GraphML-SBGN bidirectional converter for metabolic networks.
GraphML
Recon2 human metabolic reconstruction
process description
systems biology graphical notation
systems biology standard
Journal
Journal of integrative bioinformatics
ISSN: 1613-4516
Titre abrégé: J Integr Bioinform
Pays: Germany
ID NLM: 101503361
Informations de publication
Date de publication:
01 Dec 2022
01 Dec 2022
Historique:
received:
27
05
2022
accepted:
12
12
2022
pubmed:
24
12
2022
medline:
3
1
2023
entrez:
23
12
2022
Statut:
epublish
Résumé
Systems biology researchers need feasible solutions for editing and visualisation of large biological diagrams. Here, we present the ySBGN bidirectional converter that translates metabolic pathways, developed in the general-purpose yEd Graph Editor (using the GraphML format) into the Systems Biology Graphical Notation Markup Language (SBGN-ML) standard format and vice versa. We illustrate the functionality of this converter by applying it to the translation of the ReconMap resource (available in the SBGN-ML format) to the yEd-specific GraphML and back. The ySBGN tool makes possible to draw extensive metabolic diagrams in a powerful general-purpose graph editor while providing results in the standard SBGN format.
Identifiants
pubmed: 36563404
pii: jib-2022-0030
doi: 10.1515/jib-2022-0030
pmc: PMC9800040
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© 2022 the author(s), published by De Gruyter, Berlin/Boston.
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