Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0

Rougny, Adrien; Touré, Vasundra; Moodie, Stuart; Balaur, Irina; Czauderna, Tobias; Borlinghaus, Hanna; Doğrusöz, Uğur; Mazein, Alexander; Dräger, Andreas; Blinov, Michael L.; Villéger, Alice; Haw, Robin; Demir, Emek; Mi, Huaiyu; Sorokin, Anatoly; Schreiber, Falk; Luna, Augustin

doi:10.1515/jib-2019-0022

Cited by 53 publications

(50 citation statements)

References 1 publication

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…To this end, our technique exploits the repeatedly observed ability of human beholders to estimate quantities most precisely when these are mapped to a lengths scale [31]. Since metabolic maps commonly represent nodes with circles [6,34], we suggest using the fill level of each node as a visual element to represent its amount at each time point.…”

Section: Resultsmentioning

confidence: 99%

Visualizing metabolic network dynamics through time-series metabolomic data

Buchweitz¹,

Yurkovich

Blessing

et al. 2020

BMC Bioinformatics

Self Cite

View full text Add to dashboard Cite

Background: New technologies have given rise to an abundance of-omics data, particularly metabolomic data. The scale of these data introduces new challenges for the interpretation and extraction of knowledge, requiring the development of innovative computational visualization methodologies. Here, we present GEM-Vis, an original method for the visualization of time-course metabolomic data within the context of metabolic network maps. We demonstrate the utility of the GEM-Vis method by examining previously published data for two cellular systems-the human platelet and erythrocyte under cold storage for use in transfusion medicine. Results: The results comprise two animated videos that allow for new insights into the metabolic state of both cell types. In the case study of the platelet metabolome during storage, the new visualization technique elucidates a nicotinamide accumulation that mirrors that of hypoxanthine and might, therefore, reflect similar pathway usage. This visual analysis provides a possible explanation for why the salvage reactions in purine metabolism exhibit lower activity during the first few days of the storage period. The second case study displays drastic changes in specific erythrocyte metabolite pools at different times during storage at different temperatures. Conclusions: The new visualization technique GEM-Vis introduced in this article constitutes a well-suitable approach for large-scale network exploration and advances hypothesis generation. This method can be applied to any system with data and a metabolic map to promote visualization and understand physiology at the network level. More broadly, we hope that our approach will provide the blueprints for new visualizations of other longitudinal-omics data types. The supplement includes a comprehensive user's guide and links to a series of tutorial videos that explain how to prepare model and data files, and how to use the software SBMLsimulator in combination with further tools to create similar animations as highlighted in the case studies.

show abstract

Section: Resultsmentioning

confidence: 99%

Visualizing metabolic network dynamics through time-series metabolomic data

Buchweitz¹,

Yurkovich

Blessing

et al. 2020

BMC Bioinformatics

Self Cite

View full text Add to dashboard Cite

show abstract

“…Expectedly, LoF for CCNB1:CDK1 which is the key driver of the G2/M transition blocked the reachability of phase M markers. The subnetwork is represented using the CellDesigner format [15], which is compatible with the SBGN Process Description language [40].…”

Section: Control Of Cell Cycle Checkpoints By Entities Of the Circadimentioning

confidence: 99%

“…The Systems Biology Graphical Notation (SBGN) [28] is a standard for the graphical representation of molecular networks. It includes three orthogonal languages: the Process Description (PD) [40], used to represent reaction networks; the Activity Flow [30], used to represent influence graphs; and the Entity Relationship [42], used to represent sets of rules and relationships. We focus hereafter on the SBGN PD language, as we are interested in representing and modelling reaction networks.…”

Section: Sbgn Pd Standard For Mapsmentioning

confidence: 99%

A Detailed Map of Coupled Circadian Clock and Cell Cycle with Qualitative Dynamics Validation

Rougny

Paulevé

Teboul

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

The temporal coordination of biological processes by the circadian clock is an important mechanism, and its disruption has negative health outcomes, including cancer. Experimental and theoretical evidence suggests that the oscillators driving the circadian clock and the cell cycle are coupled through phase locking. We present a detailed and documented SBGN PD map of known mechanisms related to the regulation of the circadian clock, and its coupling with an existing cell cycle SBGN PD map which includes main interactions of the mammalian cell cycle. The coherence of the merged map has been validated with a qualitative dynamics analysis. We verified that the coupled circadian clock and cell cycle maps allow reproducing the observed sequence of phase markers. Moreover, we predicted mutations that contribute to regulating checkpoints of the two oscillators. Strikingly, our approach underlines the potential key role of the core clock protein NR1D1 in regulating cell cycle progression. We predicted that its activity influences negatively the progression of the cell cycle from phase G2 to M. It is consistent with the earlier experimental finding that pharmacological activation of NR1D1 inhibits tumour cell proliferation and shows that our approach can identify biologically relevant species in the context of large and complex networks.

show abstract

“…*NEW* SBGN Process Description Level 1 Version 2 [16] – which includes new developments such as the addition of equivalence operator, subunit, and annotation glyphs, modification to the usage of submaps, and updates to clarify the use of various glyphs;…”

Section: Latest Versions Of Combine Standardsmentioning

confidence: 99%

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019

Schreiber

Sommer

Bader

et al. 2019

Journal of Integrative Bioinformatics

Self Cite

View full text Add to dashboard Cite

This special issue of the Journal of Integrative Bioinformatics presents an overview of COMBINE standards and their latest specifications. The standards cover representation formats for computational modeling in synthetic and systems biology and include BioPAX, CellML, NeuroML, SBML, SBGN, SBOL and SED-ML. The articles in this issue contain updated specifications of SBGN Process Description Level 1 Version 2, SBML Level 3 Core Version 2 Release 2, SBOL Version 2.3.0, and SBOL Visual Version 2.1.

show abstract

Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0

Cited by 53 publications

References 1 publication

Visualizing metabolic network dynamics through time-series metabolomic data

Visualizing metabolic network dynamics through time-series metabolomic data

A Detailed Map of Coupled Circadian Clock and Cell Cycle with Qualitative Dynamics Validation

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019

Contact Info

Product

Resources

About