# GrameneOryza

An Ensembl-based genome browser, search interface, and FTP serving the 19K-RGP across all five references — with the stable Ensembl REST API for gene, region, variant-effect, and sequence queries.

Open GrameneOryza ↗ Jump to examples

## README — what it is & what it hosts

The FTP holds the per-reference variant calls and their predicted effects; the browser visualizes them on the location, gene, and variation pages. Because GrameneOryza is built on Ensembl, the Ensembl REST API (`rest.ensembl.org`) gives documented, stable access for Oryza sativa.

Use this when… you need gene models, the predicted consequence of a variant (VEP), cross-reference coordinates, or to stream a VCF slice via a track hub / tabix.

## Tutorial — the genome browser (OsMADS50)

1. From the location page, search `OsMADS50` to reach its gene page.
2. Open the variation page and enable the 19K-RGP variation track.
3. Click a variant to inspect its predicted effect.

A video walkthrough is available at oryza.gramene.org/videotutorials.

## Workflow — a locus' variants & effects via REST (no download)

Goal: for MADS14 (`Os03g0752800`), pull the gene model, all overlapping variants, and their predicted consequences. `lookup/id` → `overlap/region` (feature=variation) → `vep` → a tidy variant×consequence table. See Workflow A.

## Examples

    # Gene -> coordinates
    curl -s "https://rest.ensembl.org/lookup/id/Os03g0752800?content-type=application/json"
    # Variants overlapping the locus
    curl -s "https://rest.ensembl.org/overlap/region/oryza_sativa/3:31031753-31041563?feature=variation;content-type=application/json"
    # Predicted consequence (region/:-/)
    curl -s "https://rest.ensembl.org/vep/oryza_sativa/region/3:31037240-31037240/A?content-type=application/json"

    import oryza19k as o19
    gene = o19.lookup_gene("Os03g0752800")                       # MADS14
    vars = o19.region_features("3:31031753-31041563", feature="variation")
    vep  = o19.vep_effects("3:31037240:A")                       # -> intron_variant

## Access & cite

Review During peer review the rice resources are served from a staging instance with reviewer credentials provided to the editor; at publication they move to public, login-free production endpoints. The durable variant archive is the European Variation Archive (PRJEB105137).

Cite: Tello-Ruiz et al. (Gramene, NAR); the GrameneOryza database paper; the Ensembl REST API.