ontomark 0.7.0

Markdown ontology vaults to standard artefacts: build, validate, gate, conflicts, find, retrieve, tree, guarded edits and migrations for Obsidian vaults and estate repositories
ontomark-0.7.0 is not a library.

ontomark (command line)

ontomark turns a vault of Markdown notes into standard artefacts — RDF 1.1 Turtle (asserted and inferred), JSON-LD 1.1, SHACL, the NGG1 graph tiers, a page API, search and scaffold indexes and a redacted publish/ tree — and gives a corpus workflow the verbs around that: validation, a quality gate, conflict detection, graph queries, guarded edits and reversible migrations. It is the installable form of the ontomark-compile crate, and a drop-in for VisionClaw's vault on the verbs both have.

Install

cargo install ontomark

or take the static Linux x86-64 binary from a GitHub release:

V=0.4.0
curl -fLO https://github.com/DreamLab-AI/ontomark/releases/download/v$V/ontomark-x86_64-unknown-linux-gnu
curl -fLO https://github.com/DreamLab-AI/ontomark/releases/download/v$V/ontomark-x86_64-unknown-linux-gnu.sha256
sha256sum --check ontomark-x86_64-unknown-linux-gnu.sha256
chmod +x ontomark-x86_64-unknown-linux-gnu && ./ontomark-x86_64-unknown-linux-gnu --help

Two kinds of repository

--repo (default: the current directory) names one of two shapes (ADR-OM-008):

  • A plain Obsidian vault. Notes at the root, .obsidian/, templates/, bases/ beside them, no ontology/ folder anywhere above. The directory itself is the knowledge vault, there is no working vault, and the generic profile and the built-in vocabulary apply. Anything that needs a working vault (--vault working|all, --scope machine) is refused with exit 2 and a message naming the layout.

    ontomark --repo ~/Vaults/Notes validate
ontomark --repo ~/Vaults/Notes build --out /tmp/notes-www
ontomark --repo ~/Vaults/Notes find --query dog

  • An estate-shaped repository. ontology/vocabulary.yaml beside the vaults the profile's layout places — knowledge/ and working/ by default. The nearest ancestor holding ontology/vocabulary.yaml is the root, and the estate profile is the default. --profile generic or --profile path/to/profile.yaml overrides it; a profile file is taken as written, including its layout.

Vault layout

A vault is an ordinary Obsidian vault (ADR-OM-007): pages at the vault root, ids are root-relative paths without .md, and the furniture folders (templates/, bases/, assets/, journals/, plus a profile's layout.excluded) are skipped and reported in the census and the validation report, never silently dropped. The profile's layout.knowledge and layout.working say where the two vault roles live under the repository root; "." means the root itself. The output contract is the same whatever the input layout: knowledge pages stage under publish/pages/, working pages under publish/working/, and reports are keyed by role name.

Every build stamps a generation, <prefix>@<commit> (+dirty when the vault paths had uncommitted changes), into .generation.json. The prefix is the profile's pin (visionGraph for the estate) or the repository's directory name, so a vault at ~/Vaults/Notes produces Notes@<sha>.

Verbs

Command What it does
validate Frontmatter grammar, vocabulary agreement, link integrity, credential scan and the public gate for the selected vaults.
gate --tier quick|full The autonomous continuation gate: validation, and with full conflicts plus the OWL 2 EL classifier.
conflicts Semantic conflict detection with a failing --severity.
build --out DIR The publication build. --scope machine writes the machine bundle (knowledge plus the working vault's public notes as plain records, no publish/); --with-rvdb adds embedded records; --publish-out stages the Markdown elsewhere; --certificate-out DIR also writes the RDFS derivation certificate of the published graph (oo-cert/1), refused with exit 2 if it does not cover the classifier's closure (ADR-OM-009).
find, retrieve, tree Title and alias search; expansion from seed pages along declared edge types; the taxonomy tree beneath a page.
edit, create, apply Guarded writes: a frontmatter edit with a declared blast radius, a new page from a staged file, a human-approved kind: amend proposal.
repair bodies|fences Logseq outliner bodies to Obsidian Markdown; unmatched code fences.
migrate list|plan|apply|rollback|status Registry-driven, journalled, reversible corpus migrations.
ingest --source <path|url> (--target <note>|--discover) --endpoint <url> --model <name> External sources to a proposal bundle (manifest/ for vault propose --diff, evidence.json with quotes and spans). Local-only endpoint unless ONTOMARK_JEV_ALLOW_CLOUD=1; --budget-calls, --budget-chars, response cache, --plan-only. Exit 0 done, 1 endpoint failed, 2 refused.

Every verb takes --json; --vault knowledge|working|all selects the roles (all means both, everywhere). ontomark <verb> --help lists the flags.

Exit codes

Code Meaning
0 Success.
1 A failed check (validation errors, a failing gate or conflict) or an execution error.
2 A refusal or an invalid request: a credential on a page selected for publication, two artefacts claiming one output path, an unsatisfiable class, a definition the reasoner would not finish on, a --scope machine build asked for with something it cannot honour, a vault role the layout does not have, a create/apply whose guards refuse the write, or an unknown --vault, --scope, --tier or --severity value. Refusals name what they refused and write nothing.

Migration journals under .ontomark/ keep the original bytes of migrated pages, private ones included: keep that directory out of git and out of publication.

Build from source

cargo build --locked -p ontomark --release
cargo test --locked -p ontomark

MIT OR Apache-2.0. The root NOTICE records the source relocation and relicensing grant; upstream sources and third-party notices accompany each release.