curation; disease mechanisms; pathway biology; systems biology; translational research; Biochemistry; Biotechnology; Computational Mathematics; Statistics and Probability; Structural Biology; Environmental Engineering
Abstract :
[en] As a conceptual model of disease mechanisms, a disease map integrates available knowledge and is applied for data interpretation, predictions and hypothesis generation. It is possible to model disease mechanisms on different levels of granularity and adjust the approach to the goals of a particular project. This rich environment together with requirements for high-quality network reconstruction makes it challenging for new curators and groups to be quickly introduced to the development methods. In this review, we offer a step-by-step guide for developing a disease map within its mainstream pipeline that involves using the CellDesigner tool for creating and editing diagrams and the MINERVA Platform for online visualisation and exploration. We also describe how the Neo4j graph database environment can be used for managing and querying efficiently such a resource. For assessing the interoperability and reproducibility we apply FAIR principles.
Disciplines :
Life sciences: Multidisciplinary, general & others
Author, co-author :
MAZEIN, Alexander ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core
ACENCIO, Marcio Luis ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core
BALAUR, Irina-Afrodita ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core
Rougny, Adrien; Independent Researcher, Massy, France
WELTER, Danielle ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine > Bioinformatics Core > Translational Informatics
Niarakis, Anna; Université Paris-Saclay, Laboratoire Européen de Recherche Pour la Polyarthrite Rhumatoïde-Genhotel, University Evry, Evry, France ; Lifeware Group, Inria Saclay-Ile de France, Palaiseau, France
Ramirez Ardila, Diana; ITTM Information Technology for Translational Medicine, Esch-sur-Alzette, Luxemburg
Dogrusoz, Ugur; Computer Engineering Department, Bilkent University, Ankara, Türkiye
GAWRON, Piotr ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine > Bioinformatics Core > Visualisation
SATAGOPAM, Venkata ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core ; ELIXIR Luxembourg, Belvaux, Luxembourg
GU, Wei ; University of Luxembourg ; ELIXIR Luxembourg, Belvaux, Luxembourg
KREMER, Andreas ; University of Luxembourg ; ITTM Information Technology for Translational Medicine, Esch-sur-Alzette, Luxemburg
SCHNEIDER, Reinhard ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core ; ELIXIR Luxembourg, Belvaux, Luxembourg
OSTASZEWSKI, Marek ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core ; ELIXIR Luxembourg, Belvaux, Luxembourg
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