Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms

Alexander Mazein; Marek  Ostaszewski; Inna  Kuperstein; Steven Watterson; Nicolas Le Novere; Diane  Lefaudeux; Bertrand  De Meulder; Johann Pellet; Irina  Balaur; Mansoor  Saqi; Maria  Manuela Nogueira; Feng  Q. HeFeng; Andrew Parton; Nathanael  Lemonnier; Piotr Gawron; Stephan  Gebel; Pierre Hainaut; Markus  Ollert; Ugur  Dogrusoz; Emmanuel  Barillot; Andrei Zinovyev; Reinhard Schneider; Rudi Balling; Charles  Auffray

doi:10.1038/s41540-018-0059-y

Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms

Alexander Mazein
, Marek Ostaszewski
, Inna Kuperstein
, Steven Watterson
, Nicolas Le Novere
, Diane Lefaudeux
, Bertrand De Meulder
, Johann Pellet
, Irina Balaur
, Mansoor Saqi
, Maria Manuela Nogueira
, Feng Q. HeFeng
, Andrew Parton
, Nathanael Lemonnier
, Piotr Gawron
, Stephan Gebel
, Pierre Hainaut
, Markus Ollert
, Ugur Dogrusoz
, Emmanuel Barillot

Andrei Zinovyev, Reinhard Schneider, Rudi Balling , Charles Auffray

Research output: Contribution to journal › Article › peer-review

86 Citations (Scopus)

89 Downloads (Pure)

Abstract

The development of computational approaches in systems biology has reached a state of maturity that allows their transition to systems medicine. Despite this progress, intuitive visualisation and context-dependent knowledge representation still present a major bottleneck. In this paper, we describe the Disease Maps Project, an effort towards a community-driven computationally readable comprehensive representation of disease mechanisms. We outline the key principles and the framework required for the success of this initiative, including use of best practices, standards and protocols. We apply a modular approach to ensure efficient sharing and reuse of resources for projects dedicated to specific diseases. Community-wide use of disease maps will accelerate the conduct of biomedical research and lead to new disease ontologies defined from mechanism-based disease endotypes rather than phenotypes.

Original language	English
Article number	21
Number of pages	10
Journal	npj Systems Biology and Applications
Volume	4
Early online date	2 Jun 2018
DOIs	https://doi.org/10.1038/s41540-018-0059-y
Publication status	Published online - 2 Jun 2018

Data Availability Statement

All relevant data are available within the paper, Supplementary Information and the Disease Maps website at http://disease-maps.io.

Funding

This work was supported by the CNRS, University of Luxembourg, Institut Curie and in part through the U-BIOPRED (IMI no. 115010 grant to C.A.) and eTRIKS (IMI no. 115446 grant to C.A., R.B. and R.S.) Consortia funded by the European Union and the European Federation of Pharmaceutical Industry Associations, the Coordinating action for the implementation of systems medicine in Europe (CASyM FP7 grant no. 305333 to C.A. and R.B.), the COLOSYS grant ANR-15-CMED-0001-04, provided by the Agence Nationale de la Recherche under the frame of ERACoSysMed-1, the ERA-Net for Systems Medicine in clinical research and medical practice (to I.K., E.B. and A.Z.). A.P. and S.W. acknowledge a research exchange grant from CASyM.

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

Diseases
Scientific Community
Systems Biology

Access to Document

10.1038/s41540-018-0059-yLicence: CC BY

s41540-018-0059-yFinal published version, 4.52 MBLicence: CC BY

Cite this

Mazein, A., Ostaszewski, M., Kuperstein, I., Watterson, S., Novere, N. L., Lefaudeux, D., De Meulder , B., Pellet , J., Balaur, I., Saqi, M., Manuela Nogueira , M., Q. HeFeng , F., Parton, A., Lemonnier , N., Gawron, P., Gebel, S., Hainaut , P., Ollert, M., Dogrusoz , U., ... Auffray, C. (2018). Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms. npj Systems Biology and Applications, 4, Article 21. Advance online publication. https://doi.org/10.1038/s41540-018-0059-y

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Mazein, A, Ostaszewski, M, Kuperstein, I, Watterson, S, Novere, NL, Lefaudeux, D, De Meulder , B, Pellet , J, Balaur, I, Saqi, M, Manuela Nogueira , M, Q. HeFeng , F, Parton, A, Lemonnier , N, Gawron, P, Gebel, S, Hainaut , P, Ollert, M, Dogrusoz , U, Barillot , E, Zinovyev, A, Schneider, R, Balling , R & Auffray, C 2018, 'Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms', npj Systems Biology and Applications, vol. 4, 21. https://doi.org/10.1038/s41540-018-0059-y

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T1 - Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms

AU - Mazein, Alexander

AU - Ostaszewski, Marek

AU - Kuperstein, Inna

AU - Watterson, Steven

AU - Novere, Nicolas Le

AU - Lefaudeux, Diane

AU - De Meulder , Bertrand

AU - Pellet , Johann

AU - Balaur, Irina

AU - Saqi, Mansoor

AU - Manuela Nogueira , Maria

AU - Q. HeFeng , Feng

AU - Parton, Andrew

AU - Lemonnier , Nathanael

AU - Gawron, Piotr

AU - Gebel, Stephan

AU - Hainaut , Pierre

AU - Ollert, Markus

AU - Dogrusoz , Ugur

AU - Barillot , Emmanuel

AU - Zinovyev, Andrei

AU - Schneider, Reinhard

AU - Balling , Rudi

AU - Auffray, Charles

PY - 2018/6/2

Y1 - 2018/6/2

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AB - The development of computational approaches in systems biology has reached a state of maturity that allows their transition to systems medicine. Despite this progress, intuitive visualisation and context-dependent knowledge representation still present a major bottleneck. In this paper, we describe the Disease Maps Project, an effort towards a community-driven computationally readable comprehensive representation of disease mechanisms. We outline the key principles and the framework required for the success of this initiative, including use of best practices, standards and protocols. We apply a modular approach to ensure efficient sharing and reuse of resources for projects dedicated to specific diseases. Community-wide use of disease maps will accelerate the conduct of biomedical research and lead to new disease ontologies defined from mechanism-based disease endotypes rather than phenotypes.

KW - Diseases

KW - Scientific Community

KW - Systems Biology

UR - https://www.nature.com/articles/s41540-025-00554-6

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SN - 2056-7189

VL - 4

JO - npj Systems Biology and Applications

JF - npj Systems Biology and Applications

M1 - 21

ER -

Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms

Abstract

Data Availability Statement

Funding

UN SDGs

Keywords

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The dynamics of cholesterol metabolism and atherosclerosis across population subgroups

Cite this

Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms

Abstract

Data Availability Statement

Funding

UN SDGs

Keywords

Access to Document

Other files and links

Fingerprint

Student theses

The dynamics of cholesterol metabolism and atherosclerosis across population subgroups

Cite this