PHI-base

Source: Wikipedia, the free encyclopedia.
PHI-base
PMID 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)

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 (

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.
    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.
    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.
    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.
    PMID 25414340
    .
  6. ^ .
  7. ^ .
  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.
    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.
    PMID 26300902
    .
  10. .
  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.
    PMID 27915230.{{cite journal}}: CS1 maint: numeric names: authors list (link
    )
  12. .
  13. .
  14. .
  15. ^ Rutherford, K. M., Lera-Ramírez, M. & Wood, V. PomBase: a Global Core Biodata Resource-growth, collaboration, and sustainability. Genetics (2024), PMID 38376816

External links