CropSNPdb

CropSNPdb is a web database of SNP array genotypes for Brassica crops and hexaploid bread wheat (Triticum aestivum). It hosts genotypes from the Illumina Infinium Brassica 60K and wheat 90K arrays and lets users search SNPs by genomic region and line, browse line metadata, and download data in bulk.

Live site: https://snpdb.appliedbioinformatics.com.au

Citation

If you use CropSNPdb, please cite:

Scheben A, Verpaalen B, Lawley CT, Chan CK, Bayer PE, Batley J, Edwards D (2019) CropSNPdb: a database of SNP array data for Brassica crops and hexaploid bread wheat. The Plant Journal 98: 142–152. https://doi.org/10.1111/tpj.14194

What's in the database

Array	Reference genomes	Lines	Accessions
Brassica 60K	B. napus Darmor v8.1 and v4.1, B. rapa v3, B. oleracea v2.1, B. juncea v1.5	526	575
Wheat 90K	IWGSC RefSeq v1.0 and wheat pangenome	309	309

Genotypes come from published studies (Mason et al. 2015; Qian et al. 2014; Xu et al. 2016; Higgins et al. 2018) and T3/Wheat. Line metadata (country, ecotype, breeding status, pedigree, genebank IDs) and Australian Grains Genebank field phenotypes were added in October 2026 from the same sources; see scripts/maintenance_2026-10.

Features

• Search – SNP genotypes for selected lines in a chromosomal region, with SNP details and genome-browser links
• Lines – all accessions with available metadata (/lines, /lines.csv, /phenotypes.csv)
• Download – per-chromosome genotype matrices
• Upload – submission of new SNP array datasets for curation

Repository layout

app/
  app.py              Flask application entry (imported by snpdb.wsgi)
  views.py            routes: search, lines, download, submit
  forms.py            WTForms definitions
  ownLib/             database queries, parsing, file handling, upload alerts (notify.py)
  templates/          Jinja2 templates
  static/             CSS, JavaScript, probe sequences and example upload files
  config.py.example   settings template (copy to config.py)
snpdb.wsgi            mod_wsgi entry point
mail.cfg.example      optional SMTP settings for upload alerts
scripts/              maintenance scripts and source data

Not included: the MySQL database dump, the bulk download files (app/data/), uploaded submissions and real configuration files. Contact the maintainers below if you need the database.

Running it

Production runs on Ubuntu 24.04 with Apache 2.4 + libapache2-mod-wsgi-py3, MySQL 8.0 and Python 3.12.

1. Database. Create the database and an application user (use a strong password; limit privileges in production):

   CREATE DATABASE snpdb;
   CREATE USER 'flask'@'localhost' IDENTIFIED BY 'CHANGE_ME';
   GRANT SELECT, INSERT, UPDATE ON snpdb.* TO 'flask'@'localhost';

   then load the database dump.
2. Python environment.

   python3 -m venv venv
   venv/bin/pip install -r requirements.txt

3. Settings. Copy app/config.py.example to app/config.py and set the MySQL credentials. Keep DEBUG = False in production. config.py is ignored by git.
4. Web server. Point an Apache WSGIScriptAlias at snpdb.wsgi (adjust the paths in it), using a WSGIDaemonProcess, plus Alias /data for the bulk files. Touch snpdb.wsgi to reload after code changes (run python3 -m py_compile on edited files first, as a syntax error takes the whole site down).
5. Upload alerts (optional). Copy mail.cfg.example to mail.cfg next to snpdb.wsgi, fill in SMTP details and make it readable only by the web server (chown root:www-data mail.cfg; chmod 640 mail.cfg). Without this file uploads still work but no email is sent. Submissions are saved under app/app/uploadFiles/.

History

Originally developed by Armin Scheben, Brent Verpaalen and colleagues (code first published at ascheben/snpdb, 2019). Moved to this repository in October 2026 after a maintenance round that fixed broken links and uploads, corrected line names and species assignments, and added line metadata and phenotypes.

Contact and licence

Applied Bioinformatics Group, The University of Western Australia – Prof. David Edwards (dave.edwards@uwa.edu.au).

Code released under the MIT Licence. Genotype data remain subject to the terms of their original publications and sources.