Browsing by Author "Niarakis, A."

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Open Access
A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance
(Frontiers Media S.A., 2023-06-22) Mazein, A.; Acencio, M. L.; Balaur, I.; Rougny, A.; Welter, D.; Niarakis, A.; Ramirez Ardila, D.; Doğrusöz, Uğur; Gawron, P.; Satagopam, V.; Gu, W.; Kremer, A.; Schneider, R.; Ostaszewski, M.
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.
Open Access
Community-driven roadmap for integrated disease maps
(Oxford University Press, 2018) Ostaszewski, M.; Gebel, S.; Kuperstein, I.; Mazein, A.; Zinovyev, A.; Doğrusöz, Uğur; Hasenauer, J.; Fleming, R. M. T.; Novere, N. L.; Gawron, P.; Ligon, T.; Niarakis, A.; Nickerson, D.; Weindl, D.; Balling, R.; Barillot, E.; Auffray, C.; Schneider, R.
The Disease Maps Project builds on a network of scientific and clinical groups that exchange best practices, share information and develop systems biomedicine tools. The project aims for an integrated, highly curated and user-friendly platform for disease-related knowledge. The primary focus of disease maps is on interconnected signaling, metabolic and gene regulatory network pathways represented in standard formats. The involvement of domain experts ensures that the key disease hallmarks are covered and relevant, up-to-date knowledge is adequately represented. Expert-curated and computer readable, disease maps may serve as a compendium of knowledge, allow for data-supported hypothesis generation or serve as a scaffold for the generation of predictive mathematical models. This article summarizes the 2nd Disease Maps Community meeting, highlighting its important topics and outcomes. We outline milestones on the roadmap for the future development of disease maps, including creating and maintaining standardized disease maps; sharing parts of maps that encode common human disease mechanisms; providing technical solutions for complexity management of maps; and Web tools for in-depth exploration of such maps. A dedicated discussion was focused on mathematical modeling approaches, as one of the main goals of disease map development is the generation of mathematically interpretable representations to predict disease comorbidity or drug response and to suggest drug repositioning, altogether supporting clinical decisions.