The next step in systems biology: simulating the temporospatial dynamics of molecular network

Abstract A comprehensible representation of a molecular network is key to communicating and understanding scientific results in systems biology. The Systems Biology Graphical Notation (SBGN) has emerged as the main standard to represent such networks graphically. It has been implemented by different software tools, and is now largely used to communicate maps in scientific publications. However, learning the standard, and using it to build large maps, can be tedious. Moreover, SBGN maps are not grounded on a formal semantic layer and therefore do not enable formal analysis. Here, we introduce a new set of patterns representing recurring concepts encountered in molecular networks, called SBGN bricks. The bricks are structured in a new ontology, the Bricks Ontology (BKO), to define clear semantics for each of the biological concepts they represent. We show the usefulness of the bricks and BKO for both the template-based construction and the semantic annotation of molecular networks. The SBGN bricks and BKO can be freely explored and downloaded at sbgnbricks.org.

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Abstract 357: A systems biology approach for rational molecular network inference

10.1158/1538-7445.am2014-357 ◽

2014 ◽

Author(s):

Megan E. Egbert ◽

Michelle L. Wynn ◽

Zhi Fen Wu ◽

Rabia A. Gilani ◽

Santiago Schnell ◽

...

Keyword(s):

Systems Biology ◽

Network Inference ◽

Molecular Network

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Towards Systems Biology of Heterosis: A Hypothesis about Molecular Network Structure Applied for the Arabidopsis Metabolome

EURASIP Journal on Bioinformatics and Systems Biology ◽

10.1155/2009/147157 ◽

2009 ◽

Vol 2009 ◽

pp. 1-12 ◽

Cited By ~ 7

Author(s):

Sandra Andorf ◽

Tanja Gärtner ◽

Matthias Steinfath ◽

Hanna Witucka-Wall ◽

Thomas Altmann ◽

...

Keyword(s):

Systems Biology ◽

Network Structure ◽

Molecular Network

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

Briefings in Bioinformatics ◽

10.1093/bib/bbz067 ◽

2019 ◽

Vol 21 (4) ◽

pp. 1249-1260 ◽

Cited By ~ 2

Author(s):

David Hoksza ◽

Piotr Gawron ◽

Marek Ostaszewski ◽

Jan Hasenauer ◽

Reinhard Schneider

Keyword(s):

Systems Biology ◽

Biological Networks ◽

Software Tools ◽

Molecular Network ◽

Large Networks ◽

Software Libraries ◽

Closing The Gap ◽

Rest Api ◽

High Level ◽

Complex Biological Networks

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.

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SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks

10.1101/2020.11.16.369330 ◽

2020 ◽

Author(s):

Adrien Rougny ◽

Vasundra Touré ◽

John Albanese ◽

Dagmar Waltemath ◽

Denis Shirshov ◽

...

Keyword(s):

Systems Biology ◽

Semantic Annotation ◽

Formal Analysis ◽

Molecular Network ◽

Molecular Networks ◽

Scientific Publications ◽

Graphical Notation ◽

Biological Concepts ◽

Scientific Results ◽

Semantic Layer

AbstractA comprehensible representation of a molecular network is key to communicating and understanding scientific results in systems biology. The Systems Biology Graphical Notation (SBGN) has emerged as the main standard to represent such networks graphically. It has been implemented by different software tools, and is now largely used to communicate maps in scientific publications. However, learning the standard, and using it to build large maps, can be tedious. Moreover, SBGN maps are not grounded on a formal semantic layer and therefore do not enable formal analysis. Here, we introduce a new set of patterns representing recurring concepts encountered in molecular networks, called SBGN bricks. The bricks are structured in a new ontology, the BricKs Ontology (BKO), to define clear semantics for each of the biological concepts they represent. We show the usefulness of the bricks and BKO for both the template-based construction and the semantic annotation of molecular networks. The SBGN bricks and BKO can be freely explored and downloaded at sbgnbricks.org.

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Combining integrated systems-biology approaches with intervention-based experimental design provides a higher-resolution path forward for microbiome research

Behavioral and Brain Sciences ◽

10.1017/s0140525x18002911 ◽

2019 ◽

Vol 42 ◽

Author(s):

J. Alfredo Blakeley-Ruiz ◽

Carlee S. McClintock ◽

Ralph Lydic ◽

Helen A. Baghdoyan ◽

James J. Choo ◽

...

Keyword(s):

Systems Biology ◽

High Resolution ◽

Experimental Design ◽

Integrated Systems ◽

Microbiome Research ◽

Constructive Criticism

Abstract The Hooks et al. review of microbiota-gut-brain (MGB) literature provides a constructive criticism of the general approaches encompassing MGB research. This commentary extends their review by: (a) highlighting capabilities of advanced systems-biology “-omics” techniques for microbiome research and (b) recommending that combining these high-resolution techniques with intervention-based experimental design may be the path forward for future MGB research.

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