OmniPath: integrated knowledgebase for multi-omics analysis
File(s)
Published version
Author(s)
Type
Journal Article
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.
Date Issued
2026-01-06
Date Acceptance
2025-10-03
Citation
Nucleic Acids Research (NAR), 2026, 54 (D1), pp.D652-D660
ISSN
0305-1048
Publisher
Oxford University Press
Start Page
D652
End Page
D660
Journal / Book Title
Nucleic Acids Research (NAR)
Volume
54
Issue
D1
Copyright Statement
© The Author(s) 2025. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https:// creativecommons.org/ licenses/by/ 4.0/ ), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
License URL
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/41251164
PII: 8326458
Subjects
Biochemistry & Molecular Biology
Life Sciences & Biomedicine
Science & Technology
Publication Status
Published
Coverage Spatial
England
Date Publish Online
2025-11-18