A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms

The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. Community-driven and highly interdisciplinary, the project is collaborative and supports community standards, open access, and the FAIR data principles. The coordination of community work allowed for an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework links key molecules highlighted from broad omics data analysis and computational modeling to dysregulated pathways in a cell-, tissue- or patient-specific manner. We also employ text mining and AI-assisted analysis to identify potential drugs and drug targets and use topological analysis to reveal interesting structural features of the map. The proposed framework is versatile and expandable, offering a significant upgrade in the arsenal used to understand virus-host interactions and other complex pathologies. ### Competing Interest Statement A. Niarakis collaborates with SANOFI-AVENTIS R&D via a public private partnership grant (CIFRE contract, no 2020/0766). D. Maier and A. Bauch are employed at Biomax Informatics AG and will be affected by any effect of this publication on the commercial version of the AILANI software. J.A. Bachman and B. Gyori received consulting fees from Two Six Labs, LLC. T. Helikar has served as a shareholder and has consulted for Discovery Collective, Inc. R. Balling and R. Schneider are founders and shareholders of MEGENO S.A. and ITTM S.A. J. Saez-Rodriguez receives funding from GSK and Sanofi and consultant fees from Travere Therapeutics. Janet Pinero and Laura I. Furlong are employees and shareholders of MedBioinformatics Solutions SL. The remaining authors have declared that they have no Conflict of interest.