23 Feb 2023

RNAcentral Release 22

We are pleased to announce RNAcentral release 22, featuring two new expert databases, EVlncRNAs and Ribocentre, a new visualisation, and updates to LitScan.

Welcome EVlncRNAs

EVlncRNAs is a database of experimentally validated long non-coding RNAs, curated from papers alongside their expression, interaction and association with disease. In release 22, we have imported the second version of the database, which expands on the original by manually curating almost 19,000 additional papers. You can explore their data here.

Welcome Ribocentre

Ribocentre aims to become a database of all natural ribozymes, and includes representative structures alongside the chemical mechanism of ribozymes. You can explore their data here.

Visualise expression

In release 21 we import cross references to Expression Atlas, we have gone further and now integrated their viewer into RNAcentral. You can now view expression information from some ncRNAs on RNAcentral. Below is one example:

Browse all sequences with data from Expression Atlas here.

LitScan updates

LitScan is our text mining tool and is used to associate papers with the RNA sequences they mention. We use our comprehensive collection of RNA names to associate sequences with papers. LitScan scanned all open access literature available on Europe PMC with 8,939,826 ids and found 865,179 articles which matched 4,497,573 unique sequences. Please reach out to us if we have missed any names!

Additionally, we are preparing exports of LitScan results. In future releases this will be part of our FTP export. Get in contact if you would like to hear about the export as soon as it is ready.

FTP export updates

RNAcentral is powered by a PostgreSQL database, which is publicly available. We are now making dumps of the latest release publically available on our FTP site. We intend to keep only the latest dump available. Power users interested in large scale analysis with RNAcentral can fetch and use our database dumps now. Take a look at some documentation, details on our schema, or reach out if you have any questions!

Database updates

These databases were updated in this release to the version stated below:

  • Ensembl 107 -> 108
  • Ensembl Fungi 54 -> 55
  • Ensembl Metazoa 54 -> 55
  • Ensembl Plants 54 -> 55
  • Ensembl Protists 54 -> 55
  • RefSeq 213 -> 216
  • Rfam 14.7 -> 14.9

The below databases were imported at their latest version as of 2023-01-25

  • ENA
  • FlyBase
  • HGNC
  • IntAct
  • PDBe
  • PomBase
  • QuickGO

Get in touch

As always, all data are freely available on the RNAcentral website, via the API, our public database, and in the FTP archive. If you have any feedback, please get in touch by email, on Twitter, or by submitting an issue on GitHub. We look forward to hearing from you!