The Pathogen-Host Interactions database (PHI-base) is a biological database that contains manually curated information on genes experimentally proven to affect the outcome of pathogen-host interactions. The database has been maintained by researchers at

Rothamsted Research Rothamsted Research, previously known as the Rothamsted Experimental Station and then the Institute of Arable Crops Research, is one of the oldest agricultural experiment station, agricultural research institutions in the world, having been founde ...

and external collaborators since 2005. PHI-base has been part of the UK node of

ELIXIR An elixir is a sweet liquid used for medical purposes, to be taken orally and intended to cure one's illness. When used as a dosage form, pharmaceutical preparation, an elixir contains at least one active ingredient designed to be taken orall ...

, the European life-science infrastructure for biological information, since 2016.

Background

The

Pathogen In biology, a pathogen (, "suffering", "passion" and , "producer of"), in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a Germ theory of d ...

Host A host is a person responsible for guests at an event or for providing hospitality during it. Host may also refer to: Places * Host, Pennsylvania, a village in Berks County * Host Island, in the Wilhelm Archipelago, Antarctica People * ...

Interactions database was developed to utilise the growing number of verified genes that mediate an organism's ability to cause disease and/or trigger host responses. The web-accessible database catalogues experimentally verified pathogenicity, virulence, and effector genes from bacterial, fungal, and

oomycete The Oomycetes (), or Oomycota, form a distinct phylogenetic lineage of fungus-like eukaryotic microorganisms within the Stramenopiles. They are filamentous and heterotrophic, and can reproduce both sexually and asexually. Sexual reproduction o ...

pathogens which infect animal, plant, and fungal hosts. PHI-base was the first online resource devoted to the identification and presentation of information on fungal and oomycete pathogenicity genes and their host interactions. PHI-base is a resource for the discovery of candidate targets in medically and agronomically important fungal and oomycete pathogens for intervention with synthetic chemistries and natural products (

fungicide Fungicides are pesticides used to kill parasitic fungi or their spores. Fungi can cause serious damage in agriculture, resulting in losses of yield and quality. Fungicides are used both in agriculture and to fight fungal infections in animals, ...

s). Each entry in PHI-base is curated by domain experts and supported by strong experimental evidence (gene disruption experiments) as well as literature references in which the experiments are described. Each gene in PHI-base is presented with its nucleotide and deduced amino acid sequence as well as a detailed structured description of the predicted protein's function during the host infection process. To facilitate data interoperability, genes are annotated using controlled vocabularies (

Gene Ontology The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and ...

terms, EC Numbers, etc.), and links to other external data sources such as

UniProt UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived fro ...

EMBL The European Molecular Biology Laboratory (EMBL) is an intergovernmental organization dedicated to molecular biology research and is supported by 29 member states, two prospect member states, and one associate member state. EMBL was created in ...

, and the

NCBI The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is loca ...

taxonomy services.

Current developments

Version 4.17 (May 2024) of PHI-base provides information on 9973 genes from 296 pathogens and 249 hosts and their impact on 22415 interactions as well on efficacy information on ~20 drugs and the target sequences in the pathogen. PHI-base currently focuses on plant pathogenic and human pathogenic organisms including fungi, oomycetes, and bacteria. The entire contents of the database can be downloaded in a tab delimited format. Since the launch of version 4, the PHI-base is also searchable using the PHIB-BLAST search tool, which uses the BLAST algorithm to compare a user's sequence against the sequences available from PHI-base. The database providers recently announced the launch o
PHI-base 5
a new gene-centric version of PHI-base, through
press release
on the Rothamsted Research website. A summary of the improvements made is als
available
In 2016 the plant portion of PHI-base was used to establish a Semantic PHI-base search tool. PHI-base has been aligned wit
Ensembl Genomes
since 2011
FungiDB
since 2016, an
Global Biotic Interactions (GloBI)
since 2018. All new PHI-base releases are integrated by these independent databases. PHI-base is a resource for many applications including: › The discovery of conserved genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention › Comparative genome analyses › Annotation of newly sequenced pathogen genomes › Functional interpretation of RNA sequencing and microarray experiments › The rapid cross-checking of phenotypic differences between pathogenic species when writing articles for peer review PHI-base use has been cited in over 900 peer-reviewed articles. Since 2015, the website has linked to an online literature curation tool calle
PHI-Canto
enabling community-driven literature curation for various pathogenic species. PHI-Canto employs a community curation framework that not only offers a curation tool but also includes a phenotype ontology and controlled vocabularies using unified languages and rules used in biology experiments. The central concept of this framework is the introduction of a 'Metagenotype', which allows the annotation and assignment of phenotypes to specific pathogen mutant-host interactions. PHI-Canto extends the single species curation tool developed for PomBase (https://www.pombase.org), the model organism database for fission yeast.

Funding

PHI-base is a National Capability funded by the

Biotechnology and Biological Sciences Research Council Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation, is a non-departmental public body (NDPB), and is the largest UK public funder of non-medical bioscience. It predominantly funds science, scient ...

(BBSRC), a UK research council.

References

External links

PHI-base
{{Bioinformatics Biological interactions Genetics databases Genetics in the United Kingdom Genomics Online databases Pathogenic microbes Plant pathogens and diseases Rothamsted Experimental Station Science and technology in Hertfordshire