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DEPENDENCY_MATRIX.md

Canonical inventory of external Rust crates and CLIs used by OntoIndex/OntoCode. Policy: ADR-0016. Do not add dependencies without updating this file.

Last updated: 2026-06-24

How to read this table

Column Meaning
Capability Product feature area
Chosen dependency Crate or external tool OntoIndex delegates to
Version pin Target for new workspace deps (workspace Cargo.toml may lag until integration)
OntoIndex facade Thin ontoindex-* crate or module
OntoIndex owns Logic that stays in-tree
ADR Decision record
Phase Roadmap milestone

Master matrix

Capability Chosen dependency Version pin OntoIndex facade OntoIndex owns ADR Phase
RDF parse + triple store + SPARQL oxigraph 0.4 (workspace) ontoindex-parser, ontoindex-query Entity extraction, catalog mapping, limits 0003 v0.2
RDF I/O ecosystem peer oxrdf, oxrdfio via Oxigraph / OntoLogos — — — —
SQL-like query parse sqlparser 0.53 (workspace) ontoindex-query Virtual tables, projection, WHERE 0011 v0.2
SQL joins / aggregations (v1.0) Extend sqlparser virtual tables first; datafusion if scope exceeds hand-rolled TBD at v1.0 ontoindex-query Table join logic or DataFusion adapter 0011 v1.0
Workspace scan + gitignore ignore 0.4 (workspace) ontoindex-core Path jail, hashing, format detection 0005 v0.2
LSP protocol lsp-server, lsp-types 0.7 / 0.97 ontoindex-lsp Custom methods, catalog JSON, path sandbox 0007 v0.2
Parse / import / prefix diagnostics oxigraph parse errors + catalog rules 0.4 ontoindex-diagnostics Lint rules: duplicate/missing labels, orphans, broken imports 0016 v0.3
OBO validation (future) fastobo-validator 0.4 ontoindex-diagnostics Map violations to LSP diagnostics 0016 v0.7b
OWL axiom model + round-trip horned-owl 1.4 ontoindex-owl Catalog bridge, patch write-back, consistency tests 0013 v0.4.0
Manchester functional syntax horned-functional 0.4 ontoindex-owl LSP range mapping, webview wire format 0016 v0.5
Manchester editor assist (optional) owl-ms-language-server evaluate at v0.5 extension / LSP Embed vs subprocess decision at implementation 0016 v0.5
Reasoner orchestration OntoLogos (ontologos-*) 0.9 → 1.0 ontoindex-reasoner ReasonerAdapter trait, cache, LSP JSON 0015 v0.6 / v1.0
Reasoner file load ontologos-parser 0.9 → 1.0 ontoindex-reasoner Workspace path → ontology input bridge 0015 v0.6
Reasoning transitive (via OntoLogos) reasonable, horned-owl, petgraph via OntoLogos — Do not depend directly 0015 v0.6
Graph structure for viz petgraph 0.8 ontoindex-lsp / export API JSON graph for React webview; layout in webview-ui 0016 v0.7
Webview panel UI react, vite evaluate at v0.7a extension/webview-ui Typed postMessage protocol, panel host, CSP 0017 v0.7a+
OBO read/write fastobo, fastobo-owl 0.15 / 0.3 ontoindex-parser or ontoindex-owl Catalog mapping, OBO id ↔ IRI 0016 v0.7b
ROBOT release pipelines ROBOT CLI external ontoindex-robot Subprocess wrapper, exit codes, settings OBO_ROBOT_SPEC v0.7b
File-watch reindex notify or ontologos-watch 9 / via OntoLogos ontoindex-lsp Debounce, catalog invalidation 0015 v0.9
Git branch / commit inputs git2 0.21 ontoindex-diff Checkout snapshots, diff presentation 0016 v0.9
Semantic axiom diff horned-owl (in-house diff logic) 1.4 ontoindex-diff Breaking-change heuristics, PR markdown 0009 v0.9
Docs export Markdown pulldown-cmark 0.13 ontoindex-docs Entity page templates, TOC 0016 v0.9
Docs export HTML minijinja 2 ontoindex-docs Template files, asset bundling 0016 v0.9
SHACL validation (P1) rudof (shapes-rs) 0.1 plugin / ontoindex-diagnostics Shape path config, LSP diagnostic mapping SHACL_SPEC v1.0 P1

Explicitly excluded dependencies

Crate / tool Reason
ELK, HermiT, Pellet (JVM) ADR-0014
whelk-rs direct Use ontologos-el via ADR-0015
reasonable direct Use ontologos-rl / ontologos-rdfs via ADR-0015
owl-dl-core / rustdl Single DL stack = OntoLogos ontologos-dl
Reimplementing ROBOT merge/report OBO_ROBOT_SPEC
Reimplementing triple store Oxigraph covers RDF/SPARQL (ADR-0003)

Intentionally in-house (no crate substitute)

Area OntoIndex owns Why
Workspace scanner security Path jail, resource limits Product-specific (path_jail.rs on GitHub)
Catalog schema + SQL virtual tables Table design, entity API Product-specific
Ontology quality lints Duplicate labels, orphans, missing labels Rules on catalog; no ontology-linter crate
LSP custom protocol ontoindex/* methods, snake_case enums ADR-0007, ADR-0012
Semantic diff UX + breaking-change report PR summaries, Git compare UI No ontology PR-diff library
VS Code extension host Tree views, commands, LSP client, webview lifecycle TypeScript orchestration only (ADR-0007)
VS Code webview UI Panel UI (inspector, query, Manchester, reasoner, graphs, diff) React + Vite in extension/webview-ui (ADR-0017)

License compatibility

See LICENSES.md. Summary:

Dependency License Notes
OntoIndex / OntoCode MIT OR Apache-2.0 Dual-licensed
horned-owl LGPL-3.0 Dynamic linking; document in distributions
reasonable (transitive via OntoLogos) BSD-3-Clause NOTICES file
oxigraph, sqlparser, OntoLogos crates MIT OR Apache-2.0 Compatible
fastobo family MIT Compatible
rudof MIT OR Apache-2.0 Compatible

MSRV alignment

Source MSRV
OntoIndex workspace (Cargo.toml) 1.86
horned-owl 1.4 1.88
OntoLogos 0.9+ 1.88

Action: Bump workspace rust-version to 1.88 when integrating ontoindex-reasoner (v0.6). (ontoindex-owl shipped in v0.4.0 at MSRV 1.88.)

OntoLogos crate map (reasoner stack)

OntoLogos crate Role OntoIndex uses via
ontologos-core OWL ontology model ontoindex-reasoner
ontologos-parser Load .owl/.ttl ontoindex-reasoner
ontologos-profile Profile detection ontoindex-reasoner, LSP warnings
ontologos-el / rl / rdfs Profile engines ontoindex-reasoner adapters
ontologos-dl OWL 2 DL (1.0.0) ontoindex-reasoner dl adapter
ontologos-facade Auto routing (1.0.0) ontoindex-reasoner auto adapter
ontologos-explain Proof graphs LSP getExplanation
ontologos-watch File-watch reload ontoindex-lsp (v0.9 eval)