PHI-base - The multi-species Pathogen-Host Interaction Database in 2025

A - Papers appearing in refereed journals

Urban, M., Cuzick, A., Seager, J., Nonavinakere, N., Sahu, J., Sahu, P., Iyer, V. L., Khamari, L., Martinez, M. C. and Hammond-Kosack, K. E. 2024. PHI-base - The multi-species Pathogen-Host Interaction Database in 2025. Nucleic Acids Research. 53 (D1), p. D826–D838. https://doi.org/10.1093/nar/gkae1084

AuthorsUrban, M., Cuzick, A., Seager, J., Nonavinakere, N., Sahu, J., Sahu, P., Iyer, V. L., Khamari, L., Martinez, M. C. and Hammond-Kosack, K. E.
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.

KeywordsPathogenicity; Virulence; Effector; Infectious disease; Comparative genomics
Year of Publication2024
JournalNucleic Acids Research
Journal citation53 (D1), p. D826–D838
Digital Object Identifier (DOI)https://doi.org/10.1093/nar/gkae1084
Open accessPublished as ‘gold’ (paid) open access
FunderBiotechnology and Biological Sciences Research Council
Wellcome Trust
Funder project or codeA FAIR community resource for pathogens, hosts and their interactions to enhance global food security and human health
BB/K020102/1
BB/I001077/1
BB/S02011X/1
Growing Health (WP1) - bio-inspired solutions for healthier agroecosystems: Understanding biointeractions
Delivering Sustainable Wheat
Delivering Sustainable Wheat (WP2): Delivering Resilience to Biotic Stress
Publisher's version
Accepted author manuscript
Supplemental file
Output statusIn press
Publication dates
Online26 Nov 2024
Publication process dates
Accepted23 Oct 2024
PublisherOxford University Press (OUP)
ISSN0305-1048

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