RefRNA is the database for RNA databases.
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.
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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 bypg_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.