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Changelog

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

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[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)