The DOI matches its Crossref record; 41 of the 41 references it cites were found in a registry or an index.
PHI-base: the pathogen–host interactions database
Open accessAbstract
The pathogen–host interactions database (PHI-base) is available at www.phi-base.org. PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen–host interactions reported in peer reviewed research articles. PHI-base also curates literature describing specific gene alterations that did not affect the disease interaction phenotype, in order to provide complete datasets for comparative purposes. Viruses are not included, due to their extensive coverage in other databases. In this article, we describe the increased data content of PHI-base, plus new database features and further integration with complementary databases. The release of PHI-base version 4.8 (September 2019) contains 3454 manually curated references, and provides information on 6780 genes from 268 pathogens, tested on 210 hosts in 13,801 interactions. Prokaryotic and eukaryotic pathogens are represented in almost equal numbers. Host species consist of approximately 60% plants (split 50:50 between cereal and non-cereal plants), and 40% other species of medical and/or environmental importance. The information available on pathogen effectors has risen by more than a third, and the entries for pathogens that infect crop species of global importance has dramatically increased in this release. We also briefly describe the future direction of the PHI-base project, and some existing problems with the PHI-base curation process.
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The FAIR Guiding Principles for scientific data management and stewardship
Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., da Silva Santos, L. B., Bourne, P. E., et al. (2016) · Scientific Data · doi:10.1038/sdata.2016.18 · Cited by 18,423
Jones, J. D. G., & Dangl, J. L. (2006) · Nature · doi:10.1038/nature05286 · Cited by 13,177
UniProt: a worldwide hub of protein knowledge
The UniProt Consortium (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1049 · Cited by 7,698
High-throughput functional annotation and data mining with the Blast2GO suite
Gotz, S., Garcia-Gomez, J. M., Terol, J., Williams, T. D., Nagaraj, S. H., Nueda, M. J., Robles, M., Talon, M., Dopazo, J., & Conesa, A. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn176 · Cited by 4,423
Hidden Killers: Human Fungal Infections
Brown, G. D., Denning, D. W., Gow, N. A. R., Levitz, S. M., Netea, M. G., & White, T. C. (2012) · Science Translational Medicine · doi:10.1126/scitranslmed.3004404 · Cited by 4,284
Emerging fungal threats to animal, plant and ecosystem health
Fisher, M. C., Henk, D. A., Briggs, C. J., Brownstein, J. S., Madoff, L. C., McCraw, S. L., & Gurr, S. J. (2012) · Nature · doi:10.1038/nature10947 · Cited by 3,310
Shifting the limits in wheat research and breeding using a fully annotated reference genome
The International Wheat Genome Sequencing Consortium (IWGSC), Appels, R., Eversole, K., Stein, N., Feuillet, C., Keller, B., Rogers, J., Pozniak, C. J., Choulet, F., Distelfeld, A., et al. (2018) · Science · doi:10.1126/science.aar7191 · Cited by 3,120
Worldwide emergence of resistance to antifungal drugs challenges human health and food security
Fisher, M. C., Hawkins, N. J., Sanglard, D., & Gurr, S. J. (2018) · Science · doi:10.1126/science.aap7999 · Cited by 1,555
MycoCosm portal: gearing up for 1000 fungal genomes
Grigoriev, I. V., Nikitin, R., Haridas, S., Kuo, A., Ohm, R., Otillar, R., Riley, R., Salamov, A., Zhao, X., Korzeniewski, F., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1183 · Cited by 1,498
Pivoting the Plant Immune System from Dissection to Deployment
Dangl, J. L., Horvath, D. M., & Staskawicz, B. J. (2013) · Science · doi:10.1126/science.1236011 · Cited by 1,252
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Bai, Z., Zhang, N., Jin, Y., Chen, L., Mao, Y., Sun, L., Fang, F., Liu, Y., Han, M., & Li, G. (2023) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.919701 · Cited by 29
Matta, T., Agrawal, K., Datta, P., Kumari, L., Bishnoi, M., Chopra, K., & Kondepudi, K. K. (2026) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-025-10628-w · Cited by 4
Metadata
- Authors
- Urban, M., Cuzick, A., Seager, J., Wood, V., Rutherford, K., Venkatesh, S. Y., De Silva, N., Martinez, M. C., Pedro, H., Yates, A. D., Hassani-Pak, K., & Hammond-Kosack, K. E.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-11-16
- Volume
- 48
- Issue
- D1
- Pages
- D613-D620
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2985884608
- Cited by
- 339
- References
- 41
- FWCI
- 27.00
- Type
- journal article
- Language
- en
- Open access
- gold
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