PHI-base

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PHI-base
PHI-base logo
Content
Description Pathogen-Host Interaction database
Data types
captured
phenotypes of microbial mutants
Organisms ~250 fungal, bacterial and protist pathogens of agronomic and medical importance tested on ~170 hosts
Contact
Research center Rothamsted Research
Primary citation PMID 27915230
Release date May 2005
Access
Data format XML, FASTA
Website PHI-base
Download URL PHI-base Download
Sparql endpoint http://linkeddata.systems:8890/sparql
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 4.2 (October 2016)
Curation policy Manual Curation

The Pathogen-Host Interaction database (PHI-base) contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions. The database was created and is maintained by researchers at Rothamsted Research and external collaborators since 2005.[1][2][3][4][5][6][7] The database and latest release is described in detail in this PDF document. Since December 2016 PHI-base is part of ELIXIR, the European life-science infrastructure for biological information via its ELIXIR-UK node.

Background[edit]

The Pathogen-Host Interaction database (http://www.phi-base.org) 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 fungal and oomycete 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 terms, EC Numbers, etc.), and links to other external data sources such as UniProt, EMBL and the NCBI taxonomy services.

Current developments[edit]

Version 4.2 (Oct 3rd, 2016) of PHI-base provides information on 4460 genes from 264 pathogens and 176 hosts and their impact on 8046 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 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" [8]


PHI-base is a useful 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 ~200 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 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[edit]

PHI-base is a National Capability funded by Biotechnology and Biological Sciences Research Council (BBSRC), a UK research council.

References[edit]

  1. ^ Winnenburg, R.; Baldwin, T.K.; Urban, M.; Rawlings, C.; Köhler, J.; Hammond-Kosack, K.E. (2014). "PHI-base: a new database for pathogen host interactions" (PDF). Nucleic Acids Research. 34 (Database Issue): D459–464. doi:10.1093/nar/gkj047. PMC 1347410Freely accessible. PMID 16381911. 
  2. ^ Baldwin, T.K.; Winnenburg, R.; Urban, M.; Rawlings, C.; Köhler, J.; Hammond-Kosack, K.E. (2006). "The pathogen-host interactions database (PHI-base) provides insights into generic and novel themes of pathogenicity". Molecular Plant-Microbe Interactions. 19 (12): 1451–1462. doi:10.1094/mpmi-19-1451. PMID 17153929. 
  3. ^ Winnenburg, R.; Urban, M.; Beacham, A.; Baldwin, T.K.; Holland, S.; Lindeberg, M.; Hansen, H.; Rawlings, C.; Hammond-Kosack, K.E.; Köhler, J. (2008). "PHI-base update: additions to the pathogen host interactions database" (PDF). Nucleic Acids Research. 36 (Database Issue): D572–576. doi:10.1093/nar/gkm858. PMC 2238852Freely accessible. PMID 17942425. 
  4. ^ Urban, M.; Pant, R.; Raghunath, A.; Irvine, A.G.; Pedro, H.; Hammond-Kosack, K.E. (2015). "The Pathogen-Host Interactions database (PHI-base): additions and future developments" (PDF). Nucleic Acids Research. 43 (Database Issue): D645–D655. doi:10.1093/nar/gku1165. PMC 4383963Freely accessible. PMID 25414340. 
  5. ^ Urban, M.; Irvine, A. G.; Raghunath, A.; Cuzick, A.; Hammond-Kosack, K.E. (2015). "Using the pathogen-host interactions database (PHI-base) to investigate plant pathogen genomes and genes implicated in virulence" (PDF). Front Plant Sci. 6: 605. doi:10.3389/fpls.2015.00605. PMC 4526803Freely accessible. PMID 26300902. 
  6. ^ Brown, N. A.; Urban, M.; Hammond-Kosack, K.E. (2016). "The trans-kingdom identification of negative regulators of pathogen hypervirulence". FEMS Microbiol Rev. 40: 19–40. doi:10.1093/femsre/fuv042. PMC 4703069Freely accessible. PMID 26468211. 
  7. ^ Urban, M.; Cuzcik, A.; Rutherford, K.; Irvine, A. G.; Pedro, H.; Pant, R.; Sadanadan, V.; Khamari, L.; Billal, S.; Mohanty, S.; Hammond-Kosack, K. "PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database". Nucleic Acids Res. 45: D604–D610. doi:10.1093/nar/gkw1089. PMC 5210566Freely accessible. PMID 27915230. 
  8. ^ Rodriguez-Iglesias, A.; Rodriguez-Gonzalez, A.; Irvine, A.G.; Sesma, A.; Urban, M.; Hammond-Kosack, K.E.; Wilkinson, M.D. (2016). "Publishing FAIR Data: An Exemplar Methodology Utilizing PHI-Base". Front Plant Sci. 7: 641. doi:10.3389/fpls.2016.00641. 

External links[edit]