PHI-base

The Pathogen-Host Interactions database (PHI-base)^[1] 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 and external collaborators since 2005.^[2][3][4][5] PHI-base has been part of the UK node of ELIXIR, the European life-science infrastructure for biological information, since 2016.^[6]

PHI-base

Content
Description	Pathogen-Host Interactions database
Data types captured	phenotypes of microbial mutants
Organisms	~290 fungal, bacterial and protist pathogens of agronomic and medical importance tested on ~240 hosts
Contact
Research center	Rothamsted Research
Primary citation	PMID 39588765
Release date	May 2005
Access
Data format	XML, FASTA
Website	phibase.org
Tools
Web	PHI-base Search PHIB-BLAST PHI-Canto (Author curation)
Miscellaneous
License	Creative Commons Attribution-NoDerivatives 4.0 International License
Versioning	Yes
Data release frequency	6 monthly
Version	4.18 (May 2025)
Curation policy	Manual Curation

Background

The Pathogen-Host 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.^[7]

The web-accessible database catalogues experimentally verified pathogenicity, virulence, and effector genes from bacterial, fungal, and oomycete 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 (fungicides).^[8][9]

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 terms, EC Numbers, etc.), and links to other external data sources such as UniProt, EMBL, and the NCBI taxonomy services.

In 2016 the plant portion of PHI-base was used to establish a Semantic PHI-base search tool. PHI-base has been aligned with Ensembl Genomes since 2011, FungiDB since 2016, Global Biotic Interactions (GloBI) since 2018 and Uniprot since 2020. All new PHI-base releases are integrated by these independent databases.

Community curation

Since 2015, the website has been linked to an online literature curation tool called PHI-Canto, enabling community-driven literature curation for various pathogenic species.^[10] 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 ^[11], the model organism database for fission yeast.

Current developments

Version 4.18 (May 2025) of PHI-base ^[1] provides information on 10,614 genes from 335 pathogens and 265 hosts and their impact on 23,497 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.^[12] A new gene-centric version of PHI-base (version 5.0) was released in March 2024 and announced in a press release on the Rothamsted Research website.^[13] PHI-base 5 reorganised the data structure to group interactions by pathogen and host genes, expanded the use of ontologies for phenotype annotation, and added support for phenotypes relating to gene-for-gene relationships as well as host and pathogen phenotypes observed in vitro. Both PHI-base version 4 and version 5 are currently available online in parallel during the transition period, giving users time to familiarise themselves with the new interface before PHI-base 4 is phased out . New data mining tools are also being developed to support version 5. All articles that cite PHI-base are listed in the database’s ‘About us’ section, ordered by year.

Applications

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.^[1]

Funding

PHI-base is funded by the Biotechnology and Biological Sciences Research Council (BBSRC)^[7] through the Growing Health and Delivering Sustainable Wheat Institute Strategic Programmes.