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Interacting Species Database (ISDB): comprehensive resource for interspecies interactions at the molecular level
Michael Mederer1, Anupam Gautam2,3, Oliver Kohlbacher2,4,5
1Department for Internal Medicine I (Gastroenterology, Hepatology, Endocrinology, and Metabolism), Medical University of Innsbruck, Innsbruck A-6020, Austria.
Bioinformatics (Oxford, England)
|June 25, 2026
Summary
The Interacting Species Database (ISDB) is a new resource cataloging molecular interactions between species. It provides valuable data for understanding ecological dynamics and interspecies relationships.
Area of Science:
- Ecology
- Bioinformatics
- Molecular Biology
Background:
- Molecular interactions mediate crucial biological processes in ecological systems, including host-pathogen recognition and symbiosis.
- Understanding these interspecies interactions at a molecular level is vital for mechanistic, evolutionary, and functional insights.
- Current research is hindered by a lack of comprehensive molecular-level databases and limited experimental data.
Purpose of the Study:
- To introduce a comprehensive resource for cataloging interspecies interactions at a molecular level.
- To facilitate research on ecological dynamics by providing searchable and downloadable interaction data.
- To enable researchers to deposit their own interspecies interaction data.
Main Methods:
- Development of the Interacting Species Database (ISDB).
- Annotation of interactions with NCBI taxonomic identifiers, interaction types, and molecular interaction details.
- Creation of a web interface for data access and deposition.
Main Results:
- The ISDB contains 858,229 interacting species pairs and 171,713 interspecies protein-protein interactions across 261,287 organisms.
- The database is accessible via a web interface, with open-source code available on GitHub.
- Data is archived on Zenodo for long-term accessibility.
Conclusions:
- The ISDB significantly enhances the study of ecological dynamics by providing a centralized, molecular-level repository of interspecies interactions.
- This resource supports diverse research domains by facilitating data sharing and analysis.
- The ISDB promotes collaborative research and accelerates discoveries in interspecies molecular interactions.
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