Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms [* Cross-Reference *]

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Alexander Mazein; Marek Ostaszewski; Inna Kuperstein; Steven Watterson; Nicolas Le Novère; Diane Lefaudeux; Bertrand De Meulder; Johann Pellet; Irina Balaur; Mansoor Saqi; Maria Manuela Nogueira; Feng He; Andrew Parton; Nicolas Lemonnier; Piotr Gawron; Stephan Gebel; Pierre Hainaut; Markus Ollert; Uğur Doğrusöz; Emmanuel Barillot; Andreï Zinovyev; Reinhard Schneider; Rudi Balling; Charles Auffray, 2018, "Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms [* Cross-Reference *]", https://lore.list.lu/citation?persistentId=perma:LIST.XX2S5I, LIST Open Repository, V1

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Description	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. (2018-05-30) *This entry has been automatically imported via OpenAlex by LIST harvest scripts. Please refer to https://doi.org/10.1038/s41540-018-0059-y for the original and latest version of the publication* (2026-07-01)
Subject	Chemistry; Medicine, Health and Life Sciences
Keyword	Computer science, Bottleneck, Context (archaeology), Representation (politics), Data science, Reuse, Disease, Modular design, Mechanism (biology), Knowledge representation and reasoning, Management science, Artificial intelligence, Medicine, Engineering, Biology
License/Data Use Agreement	CC BY 4.0


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Citation Metadata

Persistent Identifier	perma:LIST.XX2S5I
Publication Date	2026-07-06
Title	Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms [* Cross-Reference *]
Other Identifier	https://doi.org/10.1038/s41540-018-0059-y OpenAlex ID: https://openalex.org/W2807615161
Author	Alexander Mazein (Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Inserm, Centre International de Recherche en Infectiologie) - ORCID: https://orcid.org/0000-0001-7137-4171 Marek Ostaszewski (University of Luxembourg, Luxembourg Institute of Science and Technology) - ORCID: https://orcid.org/0000-0003-1473-370X Inna Kuperstein (Inserm, Université Paris Sciences et Lettres, Médecins Sans Frontières, École Nationale Supérieure des Mines de Paris, Institut Curie) - ORCID: https://orcid.org/0000-0001-8086-8915 Steven Watterson (University of Ulster, Altnagelvin Area Hospital) - ORCID: https://orcid.org/0000-0002-2750-6410 Nicolas Le Novère (Babraham Institute) Diane Lefaudeux (Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Inserm, Centre International de Recherche en Infectiologie) - ORCID: https://orcid.org/0000-0001-7075-5781 Bertrand De Meulder (Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Inserm, Centre International de Recherche en Infectiologie) - ORCID: https://orcid.org/0000-0002-2108-7657 Johann Pellet (Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Inserm, Centre International de Recherche en Infectiologie) - ORCID: https://orcid.org/0000-0002-9346-0190 Irina Balaur (Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Inserm, Centre International de Recherche en Infectiologie) - ORCID: https://orcid.org/0000-0002-3671-895X Mansoor Saqi (Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Inserm, Centre International de Recherche en Infectiologie) - ORCID: https://orcid.org/0000-0003-1222-475X Maria Manuela Nogueira (Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Inserm, Centre International de Recherche en Infectiologie) - ORCID: https://orcid.org/0000-0002-8353-1979 Feng He - ORCID: https://orcid.org/0000-0003-2657-7361 Andrew Parton (University of Ulster, Altnagelvin Area Hospital) - ORCID: https://orcid.org/0000-0002-8562-0975 Nicolas Lemonnier (Centre National de la Recherche Scientifique, Inserm, Université Grenoble Alpes) - ORCID: https://orcid.org/0000-0002-3994-8697 Piotr Gawron (University of Luxembourg, Luxembourg Institute of Science and Technology) - ORCID: https://orcid.org/0000-0002-9328-8052 Stephan Gebel (University of Luxembourg, Luxembourg Institute of Science and Technology) - ORCID: https://orcid.org/0000-0001-5086-8324 Pierre Hainaut (Centre National de la Recherche Scientifique, Inserm, Université Grenoble Alpes) - ORCID: https://orcid.org/0000-0002-1303-1610 Markus Ollert (University of Southern Denmark, Luxembourg Institute of Health) - ORCID: https://orcid.org/0000-0002-8055-0103 Uğur Doğrusöz (Bilkent University) - ORCID: https://orcid.org/0000-0002-7153-0784 Emmanuel Barillot (Inserm, Université Paris Sciences et Lettres, Médecins Sans Frontières, École Nationale Supérieure des Mines de Paris, Institut Curie) - ORCID: https://orcid.org/0000-0003-2724-2002 Andreï Zinovyev (Inserm, Université Paris Sciences et Lettres, Médecins Sans Frontières, École Nationale Supérieure des Mines de Paris, Institut Curie) - ORCID: https://orcid.org/0000-0002-9517-7284 Reinhard Schneider (University of Luxembourg, Luxembourg Institute of Science and Technology) - ORCID: https://orcid.org/0000-0002-8278-1618 Rudi Balling (University of Luxembourg, Luxembourg Institute of Science and Technology) - ORCID: https://orcid.org/0000-0003-2902-5650 Charles Auffray (Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Inserm, Centre International de Recherche en Infectiologie) - ORCID: https://orcid.org/0000-0003-2226-7411
Point of Contact	Use email button above to contact. LIST QDKM (LIST)
Description	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. (2018-05-30) *This entry has been automatically imported via OpenAlex by LIST harvest scripts. Please refer to https://doi.org/10.1038/s41540-018-0059-y for the original and latest version of the publication* (2026-07-01)
Subject	Chemistry; Medicine, Health and Life Sciences
Keyword	Computer science Bottleneck Context (archaeology) Representation (politics) Data science Reuse Disease Modular design Mechanism (biology) Knowledge representation and reasoning Management science Artificial intelligence Medicine Engineering Biology
Topic Classification	Bioinformatics and Genomic Networks Biomedical Text Mining and Ontologies Microbial Metabolic Engineering and Bioproduction
Deposit Date	2018-05-30
Data Type	Article
Data Source	npj Systems Biology and Applications

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