RNA interaction format: a general data format for RNA interactions

Richard A Schäfer; Dominik Rabsch; Guillaume E Scholz; Peter F Stadler; Wolfgang R Hess; Rolf Backofen; Jörg Fallmann; Björn Voß

doi:10.1093/bioinformatics/btad665

RNA interaction format: a general data format for RNA interactions

Bioinformatics. 2023 Nov 1;39(11):btad665. doi: 10.1093/bioinformatics/btad665.

Authors

Richard A Schäfer¹, Dominik Rabsch², Guillaume E Scholz³, Peter F Stadler³, Wolfgang R Hess⁴, Rolf Backofen², Jörg Fallmann³, Björn Voß¹

Affiliations

¹ RNA-Biology and Bioinformatics, Institute of Biomedical Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
² Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany.
³ Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany.
⁴ Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.

Abstract

Summary: RNA molecules play crucial roles in various biological processes. They mediate their function mainly by interacting with other RNAs or proteins. At present, information about these interactions is distributed over different resources, often providing the data in simple tab-delimited formats that differ between the databases. There is no standardized data format that can capture the nature of all these different interactions in detail.

Availability and implementation: Here, we propose the RNA interaction format (RIF) for the detailed representation of RNA-RNA and RNA-Protein interactions and provide reference implementations in C/C++, Python, and JavaScript. RIF is released under licence GNU General Public License version 3 (GNU GPLv3) and is available on https://github.com/RNABioInfo/rna-interaction-format.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Databases, Factual
Proteins
RNA*
Software*

Substances

RNA
Proteins