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

• Read .env to get OBSIDIAN_VAULT_PATH

• Confirm the vault has pages to export — if fewer than 5 pages exist, warn the user and stop

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 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/ , .obsidian/ , index.md , log.md , _insights.md ). In filtered mode, also skip pages whose tags contain visibility/internal or visibility/pii .

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

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 four 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" } ] }

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="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> <edge source="concepts/transformers" target="entities/vaswani"> <data key="relation">wikilink</data> <data key="confidence">EXTRACTED</data> </edge> </graph> </graphml>

Write one <node> per page and one <edge> per wikilink.

3c. cypher.txt

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

// Wiki knowledge graph export — <TIMESTAMP> // Load with: cypher-shell -u neo4j -p password < cypher.txt

// Nodes MERGE (n:Page {id: "concepts/transformers"}) SET n.label = "Transformer Architecture", n.category = "concepts", n.tags = ["ml","architecture"], n.community = 0; MERGE (n:Page {id: "entities/vaswani"}) SET n.label = "Ashish Vaswani", n.category = "entities", n.tags = ["person","ml"], n.community = 0;

// Relationships MATCH (a:Page {id: "concepts/transformers"}), (b:Page {id: "entities/vaswani"}) MERGE (a)-[:WIKILINK {relation: "wikilink", confidence: "EXTRACTED"}]->(b);

Write one MERGE node statement per page, then one MATCH /MERGE relationship statement per edge.

3d. graph.html

A self-contained interactive visualization using the vis.js CDN (no local dependencies). The user opens this file in any browser — no server needed.

Build the HTML file by:

• Generating a JSON array of node objects for vis.js:

{id: "concepts/transformers", label: "Transformer Architecture", color: {background: "#4E79A7"}, size: <degree * 3 + 8>, title: "concepts | #ml #architecture", community: 0}

• Color by community (cycle through: #4E79A7 , #F28E2B , #E15759 , #76B7B2 , #59A14F , #EDC948 , #B07AA1 , #FF9DA7 , #9C755F , #BAB0AC )

• Size by degree (incoming + outgoing link count): size = degree * 3 + 8 , capped at 60

• title = tooltip text shown on hover: category, tags, summary (if available)

• Generating a JSON array of edge objects for vis.js:

{from: "concepts/transformers", to: "entities/vaswani", dashes: false, width: 1, color: {color: "#666", opacity: 0.6}}

• dashes: true for INFERRED edges

• dashes: [4,8] for AMBIGUOUS edges

• Writing the full HTML file:

<!DOCTYPE html> <html> <head> <meta charset="utf-8"> <title>Wiki Knowledge Graph</title> <script src="https://unpkg.com/vis-network/standalone/umd/vis-network.min.js">&#x3C;/script> <style>

• { box-sizing: border-box; margin: 0; padding: 0; } body { background: #0f0f1a; color: #e0e0e0; font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", sans-serif; display: flex; height: 100vh; } #graph { flex: 1; } #sidebar { width: 260px; background: #1a1a2e; border-left: 1px solid #2a2a4e; padding: 14px; overflow-y: auto; font-size: 13px; } #sidebar h3 { color: #aaa; font-size: 11px; text-transform: uppercase; letter-spacing: 0.05em; margin: 0 0 10px; } #info { margin-bottom: 16px; line-height: 1.6; color: #ccc; } .legend-item { display: flex; align-items: center; gap: 8px; padding: 3px 0; font-size: 12px; } .dot { width: 10px; height: 10px; border-radius: 50%; flex-shrink: 0; } #stats { margin-top: 16px; color: #555; font-size: 11px; } </style> </head> <body> <div id="graph"></div> <div id="sidebar"> <h3>Wiki Knowledge Graph</h3> <div id="info">Click a node to see details.</div> <h3 style="margin-top:12px">Communities</h3> <div id="legend"><!-- populated by JS --></div> <div id="stats"><!-- populated by JS --></div> </div> <script> const NODES_DATA = /* NODES_JSON /; const EDGES_DATA = / EDGES_JSON */; const COMMUNITY_COLORS = ["#4E79A7","#F28E2B","#E15759","#76B7B2","#59A14F","#EDC948","#B07AA1","#FF9DA7","#9C755F","#BAB0AC"];

const nodes = new vis.DataSet(NODES_DATA); const edges = new vis.DataSet(EDGES_DATA); const network = new vis.Network(document.getElementById('graph'), {nodes, edges}, { physics: { solver: 'forceAtlas2Based', forceAtlas2Based: { gravitationalConstant: -60, springLength: 120 }, stabilization: { iterations: 200 } }, interaction: { hover: true, tooltipDelay: 100 }, nodes: { shape: 'dot', borderWidth: 1.5 }, edges: { smooth: { type: 'continuous' }, arrows: { to: { enabled: true, scaleFactor: 0.4 } } } }); network.once('stabilizationIterationsDone', () => network.setOptions({ physics: { enabled: false } }));

network.on('click', ({nodes: sel}) => { if (!sel.length) return; const n = NODES_DATA.find(x => x.id === sel[0]); if (!n) return; document.getElementById('info').innerHTML = <b>${n.label}</b><br>Category: ${n.category||'—'}<br>Tags: ${n.tags||'—'}<br>${n.summary ? '<br>'+n.summary : ''}; });

// Build legend const communities = {}; NODES_DATA.forEach(n => { if (n.community != null) communities[n.community] = (communities[n.community]||0)+1; }); const leg = document.getElementById('legend'); Object.entries(communities).sort((a,b)=>b[1]-a[1]).forEach(([cid, count]) => { const color = COMMUNITY_COLORS[cid % COMMUNITY_COLORS.length]; leg.innerHTML += <div class="legend-item"><div class="dot" style="background:${color}"></div>Community ${cid} (${count})</div>; }); document.getElementById('stats').textContent = ${NODES_DATA.length} pages · ${EDGES_DATA.length} links; </script> </body> </html>

Replace /* NODES_JSON / and / EDGES_JSON */ with the actual JSON arrays you generated in step 1.

Step 4: Print Summary

Wiki export complete → wiki-export/ graph.json — N nodes, M edges (NetworkX node_link format) graph.graphml — N nodes, M edges (Gephi / yEd / Cytoscape) cypher.txt — N MERGE nodes + M MERGE relationships (Neo4j) graph.html — interactive browser visualization (open in any browser)

In filtered mode, append a line showing what was excluded:

(filtered: X of Y pages excluded — visibility/internal, visibility/pii)

Notes

• Re-running is safe — all output files are overwritten on each run

• Broken wikilinks are skipped — only edges to pages that exist in the vault are exported

• The wiki-export/ directory should be gitignored if the vault is version-controlled — these are derived artifacts

• graph.json is the primary format — the others are derived from it. If a future tool supports graph queries natively, point it at graph.json