The Experts below are selected from a list of 306 Experts worldwide ranked by ideXlab platform
Falk Schreiber - One of the best experts on this subject based on the ideXlab platform.
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translation of sbgn maps Process Description to activity flow
BMC Systems Biology, 2013Co-Authors: Falk Schreiber, Tobias Czauderna, Torsten VogtAbstract:Background The Systems Biology Graphical Notation (SBGN) provides standard graphical languages for representing cellular Processes, interactions, and biological networks. SBGN consists of three languages: Process Descriptions (PD), Entity Relationships (ER), and Activity Flows (AF). Maps in SBGN PD are often large, detailed, and complex, therefore there is a need for a simplified illustration.
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Translation of SBGN maps: Process Description to Activity Flow
BMC Systems Biology, 2013Co-Authors: Torsten Vogt, Tobias Czauderna, Falk SchreiberAbstract:Background The Systems Biology Graphical Notation (SBGN) provides standard graphical languages for representing cellular Processes, interactions, and biological networks. SBGN consists of three languages: Process Descriptions (PD), Entity Relationships (ER), and Activity Flows (AF). Maps in SBGN PD are often large, detailed, and complex, therefore there is a need for a simplified illustration. Results To solve this problem we define translations of SBGN PD maps into the more abstract SBGN AF maps. We present a template-based translation which allows the user to focus on different aspects of the underlying biological system. We also discuss aspects of laying out the AF map and of interactive navigation between both the PD and the AF map. The methods developed here have been implemented as part of SBGN-ED ( http://www.sbgn-ed.org ). Conclusions SBGN PD maps become much smaller and more manageable when translated into SBGN AF. The flexible translation of PD into AF and related interaction methods are an initial step in translating the different SBGN languages and open the path to future research for translation methods between other SBGN languages.
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Systems Biology Graphical Notation: Process Description language Level 1
Nature Precedings, 2009Co-Authors: Stuart Moodie, Huaiyu Mi, Nicolas Le Novère, Anatoly Sorokin, Falk SchreiberAbstract:Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the Process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous Descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical representation crafted over several years by a community of biochemists, modellers and computer scientists. Three orthogonal and complementary languages have been created, the Process Diagrams, the Entity Relationship Diagrams and the Activity Flow Diagrams. Using these three idioms a scientist can represent any network of biochemical interactions, which can then be interpreted in an unambiguous way. The set of symbols used is limited, and the grammar quite simple, to allow its usage in textbooks and its teaching directly in high schools. The first level of the SBGN Process Diagram has been publicly released. Software support for SBGN Process Diagram was developed concurrently with its specification in order to speed-up public adoption. Shared by the communities of biochemists, genomicians, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signalling pathways, metabolic networks and gene regulatory maps.
Loïc Paulevé - One of the best experts on this subject based on the ideXlab platform.
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Qualitative dynamics semantics for SBGN Process Description.
BMC systems biology, 2016Co-Authors: Adrien Rougny, Christine Froidevaux, Laurence Calzone, Loïc PaulevéAbstract:Background Qualitative dynamics semantics provide a coarse-grain modeling of networks dynamics by abstracting away kinetic parameters. They allow to capture general features of systems dynamics, such as attractors or reachability properties, for which scalable analyses exist. The Systems Biology Graphical Notation Process Description language (SBGN-PD) has become a standard to represent reaction networks. However, no qualitative dynamics semantics taking into account all the main features available in SBGN-PD had been proposed so far.
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Qualitative dynamics semantics for SBGN Process Description
BMC Systems Biology, 2016Co-Authors: Adrien Rougny, Christine Froidevaux, Laurence Calzone, Loïc PaulevéAbstract:Background: Qualitative dynamics semantics provide a coarse-grain modeling of networks dynamics by abstracting away kinetic parameters. They allow to capture general features of systems dynamics, such as attractors or reachability properties, for which scalable analyses exist. The Systems Biology Graphical Notation Process Description language (SBGN-PD) has become a standard to represent reaction networks. However, no qualitative dynamics semantics taking into account all the main features available in SBGN-PD had been proposed so far. Results: We propose two qualitative dynamics semantics for SBGN-PD reaction networks, namely the general semantics and the stories semantics, that we formalize using asynchronous automata networks. While the general semantics extends standard Boolean semantics of reaction networks by taking into account all the main features of SBGN-PD, the stories semantics allows to model several molecules of a network by a unique variable. The obtained qualitative models can be checked against dynamical properties and therefore validated with respect to biological knowledge. We apply our framework to reason on the qualitative dynamics of a large network (more than 200 nodes) modeling the regulation of the cell cycle by RB/E2F. Conclusion: The proposed semantics provide a direct formalization of SBGN-PD networks in dynamical qualitative models that can be further analyzed using standard tools for discrete models. The dynamics in stories semantics have a lower dimension than the general one and prune multiple behaviors (which can be considered as spurious) by enforcing the mutual exclusiveness between the activity of different nodes of a same story. Overall, the qualitative semantics for SBGN-PD allow to capture efficiently important dynamical features of reaction network models and can be exploited to further refine them.
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Two Qualitative Dynamics Semantics for SBGN Process Description Maps
2015Co-Authors: Adrien Rougny, Christine Froidevaux, Loïc PaulevéAbstract:Qualitative dynamics semantics allow to model large reaction networks with un- known kinetic parameters. In this poster, we present two qualitative dynamics seman- tics for reaction networks formalized into the SBGN Process Description language (SBGN-PD). These two semantics, namely the general semantics and the stories se- mantics, allow to model any SBGN-PD map into an automata network, that can then be simulated to catch the main dynamical features of the network. While the general semantics refines the standard Boolean semantics of reaction networks by taking into account all the main features of SBGN-PD, the stories semantics allows to model several molecules of a network by a unique variable, reducing in this way the size of the models. We present those two semantics and compare them on two biological network examples.
Adrien Rougny - One of the best experts on this subject based on the ideXlab platform.
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systems biology graphical notation Process Description language level 1 version 2 0
Journal of Integrative Bioinformatics, 2019Co-Authors: Adrien Rougny, Ugur Dogrusoz, Stuart L Moodie, Vasundra Toure, Irina Balaur, Tobias Czauderna, Hanna Borlinghaus, Alexander MazeinAbstract:The Systems Biology Graphical Notation (SBGN) is an international community effort that aims to standardise the visualisation of pathways and networks for readers with diverse scientific backgrounds as well as to support an efficient and accurate exchange of biological knowledge between disparate research communities, industry, and other players in systems biology. SBGN comprises the three languages Entity Relationship, Activity Flow, and Process Description (PD) to cover biological and biochemical systems at distinct levels of detail. PD is closest to metabolic and regulatory pathways found in biological literature and textbooks. Its well-defined semantics offer a superior precision in expressing biological knowledge. PD represents mechanistic and temporal dependencies of biological interactions and transformations as a graph. Its different types of nodes include entity pools (e.g. metabolites, proteins, genes and complexes) and Processes (e.g. reactions, associations and influences). The edges describe relationships between the nodes (e.g. consumption, production, stimulation and inhibition). This document details Level 1 Version 2.0 of the PD specification, including several improvements, in particular: 1) the addition of the equivalence operator, subunit, and annotation glyphs, 2) modification to the usage of submaps, and 3) updates to clarify the use of various glyphs (i.e. multimer, empty set, and state variable).
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Qualitative dynamics semantics for SBGN Process Description.
BMC systems biology, 2016Co-Authors: Adrien Rougny, Christine Froidevaux, Laurence Calzone, Loïc PaulevéAbstract:Background Qualitative dynamics semantics provide a coarse-grain modeling of networks dynamics by abstracting away kinetic parameters. They allow to capture general features of systems dynamics, such as attractors or reachability properties, for which scalable analyses exist. The Systems Biology Graphical Notation Process Description language (SBGN-PD) has become a standard to represent reaction networks. However, no qualitative dynamics semantics taking into account all the main features available in SBGN-PD had been proposed so far.
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Qualitative dynamics semantics for SBGN Process Description
BMC Systems Biology, 2016Co-Authors: Adrien Rougny, Christine Froidevaux, Laurence Calzone, Loïc PaulevéAbstract:Background: Qualitative dynamics semantics provide a coarse-grain modeling of networks dynamics by abstracting away kinetic parameters. They allow to capture general features of systems dynamics, such as attractors or reachability properties, for which scalable analyses exist. The Systems Biology Graphical Notation Process Description language (SBGN-PD) has become a standard to represent reaction networks. However, no qualitative dynamics semantics taking into account all the main features available in SBGN-PD had been proposed so far. Results: We propose two qualitative dynamics semantics for SBGN-PD reaction networks, namely the general semantics and the stories semantics, that we formalize using asynchronous automata networks. While the general semantics extends standard Boolean semantics of reaction networks by taking into account all the main features of SBGN-PD, the stories semantics allows to model several molecules of a network by a unique variable. The obtained qualitative models can be checked against dynamical properties and therefore validated with respect to biological knowledge. We apply our framework to reason on the qualitative dynamics of a large network (more than 200 nodes) modeling the regulation of the cell cycle by RB/E2F. Conclusion: The proposed semantics provide a direct formalization of SBGN-PD networks in dynamical qualitative models that can be further analyzed using standard tools for discrete models. The dynamics in stories semantics have a lower dimension than the general one and prune multiple behaviors (which can be considered as spurious) by enforcing the mutual exclusiveness between the activity of different nodes of a same story. Overall, the qualitative semantics for SBGN-PD allow to capture efficiently important dynamical features of reaction network models and can be exploited to further refine them.
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Two Qualitative Dynamics Semantics for SBGN Process Description Maps
2015Co-Authors: Adrien Rougny, Christine Froidevaux, Loïc PaulevéAbstract:Qualitative dynamics semantics allow to model large reaction networks with un- known kinetic parameters. In this poster, we present two qualitative dynamics seman- tics for reaction networks formalized into the SBGN Process Description language (SBGN-PD). These two semantics, namely the general semantics and the stories se- mantics, allow to model any SBGN-PD map into an automata network, that can then be simulated to catch the main dynamical features of the network. While the general semantics refines the standard Boolean semantics of reaction networks by taking into account all the main features of SBGN-PD, the stories semantics allows to model several molecules of a network by a unique variable, reducing in this way the size of the models. We present those two semantics and compare them on two biological network examples.
Torsten Vogt - One of the best experts on this subject based on the ideXlab platform.
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Translation of SBGN maps: Process Description to Activity Flow
BMC Systems Biology, 2013Co-Authors: Torsten Vogt, Tobias Czauderna, Falk SchreiberAbstract:Background The Systems Biology Graphical Notation (SBGN) provides standard graphical languages for representing cellular Processes, interactions, and biological networks. SBGN consists of three languages: Process Descriptions (PD), Entity Relationships (ER), and Activity Flows (AF). Maps in SBGN PD are often large, detailed, and complex, therefore there is a need for a simplified illustration. Results To solve this problem we define translations of SBGN PD maps into the more abstract SBGN AF maps. We present a template-based translation which allows the user to focus on different aspects of the underlying biological system. We also discuss aspects of laying out the AF map and of interactive navigation between both the PD and the AF map. The methods developed here have been implemented as part of SBGN-ED ( http://www.sbgn-ed.org ). Conclusions SBGN PD maps become much smaller and more manageable when translated into SBGN AF. The flexible translation of PD into AF and related interaction methods are an initial step in translating the different SBGN languages and open the path to future research for translation methods between other SBGN languages.
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translation of sbgn maps Process Description to activity flow
BMC Systems Biology, 2013Co-Authors: Falk Schreiber, Tobias Czauderna, Torsten VogtAbstract:Background The Systems Biology Graphical Notation (SBGN) provides standard graphical languages for representing cellular Processes, interactions, and biological networks. SBGN consists of three languages: Process Descriptions (PD), Entity Relationships (ER), and Activity Flows (AF). Maps in SBGN PD are often large, detailed, and complex, therefore there is a need for a simplified illustration.
Emek Demir - One of the best experts on this subject based on the ideXlab platform.
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systems biology graphical notation Process Description language level 1 version 1 3
Journal of Integrative Bioinformatics, 2015Co-Authors: Stuart L Moodie, Nicolas Le Novère, Emek Demir, Alice VillegerAbstract:The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Process Description language represents biological entities and Processes between these entities within a network. SBGN PD focuses on the mechanistic Description and temporal dependencies of biological interactions and transformations. The nodes (elements) are split into entity nodes describing, e.g., metabolites, proteins, genes and complexes, and Process nodes describing, e.g., reactions and associations. The edges (connections) provide Descriptions of relationships (or influences) between the nodes, such as consumption, production, stimulation and inhibition. Among all three languages of SBGN, PD is the closest to metabolic and regulatory pathways in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.
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sbgnviz a tool for visualization and complexity management of sbgn Process Description maps
PLOS ONE, 2015Co-Authors: Mecit Sari, Ugur Dogrusoz, Istemi Bahceci, Selcuk Onur Sumer, Bulent Arman Aksoy, Ozgun Babur, Emek DemirAbstract:BACKGROUND Information about cellular Processes and pathways is becoming increasingly available in detailed, computable standard formats such as BioPAX and SBGN. Effective visualization of this information is a key recurring requirement for biological data analysis, especially for -omic data. Biological data analysis is rapidly migrating to web based platforms; thus there is a substantial need for sophisticated web based pathway viewers that support these platforms and other use cases. RESULTS Towards this goal, we developed a web based viewer named SBGNViz for Process Description maps in SBGN (SBGN-PD). SBGNViz can visualize both BioPAX and SBGN formats. Unique features of SBGNViz include the ability to nest nodes to arbitrary depths to represent molecular complexes and cellular locations, automatic pathway layout, editing and highlighting facilities to enable focus on sub-maps, and the ability to inspect pathway members for detailed information from EntrezGene. SBGNViz can be used within a web browser without any installation and can be readily embedded into web pages. SBGNViz has two editions built with ActionScript and JavaScript. The JavaScript edition, which also works on touch enabled devices, introduces novel methods for managing and reducing complexity of large SBGN-PD maps for more effective analysis. CONCLUSION SBGNViz fills an important gap by making the large and fast-growing corpus of rich pathway information accessible to web based platforms. SBGNViz can be used in a variety of contexts and in multiple scenarios ranging from visualization of the results of a single study in a web page to building data analysis platforms.
