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# 19K-RGP — Data Access & Usability Package

Resource: Unity in Diversity: A Global Atlas of 19,035 Rice Genomes (19K Rice Genome Project, 19K-RGP) Purpose: a unified, reproducible guide to how to access, query, and analyze the 19K-RGP across its data platforms — APIs, precomputed summaries, and runnable example workflows.

This package was assembled to make a large, multi-platform genomics resource easy to use: clear documentation, copy-paste API recipes, end-to-end example notebooks, and precomputed summary tables, tied together by a small website and an in-page assistant.

## The resource at a glance

Rice genomes | 19,035 (9,309 newly sequenced + 9,726 public)
Reference assemblies | 5 platinum genomes — Nipponbare IRGSP‑1.0 (GJ), IR64RS2 (XI, new gap‑free), MH63RS3 (XI), ARC 10497 (cB), N22 (cA)
Variants | ~57 million across references; 2.02M high‑effect regulatory variants
Analyses | population genomics · rare variants · regulatory (HEV) modeling · genome × environment · small RNA · AlphaFold3 protein models · AI trait prediction

## The platforms (one documentation page each)

Platform | What it's for | Programmatic access
--- | --- | ---
SNP‑Seek v3 (`snp-seek.irri.org`) | Interactive genotypes, haplotypes, allele frequencies, phenotypes | REST API (endpoints to confirm with IRRI)
GrameneOryza (`oryza.gramene.org`) | Genome browser, search, FTP of extended variants + predicted effects | Ensembl REST · BioMart · remote `tabix`
Oryza CLIMtools (`gramene.org/CLIMtools/oryza_19K-RGP`) | Climate ↔ genome (G×E) associations | Downloadable tables (no REST API)
Code & Models (`github.com/YongZhou2019/19K-RGP`) | Pipelines + pre‑trained AI trait‑prediction models | Git, Docker, Colab
Archives & Bulk (NCBI · EVA · KAUST) | Raw reads, full variant archives, citable DOIs | Accession download

## What this package contains

    Reviewer_webpage/
    ├── README.md                  ← you are here
    ├── supplementary_note_10/     Expanded "Data Access and Visualization" note (§§10.1–10.6)
    ├── notebooks/                 Runnable example workflows + the `oryza19k` access-cookbook helper
    ├── precomputed_tables/        DOI-citable summary tables (+ Zenodo deposit manifest)
    ├── response/                  Point-by-point reply to the reviewer + rebuttal paragraph
    └── site/                      Static documentation website (vanilla HTML/CSS/JS)
        ├── index.html  start.html  workflows.html  api.html  about.html
        ├── platforms/             one page per platform (README · Tutorial · Workflow · Examples)
        ├── partials/              shared header/footer/assistant
        └── assets/                css · js · data · fonts · img · icons

## How it maps to the three asks

- APIs → `site/api.html` (Access matrix + endpoint reference) and §§10.1–10.5 of the note; honest per‑platform tiers, copy‑paste curl/Python/R.
- Precomputed summaries → `precomputed_tables/` (allele frequencies, per‑gene variant summaries, the core‑SNP matrix, trait tables, benchmarks), published to Zenodo with a DOI.
- Example workflows → `notebooks/` + `site/workflows.html`: three end‑to‑end recipes anchored to results in the paper, runnable in Colab or Docker, with committed outputs and offline fallback.

## Efficient data access — the headline technique

You do not need to download 19,035 genomes to query a locus. The package documents remote `tabix` streaming of the bgzipped VCFs (slice any region across all accessions over HTTPS), plus precomputed summary tables for the most common questions.

## Conventions & compliance (please read before contributing)

- No credentials in any tracked file. Review‑only passwords live solely in the editor/cover‑letter channel. The website ships credential‑free; any review build toggle lives in an untracked `site/assets/js/config.local.js`.
- No endpoint is documented unless it returns HTTP 200 with no login. Endpoints are tagged by access tier; anything unverified is served as a precomputed table instead.
- Notebooks always run for a reader — every networked cell ships with committed output and falls back to a precomputed table if a live service is unavailable.
- Cite DOIs, not bare hostnames, for anything durable.

## Status

Local‑first build (this folder). Public deployment (org GitHub Pages) and a Zenodo DOI are prepared but minted only after co‑author sign‑off. See the approved plan for the full design and open items.