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

2021 ◽  
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

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.

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

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.

scholarly journals Inhibitory effect of sodium butyrate on colorectal cancer cells and construction of the related molecular network

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yang Xi ◽  
Zhuang Jing ◽  
Wu Wei ◽  
Zhang Chun ◽  
Qi Quan ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Sodium Butyrate ◽  
Molecular Network ◽  
Differentially Expressed ◽  
Cell Counting ◽  
Molecular Networks ◽  
Ppi Network ◽  
Invasion And Metastasis ◽  
Cerna Network ◽  
Proliferation Ability

Abstract Background Sodium butyrate (NaB) is produced through the fermentation of dietary fiber that is not absorbed and digested by the small intestine. Purpose Here, we aimed to investigate the effects of NaB on the proliferation, invasion, and metastasis of CRC cells and their potential underlying molecular mechanism(s). Methods The cell counting kit-8 (CCK-8) assay and EdU assay were used to detect cell proliferation ability, flow cytometry was used to investigate the induction of apoptosis and cell cycle progression, and the scratch-wound healing and transwell assays were used to evaluate cell migration and invasion, respectively. The human CRC genome information for tissues and CRC cells treated with NaB obtained from the NCBI GEO database was reannotated and used for differential RNA analysis. Functional and pathway enrichment analyses were performed for differentially expressed lncRNAs and mRNAs. A protein-protein interaction (PPI) network for the hub genes was constructed using the Cytoscape software. Targeted miRNAs were predicted based on the lnCeDB database, and a ceRNA network was constructed using the Cytoscape software. The Kaplan-Meier method was used to analyze patient prognosis using the clinical information and exon-seq data for CRC obtained from the Broad Institute’s GDAC Firehose platform. Results NaB decreased the proliferation ability of CRC cells in a dose- and time-dependent manner. The number of apoptotic CRC cells increased with the increase in NaB concentrations, and NaB induced a G1 phase block in CRC cells. Moreover, NaB suppressed the migratory and invasive capabilities of CRC cells. There were 666 differentially expressed mRNAs and 30 differentially expressed lncRNAs involved in the CRC inhibition by NaB. The PPI network and ceRNA network were constructed based on the differentially expressed mRNAs and lncRNAs. Three differentially expressed mRNAs, including HMGA2, LOXL2, and ST7, were significantly correlated with the prognosis of CRC. Conclusion NaB induces the apoptosis and inhibition of CRC cell proliferation, invasion, and metastasis by modulating complex molecular networks. RNA prediction and molecular network construction need to be the focus of further research in this direction.

scholarly journals Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation

2018 ◽  
Vol 14 (2) ◽  
pp. e1005740 ◽  
Author(s):  
Vasundra Touré ◽  
Nicolas Le Novère ◽  
Dagmar Waltemath ◽  
Olaf Wolkenhauer
Keyword(s):  
Systems Biology ◽  
Biological Pathways ◽  
Graphical Notation

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

BioEssays ◽  
2003 ◽  
Vol 26 (1) ◽  
pp. 68-72 ◽  
Author(s):  
Hao Zhu ◽  
Sui Huang ◽  
Pawan Dhar
Keyword(s):  
Systems Biology ◽  
Molecular Network

Beacon Editor: Capturing Signal Transduction Pathways Using the Systems Biology Graphical Notation Activity Flow Language

2017 ◽  
Vol 24 (12) ◽  
pp. 1226-1229 ◽  
Author(s):  
Haitham Elmarakeby ◽  
Mostafa Arefiyan ◽  
Elijah Myers ◽  
Song Li ◽  
Ruth Grene ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Systems Biology ◽  
Signal Transduction Pathways ◽  
Graphical Notation

scholarly journals Systems Biology Graphical Notation: Process Description language Level 1

2010 ◽  
Author(s):  
Stuart Moodie ◽  
Nicolas Le Novere ◽  
Emek Demir ◽  
Huaiyu Mi ◽  
Falk Schreiber
Keyword(s):  
Systems Biology ◽  
Description Language ◽  
Graphical Notation ◽  
Language Level ◽  
Level 1

scholarly journals Oak Species Quercus robur L. and Quercus petraea Liebl. Identification Based on UHPLC-HRMS/MS Molecular Networks

Metabolites ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 684
Author(s):  
Gaëlle Buche ◽  
Cyril Colas ◽  
Laëtitia Fougère ◽  
Emilie Destandau
Keyword(s):  
Quercus Robur ◽  
Quercus Petraea ◽  
Molecular Network ◽  
Molecular Networks ◽  
Venn Diagram ◽  
Pedunculate Oak ◽  
Pure Species ◽  
Wide Range ◽  
Fragmentation Patterns ◽  
The Individual

Two species of oak are dominant in French forests: pedunculate oak (Quercus robur L.) and sessile oak (Quercus petraea Liebl.). Their differentiation is not straightforward but is essential to better understand their respective molecular content in order to better valorize them. Thus, to improve oak species identification, an untargeted UHPLC-HRMS/MS method associated with a two-step data treatment was developed to analyze a wide range of specialized metabolites enabling the comparison of both species of oak extracts. Pooled extracts from sessile and pedunculate oaks, composed of extracts from several trees of pure species from various origins, were compared using first the Venn diagram, as a quick way to get an initial idea of how close the extracts are, and then using a molecular network to visualize, on the one hand, the ions shared between the two species and, on the other hand, the compounds specific to one species. The molecular network showed that the two species shared common clusters mainly representative of tannins derivatives and that each species has specific molecules with similar fragmentation patterns, associated in specific clusters. This methodology was then applied to compare these two pooled extracts to unknown individuals in order to determine the species. The Venn diagram allowed for the quick presumption of the species of the individual and then the species could be assigned more precisely with the molecular network, at the level of specific clusters. This method, developed for the first time, has several interests. First, it makes it possible to discriminate the species and to correctly assign the species of unknown samples. Moreover, it gave an overview of the metabolite composition of each sample to better target oak tree utilization and valorization.

scholarly journals Advancing Drug Discovery and Development from Active Constituents of Yinchenhao Tang, a Famous Traditional Chinese Medicine Formula

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Aihua Zhang ◽  
Hui Sun ◽  
Shi Qiu ◽  
Xijun Wang
Keyword(s):  
Systems Biology ◽  
Drug Discovery ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Molecular Mechanisms ◽  
Synergistic Effects ◽  
Molecular Networks ◽  
Agile Development ◽  
Therapeutic Effects ◽  
Systematic Analysis

Traditional Chinese medicine (TCM) formula has been playing a very important role in health protection and disease control for thousands of years. Guided by TCM syndrome theories, formula are designed to contain a combination of various kinds of crude drugs that, when combined, will achieve synergistic efficacy. However, the precise mechanism of synergistic action remains poorly understood. One example is a famous TCM formula Yinchenhao Tang (YCHT), whose efficacy in treating hepatic injury (HI) and Jaundice syndrome, has recently been well established as a case study. We also conducted a systematic analysis of synergistic effects of the principal compound using biochemistry, pharmacokinetics and systems biology, to explore the key molecular mechanisms. We had found that the three component (6,7-dimethylesculetin (D), geniposide (G), and rhein (R)) combination exerts a more robust synergistic effect than any one or two of the three individual compounds by hitting multiple targets. They can regulate molecular networks through activating both intrinsic and extrinsic pathways to synergistically cause intensified therapeutic effects. This paper provides an overview of the recent and potential developments of chemical fingerprinting coupled with systems biology advancing drug discovery towards more agile development of targeted combination therapies for the YCHT.

scholarly journals Neurons, Glia, Extracellular Matrix and Neurovascular Unit: A Systems Biology Approach to the Complexity of Synaptic Plasticity in Health and Disease

2020 ◽  
Vol 21 (4) ◽  
pp. 1539 ◽  
Author(s):  
Ciro De Luca ◽  
Anna Maria Colangelo ◽  
Assunta Virtuoso ◽  
Lilia Alberghina ◽  
Michele Papa
Keyword(s):  
Extracellular Matrix ◽  
Synaptic Plasticity ◽  
Systems Biology ◽  
Synapse Formation ◽  
Neurovascular Unit ◽  
Synaptic Cleft ◽  
Adult Brain ◽  
Molecular Networks ◽  
Maladaptive Plasticity ◽  
Health And Disease

The synaptic cleft has been vastly investigated in the last decades, leading to a novel and fascinating model of the functional and structural modifications linked to synaptic transmission and brain processing. The classic neurocentric model encompassing the neuronal pre- and post-synaptic terminals partly explains the fine-tuned plastic modifications under both pathological and physiological circumstances. Recent experimental evidence has incontrovertibly added oligodendrocytes, astrocytes, and microglia as pivotal elements for synapse formation and remodeling (tripartite synapse) in both the developing and adult brain. Moreover, synaptic plasticity and its pathological counterpart (maladaptive plasticity) have shown a deep connection with other molecular elements of the extracellular matrix (ECM), once considered as a mere extracellular structural scaffold altogether with the cellular glue (i.e., glia). The ECM adds another level of complexity to the modern model of the synapse, particularly, for the long-term plasticity and circuit maintenance. This model, called tetrapartite synapse, can be further implemented by including the neurovascular unit (NVU) and the immune system. Although they were considered so far as tightly separated from the central nervous system (CNS) plasticity, at least in physiological conditions, recent evidence endorsed these elements as structural and paramount actors in synaptic plasticity. This scenario is, as far as speculations and evidence have shown, a consistent model for both adaptive and maladaptive plasticity. However, a comprehensive understanding of brain processes and circuitry complexity is still lacking. Here we propose that a better interpretation of the CNS complexity can be granted by a systems biology approach through the construction of predictive molecular models that enable to enlighten the regulatory logic of the complex molecular networks underlying brain function in health and disease, thus opening the way to more effective treatments.

Sign in / Sign up

Export Citation Format

Share Document