RNAcentral: A vision for an international database of RNA sequences

Abstract

During the last decade there has been a great increase in the number of noncoding RNA genes identified, including new classes such as microRNAs and piRNAs. There is also a large growth in the amount of experimental characterization of these RNA components. Despite this growth in information, it is still difficult for researchers to access RNA data, because key data resources for noncoding RNAs have not yet been created. The most pressing omission is the lack of a comprehensive RNA sequence database, much like UniProt, which provides a comprehensive set of protein knowledge. In this article we propose the creation of a new open public resource that we term RNAcentral, which will contain a comprehensive collection of RNA sequences and fill an important gap in the provision of biomedical databases. We envision RNA researchers from all over the world joining a federated RNAcentral network, contributing specialized knowledge and databases. RNAcentral would centralize key data that are currently held across a variety of databases, allowing researchers instant access to a single, unified resource. This resource would facilitate the next generation of RNA research and help drive further discoveries, including those that improve food production and human and animal health. We encourage additional RNA database resources and research groups to join this effort. We aim to obtain international network funding to further this endeavor.

FIGURE 1.

The cumulative number of papers in PubMed that contain noncoding RNA-related keywords in the title or abstract.

FIGURE 2.

Organization of RNAcentral and the RNAcentral expert databases. Many RNAcentral expert databases exist already (such as Rfam, RNAdb, piRNAbank, etc.), but the scheme can flexibly include new databases that are created over time. The RNAcentral expert databases provide their content via standard exchange formats to the RNAcentral database, which holds information about all ncRNAs and links special features (such as alignments or predicted 3D-structure) back to RNAcentral expert databases. All information is freely available for the RNA community both through the RNAcentral database as well as the expert databases. In the case of novel ncRNA sequences that do not fit into a class covered by the RNAcentral expert databases, the RNA community will be able to communicate with and submit their data directly to the RNAcentral database.