Public Postgres database

In addition to downloadable files, an API, and the text search, RNAcentral provides a public Postgres database that can be used to query the data using SQL syntax. The database is updated with every RNAcentral release and contains a copy of the data available through the RNAcentral website.

Connection details

Main database

  • Hostname: hh-pgsql-public.ebi.ac.uk
  • Port: 5432
  • Database: pfmegrnargs
  • User: reader
  • Password: NWDMCE5xdipIjRrp

Connecting to the database

To connect to the database using command line:

psql postgres://reader:NWDMCE5xdipIjRrp@hh-pgsql-public.ebi.ac.uk:5432/pfmegrnargs

Pro tip: if you don't have psql installed on your machine, consider using Docker to get started with a pre-configured Postgres image:

docker pull postgres docker run -it postgres psql postgres://reader:NWDMCE5xdipIjRrp@hh-pgsql-public.ebi.ac.uk:5432/pfmegrnargs

Alternatively, you can use a Postgres client like DBeaver or PgAdmin.

If your computer is behind a firewall, please ensure that outgoing TCP/IP connections to the corresponding ports are allowed.

Database Schema

The following diagram was generated based on RNAcentral release 16.

Main tables

The entire RNAcentral schema contains more than 40 tables, but the following tables are good starting points for exploring the data:

  • rna - contains RNA sequences and URS identifiers
  • xref - contains cross-references to Expert Databases
  • rnc_database - contains a list of Expert Databases
  • rnc_accessions - contains metadata associated with each cross-reference
  • rnc_rna_precomputed - contains RNA types and descriptions for all sequences

Example queries

Search by external accessions

Although the VEGA database has been archived and its identifiers are no longer searchable using the RNAcentral text search, you can still query RNAcentral using VEGA identifiers:

SELECT
  upi,     -- RNAcentral URS identifier
  taxid,   -- NCBI taxid
  ac       -- external accession
FROM xref
WHERE ac IN ('OTTHUMT00000106564.1', 'OTTHUMT00000416802.1')

Example output:

URS00000B15DA   9606    OTTHUMT00000106564.1
URS00000A54A6   9606    OTTHUMT00000416802.1

Example workflow to extract all bacterial rRNA sequences

The RNAcentral text search can only export up to 1,000,000 search results. If you need to export more sequences, you can use the following workflow:

  1. Create a file query.sql:

    SELECT
      precomputed.id
    FROM rnc_rna_precomputed precomputed
    JOIN rnc_taxonomy tax
    ON
      tax.id = precomputed.taxid
    WHERE
      tax.lineage LIKE 'cellular organisms; Bacteria; %'
      AND precomputed.is_active = true    -- exclude sequences without active cross-references
      AND rna_type = 'rRNA'
    
  2. Run the following command to execute the query:

    docker run -v `pwd`:/rnacentral -it postgres /bin/sh -c 'cd /rnacentral && psql -t -A -f query.sql postgres://reader:NWDMCE5xdipIjRrp@hh-pgsql-public.ebi.ac.uk:5432/pfmegrnargs > ids.txt'  
    

    The command will create a file ids.txt with a list of RNAcentral identifiers.

  3. Download the following RNAcentral FASTA file:

    http://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/sequences/rnacentral_species_specific_ids.fasta.gz

  4. Extract the sequences using seqkit:

    seqkit grep -f ids.txt rnacentral_species_specific_ids.fasta.gz > output.fasta
    

    The file output.fasta will contain the desired subset of RNAcentral sequences in FASTA format.

Example Python script

Requires psycopg2 to connect to Postgres:

pip install psycopg2

Contributing to the RNAcentral website

The public Postgres database allows anyone to run the RNAcentral website locally and contribute new code to RNAcentral using the instructions available on GitHub.


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