Organ–FTU–Expression Explorer

A React + TypeScript research interface for exploring Human Reference Atlas organ context, Functional Tissue Unit illustrations, and AS-B-style anatomical structure expression. The app is intentionally data-aware: unavailable upstream data remains unavailable instead of being replaced with fake colors or zeros.

Run the web app

npm install
cp .env.example .env
npm run dev

The browser app runs at http://localhost:5173. To run the API in another terminal:

python3 -m venv .venv
source .venv/bin/activate
pip install -r api/requirements.txt
uvicorn api.app.main:app --reload --port 8000

Set VITE_API_BASE_URL=http://localhost:8000 when using the API. The API serves /api/v1/health, /organs, /genes, and /expression. A verified XIAP ETL snapshot is included at data/processed/expression.json; regenerate it from the locked raw downloads with python3 scripts/build_expression_snapshot.py when the upstream release changes.

Section C uses the HRApop v1.1 XIAP snapshot and verified HRA reference-organ anatomy. Large Intestine uses the organ-specific HRA v1.3 GLBs recorded in docs/section-c-model-probe.md; Kidney uses the verified local kidney GLBs when the selected side is available. The left panel colors real meshes by the pooled AS-level expression values, while the right panel shows the same real mesh in neutral color and states HPO data not yet available. No HPO data are fetched or inferred. Implementation details and the future HPO contract are documented in docs/section-c-implementation-notes.md and docs/hpo-future-integration.md.

Checks

npm run typecheck
npm run build
npm run test
npm run test:e2e
python3 scripts/probe_sources.py
python3 scripts/build_expression_snapshot.py

Data and deployment notes

External URLs are configurable in .env.example and recorded in data-sources.lock.json. The 2026-10-26 probe succeeded; four verified kidney GLBs and a compact XIAP expression snapshot are included. The complete male/female HRA v1.5 body GLBs are reproducible source assets and are intentionally ignored because of their size. Fetch them before running the full-body viewer:

python3 scripts/fetch_reference_models.py --allow-network

Do not commit the large raw JSON/CSV/GLB downloads. Run the probe and ETL again when the upstream release changes.

The UI has no tissue-block or donor data dependency. sex selects anatomy geometry; expression is labelled pooled until a validated sex-specific dataset exists. The footer carries the research and educational use disclaimer.

See docs/integration-probe.md, docs/data-dictionary.md, docs/data-provenance.md, and docs/validation-report.md.