[Atlas] Bidirectional KG-Wiki navigation system
Goal
Create seamless bidirectional navigation between knowledge graph nodes and wiki content to unify SciDEX's knowledge representation.
Acceptance Criteria
☐ /wiki/{slug} route implemented showing KG edges and related hypotheses
☐ Breadcrumb navigation added to entity pages
☐ Wiki snippets shown on hypothesis detail pages for target genes with wiki pages
☐ Auto-linking of KG entity mentions in wiki content
☐ All pages load correctly (200 status)
☐ No broken links introduced
Approach
Create /wiki/{slug} route handler that:
- Fetches wiki content from NeuroWiki
- Shows KG neighborhood (edges involving this entity)
- Displays related hypotheses mentioning this entity
- Links to /entity/{name} page
Add breadcrumb navigation to entity pages:
- Entity Type > Entity Name > (Wiki | Graph | Hypotheses)
Enhance hypothesis detail pages:
- Check if target_gene has wiki_entities entry
- Display wiki summary snippet if available
- Link to full /wiki/ and /entity/ pages
Implement auto-linking of KG entities in wiki content:
- Scan wiki summary text for mentions of KG entity names
- Create hyperlinks to /entity/{name} pages
Test all routes and verify navigation works bidirectionallyCurrent State
Entity pages (/entity/{name}) already have:
- ✅ Wiki content embedded inline
- ✅ KG neighborhood visualization
- ✅ Related hypotheses
- ✅ Papers cited in analyses
Still needed:
- ❌ /wiki/{slug} route
- ❌ Breadcrumb navigation
- ❌ Wiki snippets on hypothesis pages
- ❌ Auto-linking in wiki content
Work Log
2026-04-01 23:27 PT — Slot 4
- Task assigned: Bidirectional KG-Wiki navigation system
- Reviewed existing entity page implementation (already quite comprehensive)
- Created task spec
- Next: Implement /wiki/{slug} route and other enhancements
2026-04-20 22:52 PT — Slot minimax:64
- Verified: Entity pages (
/entity/{name}) already have wiki content embedded, KG neighborhood, related hypotheses
- Verified:
/wiki/{slug} route already shows KG edges + related hypotheses + auto-linking in sidebar
- Verified: Graph visualization already has node click panel with wiki/KG connections
- Found: The two remaining gaps from spec were:
1. Wiki snippets on hypothesis detail pages (target_gene wiki lookup)
2. Auto-linking in wiki content (server-side via entity_auto_linking)
- Implemented wiki snippet for target genes on hypothesis detail pages at line ~32957 in hypothesis_detail_page
- Implemented server-side auto-linking of KG entities in wiki content using link_entities_in_markdown at wiki_page route
- Rebased on latest origin/main (clean rebase, no conflicts)
- Committed and pushed to branch orchestra/task/b5d9421e-bidirectional-kg-wiki-navigation-system
- Result: Done — Two remaining spec items implemented and pushed