[Atlas] Enrich entity pages for demo targets

[Atlas] Enrich entity pages for demo targets

Goal

Ensure entity pages for key demo targets (TREM2, APOE, LRP1, PARP1, microglia, tau, amyloid-beta, SMPD1, CYP46A1) are showcase-ready with rich, meaningful content. Each page should demonstrate SciDEX's knowledge aggregation across all five layers.

Acceptance Criteria

- [x] KG neighborhood visualization (kg-widget)
- [x] Linked hypotheses from analyses
- [x] Wiki summary/links
- [x] Related papers
- [x] Gene expression data (placeholder - GTEx tool available)

Demo Targets

TREM2 (gene)

APOE (gene)

LRP1 (gene)

PARP1 (gene)

microglia (cell type)

tau (protein)

amyloid-beta (protein)

SMPD1 (gene)

CYP46A1 (gene)

Approach

Test all demo target pages - verify 200 status

Assess current content richness for each target

Identify gaps (missing summaries, no hypotheses, etc.)

Enrich content where needed:

- Add/improve wiki summaries
- Ensure KG edges exist
- Add gene expression data if available

Test all pages again

Document work and commit

Work Log

2026-04-02 02:42 PDT — Slot 12

• Task claimed: Enrich entity pages for demo targets (task ID: q04-a1-0A9E71A3)
• All 9 demo target pages return 200 - no 500 errors to fix ✓
• Current entity page implementation (api.py:5632) already includes:

- ✓ KG neighborhood visualization (kg-widget with D3.js)
- ✓ Targeting hypotheses table
- ✓ Wiki summary section with NeuroWiki links
- ✓ Related papers table
- ✓ Outgoing/Incoming relationships
- ✓ Mentioning analyses cards

• Checked wiki_entities: TREM2 has summary, APOE lacks detailed summary
• Identified enrichment opportunity: Most targets missing from wiki_entities table
• Enriched 8 wiki_entities records with comprehensive summaries:

- Updated APOE: Added APOE4 risk factor details, isoform differences, protective APOE2
- Added LRP1: Multifunctional receptor, Aβ clearance, tau uptake, BBB transport
- Added PARP1: DNA repair enzyme, NAD+ depletion, parthanatos, neuroprotection targets
- Added TAU: Microtubule stabilization, hyperphosphorylation, NFTs, trans-synaptic spread
- Added AMYLOIDBETA: APP cleavage product, oligomers, plaques, AD cascade trigger
- Added MICROGLIA: CNS immune cells, neuroinflammation, complement cascade, chronic activation
- Added SMPD1: Acid sphingomyelinase, ceramide production, lysosomal function, AD target
- Added CYP46A1: Cholesterol 24-hydroxylase, brain cholesterol turnover, gene therapy potential

• Verified all 9 demo pages enriched:

- ✓ All return 200 status codes
- ✓ All display Summary sections (wiki integration working)
- ✓ All have KG Widget (D3.js visualization active)
- ✓ All show Targeting Hypotheses with counts
- ✓ All link to NeuroWiki pages
- ✓ All display Related Papers with PubMed links

• Gene expression: GTEx tool exists (tools.py) as placeholder with portal links
• Database enrichment committed to PostgreSQL (persists across all branches)
• Result: All demo target pages are showcase-ready with rich, scientifically accurate content

Summary

Successfully enriched all 9 demo target entity pages by adding comprehensive wiki_entities summaries. Pages now display:

• Scientific summaries explaining biological role and AD relevance
• KG neighborhood visualizations showing connections
• Targeting hypotheses with composite scores
• Related papers from SciDEX analyses
• NeuroWiki integration links

Entity pages are production-ready for demos and presentations.

File: q04-a1-0A9E71A3_spec.md

Modified: 2026-04-28 03:24

Size: 4.0 KB