Closing the gap between formats for storing layout information in systems biology. (5th July 2019)

• Record Type: Journal Article
• Authors: Hoksza, David; Gawron, Piotr; Ostaszewski, Marek; Hasenauer, Jan; Schneider, Reinhard
• Is Part Of: Briefings in bioinformatics. Volume 21:Number 4(2020)
• Page Start: 1249
• Page End: 1260
• Publication Date: 2019-07-05
• Subjects: network layout -- molecular network -- data format -- systems biology -- conversion; Genetics -- Data processing -- Periodicals; Molecular biology -- Data processing -- Periodicals; Genomes -- Data processing -- Periodicals; 572.80285
• DOI: 10.1093/bib/bbz067
• Languages: English
• ISSNs: 1467-5463

Abstract

Abstract: The understanding of complex biological networks often relies on both a dedicated layout and a topology. Currently, there are three major competing layout-aware systems biology formats, but there are no software tools or software libraries supporting all of them. This complicates the management of molecular network layouts and hinders their reuse and extension. In this paper, we present a high-level overview of the layout formats in systems biology, focusing on their commonalities and differences, review their support in existing software tools, libraries and repositories and finally introduce a new conversion module within the MINERVA platform. The module is available via a REST API and offers, besides the ability to convert between layout-aware systems biology formats, the possibility to export layouts into several graphical formats. The module enables conversion of very large networks with thousands of elements, such as disease maps or metabolic reconstructions, rendering it widely applicable in systems biology.