version: 2
project_id: example-ontology-v2
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

prefixes:
  skos: http://www.w3.org/2004/02/skos/core#

filesystem:
  allow_external_paths: false
audit:
  retention_days: 90
  max_file_bytes: 10485760
  max_files: 10
network:
  default: deny
  allowed_hosts: []

# Endpoints and credential bindings for this alias stay in owner-local configuration.
external_terms:
  providers:
    - id: ebi-ols
      profile: ols4
      enabled: false
      origin_alias: ebi-ols
      ontologies: [efo]
      languages: [en]
      ttl_seconds: 900
      freshness: cache_ok
      required_evidence_for: [reuse]
      max_results: 25

mappings:
  path: .protege-mcp/mappings.sssom.tsv
  allowed_predicates: [skos:exactMatch, skos:broadMatch, skos:narrowMatch]
  allowed_sources: [ebi-ols]
  allowed_licenses: [CC-BY-4.0]
  require_license: true
  required_findings: [missing_source, missing_target, predicate_not_allowed, license_not_allowed]
  directional_cycle_policy:
    skos:broadMatch: error
    skos:narrowMatch: error
  many_to_one_rules: []

jobs:
  allowed_types: [classification, project_qc, semantic_diff, inference_materialization]
  workers: 2
  queue_capacity: 32
  active_per_principal: 8
  retained_per_principal: 32
  retained_per_backend: 128
  retention_seconds: 3600

materialization:
  allowed_reasoners: [HermiT]
  allowed_categories: [subclass_axioms, equivalent_class_axioms, class_assertions,
    property_hierarchy_axioms, object_property_assertions, data_property_assertions]
  allowed_destinations: [new_ontology, project_file]
  allow_source_write: false
  max_axioms_per_category: 50000
  max_axioms_total: 50000
  max_bytes: 67108864
  timeout_ms: 120000

imports:
  mode: unlocked
  fail_on_missing: true
  network: deny

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

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