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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.

Nucleic Acids Research
|November 17, 2019
PubMed
Summary
This summary is machine-generated.

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.

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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.