OmniPath: integrated knowledgebase for multi-omics analysis

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Abstract Analysis and interpretation of omics data largely benefit from the use of prior knowledge. However, this knowledge is fragmented across resources and often is not directly accessible for analytical methods. We developed OmniPath ( https://omnipathdb.org/ ), a database combining diverse molecular knowledge from 168 resources. It covers causal protein-protein, gene regulatory, miRNA, and enzyme-PTM (post-translational modification) interactions, cell-cell communication, protein complexes, and information about the function, localization, structure, and many other aspects of biomolecules. It prioritizes literature curated data, and complements it with predictions and large scale databases. To enable interactive browsing of this large corpus of knowledge, we developed OmniPath Explorer, which also includes a large language model (LLM) agent that has direct access to the database. Python and R/Bioconductor client packages and a Cytoscape plugin create easy access to customized prior knowledge for omics analysis environments, such as scverse. OmniPath can be broadly used for the analysis of bulk, single-cell and spatial multi-omics data, especially for mechanistic and causal modeling. Graphical Abstract

Authors 32

1. Dénes Türei corresponding

   Heidelberg University · University Hospital Heidelberg

   Affiliation as printed

   Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany

2. Jonathan Schaul

   Heidelberg University · University Hospital Heidelberg

   Affiliation as printed

   Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany

3. Nicolàs Palacio‐Escat

   Heidelberg University · University Hospital Heidelberg

   Affiliation as printed

   Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany

4. Balázs Bohár

   Imperial College London

   Affiliation as printed

   Imperial College London, Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, London, UK

5. Yunfan Bai

   Heidelberg University · University Hospital Heidelberg

   Affiliation as printed

   Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany

6. Francesco Ceccarelli

   University of Cambridge

   Affiliation as printed

   Department of Computer Science and Technology, University of Cambridge, Cambridge, UK

7. Elif Çevrim

   Hacettepe University

   Affiliation as printed

   Biological Data Science Lab, Dept. of Computer Engineering, Hacettepe University, Ankara, Turkey

   Dept. of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, Ankara, Turkey

8. Macabe Daley

   Heidelberg University · University Hospital Heidelberg

   Affiliation as printed

   Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany

9. Melih Darcan

   Hacettepe University

   Affiliation as printed

   Biological Data Science Lab, Dept. of Computer Engineering, Hacettepe University, Ankara, Turkey

   Dept. of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, Ankara, Turkey

10. Daniel Dimitrov

    Heidelberg University · University Hospital Heidelberg

    Affiliation as printed

    Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany

11. Tunca Doğan

    Hacettepe University

    Affiliation as printed

    Biological Data Science Lab, Dept. of Computer Engineering, Hacettepe University, Ankara, Turkey

    Dept. of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, Ankara, Turkey

    Dept. of Health Informatics, Institute of Informatics, Hacettepe University, Ankara, Turkey

12. Daniel Domingo‐Fernándéz

    Fraunhofer Institute for Algorithms and Scientific Computing

    Affiliation as printed

    Fraunhofer Institute for Algorithms and Scientific Computing

13. Aurélien J. F. Dugourd

    European Bioinformatics Institute

    Affiliation as printed

    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK

14. Attila Gábor

    Heidelberg University · University Hospital Heidelberg

    Affiliation as printed

    Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany

15. Lejla Potari-Gul

    Imperial College London

    Affiliation as printed

    Imperial College London, Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, London, UK

16. Benjamin A. Hall

    University College London

    Affiliation as printed

    Department of Medical Physics and Biomedical Engineering, University College London, London, UK

17. Charles Tapley Hoyt Aachen Institute of Inorganic Chemistry

    RWTH Aachen University

    Affiliation as printed

    RWTH Aachen University, Institute of Inorganic Chemistry, Aachen, Germany

18. Olga Ivanova

    German Cancer Research Center · Heidelberg University · University Hospital Heidelberg

    Affiliation as printed

    Division of Vascular Oncology and Metastasis, German Cancer Research Center (DKFZ), Heidelberg, Germany

    Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany

19. Michal Klein

    Helmholtz Munich · Apple (United States) · Institute of Computational Biology

    Affiliation as printed

    Apple Inc; Work done while at Institute of Computational Biology, Helmholtz Center, Munich, Germany

    Apple Inc

20. Toby Lawrence

    Imperial College London

    Affiliation as printed

    Imperial College London, Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, London, UK

21. Diego Mañanes

    Heidelberg University · University Hospital Heidelberg · Spanish National Centre for Cardiovascular Research

    Affiliation as printed

    Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain

    Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany

22. Dezső Módos

    Imperial College London

    Affiliation as printed

    Imperial College London, Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, London, UK

23. Sophia Müller‐Dott

    Heidelberg University · University Hospital Heidelberg

    Affiliation as printed

    Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany

24. Marton L. Olbei

    Imperial College London

    Affiliation as printed

    Imperial College London, Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, London, UK

25. Christina Schmidt

    Heidelberg University · University Hospital Heidelberg

    Affiliation as printed

    Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany

26. Bünyamin Şen

    Hacettepe University

    Affiliation as printed

    Biological Data Science Lab, Dept. of Computer Engineering, Hacettepe University, Ankara, Turkey

    Dept. of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, Ankara, Turkey

27. Fabian Joachim Theis

    Helmholtz Munich · Institute of Computational Biology · Technical University of Munich

    Affiliation as printed

    Institute of Computational Biology, Helmholtz Center, Munich, Germany

    TUM School of Life Sciences, Technical University of Munich, Germany

    TUM, School of Computation, Information and Technology, Technical University of Munich, Germany

28. Atabey Ünlü

    Hacettepe University

    Affiliation as printed

    Biological Data Science Lab, Dept. of Computer Engineering, Hacettepe University, Ankara, Turkey

    Dept. of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, Ankara, Turkey

29. Erva Ulusoy

    Hacettepe University

    Affiliation as printed

    Biological Data Science Lab, Dept. of Computer Engineering, Hacettepe University, Ankara, Turkey

    Dept. of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, Ankara, Turkey

30. Alberto Valdeolivas

    Heidelberg University · University Hospital Heidelberg

    Affiliation as printed

    Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany

31. Tamas Douglas Korcsmaros

    Imperial College London

    Affiliation as printed

    Imperial College London, Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, London, UK

32. Julio Sáez-Rodríguez corresponding

    European Bioinformatics Institute · Heidelberg University · University Hospital Heidelberg

    Affiliation as printed

    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK

    Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany