glam/RDF_UML_GENERATION_COMPLETE_20251122_old.md

RDF and UML Generation Complete

Date: 2025-11-22
Schema Version: 20251121
Status: ✅ COMPLETE

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Summary

Successfully generated all RDF serializations and UML diagrams for the Heritage Custodian Ontology with the new legal entity model (v0.2.2).

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Generated Files

RDF Formats (7 serializations)

All generated from: schemas/20251121/linkml/01_custodian_name_modular.yaml

Format	File	Size	Lines	Triples	Description
Turtle	01_custodian_name_modular.owl.ttl	140K	2,328	2,701	Primary OWL ontology (human-readable)
N-Triples	01_custodian_name_modular.nt	452K	2,701	2,701	Line-based triple format (machine-readable)
JSON-LD	01_custodian_name_modular.jsonld	336K	7,451	2,701	JSON Linked Data (web-friendly)
RDF/XML	01_custodian_name_modular.rdf	324K	10,810	2,701	XML serialization (legacy compatibility)
N3	01_custodian_name_modular.n3	196K	5,144	2,701	Notation3 (Turtle superset)
TriG	01_custodian_name_modular.trig	196K	5,144	2,701	Named graphs extension
TriX	01_custodian_name_modular.trix	644K	21,377	2,701	XML with named graphs

Total RDF Size: ~2.3 MB
Total RDF Lines: 40,955 lines

UML Diagrams (2 formats)

Format	File	Size	Description
Mermaid	uml/mermaid/01_custodian_name_modular.mmd	6.0K	Markdown-based class diagram (GitHub-friendly)
PlantUML	uml/plantuml/01_custodian_name_modular.puml	7.5K	UML class diagram with color-coded packages

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Validation Results

RDF Validation ✅

Using rdflib Python library:

✅ Turtle validation: SUCCESS
   Triples: 2,701
   Subjects: 652
   Predicates: 36
   Objects: 1,325

Key Statistics:

• 2,701 triples - All class/slot/enum definitions and mappings
• 652 unique subjects - Classes, slots, enums, and their components
• 36 unique predicates - RDF/RDFS/OWL properties
• 1,325 unique objects - Property values and types

Ontology Coverage

The generated RDF includes:

Classes (17):

• Custodian (hub)
• CustodianObservation, CustodianName (observation pattern)
• CustodianReconstruction (reconstruction pattern)
• LegalEntityType (NEW)
• LegalForm (NEW)
• LegalName (NEW)
• RegistrationNumber (NEW, within RegistrationInfo)
• RegistrationAuthority (NEW, within RegistrationInfo)
• GovernanceStructure (NEW, within RegistrationInfo)
• LegalStatus (NEW, within RegistrationInfo)
• SourceDocument, TimeSpan, ConfidenceMeasure
• ReconstructionActivity, ReconstructionAgent
• Identifier, LanguageCode, Appellation

Enums (6):

• AppellationTypeEnum
• AgentTypeEnum
• EntityTypeEnum (DEPRECATED, use LegalEntityType)
• LegalStatusEnum (DEPRECATED, use LegalStatus class)
• ReconstructionActivityTypeEnum
• SourceDocumentTypeEnum

Slots (59+):

• All 59 modular slot definitions
• Including new legal entity slots: legal_entity_type, registration_numbers

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UML Diagram Features

Mermaid Diagram

Features:

• Class diagram with all 17 classes
• Hub-Observation-Reconstruction pattern visualization
• Legal entity model highlighted (8 new classes)
• Relationship arrows with cardinality
• Inline notes for key classes
• GitHub-renderable (displays directly in markdown files)

Sections:

1. Hub Pattern (Custodian)
2. Observation Pattern (CustodianObservation, CustodianName)
3. Reconstruction Pattern (CustodianReconstruction)
4. Legal Entity Model (8 classes, highlighted)
5. Supporting Classes (9 classes)

PlantUML Diagram

Features:

• Color-coded packages:
  • 🔵 Light Blue: Hub (Custodian)
  • 🟢 Light Green: Observations
  • 🔴 Light Coral: Reconstructions
  • 🟡 Gold: Legal Entity classes
  • ⚪ Light Gray: Supporting classes
• Detailed class attributes with types
• Relationship arrows with labels
• Comprehensive notes explaining:
  • Hub pattern (minimal entity)
  • Observation pattern (source evidence)
  • Reconstruction pattern (formal entity)
  • Legal entity classes (NEW in v0.2.2)
• ISO 20275 and TOOI references

Rendering:

• Use PlantUML server: https://www.plantuml.com/plantuml/
• Or local PlantUML CLI: plantuml 01_custodian_name_modular.puml

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Generation Process

Step 1: Generate OWL/Turtle

gen-owl -f ttl schemas/20251121/linkml/01_custodian_name_modular.yaml 2>/dev/null \
  > schemas/20251121/rdf/01_custodian_name_modular.owl.ttl

Output: 138K Turtle file with 2,328 lines

Step 2: Convert to Other RDF Formats

cd schemas/20251121/rdf
rdfpipe -i turtle -o nt 01_custodian_name_modular.owl.ttl > 01_custodian_name_modular.nt
rdfpipe -i turtle -o json-ld 01_custodian_name_modular.owl.ttl > 01_custodian_name_modular.jsonld
rdfpipe -i turtle -o xml 01_custodian_name_modular.owl.ttl > 01_custodian_name_modular.rdf
rdfpipe -i turtle -o n3 01_custodian_name_modular.owl.ttl > 01_custodian_name_modular.n3
rdfpipe -i turtle -o trig 01_custodian_name_modular.owl.ttl > 01_custodian_name_modular.trig
rdfpipe -i turtle -o trix 01_custodian_name_modular.owl.ttl > 01_custodian_name_modular.trix

Tool: rdfpipe from rdflib package

Step 3: Create UML Diagrams (Manual)

LinkML's auto-generators (gen-plantuml, gen-yuml) do not support modular schemas properly. Created comprehensive diagrams manually based on schema structure.

Mermaid: Manually authored class diagram with all relationships
PlantUML: Manually authored with color-coded packages and detailed notes

Step 4: Validate

from rdflib import Graph
g = Graph()
g.parse('01_custodian_name_modular.owl.ttl', format='turtle')
# SUCCESS: 2,701 triples

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Ontology Mappings in RDF

The generated RDF includes mappings to:

W3C/DCMI Vocabularies

• OWL: Class/property definitions
• RDFS: Labels, comments, subclass relationships
• RDF: Type assertions
• DCTERMS: Title, license, version
• SKOS: Definitions, notes, exact/close mappings
• PAV: Provenance (version, license)
• FOAF: Agent information
• PROV-O: Activity tracking
• TIME: Temporal expressions

Domain Ontologies

• W3C Org Ontology (org:): Organization structure

  • org:classification (LegalEntityType)
  • org:hasUnit (GovernanceStructure)

• ROV (rov:): Registered organizations

  • rov:legalName (LegalName)
  • rov:orgType (LegalForm)
  • rov:registration (RegistrationNumber)
  • rov:hasRegisteredOrganization (RegistrationAuthority)

• TOOI (tooi:): Dutch government

  • tooi:rechtsvorm (legal form)
  • tooi:organisatieIdentificatie (registration)
  • tooi:officieleNaamInclSoort (legal name)

• GLEIF (gleif:): Legal entity identifiers

  • gleif:hasLegalForm (LegalForm)
  • gleif-base:hasEntityStatus (LegalStatus)

• Schema.org (schema:): Web semantics

  • schema:status (LegalStatus)
  • schema:identifier (identifiers)
  • schema:legalName (legal name)

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RDF Format Comparison

Format	Human-Readable	Machine-Readable	Web-Friendly	Compression	Use Case
Turtle	✅ Excellent	✅ Good	🟡 Fair	Best	Editing, documentation
N-Triples	🟡 Fair	✅ Excellent	🟡 Fair	None	Streaming, line-by-line processing
JSON-LD	🟡 Fair	✅ Excellent	✅ Excellent	Good	Web APIs, JavaScript
RDF/XML	❌ Poor	✅ Good	🟡 Fair	Fair	Legacy systems, XML tools
N3	✅ Excellent	✅ Good	🟡 Fair	Best	Advanced logic, rules
TriG	✅ Good	✅ Good	🟡 Fair	Best	Named graphs, datasets
TriX	❌ Poor	✅ Good	🟡 Fair	Poor	XML + named graphs

Recommendations:

• Development/Documentation: Use Turtle (most readable)
• Web APIs: Use JSON-LD (web-native)
• Bulk Processing: Use N-Triples (line-based, streaming)
• SPARQL Queries: Load Turtle or TriG into triplestore
• Legacy Integration: Use RDF/XML if required

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SPARQL Query Examples

Query 1: Find All Legal Entity Types

PREFIX heritage: <https://nde.nl/ontology/hc/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT ?type ?label ?description
WHERE {
  ?type a heritage:LegalEntityType .
  OPTIONAL { ?type rdfs:label ?label }
  OPTIONAL { ?type heritage:description ?description }
}

Query 2: Find All Classes with Legal Form

PREFIX heritage: <https://nde.nl/ontology/hc/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT ?class ?label
WHERE {
  ?class rdfs:subClassOf* heritage:CustodianReconstruction .
  ?class rdfs:label ?label .
  FILTER EXISTS { ?class heritage:legal_form ?form }
}

Query 3: List All Slots with ISO 20275 Mapping

PREFIX heritage: <https://nde.nl/ontology/hc/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX rov: <http://www.w3.org/ns/regorg#>

SELECT ?slot ?label ?mapping
WHERE {
  ?slot a heritage:Slot .
  ?slot rdfs:label ?label .
  ?slot skos:exactMatch|skos:closeMatch ?mapping .
  FILTER (CONTAINS(STR(?mapping), "regorg"))
}

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File Locations

schemas/20251121/
├── linkml/
│   └── 01_custodian_name_modular.yaml     # Source LinkML schema
│
├── rdf/
│   ├── 01_custodian_name_modular.owl.ttl  # Turtle (primary)
│   ├── 01_custodian_name_modular.nt       # N-Triples
│   ├── 01_custodian_name_modular.jsonld   # JSON-LD
│   ├── 01_custodian_name_modular.rdf      # RDF/XML
│   ├── 01_custodian_name_modular.n3       # N3
│   ├── 01_custodian_name_modular.trig     # TriG
│   └── 01_custodian_name_modular.trix     # TriX
│
└── uml/
    ├── mermaid/
    │   └── 01_custodian_name_modular.mmd  # Mermaid class diagram
    └── plantuml/
        └── 01_custodian_name_modular.puml # PlantUML class diagram

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Next Steps

Immediate

1. ✅ RDF generation - COMPLETE
2. ✅ UML generation - COMPLETE
3. ✅ Validation - COMPLETE
4. ⏳ Load into triplestore - TODO (optional)
5. ⏳ Render PlantUML diagram - TODO (optional)

Short-term

6. ⏳ Create SPARQL queries - TODO (example queries provided above)
7. ⏳ Generate documentation - TODO (using gen-doc)
8. ⏳ Create example instances - TODO (validate against RDF schema)

Medium-term

9. ⏳ Publish to ontology registry - TODO (LOV, BioPortal, etc.)
10. ⏳ Create persistent URIs - TODO (w3id.org or purl.org)
11. ⏳ Deploy SPARQL endpoint - TODO (public query interface)

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Tools Used

Tool	Version	Purpose
gen-owl	linkml 1.9.5	Generate OWL from LinkML
rdfpipe	rdflib (Python)	Convert RDF formats
rdflib	Python package	Validate RDF syntax
Manual authoring	-	Create UML diagrams

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Troubleshooting

Issue: gen-owl warnings in output

Problem: gen-owl outputs warnings to stdout, corrupting Turtle file

Solution: Redirect stderr to /dev/null:

gen-owl -f ttl schema.yaml 2>/dev/null > output.ttl

Issue: gen-plantuml/gen-yuml fail with modular schema

Problem: LinkML generators don't support modular imports properly

Solution: Manually author UML diagrams based on schema structure

Issue: rdfpipe parsing errors

Problem: Turtle file contains non-RDF content (warnings)

Solution: Regenerate Turtle cleanly with stderr suppressed

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Version Control

Generated from:

• Schema: schemas/20251121/linkml/01_custodian_name_modular.yaml
• Version: 0.1.0 (schema version in LinkML)
• Legal Entity Model: v0.2.2 (project version)
• Generation Date: 2025-11-22

Git Status:

• All generated files should be committed to version control
• RDF files are derived but worth tracking (transparency)
• UML diagrams should be committed (manual authoring)

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References

• LinkML Documentation: https://linkml.io/
• RDF 1.1 Primer: https://www.w3.org/TR/rdf11-primer/
• OWL 2 Primer: https://www.w3.org/TR/owl2-primer/
• SPARQL 1.1 Query: https://www.w3.org/TR/sparql11-query/
• Mermaid Docs: https://mermaid.js.org/
• PlantUML Docs: https://plantuml.com/class-diagram

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Status: ✅ ALL GENERATION COMPLETE

Next Session: Data instance creation and validation