Community-driven roadmap for integrated disease maps

Abstract

The Disease Maps Project builds upon 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 in order to predict disease comorbidity or drug response and to suggest drug repositioning, altogether supporting clinical decisions.

COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

“…First, it is a graphical, interactive representation of disease-relevant molecular mechanisms linking different knowledge bases. Second, it is a computational resource of reviewed content for graph-based analyses 12 and disease modelling 13 . Thus, it provides a platform for domain experts, such as clinicians, virologists, and immunologists, to collaborate with data scientists and computational biologists for a rigorous model building, accurate data interpretation and drug repositioning.…”

Towards a European health research and innovation cloud (HRIC)

“…The Health Research and Innovation Cloud (HRIC), as described in this manuscript, would help to facilitate this transition, providing access to larger datasets, cutting-edge tools, and knowledge, as envisioned by Auffray et al [3]. For example, the HRIC should ease the incorporation of domain expert knowledge into systems disease maps in a format that can be both understood by all stakeholders (patients and clinicians, scientists, and drug developers) and processed by highperformance computers, thus supporting the development of innovative medicines and diagnostics [4,5]. Cloud technologies (accessed through Hadoop applications, for example) also make it possible to collaborate and to access and reuse data in situations when privacy concerns or regulation prohibits remote users from downloading data-an important benefit in Europe where national regulations can differ significantly.…”

Mechanistic modeling of the SARS-CoV-2 disease map

“…Understanding the molecular mechanisms that mediate SARS-CoV-2 infection is key for the rapid development of efficient preventive or therapeutic interventions against the COVID-19. A comprehensive description of such molecular mechanisms is represented in the corresponding disease map, that is, the fragment of the whole network of known human protein interactions that are relevant for the disease 2 . The recent availability of a detailed catalog of viral-human protein interactions 3 has facilitated the construction of a first version of the map of human molecular pathways involved in the viral infection.…”