Community-driven roadmap for integrated disease maps.

Marek Ostaszewski,Charles Auffray,Jan Hasenauer,Andrei Zinovyev,Anna Niarakis,Emmanuel Barillot,Thomas Ligon,David Nickerson,Rudi Balling,Piotr Gawron,Reinhard Schneider,Inna Kuperstein,Ugur Dogrusoz,Alexander Mazein,Nicolas Le Novère,Stephan Gebel,Ronan M T Fleming,Daniel Weindl

doi:10.1093/bib/bby024

Abstract

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

Highlights

The concept of disease maps emerged to bridge the domains of biological and computational research on various human disorders
One of the first platforms for sharing disease maps as CellDesigner diagrams was Payao [16], followed by iPathwaysþ [4]. Their functionality was extended by tools like Molecular Interaction NEtwoRks VisuAlization (MINERVA) platform [6] and NaviCell [14], developed by the Disease Maps Community (DMC) members
They allow for visualization of large CellDesigner and Systems Biology Graphical Notation (SBGN) diagrams using the Google Maps Application Programming Interface (API) to provide interactive annotation to maps’ elements and enable overlay of experimental data on top of these maps

Summary

Introduction

The concept of disease maps emerged to bridge the domains of biological and computational research on various human disorders. Their functionality was extended by tools like Molecular Interaction NEtwoRks VisuAlization (MINERVA) platform [6] and NaviCell [14], developed by the DMC members They allow for visualization of large CellDesigner and SBGN diagrams using the Google Maps Application Programming Interface (API) to provide interactive annotation to maps’ elements and enable overlay of experimental data on top of these maps. Disease maps are created for various purposes, for instance as a didactic resource, a knowledge repository, a platform to visualize data or a collection of predictive molecular signatures These use cases reflect different stages of development of a disease map, when its contents are continuously refined from a collection of most known mechanisms of a given disease (‘hallmarks’) through verification against established expertise and available experimental data. Disease-related functional variants need to be implemented to benefit from comprehensive sequencing and genome-wide association studies (GWAS)

Summary

Key Points