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Published on: March 5, 2022
PHI-base: the pathogen-host interactions database
Martin Urban1, Alayne Cuzick1, James Seager1
1Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden AL5 2JQ, UK.
Abstract:
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.
Insights
The pathogen-host interactions database (PHI-base) now includes more data on genes affecting host interactions, with a focus on crop pathogens. This updated resource aids research into plant and animal diseases.
Area of Science:
- * Molecular biology and bioinformatics
- * Pathogen-host interaction research
- * Genetics and genomics
Background:
- * Pathogen-Host Interactions Database (PHI-base) is a curated resource for genes impacting pathogen-host interactions.
- * PHI-base excludes viral data, focusing on prokaryotic and eukaryotic pathogens affecting plants, animals, and environmental species.
- * The database supports comparative analysis by including data on gene alterations that do not affect disease phenotypes.
Purpose of the Study:
- * To report on the expanded data content and new features of PHI-base version 4.8.
- * To highlight improved integration with complementary biological databases.
- * To detail advancements in curated information on pathogen effectors and crop-infecting pathogens.
Main Methods:
- * Manual curation of peer-reviewed literature on pathogen-host interactions.
- * Data compilation on genes, pathogens, hosts, and interaction outcomes.
- * Integration of PHI-base with other relevant biological databases.
Main Results:
- * PHI-base version 4.8 (September 2019) contains 3454 references, 6780 genes, 268 pathogens, 210 hosts, and 13,801 interactions.
- * Significant increase in data on pathogen effectors (over 33%) and pathogens affecting agriculturally important crops.
- * Balanced representation of prokaryotic and eukaryotic pathogens, with a majority of plant hosts (60%).
Conclusions:
- * PHI-base version 4.8 offers a substantially enriched dataset for studying pathogen-host interactions.
- * The database enhancements facilitate deeper insights into the genetic basis of diseases affecting crops and other species.
- * Future development will address challenges in the curation process and expand database functionalities.
