@skaterqiang/protege-js

v0.1.0

Published

a month ago

Zero-dependency OWL 2 / RDF / SWRL library for Node.js: 6 parsers, 3 serializers, and a forward-chaining reasoner covering all 78 W3C OWL 2 RL rules plus QL/EL profiles. A Node.js port of Protégé's non-UI core.

Protégé JS

A zero-dependency OWL 2 / RDF / SWRL library for Node.js — 6 parsers, 3 round-trip serializers, and a forward-chaining reasoner covering all 78 W3C OWL 2 RL rules plus QL / EL profiles.

Install

npm install @skaterqiang/protege-js

// Flat imports
const { OWL2RLReasoner, TripleStore, TurtleParser, checkRL } = require('@skaterqiang/protege-js');

// Or namespaced
const protege = require('@skaterqiang/protege-js');
protege.inference.OWL2RLReasoner;   // reasoners, triple store, queries
protege.io.TurtleParser;            // parsers + writers + loader
protege.model.OWLClass;             // entities, axioms, class expressions
protege.profiles.checkRL;           // RL / QL / EL profile validators

// Deep imports also work
const { OWL2RLReasoner } = require('@skaterqiang/protege-js/src/inference/OWL2RLReasoner');

Why the scoped name? The unscoped name protege-js is rejected by npm's name-similarity rule because protegejs already exists — an unrelated 2018 jQuery/Prototype.js shim that happens to share the French word protégé. This package is scoped to make authorship unambiguous, which is exactly what npm's package name guidelines ask for. The GitHub repository keeps the shorter name: skaterqiang/protege-js.

Full API reference: docs/API.md.

What this is

Protégé is a large Java/Swing application (~1498 files; ~1205 are Swing UI). This project ports the non-UI core to Node.js and presents it through a web UI served by Node, which can be wrapped in an Electron desktop window.

Only the model layer is reimplemented — the part that is genuinely useful in Node.js and reusable by other projects (such as Synapse). Swing views, OSGi plugin plumbing, and the Java desktop workspace are intentionally not ported.

Attribution: protege-js is an independent reimplementation and is not affiliated with or endorsed by Stanford University or the Protégé team. Protégé is a trademark of Stanford University; the name is used for descriptive purposes only. See LICENSE for details. Sample ontologies under sample/ontologies/ (BFO / OGMS / IAO / RO-core) come from the OBO Foundry under CC-BY 4.0 / CC0 1.0 — see sample/README.md.

Run

# As a library (no server needed):
node -e "const {TurtleParser}=require('@skaterqiang/protege-js'); console.log(new TurtleParser().parse('@prefix ex: <http://e.org/> . ex:a ex:p ex:b .').size)"

# Web UI only (no Electron dependency needed):
npm run start:web
# then open http://localhost:8899/

# Desktop (requires electron, `npm install` first):
npm start

Test

npm test    # 281 tests: core model + 80 OWL 2 RL rule tests + OWL 2 full-spec + 业务案例 e2e + exports map

OWL 2 全覆盖

完整覆盖 W3C OWL 2 规范，包括：

OWL 2 RL 推理：78 条规则前向链接物化（见下文）
OWL 2 QL / EL 推理：基于 RL 规则子集的最小推理机（OWL2QLReasoner / OWL2ELReasoner）
OWL 2 全结构规范：38 种公理类型、26 种类表达式、SWRL 规则
解析器：Functional Syntax、Turtle、RDF/XML、Manchester Syntax、OWL/XML
序列化器：Functional Syntax、Turtle、RDF/XML
桥接：RDFGraphToOntology（TripleStore → OWLOntology）、OntologyLoader（含 imports 闭包）
验证：OWL2Profiles（RL/QL/EL profile 检查）、GlobalRestrictionsValidator
查询：ReasonerQueries（getSubClasses / getInstances / isSubClassOf / isSatisfiable）
SWRL：模型 + 解析器 + 求值器（含长尾 builtins）
详见 docs/design/OWL2-缺口分析.md（全部缺口已实施完成）

OWL 2 RL inference engine

A forward-chaining, semi-naive materialization engine covering all 78 rules of the OWL 2 RL profile (6 categories: eq / prp / cls / cax / dt / scm). See docs/owl2-rl/OWL2-RL-规则细则.md for the full rule list with W3C references, and docs/owl2-rl/owl2-profiles-spec.html for the original W3C specification snapshot.

const { OWL2RLReasoner } = require('./src/inference/OWL2RLReasoner');
const r = new OWL2RLReasoner();
r.store.add('ex:A', 'http://www.w3.org/2000/01/rdf-schema#subClassOf', 'ex:B');
r.store.add('ex:x', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#type', 'ex:A');
r.materialize();                                  // runs all 78 rules to fixpoint
r.entails('ex:x', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#type', 'ex:B'); // true
r.isConsistent();                                  // true / false (false-consequent rules)

Files:

src/inference/
  TripleStore.js        triple store with pattern matching + RDF-list walker
  rdf.js                namespace constants + literal helpers
  OWL2RLReasoner.js     fixpoint engine, inconsistency collector
  rules/owl2rl.js       the 78 OWL 2 RL rules
test/owl2rl/            80 rule tests (>=1 per rule)
docs/owl2-rl/           W3C spec snapshot + rule catalog + Chinese细则

OWL 2 full structural spec

Beyond the RL profile, the model layer covers the complete OWL 2 structural specification:

38 axiom types (every axiom in the spec): declaration, subclass, equivalent/disjoint classes, disjoint union, property hierarchy (sub/equivalent/disjoint/inverse/chain), property domain/range, all 7 object-property characteristics (functional, inverse-functional, reflexive, irreflexive, symmetric, asymmetric, transitive), functional data property, datatype definition, has-key, same/different individuals, class/object/data property assertion (positive + negative), annotation assertion, annotation property hierarchy + domain/range.
26 class expression kinds, object and data sides: intersection, union, complement, one-of, some/all/has-value/has-self, min/max/exact cardinality (qualified and unqualified), data intersection/union/complement/one-of, datatype restriction with facets.
SWRL rules with class/object/data property atoms, sameAs/differentFrom atoms, and 30+ built-ins (math, string, comparison). Forward-chaining materialization over the same TripleStore used by OWL 2 RL.

Parsers

Five syntax parsers:

RDF/XML — src/io/RDFXMLParser.js: classic OWL/XML, extended to recognize disjointWith, inverseOf, sameAs, differentFrom, all 7 property characteristics, nested class expressions (owl:Restriction / intersectionOf / unionOf / ...), owl:hasKey, anonymous individuals and punning.
Turtle — src/io/TurtleParser.js: W3C Turtle 1.1 with @prefix/@base, SPARQL PREFIX/BASE, typed/lang literals, blank nodes, collections, auto-typed numbers/booleans.
OWL 2 Functional-Style — src/io/FunctionalSyntaxParser.js: parses the complete functional syntax including Prefix(...), Ontology(...) (with imports / versionIRI), all 38 axiom forms, and all class expressions / data ranges.
Manchester Syntax — src/io/ManchesterSyntaxParser.js.
OWL/XML — src/io/OWLXMLParser.js.
SWRL text — src/io/SWRLParser.js.

Serializers (writers)

Turtle — src/io/TurtleWriter.js
OWL 2 Functional-Style — src/io/FunctionalSyntaxWriter.js
RDF/XML — src/io/RDFXMLWriter.js

All three writers round-trip: Turtle/Functional/RDF/XML 导入 → 结构化 → 导出 → 再导入不丢公理（见 sample/case4、case6、case7）。

const { TurtleParser } = require('./src/io/TurtleParser');
const { FunctionalSyntaxParser } = require('./src/io/FunctionalSyntaxParser');
const { SWRLReasoner } = require('./src/inference/SWRLReasoner');

const store = new TurtleParser().parse(`
  @prefix ex: <http://example.org/> .
  ex:alice a ex:Person ; ex:age 30 .
`);

const onto = new FunctionalSyntaxParser().parse(`
  Prefix(ex:=<http://example.org/>)
  Ontology( Declaration(Class(ex:Person)) )
`);

Architecture

main.js                        Electron shell (falls back to headless web server)
src/
  index.js                     public API entry (flat + namespaced exports)
  model/                       org.protege.editor.owl.model equivalents
    IRI.js                     org.semanticweb.owlapi.model.IRI
    OWLEntity.js               OWLClass / OWLObjectProperty / OWLDataProperty /
                               OWLNamedIndividual / OWLDatatype / OWLAnnotationProperty
    OWLAxiom.js                OWLSubClassOfAxiom, OWLDeclarationAxiom, domain/range,
                               class/property assertions, annotation assertions, ...
    OWLClassExpression.js      anonymous expressions: intersection/union/some/only/...
    OWLLiteral.js              org.semanticweb.owlapi.model.OWLLiteral
    OWLOntology.js             OWLOntology + OWLOntologyID (in-memory axiom set)
    OWLModelManager.js         OWLModelManager / OWLModelManagerImpl
    SWRL.js                    SWRLRule + class/object/data property/builtin atoms
    event/
      OWLModelManagerEvent.js  model.event.EventType + OWLModelManagerChangeEvent
    hierarchy/
      HierarchyProvider.js     AssertedClassHierarchyProvider,
                               OWLObject/DataPropertyHierarchyProvider
  io/
    RDFXMLParser.js            dependency-free RDF/XML reader (typed-node + Description style)
    RDFXMLWriter.js            RDF/XML serializer
    TurtleParser.js            W3C Turtle 1.1 reader
    TurtleWriter.js            Turtle serializer
    FunctionalSyntaxParser.js  OWL 2 functional-style reader
    FunctionalSyntaxWriter.js  functional-style serializer
    ManchesterSyntaxParser.js  Manchester Syntax reader
    OWLXMLParser.js            OWL/XML reader
    SWRLParser.js              SWRL text rule reader
    RDFGraphToOntology.js      TripleStore → OWLOntology bridge
    OntologyLoader.js          model.io.OntologyLoader (imports closure)
  inference/
    TripleStore.js             triple store with pattern matching + RDF-list walker
    rdf.js                     namespace constants + literal helpers
    OWL2RLReasoner.js          fixpoint engine, inconsistency collector (78 rules)
    rules/owl2rl.js            the 78 OWL 2 RL rules (eq / prp / cls / cax / dt / scm)
    OWL2ProfileReasoners.js    OWL2QLReasoner / OWL2ELReasoner (RL-rule subsets)
    SWRLReasoner.js            SWRL forward-chaining engine (30+ builtins)
    ReasonerQueries.js         getSubClasses / getInstances / isSubClassOf / isSatisfiable
  profiles/
    OWL2Profiles.js            OWL 2 RL / QL / EL profile validators
  validation/
    GlobalRestrictionsValidator.js  global-restriction checks
  server/
    webServer.js               Node http server + JSON API (/api/load, /api/tree, /api/stats)
    public/                    web UI (class/property hierarchy tree browser)
test/
  core.test.js                 node:test unit tests (model layer)
  owl2rl/                      80 rule tests (>=1 per OWL 2 RL rule)
  owl2/                        full-spec tests: axioms / class expressions / parsers /
                               writers / profiles / reasoner queries / sample e2e
sample/                        10 个真实业务案例 + ontologies/ 真实公开本体
                               (BFO / OGMS / RO-core / IAO, OBO Foundry 官方 PURL)

Java → JS mapping notes

| Protégé / OWLAPI (Java) | protege-js (Node) | |------------------------------------------|--------------------------------------------| | org.semanticweb.owlapi.model.IRI | src/model/IRI.js | | OWLEntity hierarchy | src/model/OWLEntity.js | | OWLAxiom hierarchy | src/model/OWLAxiom.js | | OWLClassExpression | src/model/OWLClassExpression.js | | OWLOntology / OWLOntologyID | src/model/OWLOntology.js | | OWLModelManager(Impl) | src/model/OWLModelManager.js | | model.event.EventType | src/model/event/OWLModelManagerEvent.js | | model.hierarchy.*HierarchyProvider | src/model/hierarchy/HierarchyProvider.js | | model.io.OntologyLoader + RDF/XML | src/io/OntologyLoader.js, RDFXMLParser.js | | OWLReasoner (RL/QL/EL) | src/inference/OWL2RLReasoner.js, OWL2ProfileReasoners.js | | OWLReasoner query API | src/inference/ReasonerQueries.js | | OWL2Profile validators | src/profiles/OWL2Profiles.js |

Scope

Implemented:

Entities, IRIs, literals, class expressions (26 kinds), full 38-axiom model
Ontology container + signature indexes + ontology headers (imports / versionIRI)
Asserted class / object property / data property hierarchy providers + tree JSON
Parsers: RDF/XML, Turtle, Functional Syntax, Manchester Syntax, OWL/XML, SWRL
Serializers: RDF/XML, Turtle, Functional Syntax (round-trip verified)
Inference: OWL 2 RL (all 78 rules), OWL 2 QL / EL, SWRL forward-chaining, inconsistency detection (disjoint / functional violations)
Validation: OWL 2 RL/QL/EL profile checkers, global-restriction validator
Query: ReasonerQueries (getSubClasses / getInstances / isSubClassOf / isSatisfiable)
RDFGraphToOntology bridge, OntologyLoader with imports closure
Web UI tree browser (Classes / Object Properties / Data Properties tabs)
10 个端到端业务案例（电商风控 / 医疗用药 / 制造 PPR / 真实 BFO-OGMS-IAO 加载 / ...）

Not implemented (out of scope for the Node core):

Tableau-based DL reasoning (HermiT/Pellet/Openllet) — 仅提供规则式 RL/QL/EL 推理
Editing operations, refactoring, search-importer, git integration
Swing workspace / views / OSGi plugin system