PHI-base - the multi-species pathogen-host interaction database in 2025

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.