OmniPath: integrated knowledgebase for multi-omics analysis

Nucleic Acids Research, vol. 54, pp. D652–D660

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, microRNA, and enzyme-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 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.

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 69120 ,

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 69120 ,

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 69120 ,

4. Balázs Bohár

   Imperial College London

   Affiliation as printed

   Imperial College London, Faculty of Medicine , Department of Metabolism, Digestion and Reproduction, London W12 0NN ,

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 69120 ,

6. Francesco Ceccarelli

   University of Cambridge

   Affiliation as printed

   University of Cambridge Department of Computer Science and Technology, , Cambridge CB3 0FD ,

7. Elif Çevrim

   Hacettepe University

   Affiliation as printed

   Biological Data Science Lab, Dept. of Computer Engineering, Hacettepe University , Ankara 06800 ,

   Graduate School of Health Sciences, Hacettepe University Department of Bioinformatics, , Ankara 06100 ,

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 69120 ,

9. Melih Darcan

   Hacettepe University

   Affiliation as printed

   Biological Data Science Lab, Dept. of Computer Engineering, Hacettepe University , Ankara 06800 ,

   Graduate School of Health Sciences, Hacettepe University Department of Bioinformatics, , Ankara 06100 ,

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 69120 ,

11. Tunca Doğan

    Hacettepe University

    Affiliation as printed

    Biological Data Science Lab, Dept. of Computer Engineering, Hacettepe University , Ankara 06800 ,

    Graduate School of Health Sciences, Hacettepe University Department of Bioinformatics, , Ankara 06100 ,

    Institute of Informatics, Hacettepe University Department of Health Informatics, , Ankara 06800 ,

12. Daniel Domingo‐Fernándéz

    Fraunhofer Institute for Algorithms and Scientific Computing

    Affiliation as printed

    Fraunhofer Institute for Algorithms and Scientific Computing Schloss Birlinghoven 53757 ,

13. Aurélien J. F. Dugourd

    European Bioinformatics Institute

    Affiliation as printed

    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Hinxton CB10 1SD ,

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 69120 ,

15. Lejla Potari-Gul

    Imperial College London

    Affiliation as printed

    Imperial College London, Faculty of Medicine , Department of Metabolism, Digestion and Reproduction, London W12 0NN ,

16. Benjamin A. Hall

    University College London

    Affiliation as printed

    University College London Department of Medical Physics and Biomedical Engineering, , London WC1E 6BT ,

17. Charles Tapley Hoyt Aachen Institute of Inorganic Chemistry

    RWTH Aachen University

    Affiliation as printed

    RWTH Aachen University, Institute of Inorganic Chemistry , Aachen 52064

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 69120 ,

    Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine , Heidelberg 69120 ,

19. Michal Klein

    Helmholtz Munich · Institute of Computational Biology

    Affiliation as printed

    Apple Inc. Work done while at Institute of Computational Biology, Helmholtz Center Munich , Neuherberg 85764 ,

20. Toby Lawrence

    Imperial College London

    Affiliation as printed

    Imperial College London, Faculty of Medicine , Department of Metabolism, Digestion and Reproduction, London W12 0NN ,

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 28029 ,

    Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine , Heidelberg 69120 ,

22. Dezső Módos

    Imperial College London

    Affiliation as printed

    Imperial College London, Faculty of Medicine , Department of Metabolism, Digestion and Reproduction, London W12 0NN ,

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 69120 ,

24. Marton L. Olbei

    Imperial College London

    Affiliation as printed

    Imperial College London, Faculty of Medicine , Department of Metabolism, Digestion and Reproduction, London W12 0NN ,

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 69120 ,

26. Bünyamin Şen

    Hacettepe University

    Affiliation as printed

    Biological Data Science Lab, Dept. of Computer Engineering, Hacettepe University , Ankara 06800 ,

    Graduate School of Health Sciences, Hacettepe University Department of Bioinformatics, , Ankara 06100 ,

27. Fabian Joachim Theis

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

    Affiliation as printed

    Institute of Computational Biology, Helmholtz Center Munich , Neuherberg 85764 ,

    TUM School of Computation, Information and Technology, Technical University of Munich , München 80333 ,

    TUM School of Life Sciences, Technical University of Munich , Freising 85354 ,

28. Atabey Ünlü

    Hacettepe University

    Affiliation as printed

    Biological Data Science Lab, Dept. of Computer Engineering, Hacettepe University , Ankara 06800 ,

    Graduate School of Health Sciences, Hacettepe University Department of Bioinformatics, , Ankara 06100 ,

29. Erva Ulusoy

    Hacettepe University

    Affiliation as printed

    Biological Data Science Lab, Dept. of Computer Engineering, Hacettepe University , Ankara 06800 ,

    Graduate School of Health Sciences, Hacettepe University Department of Bioinformatics, , Ankara 06100 ,

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 69120 ,

31. Tamas Douglas Korcsmaros

    Imperial College London

    Affiliation as printed

    Imperial College London, Faculty of Medicine , Department of Metabolism, Digestion and Reproduction, London W12 0NN ,

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 CB10 1SD ,

    Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine , Heidelberg 69120 ,