Search Results - "Toure, Vasundra"

The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling by Touré, Vasundra, Flobak, Åsmund, Niarakis, Anna, Vercruysse, Steven, Kuiper, Martin

“…Abstract Causal molecular interactions represent key building blocks used in computational modeling, where they facilitate the assembly of regulatory networks…”
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UniBioDicts: Unified access to Biological Dictionaries by Zobolas, John, Touré, Vasundra, Kuiper, Martin, Vercruysse, Steven

“…Abstract Summary We present a set of software packages that provide uniform access to diverse biological vocabulary resources that are instrumental for current…”
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CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator by Touré, Vasundra, Zobolas, John, Kuiper, Martin, Vercruysse, Steven

“…Molecular causal interactions are defined as regulatory connections between biological components. They are commonly retrieved from biological experiments and…”
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A National, Semantic-Driven, Three-Pillar Strategy to Enable Health Data Secondary Usage Interoperability for Research Within the Swiss Personalized Health Network: Methodological Study by Gaudet-Blavignac, Christophe, Raisaro, Jean Louis, Touré, Vasundra, Österle, Sabine, Crameri, Katrin, Lovis, Christian

“…Interoperability is a well-known challenge in medical informatics. Current trends in interoperability have moved from a data model technocentric approach to…”
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Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation by Touré, Vasundra, Le Novère, Nicolas, Waltemath, Dagmar, Wolkenhauer, Olaf

“…[...]SBGN ER visualises independent interactions between biological entities without any temporal aspect. [...]the forth diagram highlights an identified…”
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GraphML-SBGN bidirectional converter for metabolic networks by Balaur, Irina, Roy, Ludovic, Touré, Vasundra, Mazein, Alexander, Auffray, Charles

“…Systems biology researchers need feasible solutions for editing and visualisation of large biological diagrams. Here, we present the ySBGN bidirectional…”
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Strategies to Enhance Logic Modeling-Based Cell Line-Specific Drug Synergy Prediction by Niederdorfer, Barbara, Touré, Vasundra, Vazquez, Miguel, Thommesen, Liv, Kuiper, Martin, Lægreid, Astrid, Flobak, Åsmund

“…Discrete dynamical modeling shows promise in prioritizing drug combinations for screening efforts by reducing the experimental workload inherent to the vast…”
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SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks by Rougny, Adrien, Touré, Vasundra, Albanese, John, Waltemath, Dagmar, Shirshov, Denis, Sorokin, Anatoly, Bader, Gary D, Blinov, Michael L, Mazein, Alexander

“…A comprehensible representation of a molecular network is key to communicating and understanding scientific results in systems biology. The Systems Biology…”
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FAIRification of health-related data using semantic web technologies in the Swiss Personalized Health Network by Touré, Vasundra, Krauss, Philip, Gnodtke, Kristin, Buchhorn, Jascha, Unni, Deepak, Horki, Petar, Raisaro, Jean Louis, Kalt, Katie, Teixeira, Daniel, Crameri, Katrin, Österle, Sabine

“…The Swiss Personalized Health Network (SPHN) is a government-funded initiative developing federated infrastructures for a responsible and efficient secondary…”
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DCC Terminology Service—An Automated CI/CD Pipeline for Converting Clinical and Biomedical Terminologies in Graph Format for the Swiss Personalized Health Network by Krauss, Philip, Touré, Vasundra, Gnodtke, Kristin, Crameri, Katrin, Österle, Sabine

“…One goal of the Swiss Personalized Health Network (SPHN) is to provide an infrastructure for FAIR (Findable, Accessible, Interoperable and Reusable)…”
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STON: exploring biological pathways using the SBGN standard and graph databases by Touré, Vasundra, Mazein, Alexander, Waltemath, Dagmar, Balaur, Irina, Saqi, Mansoor, Henkel, Ron, Pellet, Johann, Auffray, Charles

“…When modeling in Systems Biology and Systems Medicine, the data is often extensive, complex and heterogeneous. Graphs are a natural way of representing…”
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Systems biology graphical notation markup language (SBGNML) version 0.3 by Bergmann, Frank T., Czauderna, Tobias, Dogrusoz, Ugur, Rougny, Adrien, Dräger, Andreas, Touré, Vasundra, Mazein, Alexander, Blinov, Michael L., Luna, Augustin

“…This document defines Version 0.3 Markup Language (ML) support for the Systems Biology Graphical Notation (SBGN), a set of three complementary visual languages…”
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A Middle-Out Modeling Strategy to Extend a Colon Cancer Logical Model Improves Drug Synergy Predictions in Epithelial-Derived Cancer Cell Lines by Tsirvouli, Eirini, Touré, Vasundra, Niederdorfer, Barbara, Vázquez, Miguel, Flobak, Åsmund, Kuiper, Martin

“…Cancer is a heterogeneous and complex disease and one of the leading causes of death worldwide. The high tumor heterogeneity between individuals affected by…”
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Evolution of computational models in BioModels Database and the Physiome Model Repository by Scharm, Martin, Gebhardt, Tom, Touré, Vasundra, Bagnacani, Andrea, Salehzadeh-Yazdi, Ali, Wolkenhauer, Olaf, Waltemath, Dagmar

“…A useful model is one that is being (re)used. The development of a successful model does not finish with its publication. During reuse, models are being…”
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Exploring the evolution of biochemical models at the network level by Gebhardt, Tom, Touré, Vasundra, Waltemath, Dagmar, Wolkenhauer, Olaf, Scharm, Martin

“…The evolution of biochemical models is difficult to track. At present, it is not possible to inspect the differences between model versions at the network…”
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Harmonizing semantic annotations for computational models in biology by Neal, Maxwell Lewis, König, Matthias, Nickerson, David, Mısırlı, Göksel, Kalbasi, Reza, Dräger, Andreas, Atalag, Koray, Chelliah, Vijayalakshmi, Cooling, Michael T, Cook, Daniel L, Crook, Sharon, de Alba, Miguel, Friedman, Samuel H, Garny, Alan, Gennari, John H, Gleeson, Padraig, Golebiewski, Martin, Hucka, Michael, Juty, Nick, Myers, Chris, Olivier, Brett G, Sauro, Herbert M, Scharm, Martin, Snoep, Jacky L, Touré, Vasundra, Wipat, Anil, Wolkenhauer, Olaf, Waltemath, Dagmar

“…Abstract Life science researchers use computational models to articulate and test hypotheses about the behavior of biological systems. Semantic annotation is a…”
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Setting the basis of best practices and standards for curation and annotation of logical models in biology—highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop by Niarakis, Anna, Kuiper, Martin, Ostaszewski, Marek, Malik Sheriff, Rahuman S, Casals-Casas, Cristina, Thieffry, Denis, Freeman, Tom C, Thomas, Paul, Touré, Vasundra, Noël, Vincent, Stoll, Gautier, Saez-Rodriguez, Julio, Naldi, Aurélien, Oshurko, Eugenia, Xenarios, Ioannis, Soliman, Sylvain, Chaouiya, Claudine, Helikar, Tomáš, Calzone, Laurence

“…Abstract The fast accumulation of biological data calls for their integration, analysis and exploitation through more systematic approaches. The generation of…”
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The SIB Swiss Institute of Bioinformatics Semantic Web of data by Altenhoff, Adrian, Bairoch, Amos, Bansal, Parit, Baratin, Delphine, Bastian, Frederic, Bolleman, Jerven, Bridge, Alan, Burdet, Frédéric, Crameri, Katrin, Dauvillier, Jérôme, Dessimoz, Christophe, Gehant, Sebastien, Glover, Natasha, Gnodtke, Kristin, Hayes, Catherine, Ibberson, Mark, Kriventseva, Evgenia, Kuznetsov, Dmitry, Frédérique, Lisacek, Mehl, Florence, Mendes de Farias, Tarcisio, Michel, Pierre-André, Moretti, Sébastien, Morgat, Anne, Österle, Sabine, Pagni, Marco, Redaschi, Nicole, Robinson-Rechavi, Marc, Samarasinghe, Kasun, Sima, Ana-Claudia, Szklarczyk, Damian, Topalov, Orlin, Touré, Vasundra, Unni, Deepak, von Mering, Christian, Wollbrett, Julien, Zahn-Zabal, Monique, Zdobnov, Evgeny

“…Abstract The SIB Swiss Institute of Bioinformatics (https://www.sib.swiss/) is a federation of bioinformatics research and service groups. The international…”
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The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST) by Touré, Vasundra, Vercruysse, Steven, Acencio, Marcio Luis, Lovering, Ruth C, Orchard, Sandra, Bradley, Glyn, Casals-Casas, Cristina, Chaouiya, Claudine, del-Toro, Noemi, Flobak, Åsmund, Gaudet, Pascale, Hermjakob, Henning, Hoyt, Charles Tapley, Licata, Luana, Lægreid, Astrid, Mungall, Christopher J, Niknejad, Anne, Panni, Simona, Perfetto, Livia, Porras, Pablo, Pratt, Dexter, Saez-Rodriguez, Julio, Thieffry, Denis, Thomas, Paul D, Türei, Dénes, Kuiper, Martin

“…Abstract Motivation A large variety of molecular interactions occurs between biomolecular components in cells. When a molecular interaction results in a…”
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Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0 by Rougny, Adrien, Touré, Vasundra, Moodie, Stuart, Balaur, Irina, Czauderna, Tobias, Borlinghaus, Hanna, Dogrusoz, Ugur, Mazein, Alexander, Dräger, Andreas, Blinov, Michael L, Villéger, Alice, Haw, Robin, Demir, Emek, Mi, Huaiyu, Sorokin, Anatoly, Schreiber, Falk, Luna, Augustin

“…The Systems Biology Graphical Notation (SBGN) is an international community effort that aims to standardise the visualisation of pathways and networks for…”
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