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Hoksza, D.* ; Gawron, P.* ; Ostaszewski, M.* ; Hasenauer, J. ; Schneider, R.*

Closing the gap between formats for storing layout information in systems biology.

Brief. Bioinform. 21, 1249-1260 (2020)
Verlagsversion Forschungsdaten DOI PMC
Open Access Hybrid
Creative Commons Lizenzvertrag
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.
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Publikationstyp Artikel: Journalartikel
Dokumenttyp Review
Schlagwörter Network Layout ; Molecular Network ; Data Format ; Systems Biology ; Conversion; Models; Cytoscape; Pathways; Kegg
Sprache englisch
Veröffentlichungsjahr 2020
Prepublished im Jahr 2019
HGF-Berichtsjahr 2019
ISSN (print) / ISBN 1467-5463
e-ISSN 1477-4054
Zeitschrift Briefings in Bioinformatics
Quellenangaben Band: 21, Heft: 4, Seiten: 1249-1260 Artikelnummer: , Supplement: ,
Verlag Oxford University Press
Verlagsort Great Clarendon St, Oxford Ox2 6dp, England
Begutachtungsstatus Peer reviewed
Institut(e) Institute of Computational Biology (ICB)
POF Topic(s) 30205 - Bioengineering and Digital Health
Forschungsfeld(er) Enabling and Novel Technologies
PSP-Element(e) G-553800-001
DOI 10.1093/bib/bbz067
WOS ID WOS:000576139100010
Scopus ID 85088265787
PubMed ID 31273380
Erfassungsdatum 2019-07-24
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