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Closing the gap between formats for storing layout information in systems biology.
Brief. Bioinform. 21, 1249-1260 (2020)
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Forschungsdaten
DOI
PMC
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
ISSN (print) / ISBN
1467-5463
e-ISSN
1477-4054
Zeitschrift
Briefings in Bioinformatics
Quellenangaben
Band: 21,
Heft: 4,
Seiten: 1249-1260
Verlag
Oxford University Press
Verlagsort
Great Clarendon St, Oxford Ox2 6dp, England
Nichtpatentliteratur
Publikationen
Begutachtungsstatus
Peer reviewed
Institut(e)
Institute of Computational Biology (ICB)