PHI-base
PHI-base logo
Content
DescriptionPathogen-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 centerRothamsted Research
Primary citationPMID 34788826
Release dateMay 2005
Access
Data formatXML, FASTA
Websitephibase.org
Tools
WebPHI-base Search

PHIB-BLAST

PHI-Canto (Author curation)
Miscellaneous
LicenseCreative Commons Attribution-NoDerivatives 4.0 International License
VersioningYes
Data release
frequency		6 monthly
Version4.16 (Nov 2023)
Curation policyManual Curation

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]

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.

Current developments

Version 4.16 (Nov 2023) of PHI-base [10] provides information on 9666 genes from 294 pathogens and 244 hosts and their impact on 21676 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.[11]

In 2016 the plant portion of PHI-base was used to establish a Semantic PHI-base search tool.[12]

PHI-base has been aligned with Ensembl Genomes since 2011, FungiDB since 2016, and Global Biotic Interactions (GloBI) since 2018.[13] 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 500 peer-reviewed articles.[6]

Since 2015, the website has linked to an online literature curation tool called PHI-Canto, enabling community-driven literature curation for various pathogenic species.[14] 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 [15] (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 (BBSRC), a UK research council.[7]

References

  1. ^ Urban, Martin; Cuzick, Alayne; Seager, James; Wood, Valerie; Rutherford, Kim; Venkatesh, Shilpa Yagwakote; Sahu, Jashobanta; Iyer, S. Vijaylakshmi; Khamari, Lokanath; De Silva, Nishadi; Martinez, Manuel Carbajo; Pedro, Helder; Yates, Andrew D.; Hammond-Kosack, Kim E. (2022-01-07). "PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions". Nucleic Acids Research. 50 (D1): D837–D847. doi:10.1093/nar/gkab1037. ISSN 1362-4962. PMC 8728202. PMID 34788826.
  2. ^ 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". Nucleic Acids Research. 34 (Database Issue): D459-464. doi:10.1093/nar/gkj047. PMC 1347410. PMID 16381911.
  3. ^ 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.
  4. ^ 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". Nucleic Acids Research. 36 (Database Issue): D572-576. doi:10.1093/nar/gkm858. PMC 2238852. PMID 17942425.
  5. ^ 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". Nucleic Acids Research. 43 (Database Issue): D645–D655. doi:10.1093/nar/gku1165. PMC 4383963. PMID 25414340.
  6. ^ a b Urban, Martin; Cuzick, Alayne; Seager, James; Wood, Valerie; Rutherford, Kim; Venkatesh, Shilpa Yagwakote; Sahu, Jashobanta; Iyer, S. Vijaylakshmi; Khamari, Lokanath; De Silva, Nishadi; Martinez, Manuel Carbajo; Pedro, Helder; Yates, Andrew D.; Hammond-Kosack, Kim E. (2022-01-07). "PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions". Nucleic Acids Research. 50 (D1): D837–D847. doi:10.1093/nar/gkab1037. ISSN 1362-4962. PMC 8728202. PMID 34788826.
  7. ^ a b Urban, M; Cuzick, A; Seager, J; Wood, V; Rutherford, K; Venkatesh, SY; De Silva, N; Martinez, MC; Pedro, H; Yates, AD; Hassani-Pak, K; Hammond-Kosack, KE (8 January 2020). "PHI-base: the pathogen-host interactions database". Nucleic Acids Research. 48 (D1): D613–D620. doi:10.1093/nar/gkz904. PMC 7145647. PMID 31733065.
  8. ^ Brown, N. A.; Urban, M.; Hammond-Kosack, K.E. (2016). "The trans-kingdom identification of negative regulators of pathogen hypervirulence". FEMS Microbiol Rev. 40 (1): 19–40. doi:10.1093/femsre/fuv042. PMC 4703069. PMID 26468211.
  9. ^ 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". Front Plant Sci. 6: 605. doi:10.3389/fpls.2015.00605. PMC 4526803. PMID 26300902.
  10. ^ Urban, Martin; Cuzick, Alayne; Seager, James; Wood, Valerie; Rutherford, Kim; Venkatesh, Shilpa Yagwakote; Sahu, Jashobanta; Iyer, S Vijaylakshmi; Khamari, Lokanath; De Silva, Nishadi; Martinez, Manuel Carbajo; Pedro, Helder; Yates, Andrew D; Hammond-Kosack, Kim E (2022-01-07). "PHI-base in 2022: a multi-species phenotype database for Pathogen–Host Interactions". Nucleic Acids Research. 50 (D1): D837–D847. doi:10.1093/nar/gkab1037. ISSN 0305-1048. PMC 8728202. PMID 34788826.
  11. ^ Urban, M.; Cuzick, A.; Rutherford10.1093/nar/gkab103, K.; Irvine, A. G.; Pedro, H.; Pant, R.; Sadanadan, V.; Khamari, L.; Billal, S.; Mohanty, S.; Hammond-Kosack, K. (2017). "PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database". Nucleic Acids Res. 45 (D1): D604–D610. doi:10.1093/nar/gkw1089. PMC 5210566. PMID 27915230.((cite journal)): CS1 maint: numeric names: authors list (link)
  12. ^ 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. PMC 4922217. PMID 27433158.
  13. ^ Basenko, Evelina Y.; Pulman, Jane A.; Shanmugasundram, Achchuthan; Harb, Omar S.; Crouch, Kathryn; Starns, David; Warrenfeltz, Susanne; Aurrecoechea, Cristina; Stoeckert, Christian J.; Kissinger, Jessica C.; Roos, David S.; Hertz-Fowler, Christiane (2018-03-20). "FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes". Journal of Fungi. 4 (1): 39. doi:10.3390/jof4010039. ISSN 2309-608X. PMC 5872342. PMID 30152809.
  14. ^ Cuzick, Alayne; Seager, James; Wood, Valerie; Urban, Martin; Rutherford, Kim; Hammond-Kosack, Kim E (2023-07-04). "A framework for community curation of interspecies interactions literature". eLife. 12. doi:10.7554/elife.84658. ISSN 2050-084X. PMC 10319440. PMID 37401199.
  15. ^ Rutherford, K. M., Lera-Ramírez, M. & Wood, V. PomBase: a Global Core Biodata Resource-growth, collaboration, and sustainability. Genetics (2024), PMID 38376816

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