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. 50, pp. D837-D847. https://doi.org/10.1093/nar/gkab1037
Authors | 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. |
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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. |
Keywords | Host-pathogen interaction; Disease; Comparative genomics; Manual curation; Human |
Year of Publication | 2021 |
Journal | Nucleic Acids Research |
Journal citation | 50, pp. D837-D847 |
Digital Object Identifier (DOI) | https://doi.org/10.1093/nar/gkab1037 |
Open access | Published as ‘gold’ (paid) open access |
Funder | Biotechnology and Biological Sciences Research Council |
Funder project or code | A FAIR community resource for pathogens, hosts and their interactions to enhance global food security and human health |
Publisher's version | |
Accepted author manuscript | |
Output status | Published |
Publication dates | |
Online | 12 Nov 2021 |
Publication process dates | |
Accepted | 03 Nov 2021 |
Publisher | Oxford University Press (OUP) |
ISSN | 0305-1048 |
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