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OmniPath: integrated knowledgebase for multi-omics analysis

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 knowl...

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Main Authors: Türei, Dénes (Author) , Schaul, Jonathan (Author) , Palacio-Escat, Nicolàs (Author) , Bohar, Balazs (Author) , Bai, Yunfan (Author) , Ceccarelli, Francesco (Author) , Cevrim, Elif (Author) , Daley, Macabe (Author) , Darcan, Melih (Author) , Dimitrov, Daniel (Author) , Dogan, Tunca (Author) , Domingo-Fernandez, Daniel (Author) , Dugourd, Aurelien (Author) , Gabor, Attila (Author) , Gul, Lejla (Author) , Hall, Benjamin A. (Author) , Hoyt, Charles Tapley (Author) , Ivanova, Olga A. (Author) , Klein, Michal (Author) , Lawrence, Toby (Author) , Mananes, Diego (Author) , Modos, Dezso (Author) , Müller-Dott, Sophia (Author) , Olbei, Marton (Author) , Schmidt, Christina (Author) , Sen, Bunyamin (Author) , Theis, Fabian J. (Author) , Unlu, Atabey (Author) , Ulusoy, Erva (Author) , Valdeolivas, Alberto (Author) , Korcsmaros, Tamas (Author) , Sáez Rodríguez, Julio (Author)
Format: Article (Journal)
Language:English
Published: 6 January 2026
In: Nucleic acids research
Year: 2026, Volume: 54, Issue: D1, Pages: D652-D660
ISSN:1362-4962
DOI:10.1093/nar/gkaf1126
Online Access:Verlag, kostenfrei, Volltext: https://doi.org/10.1093/nar/gkaf1126
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Author Notes:Denes Turei, Jonathan Schaul, Nicolas Palacio-Escat, Balazs Bohar, Yunfan Bai, Francesco Ceccarelli, Elif Cevrim, Macabe Daley, Melih Darcan, Daniel Dimitrov, Tunca Dogan, Daniel Domingo-Fernandez, Aurelien Dugourd, Attila Gabor, Lejla Gul, Benjamin A. Hall, Charles Tapley Hoyt, Olga Ivanova, Michal Klein, Toby Lawrence, Diego Mananes, Dezso Modos, Sophia Muller-Dott, Marton Olbei, Christina Schmidt, Bunyamin Sen, Fabian J. Theis, Atabey Unlu, Erva Ulusoy, Alberto Valdeolivas, Tamas Korcsmaros, Julio Saez-Rodriguez
Description
Summary: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.
Item Description:Veröffentlicht: 18 November 2025
Gesehen am 10.03.2026
Physical Description:Online Resource
ISSN:1362-4962
DOI:10.1093/nar/gkaf1126

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