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Changelog

All notable changes to ontoink are documented here. This project follows Semantic Versioning.

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[0.6.3] — 2026-06-10

PyPI · Release

Added

  • Full in-browser SHACL validation — interactive Validate now runs a standards-compliant SHACL Core engine (rdf-validate-shacl) entirely in the browser, replacing the old cardinality-only checker. It catches sh:datatype, sh:class, sh:nodeKind, sh:pattern, value ranges, sh:in/sh:hasValue/closed, logical/shape-based constraints, property paths and inline blank-node shapes — verified against pyshacl. Ships as a committed same-origin bundle (assets/shacl/shacl.mjs), so it works on the static demo with no server. (SHACL-SPARQL constraints and SHACL-AF sh:rule still need the server/build-time pyshacl.)
  • Server-side ontology dereference proxy (/deref) — a generic, CORS-free, SSRF-guarded alternative to the hard-coded mirror registry; the "More…" dereference prefers it when a server is reachable and works for any ontology (including FOAF)

Fixed

  • Dead ontology-mirror URLs — the BFO and IAO entries in the known-ontology registry returned 404 (files moved); nfdicore is now version-less. Browser dereferencing of those namespaces works again
  • Legend edge arrowheads — the legend ignored the pointer shape chosen in Edit Layout and always drew a triangle; it now renders tee / vee / diamond / circle to match the graph
  • Playground "Edit & Validate" now has a SHACL Shapes pane — the playground's editor was missing the shapes editor, so an uploaded or ?shape=-linked SHACL file was never shown and validation ran against empty shapes. The panel now matches the fence-rendered editor (Source | SHACL Shapes + Validation Report), and validation falls back to the loaded shapes so ?data=…&shape=… links validate even before the editor is opened

[0.6.2] — 2026-06-08

PyPI · Release

Fixed

  • All four OWL reasoner backends now return inferences — owlready2/HermiT, native konclude, and konclude-wasm each failed silently before (Turtle vs RDF/XML, OWL-XML output parsed as RDF/XML, N-Quads vs N-Triples), so only owlrl ever produced results. All four now work on OWL 2 property-restriction ontologies
  • owl:equivalentClass (and intersectionOf-nested) restrictions are now visualised — previously only rdfs:subClassOf restrictions were drawn. The two are distinguished: ⊑ (solid triangle) for a necessary condition vs ≡ (hollow diamond) for a definition
  • Browser (in-page) Konclude WASM Error: unwind — the Emscripten exit sentinel is now caught and the inferred graph harvested
  • Edit & Validate → Update Graph (and the playground) no longer destroy restrictions — a new blank-node-aware client-side parser collapses owl:Restriction into the same ⊑/≡ edges as the server-rendered diagrams, instead of exploding into raw [ ]/owl:Restriction nodes

Added

  • reasoner: fence option — set a diagram's default reasoner backend, e.g. reasoner: owlrl
  • Comprehensive Reasoning & Inference demo — examples/reasoning-demo.md now walks every RDF/RDFS/OWL/OWL2 reasoning feature with a small self-contained example each

Changed

  • OLS IRI-dereference link — dropped the "Found in: N ontologies" line; the cross-ontology link now reads "Ontologies using this IRI on OLS"

[0.6.1] — 2026-06-04

PyPI · Release

Added

  • SHACL Shapes editor pane in Edit & Validate — two-column editor (data TTL + SHACL shapes) with CodeMirror Turtle highlighting and a constraint-count in the report line
  • Resizable popups — drag the bottom-right corner to enlarge a popup

Fixed

  • "Ontologies reusing this IRI on OLS" link returned zero results — now derives the OBO short ID (e.g. IAO:0000300) so OLS search matches
  • Sticky toolbar bleeding over host-page chrome — .ontoink-container now isolates its stacking context

[0.6.0] — 2026-05-17

Added

  • Browser-side reasoning in the playground — Reasoning button with backend dropdown (Auto / Browser Konclude WASM / Server backends). Browser option enabled when cross-origin isolated; server options enabled when /health reachable
  • COOP/COEP service worker so the playground's WASM Konclude works on GitHub Pages without server-side header support
  • Per-request reasoner override on POST /reason — clients can choose the backend without restarting the server
  • Playground parity — Abstract View and reasoning panel match the MkDocs fence path
  • Production Docker image with ONTOINK_MODE env switch (serve / build / api / all) and ONTOINK_REASONER selector. The new all mode builds the docs once and serves them via FastAPI on the same origin as /reason — so the playground's "Server" reasoner works without a reverse proxy
  • Konclude two-pass reasoning — native Konclude wrapper runs both classification and realization. Note: Konclude expects OWL/XML input; for TTL input use owlready2 or konclude-wasm
  • Native Konclude reasoner (ONTOINK_REASONER=konclude) — upstream Konclude C++ tableau binary, downloaded into the production Docker image
  • rdf-reasoner-konclude (ONTOINK_REASONER=konclude-wasm) — WASM Konclude port for browsers and Node.js, no Java required
  • FastAPI mode — /reason, /validate, /health endpoints when ONTOINK_MODE=api
  • SHACL constraint edges in the playground — shapes now render as cyan dashed cardinality-labelled edges, matching the MkDocs build path
  • SHACL shape IRI dereferencing — labels and axioms auto-fetched for sh:path, sh:targetClass, sh:class, sh:datatype, sh:node IRIs on graph load
  • GitHub Actions workflow to build & push the Docker image to GHCR on each v* tag
  • TESTING.md with end-to-end manual test plan (Python, JS, MkDocs, playground, Docker)
  • .env.sample, NOTICE, and CITATION.cff files for deployment config and third-party attribution

Fixed

  • Reasoning UI lock state — the Reasoning button and dropdown disable while reasoning runs, with a visible Cancel button. Server requests are aborted via AbortController
  • SPARQL autocomplete on macOS — added Alt+/ as a universal trigger; macOS reserves Ctrl+Space for input source switching by default
  • Browser WASM reasoner module loading — switched from jsdelivr's /+esm to esm.sh
  • Demo pages looked unstyled in all mode — switched Cross-Origin-Embedder-Policy from require-corp to credentialless
  • Legend and namespace overlay now refresh when the layout is switched
  • Edit Layout customizations propagate to the legend — node color / node shape / edge color / line style / arrow shape changes immediately update the on-page legend
  • PNG and SVG exports now embed Edit Layout customizations in the legend (previously the export legend always showed default styles)

Changed

  • Reasoner selection is now user-configurable via env var

[0.5.2] — 2026-04-17

PyPI · Release

Fixed

  • Broken parsing of TTL with periods inside strings — the statement splitter now respects quoted strings, so descriptions like "...time frame. Every batch..." no longer break parsing
  • Hyphenated prefixes not recognized — prefixes like samm-c:, ext-built:, ext-classification: are now correctly captured

[0.5.1] — 2026-04-17

PyPI · Release

Fixed

  • Playground hang on non-HTTP namespaces — urn:, oid:, and other non-HTTP URI schemes are skipped during auto-dereference

[0.5.0] — 2026-04-10

PyPI · Release

Highlight: Automatic Ontology Label Resolution

ontoink now automatically fetches and resolves human-readable labels from referenced ontologies. When your shape graph uses IRIs from nfdicore, BFO, IAO, or other ontologies, ontoink fetches the ontology source files and extracts rdfs:label, rdfs:comment, type information, and more — so you see "contributor role" instead of NFDI_0000118 everywhere.

This works across:

  • Click popups — "More..." shows label, comment, type, subclass, deprecation status
  • SPARQL autocomplete — Ctrl+Space shows both human label and IRI local name
  • SPARQL class/property dropdowns — contributor role (NFDI_0000118) instead of just NFDI_0000118
  • Query results — IRIs rendered as label (prefixed:name)
  • SPARQL Explorer — when the endpoint lacks labels, fetches ontology source files as fallback

Added

  • Automatic ontology label resolution — background fetch of all referenced ontology namespaces on graph init
    • Known ontology URL registry bypasses CORS-broken redirects for nfdicore, BFO, IAO, RO, FOAF, Schema.org, SKOS
    • Robust line-based OWL TTL parser handles Protégé-style files with nested blank nodes, collections, and """ strings
    • Dual parser strategy: merges results from minimal + robust parsers for maximum coverage
  • Enhanced IRI dereferencing — "More..." button shows label, comment, type, subClassOf, deprecation, SKOS definitions, editorial notes
  • Scrollable popups — popup containers capped at 70vh with overflow scroll; deref results independently scrollable
  • Sticky toolbar — toolbar stays fixed at viewport top while scrolling
  • SPARQL Explorer ontology fallback — fetches nfdicore, BFO, IAO, FOAF, etc. when endpoint lacks rdfs:label
  • SPARQL results with labels — query result IRIs shown as label (prefixed:name)
  • SPARQL dropdowns always fresh — class/property selects rebuild with latest labels every time panel opens
  • OntoSniff — ontology smell detector with 9 anti-patterns, quality score (0-100), standalone page
  • SPARQL Explorer — endpoint connection, schema discovery, query builder, Ctrl+Space autocomplete
  • Abstract Model View, Search & Highlight, Layout Switcher, Graph Statistics, Path Finder, Minimap, Neighborhood Focus, Playground, SHACL Editor

Fixed

  • IRI dereferencing for nfdicore and ontologies with CORS-broken 302 redirects
  • SPARQL Explorer label fetching with batch loading and ontology source fallback
  • SPARQL dropdowns refresh labels on every panel open (not just first build)
  • PNG/SVG export: minimap hidden, scale 2x, reliable overlay positioning

[0.3.0] — 2026-04-09

PyPI · Release

Added

  • OWL Reasoning — HermiT reasoner (via owlready2) runs at build time for full OWL DL reasoning, with owlrl fallback for OWL-RL profile
    • Reasoning toolbar button opens an inferences panel showing all inferred triples in a table
    • "Show on graph" checkbox overlays inferred triples as purple dotted edges and nodes
    • "Validate with Inferences" button runs SHACL validation with inferred triples included
    • Smart filtering removes reflexive triples, built-in namespace noise, and domain/range propagation
    • Configuration option: reasoning: true/false per diagram
  • OWL Reasoning demo — new example with class hierarchy, inverse, transitive, and symmetric properties
  • Draggable popups — node and edge popups can be repositioned by dragging the header
  • Collapsible popup sections — Connections and SHACL Constraints are collapsed by default (click to expand)
  • IRI dereferencing — "More…" button in popups fetches structured data from the IRI via content negotiation
  • Prefix editing — toggle prefix visibility from the Edit Layout panel

Fixed

  • Prefix overlay only shows prefixes declared in the TTL source (not rdflib built-ins like dc, dcterms, skos, etc.)
  • Popup toggle sections work correctly for all node types (fixed special character issue in IRI-based IDs)
  • PNG/SVG export captures the exact viewport with overlays at their on-screen positions

[0.2.0] — 2026-04-08

PyPI · Release

Added

  • Edge click popup — click any edge to see its label, type, IRI, source/target nodes, cardinality, and copy buttons
  • Edit Layout panel — renamed from "Colors"; now includes:
    • Node shape selector (rectangle, ellipse, diamond, hexagon, triangle, star, and more)
    • Edge line style selector (solid, dashed, dotted)
    • Edge arrow shape selector (triangle, vee, circle, diamond, chevron, none, and more)
    • Color pickers for node types, edge types, and namespace groups
  • Documentation site — full Material for MkDocs documentation with getting started guide, examples, contributing guide, citation info, and changelog

Fixed

  • Export layout fidelity — PNG and SVG exports now capture the exact viewport the user sees (zoom, pan, node positions) instead of re-fitting all elements
  • Export overlay positioning — legend and namespace prefix boxes are drawn at their actual on-screen positions (respects user dragging)
  • Export overlay sizing — legend and prefix boxes match their DOM dimensions; font sizes aligned to CSS (11px entries, 12px titles, 10px prefixes)

Changed

  • Toolbar button renamed from "Colors" to "Edit Layout"
  • Package renamed to ontoink (from ontoviz)

[0.1.0] — 2026-04-07

PyPI · Release

Initial public release.

Added

  • Interactive ontology visualization using Cytoscape.js with dagre layout
  • Formal visual notation: classes (rectangles), individuals (ellipses), literals (dashed ellipses), datatypes (diamonds)
  • Edge styles: object properties (blue), data properties (green), rdf:type (grey dashed), rdfs:subClassOf (black), SHACL constraints (cyan dashed bold)
  • SHACL constraint overlay with cardinality badges [min..max]
  • Click popup for nodes with IRI, type badge, ontology source, connections, copy buttons
  • Inline TTL editor with CodeMirror and Turtle syntax highlighting
  • Live SHACL validation with constraint checking (browser-side)
  • Build-time SHACL validation using pySHACL
  • Publication-ready PNG (3x hi-DPI) and SVG export with legend and namespace boxes
  • Auto-generated interactive legend (draggable, resizable)
  • Namespace prefix overlay with "show all" toggle
  • Toolbar: zoom in/out, fit, fullscreen, export PNG/SVG/TTL, colors
  • Color coding by ontology source (BFO, IAO, nfdicore, RO, OBI, PMD, QUDT, Schema.org, FOAF)
  • Color customization panel for node types and namespace groups
  • MkDocs plugin with pymdownx.superfences custom fence integration
  • Configuration options: source, shape, height, editor, legend, namespaces
  • Demo site with GitHub Pages deployment
  • Comprehensive test suite with pytest (20 tests)