RO-Crate and RDFC interoperability

Protégé MCP 0.6.0 gives an ontology project a portable metadata record and a reproducible RDF dataset identity. RO-Crate describes the project and its root ontology artifact; RDFC-1.0 + SHA-256 identifies the asserted root RDF dataset independently of statement order and blank-node labels.

Table of contents

  1. What each part does
  2. Project layout
  3. Minimal RO-Crate metadata
  4. Supported RO-Crate versions
  5. Validate and run the interoperability gate
  6. What the RDFC digest covers
  7. Offline and bounded validation

What each part does

Part Role Where you see it
RO-Crate Portable JSON-LD metadata for the ontology project, its root file, profile, title, publication date, and license. ro-crate-metadata.json (or .jsonld for RO-Crate 1.0)
RDFC-1.0 + SHA-256 Canonicalizes the root RDF dataset and hashes the canonical N-Quads, so insignificant ordering and blank-node labels do not change its identity. rdf_dataset_fingerprint from run_project_qc
Protégé MCP project policy Tells Protégé MCP which crate, root artifact, canonicalization, reasoner, and QC stages the project requires. It is an execution overlay, not an exchange standard. .protege-mcp/project.yaml

RO-Crate metadata can be read by another RO-Crate-aware application without understanding project.yaml. Conversely, the RDFC digest identifies RDF content; it does not replace project metadata, a file checksum, or an import lock.

Project layout

A minimal project keeps the policy, crate metadata, and ontology artifact under one project root:

my-ontology/
├── .protege-mcp/
│   └── project.yaml
├── ontology.ttl
└── ro-crate-metadata.json

The policy declares the portable layer explicitly:

version: 1
project_id: example-ontology
root_ontology: https://example.org/ontology
project_root: .

interoperability:
  profile: https://hakjuoh.github.io/protege-mcp/profiles/project-v1/
  additional_profiles: []
  root_artifact: ontology.ttl
  metadata:
    path: ro-crate-metadata.json
    format: ro-crate-1.1
  canonicalization:
    algorithm: RDFC-1.0
    hash: SHA-256
    scope: root-ontology
    timeout_ms: 120000

filesystem:
  allow_external_paths: false
network:
  default: deny
  allowed_hosts: []

reasoning:
  reasoner: HermiT
  owl_profile: DL
  required: true
  timeout_ms: 120000

imports:
  mode: unlocked
  fail_on_missing: true
  network: deny

validation:
  required_stages: [interoperability, reasoner, profile, governance, structural]
  fail_on: warning

Paths are resolved from the effective project root, not from the process working directory. Protégé MCP rejects URL-shaped paths, traversal, and symlink escapes unless the local administrator has explicitly enabled the external-path compatibility profile.

Minimal RO-Crate metadata

For the policy above, a matching RO-Crate 1.1 descriptor is:

{
  "@context": "https://w3id.org/ro/crate/1.1/context",
  "@graph": [
    {
      "@id": "ro-crate-metadata.json",
      "@type": "CreativeWork",
      "about": {"@id": "./"},
      "conformsTo": {"@id": "https://w3id.org/ro/crate/1.1"}
    },
    {
      "@id": "./",
      "@type": "Dataset",
      "name": "Example ontology project",
      "description": "An ontology project packaged for reproducible validation.",
      "datePublished": "2026-07-16",
      "license": "https://spdx.org/licenses/BSD-2-Clause.html",
      "identifier": "example-ontology",
      "conformsTo": {
        "@id": "https://hakjuoh.github.io/protege-mcp/profiles/project-v1/"
      },
      "mainEntity": {"@id": "ontology.ttl"},
      "hasPart": {"@id": "ontology.ttl"}
    },
    {
      "@id": "https://hakjuoh.github.io/protege-mcp/profiles/project-v1/",
      "@type": "CreativeWork",
      "name": "Ontology project RO-Crate profile v1"
    },
    {
      "@id": "ontology.ttl",
      "@type": "File",
      "encodingFormat": "text/turtle",
      "about": {"@id": "https://example.org/ontology"}
    },
    {
      "@id": "https://example.org/ontology",
      "@type": "Dataset",
      "conformsTo": {"@id": "https://www.w3.org/TR/owl2-overview/"}
    }
  ]
}

The root identifier must equal the policy’s project_id. The root artifact and ontology IRI must also agree with root_artifact and root_ontology.

Supported RO-Crate versions

Policy format Required context Metadata filename Profile entity
ro-crate-1.0 https://w3id.org/ro/crate/1.0/context ro-crate-metadata.jsonld CreativeWork
ro-crate-1.1 https://w3id.org/ro/crate/1.1/context ro-crate-metadata.json CreativeWork
ro-crate-1.2 https://w3id.org/ro/crate/1.2/context ro-crate-metadata.json Profile
ro-crate-1.3 https://w3id.org/ro/crate/1.3/context ro-crate-metadata.json Profile

RO-Crate 1.1 is the compatibility default. Select another version when the receiving environment requires it. If both metadata.format and metadata.path are omitted, Protégé MCP can retain an unambiguous 1.2 or 1.3 context from an existing ro-crate-metadata.json; otherwise it materializes the 1.1 defaults. It never silently rewrites a crate from one declared version to another.

The complete required graph and version rules are defined by the Ontology project RO-Crate profile v1.

Validate and run the interoperability gate

Use these v0.6.0 tools:

  1. get_project_policy shows the discovered policy, effective defaults, resolved crate/root-artifact paths, and validation messages.
  2. validate_project_policy requires a policy and validates its RO-Crate metadata without running ontology QC.
  3. run_project_qc runs the required interoperability stage on the same isolated snapshot as the other stages.

A successful project-QC result includes:

  • rdf_dataset_fingerprint: sha256:<lowercase hex> over RDFC-1.0 canonical N-Quads;
  • rdf_dataset_identity: the canonicalization, hash, scope, RO-Crate version, and profile coordinates;
  • semantic_fingerprint: Protégé MCP’s separate OWL/editor revision identity;
  • an interoperability stage with status=pass.

An invalid/missing crate, a canonicalization timeout, or a dataset that cannot be rendered losslessly makes the required stage an execution error; it cannot become a false pass.

What the RDFC digest covers

The root-ontology scope includes:

  • ontology and version IRIs;
  • ontology annotations;
  • asserted axioms, including axiom annotations;
  • direct owl:imports coordinates.

It excludes the contents of imported ontologies. Use write_import_lock and verify_import_lock to checksum local dependency artifacts.

RDFC-1.0 canonicalizes the RDF dataset before hashing, so triple/quad order and parser-assigned blank-node identifiers do not affect the result. Protégé MCP verifies the serialized dataset before hashing and fails closed when the host RDF renderer would omit an asserted anonymous-individual structure.

Do not compare rdf_dataset_fingerprint with semantic_fingerprint: they intentionally use different contracts. The former is the standards-facing RDF dataset identity; the latter is the editor-aware revision token used by transactional previews and optimistic concurrency.

Offline and bounded validation

RO-Crate validation never dereferences JSON-LD contexts, profiles, imports, or arbitrary entity IRIs. Metadata is limited to 4 MiB, 20,000 graph entities, and 100 JSON nesting levels, with duplicate JSON keys rejected. Canonicalization is bounded by the policy timeout (120 seconds by default).

Protégé MCP validates this exchange boundary but does not ship a vendor-specific repository connector. Move the ontology file, RO-Crate metadata, policy, and verified import artifacts through the file/API workflow supported by the receiving system. See Commercial platform interoperability for the current product profiles, non-goals, and connector requirements.

Protégé MCP is licensed under the BSD 2-Clause License. Protégé is a trademark of Stanford University.

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