AUTHOR=Gawron Piotr , Hoksza David , Piñero Janet , Peña-Chilet Maria , Esteban-Medina Marina , Fernandez-Rueda Jose Luis , Colonna Vincenza , Smula Ewa , Heirendt Laurent , Ancien François , Groues Valentin , Satagopam Venkata P. , Schneider Reinhard , Dopazo Joaquin , Furlong Laura I. , Ostaszewski Marek
TITLE=Visualization of automatically combined disease maps and pathway diagrams for rare diseases
JOURNAL=Frontiers in Bioinformatics
VOLUME=3
YEAR=2023
URL=https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2023.1101505
DOI=10.3389/fbinf.2023.1101505
ISSN=2673-7647
ABSTRACT=Introduction: Investigation of molecular mechanisms of human disorders, especially rare diseases, require exploration of various knowledge repositories for building precise hypotheses and complex data interpretation. Recently, increasingly more resources offer diagrammatic representation of such mechanisms, including disease-dedicated schematics in pathway databases and disease maps. However, collection of knowledge across them is challenging, especially for research projects with limited manpower.
Methods: In this article we present an automated workflow for construction of maps of molecular mechanisms for rare diseases. The workflow requires a standardized definition of a disease using Orphanet or HPO identifiers to collect relevant genes and variants, and to assemble a functional, visual repository of related mechanisms, including data overlays. The diagrams composing the final map are unified to a common systems biology format from CellDesigner SBML, GPML and SBML+layout+render. The constructed resource contains disease-relevant genes and variants as data overlays for immediate visual exploration, including embedded genetic variant browser and protein structure viewer.
Results: We demonstrate the functionality of our workflow on two examples of rare diseases: Kawasaki disease and retinitis pigmentosa. Two maps are constructed based on their corresponding identifiers. Moreover, for the retinitis pigmentosa use-case, we include a list of differentially expressed genes to demonstrate how to tailor the workflow using omics datasets.
Discussion: In summary, our work allows for an ad-hoc construction of molecular diagrams combined from different sources, preserving their layout and graphical style, but integrating them into a single resource. This allows to reduce time consuming tasks of prototyping of a molecular disease map, enabling visual exploration, hypothesis building, data visualization and further refinement. The code of the workflow is open and accessible at https://gitlab.lcsb.uni.lu/minerva/automap/.