Wiki Export

Wiki Export — Knowledge Graph Export

You are exporting the wiki's wikilink graph to structured formats so it can be used in external tools (Gephi, Neo4j, custom scripts, browser visualization).

Before You Start

1. Resolve config — follow the Config Resolution Protocol in llm-wiki/SKILL.md (inline @name override → walk up CWD for .env → global config → prompt setup). This gives OBSIDIAN_VAULT_PATH
2. Confirm the vault has pages to export — if fewer than 5 pages exist, warn the user and stop

Project Filter (optional)

If the user's invocation includes a project name — e.g. /wiki-export prismor, "export the prismor project", "export project:security" — activate project filter mode:

1. Extract the project name from the argument or phrase. Normalise: lowercase, strip the word "project".
2. Keep only pages where either condition holds:

• The page id starts with projects/<name>/ (path-based match)
• The page's tags array contains <name> (tag-based match)

1. Drop any edge where either endpoint was excluded.
2. Note the filter in the summary: (filtered: project:<name> — X of Y pages)
3. Set graph.graph.filter = "project:<name>" in the JSON output.

If both a project filter and a visibility filter are active, apply both (project filter first, then visibility filter on the remaining set).

Visibility Filter (optional)

By default, all pages are exported regardless of visibility tags. This preserves existing behavior.

If the user requests a filtered export — phrases like "public export", "user-facing export", "exclude internal", "no internal pages" — activate visibility filtered mode:

• Build a blocked tag set: {visibility/internal, visibility/pii}
• Skip any page whose frontmatter tags contain a blocked tag when building the node list
• Skip any edge where either endpoint was excluded
• Note the filter in the summary: (filtered: visibility/internal, visibility/pii excluded)

Pages with no visibility/ tag, or tagged visibility/public, are always included.

Step 1: Build the Node and Edge Lists

Glob all .md files in the vault (excluding _archives/, _raw/, _readouts/, .obsidian/, index.md, log.md, _insights.md). Apply any active filters (project and/or visibility) after collecting the full file list.

For each page, extract from frontmatter:

• id — relative path from vault root, without .md extension (e.g. concepts/transformers)
• label — title field from frontmatter, or filename if missing
• category — directory prefix (concepts, entities, skills, references, synthesis, projects, or journal)
• tags — array from frontmatter tags field
• summary — frontmatter summary field if present

This is your node list.

For each page, Grep the body for \[\[.*?\]\] to extract all wikilinks:

• Parse each [[target]] or [[target|display]] — use the target part only
• Resolve the target to a node id (normalize: lowercase, spaces→hyphens, strip .md)
• Skip links that point outside the node list (broken links)
• Each resolved link becomes an edge: {source: page_id, target: linked_id, relation: "wikilink", confidence: "EXTRACTED"}
• If the linking sentence ends with ^[inferred] or ^[ambiguous], override confidence accordingly

Typed edge enrichment: After building the wikilink edge list, read each page's relationships: frontmatter block. For each {target, type} entry:

• The target YAML value is a quoted wikilink string such as "[[concepts/lstm]]". Strip the surrounding [[ and ]] characters, then apply the same normalization (lowercase, spaces→hyphens, strip .md) to get the node id.
• Skip entries whose resolved target is not in the node list (broken link)
• If an edge for this (source, target) pair already exists, override its relation field with the typed value (e.g., "contradicts") and set typed: true
• If no edge exists yet for this pair, add one: {source: page_id, target: target_id, relation: <type>, confidence: "EXTRACTED", typed: true}

This means relation: "wikilink" is the default for plain untyped links; a relationships: entry promotes it to a named semantic type. Edges that originated from both a body wikilink and a relationships: entry keep a single record — the typed version wins.

This is your edge list.

Step 2: Assign Community IDs

Group pages into communities by tag clustering:

• Pages sharing the same dominant tag belong to the same community
• Dominant tag = the first tag in the page's frontmatter tags array
• Pages with no tags get community id null
• Number communities starting from 0, ordered by size descending (largest community = 0)

This enables community-based coloring in the HTML visualization and tools like Gephi.

Step 3: Write the Output Files

Create wiki-export/ at the vault root if it doesn't exist. Write all five files:

3a. graph.json

NetworkX node_link format — standard for graph tools and scripts:

{
  "directed": false,
  "multigraph": false,
  "graph": {
    "exported_at": "<ISO timestamp>",
    "vault": "<OBSIDIAN_VAULT_PATH>",
    "total_nodes": N,
    "total_edges": M
  },
  "nodes": [
    {
      "id": "concepts/transformers",
      "label": "Transformer Architecture",
      "category": "concepts",
      "tags": ["ml", "architecture"],
      "summary": "The attention-based architecture introduced in Attention Is All You Need.",
      "community": 0
    }
  ],
  "links": [
    {
      "source": "concepts/transformers",
      "target": "entities/vaswani",
      "relation": "wikilink",
      "confidence": "EXTRACTED"
    },
    {
      "source": "concepts/transformers",
      "target": "concepts/lstm",
      "relation": "contradicts",
      "confidence": "EXTRACTED",
      "typed": true
    }
  ]
}

3b. graph.graphml

GraphML XML format — loadable in Gephi, yEd, and Cytoscape:

<?xml version="1.0" encoding="UTF-8"?>
<graphml xmlns="http://graphml.graphdrawing.org/graphml">
  <key id="label" for="node" attr.name="label" attr.type="string"/>
  <key id="category" for="node" attr.name="category" attr.type="string"/>
  <key id="tags" for="node" attr.name="tags" attr.type="string"/>
  <key id="community" for="node" attr.name="community" attr.type="int"/>
  <key id="relation" for="edge" attr.name="relation" attr.type="string"/>
  <key id="type" for="edge" attr.name="type" attr.type="string"/>
  <key id="confidence" for="edge" attr.name="confidence" attr.type="string"/>
  <graph id="wiki" edgedefault="undirected">
    <node id="concepts/transformers">
      <data key="label">Transformer Architecture</data>
      <data key="category">concepts</data>
      <data key="tags">ml, architecture</data>
      <data key="community">0</data>
    </node>
    <!-- Untyped wikilink — no <data key="type"> element -->
    <edge source="concepts/transformers" target="entities/vaswani">
      <data key="relation">wikilink</data>
      <data key="confidence">EXTRACTED</data>
    </edge>
    <!-- Typed edge from relationships: block -->
    <edge source="concepts/transformers" target="concepts/lstm">
      <data key="relation">contradicts</data>
      <data key="type">contradicts</data>
      <data key="confidence">EXTRACTED</data>
    </edge>
  </graph>
</graphml>

Write one <node> per page and one <edge> per link. For typed edges (those where typed: true in the edge list), emit both <data key="relation"> with the semantic type value and <data key="type"> with the same value — this keeps relation readable for tools that already consume it while letting type-aware tools filter on the dedicated type key. Untyped wikilinks omit the <data key="type"> element entirely.

3c. cypher.txt

Neo4j Cypher MERGE statements — paste into Neo4j Browser or run with cypher-shell:

// Wiki knowledge graph export — <TIMESTAMP>