High-quality Reconstruction of Disease Mechanisms: Planning, Development and Maintenance

Alexander Mazein; Marcio Luis Acencio; Irina Balaur; Adrien Rougny; Danielle Welter; Anna Niarakis; Diana Ramirez Ardila; Ugur Dogrusoz; Piotr Gawron; Venkata Satagopam; Wei Gu; Andreas Kremer; Reinhard Schneider; Marek Ostaszewski

doi:10.20944/preprints202212.0209.v1

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preprints.org > biology and life sciences > biology and biotechnology > doi: 10.20944/preprints202212.0209.v1

Preprint Review Version 1 Preserved in Portico This version is not peer-reviewed

High-quality Reconstruction of Disease Mechanisms: Planning, Development and Maintenance

^* ,

Version 1 : Received: 9 December 2022 / Approved: 13 December 2022 / Online: 13 December 2022 (01:06:32 CET)

How to cite: Mazein, A.; Acencio, M.L.; Balaur, I.; Rougny, A.; Welter, D.; Niarakis, A.; Ramirez Ardila, D.; Dogrusoz, U.; Gawron, P.; Satagopam, V.; Gu, W.; Kremer, A.; Schneider, R.; Ostaszewski, M. High-quality Reconstruction of Disease Mechanisms: Planning, Development and Maintenance. Preprints 2022, 2022120209. https://doi.org/10.20944/preprints202212.0209.v1 Mazein, A.; Acencio, M.L.; Balaur, I.; Rougny, A.; Welter, D.; Niarakis, A.; Ramirez Ardila, D.; Dogrusoz, U.; Gawron, P.; Satagopam, V.; Gu, W.; Kremer, A.; Schneider, R.; Ostaszewski, M. High-quality Reconstruction of Disease Mechanisms: Planning, Development and Maintenance. Preprints 2022, 2022120209. https://doi.org/10.20944/preprints202212.0209.v1

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MDPI and ACS Style

Mazein, A.; Acencio, M.L.; Balaur, I.; Rougny, A.; Welter, D.; Niarakis, A.; Ramirez Ardila, D.; Dogrusoz, U.; Gawron, P.; Satagopam, V.; Gu, W.; Kremer, A.; Schneider, R.; Ostaszewski, M. High-quality Reconstruction of Disease Mechanisms: Planning, Development and Maintenance. Preprints 2022, 2022120209. https://doi.org/10.20944/preprints202212.0209.v1

APA Style

Mazein, A., Acencio, M.L., Balaur, I., Rougny, A., Welter, D., Niarakis, A., Ramirez Ardila, D., Dogrusoz, U., Gawron, P., Satagopam, V., Gu, W., Kremer, A., Schneider, R., & Ostaszewski, M. (2022). High-quality Reconstruction of Disease Mechanisms: Planning, Development and Maintenance. Preprints. https://doi.org/10.20944/preprints202212.0209.v1

Chicago/Turabian Style

Mazein, A., Reinhard Schneider and Marek Ostaszewski. 2022 "High-quality Reconstruction of Disease Mechanisms: Planning, Development and Maintenance" Preprints. https://doi.org/10.20944/preprints202212.0209.v1

Abstract

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.

Keywords

Systems Biology; Systems Medicine; Disease Mechanisms; Disease Maps; Network Biology

Subject

Biology and Life Sciences, Biology and Biotechnology

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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