kempersc fa5680f0dd Add initial versions of custodian hub UML diagrams in Mermaid and PlantUML formats

- Introduced custodian_hub_v3.mmd, custodian_hub_v4_final.mmd, and custodian_hub_v5_FINAL.mmd for Mermaid representation.
- Created custodian_hub_FINAL.puml and custodian_hub_v3.puml for PlantUML representation.
- Defined entities such as CustodianReconstruction, Identifier, TimeSpan, Agent, CustodianName, CustodianObservation, ReconstructionActivity, Appellation, ConfidenceMeasure, Custodian, LanguageCode, and SourceDocument.
- Established relationships and associations between entities, including temporal extents, observations, and reconstruction activities.
- Incorporated enumerations for various types, statuses, and classifications relevant to custodians and their activities.

2025-11-22 14:33:51 +01:00

4.7 KiB

Raw Blame History

RDF Regeneration After Agent → ReconstructionAgent Rename

Date: 2025-11-22
Reason: Class rename from Agent to ReconstructionAgent for clarity
Schema Version: v0.1.0 (modular LinkML)

Summary

Successfully regenerated RDF/OWL ontology files in 7 serialization formats after renaming the Agent class to ReconstructionAgent.

Changes in Generated RDF

Class URI Updated

Old: https://nde.nl/ontology/hc/class/Agent/Agent
New: https://nde.nl/ontology/hc/class/ReconstructionAgent/ReconstructionAgent

RDF Label Updated

# Before
<.../Agent/Agent> a owl:Class ;
    rdfs:label "Agent" .

# After
<.../ReconstructionAgent/ReconstructionAgent> a owl:Class ;
    rdfs:label "ReconstructionAgent" .

Property References Updated

# responsible_agent property now references ReconstructionAgent
:responsible_agent a owl:ObjectProperty ;
    rdfs:range <.../ReconstructionAgent/ReconstructionAgent> ;
    owl:equivalentProperty prov:wasAssociatedWith .

Generated Files (7 formats)

Format	File	Size	Lines/Triples
Turtle	`01_custodian_name.owl.ttl`	91 KB	1,555 lines
N-Triples	`01_custodian_name.nt`	273 KB	1,835 triples
RDF/XML	`01_custodian_name.rdf`	195 KB	-
N3	`01_custodian_name.n3`	91 KB	-
N-Quads	`01_custodian_name.nq`	337 KB	1,834 quads
TriG	`01_custodian_name.trig`	122 KB	-
TriX	`01_custodian_name.trix`	406 KB	-

Note: JSON-LD generation skipped (plugin not available in current rdflib installation)

Triple Count Verification

✅ Consistent across formats:

N-Triples: 1,835 triples
N-Quads: 1,834 quads (1 fewer due to default graph handling)

Ontology Mappings Preserved

All ontology mappings from the original Agent class were preserved in ReconstructionAgent:

Exact Mappings

prov:Agent - PROV-O agent
foaf:Agent - FOAF agent
rico:Agent - RiC-O archival agent

Close Mappings

schema:Person, schema:Organization, schema:SoftwareApplication
prov:SoftwareAgent, dcterms:Agent
org:Organization, rico:CorporateBody
cpov:PublicOrganisation - EU public organizations (research institutions)

pico:Agent - PiCo agent model
tooi:Overheidsorganisatie - Dutch government organizations

Verification Steps

1. Class Presence Check

grep -c "ReconstructionAgent" 01_custodian_name.owl.ttl
# Output: 6 occurrences

2. No Orphaned References

grep "Agent" 01_custodian_name.owl.ttl | grep -v "ReconstructionAgent" | grep -v "AgentType"
# Output: Only ontology mappings (prov:Agent, foaf:Agent, etc.)

3. Property Range Updated

grep "range.*ReconstructionAgent" 01_custodian_name.nt
# Output: responsible_agent property correctly references ReconstructionAgent

Generation Command

# 1. Generate base OWL/TTL from LinkML
gen-owl -f ttl schemas/20251121/linkml/01_custodian_name_modular.yaml \
  2>/dev/null > schemas/20251121/rdf/01_custodian_name.owl.ttl

# 2. Convert to other RDF formats
cd schemas/20251121/rdf
rdfpipe 01_custodian_name.owl.ttl -o nt > 01_custodian_name.nt
rdfpipe 01_custodian_name.owl.ttl -o xml > 01_custodian_name.rdf
rdfpipe 01_custodian_name.owl.ttl -o n3 > 01_custodian_name.n3
rdfpipe 01_custodian_name.owl.ttl -o nquads > 01_custodian_name.nq
rdfpipe 01_custodian_name.owl.ttl -o trig > 01_custodian_name.trig
rdfpipe 01_custodian_name.owl.ttl -o trix > 01_custodian_name.trix

Next Steps

✅ COMPLETE: RDF/OWL regeneration
✅ COMPLETE: Documentation updates (ONTOLOGY_MAPPINGS.md)
⏳ TODO: Update UML diagrams (Mermaid, PlantUML)
⏳ TODO: Regenerate example instance data
⏳ TODO: Update README files referencing Agent class

Compatibility Notes

Breaking Change

⚠️ This is a breaking change for:

External systems consuming RDF endpoints
SPARQL queries referencing the old Agent class URI
RDF datasets serialized before 2025-11-22

Migration Path

Update SPARQL queries:

# Old query
SELECT ?agent WHERE {
  ?activity prov:wasAssociatedWith ?agent .
  ?agent a <.../Agent/Agent> .
}

# New query
SELECT ?agent WHERE {
  ?activity prov:wasAssociatedWith ?agent .
  ?agent a <.../ReconstructionAgent/ReconstructionAgent> .
}

References

Schema Source: schemas/20251121/linkml/01_custodian_name_modular.yaml
Class Definition: schemas/20251121/linkml/modules/classes/ReconstructionAgent.yaml
Rename Documentation: RENAME_AGENT_TO_RECONSTRUCTION_AGENT.md
Verification Report: VERIFICATION_REPORT.md

Status: ✅ COMPLETE
Generated: 2025-11-22 12:13 UTC
Tool: LinkML gen-owl + rdflib rdfpipe

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