The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways

Freeman, Tom C.; Raza, Sobia; Theocharidis, Athanasios; Ghazal, Peter

doi:10.1186/1752-0509-4-65

Cited by 18 publications

(28 citation statements)

References 44 publications

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“…This diagram is built using the standardised graphical notation Modified Edinburgh Pathway Notation (mEPN) [26]. It depicts every entity used in the final model, the reactions they are involved in, and in what way they react (binding, phosphorylation, etc.).…”

Section: Resultsmentioning

confidence: 99%

A Computational Model of Lipopolysaccharide-Induced Nuclear Factor Kappa B Activation: A Key Signalling Pathway in Infection-Induced Preterm Labour

Sharp

Saunders

et al. 2013

PLoS ONE

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Preterm birth is the single biggest cause of significant neonatal morbidity and mortality, and the incidence is rising. Development of new therapies to treat and prevent preterm labour is seriously hampered by incomplete understanding of the molecular mechanisms that initiate labour at term and preterm. Computational modelling provides a new opportunity to improve this understanding. It is a useful tool in (i) identifying gaps in knowledge and informing future research, and (ii) providing the basis for an in silico model of parturition in which novel drugs to prevent or treat preterm labour can be “tested”. Despite their merits, computational models are rarely used to study the molecular events initiating labour. Here, we present the first attempt to generate a dynamic kinetic model that has relevance to the molecular mechanisms of preterm labour. Using published data, we model an important candidate signalling pathway in infection-induced preterm labour: that of lipopolysaccharide (LPS) -induced activation of Nuclear Factor kappa B. This is the first model of this pathway to explicitly include molecular interactions upstream of Nuclear Factor kappa B activation. We produced a formalised graphical depiction of the pathway and built a kinetic model based on ordinary differential equations. The kinetic model accurately reproduced published in vitro time course plots of Lipopolysaccharide-induced Nuclear Factor kappa B activation in mouse embryo fibroblasts. In this preliminary work we have provided proof of concept that it is possible to build computational models of signalling pathways that are relevant to the regulation of labour, and suggest that models that are validated with wet-lab experiments have the potential to greatly benefit the field.

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Section: Resultsmentioning

confidence: 99%

A Computational Model of Lipopolysaccharide-Induced Nuclear Factor Kappa B Activation: A Key Signalling Pathway in Infection-Induced Preterm Labour

Sharp

Saunders

et al. 2013

PLoS ONE

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“…We selected a set of 51 SBO classes for reactions, pathways and molecules as a first resource of subclasses of processes and participants, respectively. The modified Edinburg Pathway Notation (mEPN) [13] is another syntactic format based on systems approach. Its components provide a refined set of reactions that complete the SBO class set.…”

Section: Ontological Upper Model: Alzheimer Disease Map Ontologymentioning

confidence: 99%

Converting Alzheimer’s Disease Map into a Heavyweight Ontology: A Formal Network to Integrate Data

Henry

Moszer

Dameron

et al. 2018

Lecture Notes in Computer Science

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Alzheimer's disease (AD) pathophysiology is still imperfectly understood and current paradigms have not led to curative outcome. Omics technologies offer great promises for improving our understanding and generating new hypotheses. However, integration and interpretation of such data pose major challenges, calling for adequate knowledge models. AlzPathway is a disease map that gives a detailed and broad account of AD pathophysiology. However, AlzPathway lacks formalism, which can lead to ambiguity and misinterpretation. Ontologies are an adequate framework to overcome this limitation, through their axiomatic definitions and logical reasoning properties. We introduce the AD Map Ontology (ADMO) an ontological upper model based on systems biology terms. We then propose to convert AlzPathway into an ontology and to integrate it into ADMO. We demonstrate that it allows one to deal with issues related to redundancy, naming, consistency, process classification and pathway relationships. Further, it opens opportunities to expand the model using elements from other resources, such as generic pathways from Reactome or clinical features contained in the ADO (AD Ontology). A version of the ontology will be made freely available to the community on Bioportal at the time of the conference.

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“…We have developed a modelling platform that combines elements of other approaches 1 . The modified Edinburgh Pathway Notation (mEPN) scheme was first published in 2008 2 , refined in 2010 3 , and is presented here in its current form (BOX 1). Representing the interactions between biological components in the context of a pathway diagram is a challenge, and a number of notation schemes have been proposed [3][4][5][6][7][8][9] .…”

Section: Introductionmentioning

confidence: 99%

“…The modified Edinburgh Pathway Notation (mEPN) scheme was first published in 2008 2 , refined in 2010 3 , and is presented here in its current form (BOX 1). Representing the interactions between biological components in the context of a pathway diagram is a challenge, and a number of notation schemes have been proposed [3][4][5][6][7][8][9] . In an effort to standardise pathway diagrams, the Systems Biology Graphical Notation (SBGN) community proposed standards for pathway depiction, including the process description (PD) language 7 based on ideas first proposed by Kitano et al 4 .…”

Section: Introductionmentioning

confidence: 99%

A graphical and computational modeling platform for biological pathways

et al. 2018

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EDITORIAL SUMMARY: This is a biologist-friendly modelling scheme facilitating the capture and 15 visualization of knowledge on biological pathways and how components interact. Moreover, when 16 parameterised, these pathway models can be used directly to run simulations of their activity and test 49a simulation run, even on a large model, typically takes only seconds. Models constructed using this 50 approach provide a means of knowledge management, information exchange, and through the computation simulation of their dynamic activity, a means to generate and test hypotheses, and predict a system's behaviour when perturbed.

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The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways

Cited by 18 publications

References 44 publications

A Computational Model of Lipopolysaccharide-Induced Nuclear Factor Kappa B Activation: A Key Signalling Pathway in Infection-Induced Preterm Labour

A Computational Model of Lipopolysaccharide-Induced Nuclear Factor Kappa B Activation: A Key Signalling Pathway in Infection-Induced Preterm Labour

Converting Alzheimer’s Disease Map into a Heavyweight Ontology: A Formal Network to Integrate Data

A graphical and computational modeling platform for biological pathways

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