The Pathogen-Host Interactions database (PHI-base) is a biological database that contains curated information on genes experimentally proven to affect the outcome of pathogen-host interactions. The database is 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 research institutions in the world, having been founded in 1843. It is located at Harp ...

, together with external collaborators since 2005. Since April 2017 PHI-base is part of

ELIXIR ELIXIR (the European life-sciences Infrastructure for biological Information) is an initiative that will allow life science laboratories across Europe to share and store their research data as part of an organised network. Its goal is to bring t ...

, the European life-science infrastructure for biological information via its ELIXIR-UK node.

Background

The

Pathogen In biology, a pathogen ( el, πάθος, "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 ...

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

oomycete Oomycota forms a distinct phylogenetic lineage of fungus-like eukaryotic microorganisms, called oomycetes (). They are filamentous and heterotrophic, and can reproduce both sexually and asexually. Sexual reproduction of an oospore is the resul ...

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

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 from ...

, EMBL and the

NCBI The National Center for Biotechnology Information (NCBI) is part of the United States 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 ...

taxonomy services.

Current developments

Version 4.11 (May 5th, 2021) of PHI-base provides information on 8070 genes from 276 pathogens and 224 hosts and their impact on 17060 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 2015 the web-site includes an online literature curation tool called PHI-Canto for community literature curation of various pathogenic species. Since the launch of version 4, the PHI-base is also searchable using the PHIB-BLAST search tool, which uses the

BLAST Blast or The Blast may refer to: *Explosion, a rapid increase in volume and release of energy in an extreme manner *Detonation, an exothermic front accelerating through a medium that eventually drives a shock front Film * ''Blast'' (1997 film), ...

algorithm to compare a user's sequence against the sequences available from PHI-base. In 2016 the plant portion of PHI-base was used to establish a Semantic PHI-base search tool". PHI-base is aligned wit
Ensembl Genomes
since 2011
Fungidb
since 2016, an
Global Biotic Interactions (GloBI)
(since August 2018). All new PHI-base releases are integrated by these independent databases. PHI-base has been cited in over 350 peer reviewed publications. Details on all these publications are cited in the ‘about us’ section of the database. 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 >500 peer reviewed articles published in International Journals. All these articles are cited in the 'About' section of the database. Several specific improvements to PHI-base are currently supported. The

PhytoPath PhytoPath was a joint scientific project between the European Bioinformatics Institute and Rothamsted Research, running from January 2012 to May 30, 2017. The project aimed to enable the exploitation of the growing body of “-omics” data bein ...

project develops a bioinformatics resource that integrates genome-scale data from important plant pathogen species with the phenotypes captured in PHI-base. Using the Ensembl Genomes browser, PhytoPath provides access to complete genome assemblies and gene models of priority crop and model-fungal and oomycete phytopathogens. An advanced PhytoPath BioMart search tool allows searches across different species of plant pathogens.

Funding

PHI-base is a National Capability funded by the Biotechnology and Biological Sciences Research Council (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