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

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.

SUBMITTER: Mazein A

PROVIDER: S-EPMC5984630 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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

Mazein Alexander A Ostaszewski Marek M Kuperstein Inna I Watterson Steven S Le Novère Nicolas N Lefaudeux Diane D De Meulder Bertrand B Pellet Johann J Balaur Irina I Saqi Mansoor M Nogueira Maria Manuela MM He Feng F Parton Andrew A Lemonnier Nathanaël N Gawron Piotr P Gebel Stephan S Hainaut Pierre P Ollert Markus M Dogrusoz Ugur U Barillot Emmanuel E Zinovyev Andrei A Schneider Reinhard R Balling Rudi R Auffray Charles C

NPJ systems biology and applications 20180602

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 ...[more]

PMID: 29872544

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Project description:BACKGROUND: To enhance our understanding of complex biological systems like diseases we need to put all of the available data into context and use this to detect relations, pattern and rules which allow predictive hypotheses to be defined. Life science has become a data rich science with information about the behaviour of millions of entities like genes, chemical compounds, diseases, cell types and organs, which are organised in many different databases and/or spread throughout the literature. Existing knowledge such as genotype-phenotype relations or signal transduction pathways must be semantically integrated and dynamically organised into structured networks that are connected with clinical and experimental data. Different approaches to this challenge exist but so far none has proven entirely satisfactory. RESULTS: To address this challenge we previously developed a generic knowledge management framework, BioXM™, which allows the dynamic, graphic generation of domain specific knowledge representation models based on specific objects and their relations supporting annotations and ontologies. Here we demonstrate the utility of BioXM for knowledge management in systems biology as part of the EU FP6 BioBridge project on translational approaches to chronic diseases. From clinical and experimental data, text-mining results and public databases we generate a chronic obstructive pulmonary disease (COPD) knowledge base and demonstrate its use by mining specific molecular networks together with integrated clinical and experimental data. CONCLUSIONS: We generate the first semantically integrated COPD specific public knowledge base and find that for the integration of clinical and experimental data with pre-existing knowledge the configuration based set-up enabled by BioXM reduced implementation time and effort for the knowledge base compared to similar systems implemented as classical software development projects. The knowledgebase enables the retrieval of sub-networks including protein-protein interaction, pathway, gene--disease and gene--compound data which are used for subsequent data analysis, modelling and simulation. Pre-structured queries and reports enhance usability; establishing their use in everyday clinical settings requires further simplification with a browser based interface which is currently under development.

Dataset Information

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

Publications

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

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