Related Experiment Video
Updated: Jun 6, 2025
Author Spotlight: Advanced Enteroid Model for Studying Host-Pathogen Interactions
Published on: April 5, 2024
PHI-base - the multi-species pathogen-host interaction database in 2025
Martin Urban1, Alayne Cuzick1, James Seager1
1Protecting Crops and the Environment, Rothamsted Research, Harpenden AL5 2JQ, UK.
Abstract:
The Pathogen-Host Interactions Database (PHI-base) has, since 2005, provided manually curated genes from fungal, bacterial and protist pathogens that have been experimentally verified to have important pathogenicity, virulence and/or effector functions during different types of interactions involving human, animal, plant, invertebrate and fungal hosts. PHI-base provides phenotypic annotation and genotypic information for both native and model host interactions, including gene alterations that do not alter the phenotype of the interaction. In this article, we describe major updates to PHI-base. The latest version of PHI-base, 4.17, contains a 19% increase in genes and a 23% increase in interactions relative to version 4.12 (released September 2022). We also describe the unification of data in PHI-base 4 with the data curated from a new curation workflow (PHI-Canto), which forms the first complete release of PHI-base version 5.0. Additionally, we describe adding support for the Frictionless Data framework to PHI-base 4 datasets, new ways of sharing interaction data with the Ensembl database, an analysis of the conserved orthologous genes in PHI-base, and the increasing variety of research studies that make use of PHI-base. PHI-base version 4.17 is freely available at www.phi-base.org and PHI-base version 5.0 is freely available at phi5.phi-base.org.
Insights
The Pathogen-Host Interactions Database (PHI-base) has updated its curated gene and interaction data, enhancing its utility for studying pathogen virulence. New versions offer expanded content and improved data sharing capabilities for researchers.
Area of Science:
- Microbiology
- Genomics
- Bioinformatics
Background:
- The Pathogen-Host Interactions Database (PHI-base) has served as a crucial resource since 2005.
- It manually curates experimentally verified genes involved in pathogenicity, virulence, and effector functions.
- PHI-base covers interactions between diverse pathogens (fungal, bacterial, protist) and various hosts (human, animal, plant, invertebrate, fungal).
Purpose of the Study:
- To report major updates and improvements to the PHI-base resource.
- To introduce the latest versions (4.17 and 5.0) and their enhanced features.
- To highlight the growing impact and diverse applications of PHI-base in research.
Main Methods:
- Manual curation of pathogen genes and host interactions.
- Data integration and unification from new curation workflows (PHI-Canto).
- Implementation of data standards like Frictionless Data framework.
- Interfacing with other databases such as Ensembl for data sharing.
Main Results:
- PHI-base version 4.17 shows a 19% increase in genes and a 23% increase in interactions compared to version 4.12.
- PHI-base version 5.0 represents the first complete release integrating data from the PHI-Canto curation workflow.
- Support for Frictionless Data framework and enhanced data sharing with Ensembl have been added.
- Analysis of conserved orthologous genes within PHI-base has been performed.
Conclusions:
- PHI-base continues to be a vital, expanding resource for understanding pathogen-host interactions.
- The latest updates enhance data accessibility, integration, and research utility.
- PHI-base 4.17 and 5.0 are freely available, supporting a wide range of scientific studies.
