Systems Biology Graphical Notation: Process Diagram Level 1

Novère, Nicolas Le; Moodie, Stuart; Sorokin, Anatoly; Hucka, Michael; Schreiber, Falk; Demir, Emek; Mi, Huaiyu; Matsuoka, Yoshikazu; Wegner, K Mathias; Kitano, Hiroaki

doi:10.1038/npre.2008.2320.1

Cited by 55 publications

(71 citation statements)

References 11 publications

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“…Currently, COMBINE covers standards for models (CellML [30], SBML [31]), synthetic designs (SBOL [32]), and pathways (BioPAX [33]); for simulation descriptions (SED-ML [34]); and for graphical representations of biological knowledge (SBGN [35]), cf. Figure 1.…”

Section: A Community Network and Standardsmentioning

confidence: 99%

How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine

Waltemath

Wolkenhauer

2016

IEEE Trans. Biomed. Eng.

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Section: A Community Network and Standardsmentioning

confidence: 99%

How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine

Waltemath

Wolkenhauer

2016

IEEE Trans. Biomed. Eng.

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“…To build confidence, the obtained literature set should include at least two, ideally three, independent reports corroborating the functional interaction. [28], Cell Designer [29], Copasi [30] and SimBiology [106] and can be done using the newly introduced, communitydriven systems biology graphical notation [31] future science group or one of its forerunners [32][33][34]. Due to the fashion in which they are compiled, the resulting diagrams represent a consensus view derived from the community's published results and not necessarily a canonical pathway that has been thoroughly validated.…”

Section: Building Pathway Modelsmentioning

confidence: 99%

Use of Logic Theory in Understanding Regulatory Pathway Signaling in Response to Infection

Watterson

Ghazal

2010

Future Microbiol.

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Biological pathways link the molecular and cellular levels of biological activity and perform complex information processing seamlessly. Systems biology aims to combine an understanding of the cause-effect relationships of each individual interaction to build an understanding of the function of whole pathways. Therapies that target the 'host' biological processes in infectious diseases are often limited to the use of vaccines and biologics rather than small molecules. The development of host drug targets for small molecules is constrained by a limited knowledge of the underlying role of each target, particularly its potential to cause harmful side effects after targeting. By considering the combinatorial complexity of pathways from the outset, we can develop modeling tools that are better suited to analyzing large pathways, enabling us to identify new causal relationships. This could lead to new drug target strategies that beneficially disrupt host-pathogen interactions, minimizing the number of side effects. We introduce logic theory as part of a pathway modeling approach that can provide a new framework for understanding pathways and refine 'host-based' drug target identification strategies.

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“…They have used Systems Biology Graphical Notation (SBGN) for representation of the pathways [24]. Therefore, we used CellDesigner Version 4.1 (http://www.celldesigner.org/) to generate the pathway map in the SBGN format (Figure 2).…”

Section: Introductionmentioning

confidence: 99%

A comprehensive curated resource for follicle stimulating hormone signaling

et al. 2011

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BackgroundFollicle stimulating hormone (FSH) is an important hormone responsible for growth, maturation and function of the human reproductive system. FSH regulates the synthesis of steroid hormones such as estrogen and progesterone, proliferation and maturation of follicles in the ovary and spermatogenesis in the testes. FSH is a glycoprotein heterodimer that binds and acts through the FSH receptor, a G-protein coupled receptor. Although online pathway repositories provide information about G-protein coupled receptor mediated signal transduction, the signaling events initiated specifically by FSH are not cataloged in any public database in a detailed fashion.FindingsWe performed comprehensive curation of the published literature to identify the components of FSH signaling pathway and the molecular interactions that occur upon FSH receptor activation. Our effort yielded 64 reactions comprising 35 enzyme-substrate reactions, 11 molecular association events, 11 activation events and 7 protein translocation events that occur in response to FSH receptor activation. We also cataloged 265 genes, which were differentially expressed upon FSH stimulation in normal human reproductive tissues.ConclusionsWe anticipate that the information provided in this resource will provide better insights into the physiological role of FSH in reproductive biology, its signaling mediators and aid in further research in this area. The curated FSH pathway data is freely available through NetPath (http://www.netpath.org), a pathway resource developed previously by our group.

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Systems Biology Graphical Notation: Process Diagram Level 1

Cited by 55 publications

References 11 publications

How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine

How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine

Use of Logic Theory in Understanding Regulatory Pathway Signaling in Response to Infection

A comprehensive curated resource for follicle stimulating hormone signaling

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