🧪 RO-Crate Full Example Guide

File: examples/full_example.py

Comprehensive example demonstrating advanced RO-Crate features: chemical synthesis workflow, circular relationships, SHACL validation, and dynamic updates.

📊 Data Model

OpenBIS Entities (`http://openbis.org/`)

Entity	Properties	Relationships
Project	code, name, description, created_date	→ space
Space	name, description, created_date	→ collections[]
Collection	name, sample_type, storage_conditions, created_date	(leaf node)
Equipment	name, model, serial_number, created_date, configuration{}	→ parent_equipment

Schema.org Entities (`https://schema.org/`)

Entity	Properties	Relationships
Molecule	name, smiles, molecular_weight, cas_number, created_date, experimental_notes	→ contains_molecules[]
Person	name, orcid, email	→ affiliation
Organization	name, country, website	(referenced by Person)
Publication	title, doi, publication_date	→ authors[], molecules[], equipment[], organization

⚡ Workflow: Setup → Experiment → Export

Created Entities:

1 Project, 1 Space, 1 Collection, 2 Equipment (nested)
5 Molecules, 2 People, 1 Organization, 1 Publication

Key Features:

✅ Circular Relationships: Person ↔ Person colleagues (auto-resolved)
✅ Mixed Namespaces: OpenBIS + schema.org with auto-context
✅ SHACL Validation: 100% compliance with 150+ rules
✅ Dynamic Updates: Experiment modifies molecules + adds new product

🔧 Key Technical Features

1. Circular Relationship Resolution

# Automatic resolution of Person ↔ Person colleagues
sarah = Person(colleagues=[marcus])
marcus = Person(colleagues=[sarah])
# → SchemaFacade.resolve_placeholders() merges duplicates

2. Chemical Data with SMILES

Benzene: c1ccccc1 → Toluene: Cc1ccccc1 → Product: (c1ccccc1).(Cc1ccccc1)

3. Scale Metrics

Entities: 15 → 16 (after synthesis)
RDF Triples: ~500 → ~530
SHACL Validation: 100% compliance

<EFBFBD> Usage

PYTHONPATH=./src python examples/full_example.py

Output: Initial Crate: full_example_initial/ Final Crate: full_example_final/ including file experimental_observations

✅ Testing

python -m pytest tests/ -v                    # Full suite (85 tests)

Production-ready RO-Crate library with automatic relationship resolution, comprehensive validation, and modern architecture.

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