| name | tool-obsidian |
| description | Optional knowledge-base integration. Writes well-formed markdown notes (with YAML frontmatter, tags, and [[wikilinks]]) into a local Obsidian vault so the user's graph picks them up. Zero plugins required — filesystem-only passthrough. Categories: data-notes, paper-notes, daily, experiments, drafts, inbox. Auto-detects vault via OBSIDIAN_VAULT env var, Obsidian's vault registry, or common paths. Use when: "save to obsidian", "add to vault", "log to daily note", "capture to inbox", "search my notes", "open in obsidian". Does NOT trigger for Organon's own context/memory/ — that stays local. Skill is OPTIONAL — framework works without Obsidian installed.
|
Tool: Obsidian (local vault passthrough)
Push Organon knowledge artifacts into the user's Obsidian vault so they land in their existing knowledge graph — search, backlinks, tags, daily notes, graph view — all handled by Obsidian itself. This skill is optional: if no vault is detected, the framework keeps working without it and the skill exits cleanly.
When to use
- Long-term research notes that the user wants alongside their personal knowledge base
- Daily session summaries that should link to other notes via
[[wikilinks]]
- Paper notes from
sci-literature-research that reference other papers, authors, methods
- Experiment logs from
sci-hypothesis that link to related experiments and datasets
- Quick inbox capture for ideas the user wants to triage in Obsidian later
When NOT to use
- Organon's own
context/memory/{date}.md session log — that's framework-internal, not knowledge-base material
- Binary deliverables (CSVs, PDFs, figures) — route those to
tool-gdrive instead
- Research projects with milestones — those belong in
sci-research-mgmt
- If the user has no Obsidian vault — skip silently, framework is unaffected
Vault detection (in order)
OBSIDIAN_VAULT environment variable (override) — set in .env for explicit control- macOS vault registry —
~/Library/Application Support/obsidian/obsidian.json (most-recently-opened vault wins)
- Common paths —
~/Documents/Obsidian/*, ~/Obsidian/*, ~/Vaults/* (picks first child with .obsidian/ directory)
If none found → skill exits with a clear message pointing at the override. Framework continues normally.
Commands
All commands go through scripts/obsidian_ops.py:
status — Check vault detection
python3 .claude/skills/tool-obsidian/scripts/obsidian_ops.py status
python3 .claude/skills/tool-obsidian/scripts/obsidian_ops.py status --json
write — Create a new note
python3 .claude/skills/tool-obsidian/scripts/obsidian_ops.py write "My Paper Notes" \
--body "## Key findings\n- Finding 1\n- Finding 2" \
--category paper-notes \
--tags "immunotherapy,review" \
--link-to "Doudna 2024,CRISPR delivery" \
--source "https://doi.org/10.1101/2024.10.18.619117"
- Auto-generates YAML frontmatter with
title, created, tags, source, links
- Converts
--link-to values into Obsidian [[wikilinks]] in the frontmatter
- Collision → appends
-1, -2, ... (unless --overwrite)
- Body can come from
--body, --from-file, or stdin
append — Add to an existing note
echo "new observation" | obsidian_ops.py append paper-notes/doudna-2024.md --heading "Follow-up"
daily — Append to today's daily note
python3 .claude/skills/tool-obsidian/scripts/obsidian_ops.py daily \
--body "Ran t-test on experiment_42 — p=0.003" \
--heading "Session notes"
Daily notes live at <vault>/organon/daily/YYYY-MM-DD.md. Created on first use per day.
list — Show staged notes
python3 .claude/skills/tool-obsidian/scripts/obsidian_ops.py list
python3 .claude/skills/tool-obsidian/scripts/obsidian_ops.py list --category experiments
search — Filesystem search across notes
python3 .claude/skills/tool-obsidian/scripts/obsidian_ops.py search "CRISPR delivery"
python3 .claude/skills/tool-obsidian/scripts/obsidian_ops.py search "p-value" --category experiments
Case-insensitive; matches filename or body. Returns a snippet of the first match per note. For heavier queries (backlinks, tag graphs, Dataview), open the vault in Obsidian.
link — Get an obsidian:// URI
python3 .claude/skills/tool-obsidian/scripts/obsidian_ops.py link /path/to/vault/organon/paper-notes/foo.md
Clicking the URI opens the note directly in Obsidian.
Categories
| Category | What goes here |
|---|
data-notes/ | Observations from sci-data-analysis (trends, anomalies, cleaned-dataset commentary) |
paper-notes/ | Literature notes from sci-literature-research with backlinks to authors/methods |
daily/ | Session summaries from meta-wrap-up, dated YYYY-MM-DD.md |
experiments/ | Hypothesis + experiment design notes from sci-hypothesis |
drafts/ | In-progress manuscript drafts from sci-writing |
inbox/ | Unsorted / quick capture — triage in Obsidian later |
Integration with other skills
This skill is optional — other skills should check status first, and only write if Obsidian is detected. Typical pattern:
status_result = run("obsidian_ops.py", "status", "--json")
if status_result["installed"]:
prompt = "Also save this to your Obsidian vault?"
The Obsidian Sync Gate in CLAUDE.md (parallel to the Drive Push Gate) governs when to ask.
Dependencies
| Required | What it provides | Fallback |
|---|
| Obsidian vault (any form) | Where notes are written | None — skill exits with OPTIONAL banner; framework is unaffected |
No plugins, no API keys, no OAuth. Pure filesystem. Compatible with Obsidian sync, iCloud-synced vaults, and plain local vaults.
Graceful degradation
Every command calls find_vault() first. If detection fails:
status returns installed: False with an explanationwrite, append, daily, search, list all exit with SystemExit and a message pointing at the OBSIDIAN_VAULT env var override- No partial writes, no garbage files
The user can enable the skill at any time by setting OBSIDIAN_VAULT=/path/to/vault in .env — no code changes, no restart.
Troubleshooting
- "Obsidian vault not detected": set
OBSIDIAN_VAULT=/absolute/path/to/vault in .env or open the vault in Obsidian at least once (registers it in obsidian.json)
- Notes not appearing in Obsidian graph: Obsidian re-indexes on file changes; give it a second, or reopen the vault
- Wikilinks not resolving: note titles in
--link-to must match existing note filenames (minus .md) — Obsidian handles the rest
- Wrong vault picked: Organon picks the most-recently-opened vault by default — override with
OBSIDIAN_VAULT if you have multiple
