PHI-base in 2022 a multi-species phenotype database for Pathogen–Host Interactions

A - Papers appearing in refereed journals

Urban, M., Cuzick, A., Seager, J., Wood, V., Rutherford, K., Venkatesh, S. Y., Sahu, J., Iyer, S. V., Khamari, L., De Silva, N., Martinez, M. C., Pedro, H., Yates, A. D. and Hammond-Kosack, K. E. 2021. PHI-base in 2022 a multi-species phenotype database for Pathogen–Host Interactions. Nucleic Acids Research. https://doi.org/10.1093/nar/gkab1037

AuthorsUrban, M., Cuzick, A., Seager, J., Wood, V., Rutherford, K., Venkatesh, S. Y., Sahu, J., Iyer, S. V., Khamari, L., De Silva, N., Martinez, M. C., Pedro, H., Yates, A. D. and Hammond-Kosack, K. E.
Abstract

Since 2005, the Pathogen–Host Interactions Database (PHI-base) has manually curated experimentally verified pathogenicity, virulence, and effector genes from fungal, bacterial, and protist pathogens which infect animal, plant, fish, insect and/or fungal hosts. PHI-base (www.phi-base.org) is devoted to the identification and presentation of phenotype information on pathogenicity and effector genes and their host interactions. PHI-base is invaluable for comparative analyses and for the discovery of candidate targets in medically and agronomically important species for intervention. Version 4.12 (September 2021) contains 4,387 references, and provides information on 8,411 genes from 279 pathogens, tested on 228 hosts in 18,190 interactions. This provides a 24% increase in gene content since Version 4.8 (September 2019). Bacterial and fungal pathogens represent the majority of the interaction data, with a 54:46 split of entries, whilst protists, protozoa, nematodes, and insects represent 3.6% of entries. Host species consist of approximately 54% plants and 46% others of medical, veterinary and/or environmental importance. PHI-base data is disseminated to UniProtKB, FungiDB and Ensembl Genomes. PHI-base will migrate to a new gene-centric version (version 5.0) in early 2022. This major development is briefly described.

KeywordsHost-pathogen interaction; Disease; Comparative genomics; Manual curation; Human
Year of Publication2021
JournalNucleic Acids Research
Digital Object Identifier (DOI)https://doi.org/10.1093/nar/gkab1037
Open accessPublished as green open access
FunderBiotechnology and Biological Sciences Research Council
Funder project or codeA FAIR community resource for pathogen, host, interactions to enhance global food security and human health
Output statusPublished
Publication dates
Online12 Nov 2021
Publication process dates
Accepted03 Nov 2021
PublisherOxford University Press (OUP)
ISSN0305-1048

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