Vasundra Touré PhD Student
Norwegian University of Science and Technology
Department of Biology
Realfagbygget, DU2-185, Gløshaugen
Research description Knowledge management and data extraction of causal statements
My research topic aims at formalizing the knowledge provided by molecular causal statements: a biological source entity that influences the activity or the quantity of a biological target entity, under certain conditions and a specific context. Causal statements are commonly used for modeling purposes, which implies that ideally their representation should be unified across resources for an easy data integration. It is therefore important to have guidelines indicating how to represent a causal statement and which metadata should be provided for a usable statement. My project focuses on the development of the Minimum Information about a Molecular Interaction Causal Statement (MI2CAST) guidelines that provides a checklist of information to be annotated when generating a causal statement. Following this formal representation, I am also building software pipelines to extract annotated causal statements from a variety of prior-knowledge resources. Furthermore, our group is developing a curation interface to facilitate the building of causal statements for curators and data providers with a template-based approach, conform to the concepts of MI2CAST.
keywords: causal statement, curation guidelines, curation interface, data extraction, knowledge management, systems biology.
Background
Education: MSc in Bioinformatics and Biostatistics, BSc in Life Sciences.
Research: PhD student at NTNU (2017-current), Scientific Staff member at University of Rostock (2015-2017).
Publications
Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0. Adrien Rougny, Vasundra Touré, …, Augustin Luna. Journal of Integrative Bioinformatics
CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. Livia Perfetto, Marcio Luis Acencio, …, Vasundra Toure, John Zobolas, Luana Licata. Bioinformatics.
Harmonizing semantic annotations for computational models in biology. Maxwell Lewis Neal, Matthias König, …, Vasundra Touré, …, Dagmar Waltemath. Briefings in Bioinformatics.
Evolution of computational models in BioModels Database and the Physiome Model Repository. Martin Scharm, Tom Gebhardt, Vasundra Touré, Andrea Bagnacani, Ali Salehzadeh-Yazdi, Olaf Wolkenhauer, Dagmar Waltemath . BMC Systems Biology.
Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation. Vasundra Touré, Nicolas Le Novère, Dagmar Waltemath, Olaf Wolkenhauer. PLOS Computational Biology.
STON: exploring biological pathways using the SBGN standard and graph databases. Vasundra Touré, Alexander Mazein, Dagmar Waltemath, Irina Balaur, Mansoor Saqi, Ron Henkel, Johann Pellet, Charles Auffray. BMC Bioinformatics.
Toward Community Standards and Software for Whole-Cell Modeling. Dagmar Waltemath, Jonathan R. Karr, …, Vasundra Touré, …, Frank Schreiber. IEEE Transactions on Biomedical Engineering.