We are pleased to announce RNAcentral release 20 featuring literature integration with LitScan, new permissive licence (CC0) to enable data reuse without restrictions, as well as a new expert database, Ribovision.
Introducing LitScan
One of the most requested features for RNAcentral has been a comprehensive, up-to-date connection with literature. In release 20, we have taken our first step toward this goal by developing RNAcentral LitScan to analyse open access articles from Europe PMC. RNAcentral LitScan is a new text mining pipeline that connects RNA sequences with the latest open access scientific literature. LitScan uses a collection of identifiers (Ids), gene names, and synonyms provided to RNAcentral by the Expert Databases to scan the papers available in Europe PMC. For this release, LitScan searched 2.7 million Ids from 19 Expert Databases and identified >387,000 papers which contain 1.6 million Ids corresponding to >280,000 unique RNA sequences.
For example, lncRNA THRIL is also known as Linc1992. Using LitScan, the corresponding RNAcentral entry includes papers about THRIL, Linc1992, and even NR_110375 which is another Id for the same gene:
LitScan features an interactive user interface that enables the users to filter the papers using facets, including year, journal, identifier, and the part of the paper where the Id is found.
Read more about the methodology here. Please reach out by email, Twitter or GitHub issue if you have any feedback or if you are interested in using the widget on your website!
All RNAcentral data is now released under CC0
As we announced previously, all RNAcentral data is now released under the Creative Commons Zero (CC0) licence. This means:
- Our terms of use are more inline with the spirit of EMBL-EBI's Terms of use and places the data in the public domain without constraints. We believe that this approach to research data sharing strengthens open science and scientific progress.
- We encourage remixing and reuse as it makes clear to any user - academic, commercial or otherwise - that the data is not owned by anyone and therefore can be used freely.
- We hope this will save researchers time when reusing the data, which speeds up the process of science.
Additionally, we have included a licence page to help clarify how the terms we release our data under and how we use data submitted to our services.
Welcome RiboVision
RiboVision is a tool for the exploration of ribosomal data using combined 1D, 2D and 3D visualisations. Using their carefully curated secondary structures they provide a way to explore the sequence and structural data for ribosomes. The RiboVision diagrams are also used in R2DT. You can explore their data here.
Database updates
- ENA
- FlyBase
- HGNC
- IntAct
- MirGeneDB
- PDBe
- PSICQUIC
- PomBase
- QuickGO
- RefSeq
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!