renatocf/nr2

RefRNA

RefRNA is the database for RNA databases.

Getting started

RefRNA is a PostgreSQL open source database that groups RNA sequences and related info available in other RNA databases.

RefRNA is powered by PostgreREST, a simple web server that allows easy access to the data through a RESTful API using HTTPS. To see how to query the database, check: https://postgrest.com/en/v0.4/api.html.

Here are some simple examples of queries you can do in RefRNA. Open your browser and try them directly!

Query	Meaning
http://localhost:3000/sequences?id\_sequence=eq.1	Get a sequence with ID 1
http://localhost:3000/organisms?id\_organism=eq.1&select=taxa{taxon}	Get taxa of the organism with ID 1
http://localhost:3000/taxa?taxon=eq.Homo&select=organisms{organism}	Get organisms from genre "Homo"

By default, results are in JSON, but they can also be returned in CSV.

Backups

• To create a backup of the database, run:

  pg_dump --format=c --no-acl --no-owner -U refrna refrna > YYYY_MM_DD.refrna.dump

  The flag --format asks the file to be compressed in a special binary compressed format that can be used by pg_restore to recreate the database. The flag --no-acl avoids restoring permissions and --no-owner avoids restoring ownership. This configuration is recommended by Heroku's documentation.

• To restore the database, run:

  pg_restore --verbose --clean --no-acl --no-owner -U refrna refrna > YYYY_MM_DD.refrna.dump

  The flag --clean asks to drop the database before recreating it. The flag --no-acl avoids restoring permissions and --no-owner avoids restoring ownership. This configuration is recommended by Heroku's documentation.