ob-wiki

name

ob-wiki

description

CLI tool for an Obsidian `_Wiki/` compiled knowledge layer. Use when the user wants to query entries (list, show, search, stats, papers, export, lint) or maintain them (new entry, extract concepts from notes/clippings, triage sources, refresh index). Trigger on: "wiki entry", "_Wiki", "ob-wiki", "add to wiki", "extract from notes", "wiki health", "papers cited in wiki", "export wiki context". Skip for Zotero/bibliography (zotero-cli), LaTeX editing (latex), or general Obsidian plugin questions.

ob-wiki skill

Use the ob-wiki CLI to manage an Obsidian _Wiki/ research wiki. Invoke this skill whenever the user asks about their wiki entries, wants to scaffold new pages, check wiki health, search concepts, export content for writing, or track which papers are cited across the wiki.

Activation triggers

• "my wiki", "in my wiki", "list wiki entries", "wiki entries about…"
• "add a wiki entry", "scaffold a new topic/method page", "create a wiki page for…"
• "lint my wiki", "wiki health check", "check for orphan entries"
• "show me [entry name]" when the name sounds like a research concept
• "search the wiki for …"
• "export wiki context", "wiki entries for my paper", "paper writing context"
• "what papers are cited in the wiki", "which papers appear across entries"
• /ob-wiki

Before you start

Verify the tool is installed and the vault is reachable:

which ob-wiki && ob-wiki stats

If ob-wiki is not found: pip install git+https://github.com/kanxh/ob-wiki.git

Before adding or editing an entry

1. Read _Wiki/spec/wiki-convention.md — writing rules, frontmatter schema, link format.
2. Check for a maintenance log (e.g. _Wiki/docs/log.md) if the vault has one.
3. Run ob-wiki list --json and inspect neighboring entries so naming, granularity, and hyper-tags stay consistent with what already exists.

Extraction standard

Only extract an item when it is already a stable retrieval unit:

• it can be defined cleanly
• it connects multiple notes, clippings, or papers
• it links naturally to neighboring wiki entries
• it is likely to recur across the vault

Do not extract:

• one-off experiment settings
• reviewer comments
• narrow pipeline details that do not stand alone
• weak clippings that only mention a term without defining it

Source priorities

When writing entry body content, prefer sources in this order:

1. Strong project notes that already synthesize a concept or method
2. High-quality institutional or dataset clippings
3. Paper PDFs or extracted notes in project folders
4. Secondary clippings that sharpen wording or edge cases

Use clippings as support, not as the only basis for a page, unless the clipping is itself an authoritative source.

Core patterns

List and filter

ob-wiki list                                   # all entries
ob-wiki list --type method --json              # methods as JSON
ob-wiki list --hyper-tag statistics --since 2026-01-01

Show a single entry

ob-wiki show "Gaussian Process"
ob-wiki show gp --json                         # partial name match

Stats

ob-wiki stats
ob-wiki stats --json

Search

ob-wiki search "state space" --json
ob-wiki search "neural network" --type method

Papers cited in wiki

ob-wiki papers --json                          # all cited papers
ob-wiki papers --hyper-tag statistics          # filtered by tag

Export for paper writing

# Clean LLM-digestible context (strips LaTeX, wikilinks, callouts)
ob-wiki export --format bibtex-context --hyper-tag statistics

# Markdown export of recent entries
ob-wiki export --format md --since 2026-01-01 --output context.md

# Full JSON export
ob-wiki export --format json > wiki.json

Lint / health check

ob-wiki lint
ob-wiki lint --json

Scaffold a new entry

# Always use --dry-run first to preview
ob-wiki new "Gaussian Process" --type method --hyper-tag statistics --dry-run
ob-wiki new "Gaussian Process" --type method --hyper-tag statistics

Refresh wiki-index.md

ob-wiki index
ob-wiki index --title "My Wiki" --subtitle "Research knowledge base"

JSON output shapes

list / search:

[{"name": "HMM", "type": "method", "hyper_tags": ["statistics"], "updated": "2026-04-09"}]

show / export json:

{"name": "HMM", "type": "method", "hyper_tags": ["statistics"], "body": "...", "related": {...}}

stats:

{"total_entries": 50, "hyper_tag_counts": [...], "recently_updated": [...]}

papers:

[{"paper": "Author et al. 2024", "cited_by": ["Entry A", "Entry B"]}]

lint:

[{"entry": "RC model", "check": "missing-related-block", "severity": "warning", "message": "..."}]

Tips

• Always pass --json when you need structured output for further processing.
• Use ob-wiki lint --json before bulk operations to check wiki state.
• Use --format bibtex-context when building a "write related work" prompt — it produces clean paragraphs with no LaTeX or Obsidian syntax.
• ob-wiki papers is the fastest way to find entries sharing a literature foundation — useful for discovering implicit clusters.
• --vault overrides auto-detection; set OB_WIKI_VAULT in the environment to avoid passing it on every call.