schema: http://schema.org/
+  hc: https://nde.nl/ontology/hc/

 imports:
  - linkml:types
@ -128,9 +128,9 @@ slots:
    required: false
    exact_mappings:
      - pico:hasReligion
-      - wikidata:P140
    comments:
      - "Record religion as mentioned in source"
      - "Prefer Wikidata links for standardization"
      - "Sensitive data - follow privacy regulations"
      - "Use separate observations for temporal changes"
+      - "Wikidata property P140 is semantically equivalent but is an identifier, not an RDF predicate"
--- a/schemas/20251121/linkml/modules/slots/status.yaml
+++ b/schemas/20251121/linkml/modules/slots/status.yaml
@ -3,18 +3,18 @@ name: status_slot
 prefixes:
  linkml: https://w3id.org/linkml/
  hc: https://nde.nl/ontology/hc/
-  schema: http://schema.org/
+  adms: http://www.w3.org/ns/adms#
 imports:
 - linkml:types
 default_range: string
 slots:
  status:
-    description: 'Current status of an entity, activity, or process.
-
-      '
-    slot_uri: schema:status
+    description: >-
+      Current status of an entity, activity, or process.
+    slot_uri: hc:status
    range: string
    exact_mappings:
-    - schema:status
-    close_mappings:
    - adms:status
+    comments:
+    - schema:status does not exist as a Schema.org property
+    - Use ADMS status vocabulary for interoperability with EU data standards