RNAcentral_features

Video Tip of the Week: RNACentral, wrangling non-coding RNA for simplifying access

Non-coding RNA data can be tricky to locate in public data sources. Sometimes it is handled with other gene sets, other times it’s not. Some ncRNA may be found in databases of one type or one species, but it’s not always clear what the best route to find them would be. The folks from RNACentral want to help solve this problem. They aim to create a resource that is essentially “UniProt for non-coding RNAs” as they described in their recent webinar.

The RNACentral team is working with database providers to generate a centralized access point to these disparate collections. RNAcentral_featuresThey have uniform, stable IDs and and also syntax so you can search by specific species. They aren’t species-restricted, but the rate of them incorporating your favorite data sets may vary. They are incorporating more collections as we speak and have plans for more in their upcoming releases. This summary slide offers some of the other main features of their services.

The members of this consortium (three dozen at this time) are working on getting all of the data in. I should say, though, that this doesn’t replace the member databases. You will still want to go to places like miRBase or the WormBase for deeper details on the items, or specific tools to work with that subset of the data. But with RNACentral you get centralized searching of everything, so it’s a great place to start.

The best way to get a sense of this, though, would be to watch this recent webinar, which will be this week’s Tip of the Week.

They also provided their slides, which you can access at the EBI training page. And they put the question segment in a separate file, but I almost always learn something from the good questions that are asked, and if you have questions you might want to see if they covered them. If you find your project requires some information about non-coding RNAs, you should know about the tools at RNACentral.

Quick link:

RNACentral: http://rnacentral.org

Reference:

RNAcentral Consortium. (2014). RNAcentral: an international database of ncRNA sequences Nucleic Acids Research, 43 (D1) DOI: 10.1093/nar/gku991