PHI-base

[1] (https://canto.phi-base.org/)https://canto.phi-base.org/

The Pathogen-Host Interactions database (PHI-

base) is a biological database that contains curated PHI-base
information on genes experimentally proven to affect
the outcome of pathogen-host interactions. The
database is maintained by researchers at Rothamsted
Research, together with external collaborators since
2005.[1][2][3][4][5][6][7][8] Since April 2017 PHI-base is
part of ELIXIR, the European life-science Content
infrastructure for biological information via its
ELIXIR-UK node. Description Pathogen-Host Interactions
database

Background Data types phenotypes of microbial

captured mutants
The Pathogen-Host Interactions database was Organisms ~280 fungal, bacterial and
developed to utilise effectively the growing number of protist pathogens of
verified genes that mediate an organism's ability to agronomic and medical
cause disease and / or to trigger host responses.[9] importance tested on ~230
hosts
The web-accessible database catalogues experimentally
verified pathogenicity, virulence and effector genes Contact
from bacterial, fungal and oomycete pathogens which Research center Rothamsted Research
infect animal, plant and fungal hosts. PHI-base is the
Primary citation PMID 31733065 (https://pub
first on-line resource devoted to the identification and
med.ncbi.nlm.nih.gov/31733
presentation of information on fungal and oomycete
pathogenicity genes and their host interactions. As 065)
such, PHI-base aims to be a resource for the discovery Release date May 2005
of candidate targets in medically and agronomically
Access
important fungal and oomycete pathogens for
intervention with synthetic chemistries and natural Data format XML, FASTA
products (fungicides). Website PHI-base (http://www.phibas
e.org)
Each entry in PHI-base is curated by domain experts
and supported by strong experimental evidence (gene Tools
disruption experiments) as well as literature references Web PHI-base Search
in which the experiments are described. Each gene in
PHI-base is presented with its nucleotide and deduced PHIB-BLAST
amino acid sequence as well as a detailed structured
description of the predicted protein's function during PHI-Canto (Author curation)
the host infection process. To facilitate data Miscellaneous
interoperability, genes are annotated using controlled
License Creative Commons
Attribution-NoDerivatives
4.0 International License
vocabularies (Gene Ontology terms, EC Numbers, Versioning Yes
etc.), and links to other external data sources such as
Data release 6 monthly
UniProt, EMBL and the NCBI taxonomy services.
frequency
Version 4.15 (May 2023)
Current developments
Curation policy Manual Curation
Version 4.15 (May 2, 2023) of PHI-base provides
information on 9377 genes from 285 pathogens and 236 hosts and their impact on 20950 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. In 2016 the plant
portion of PHI-base was used to establish a Semantic PHI-base search tool".[10]

PHI-base is aligned with Ensembl Genomes (http://ensemblgenomes.org/) since 2011, Fungidb (https://fung
idb.org/fungidb/) since 2016, and Global Biotic Interactions (GloBI) (https://www.globalbioticinteractions.
org/) (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.

Since 2015, the website has linked to an online literature curation tool called PHI-Canto (https://canto.phi-b
ase.org/), enabling community-driven literature curation for various pathogenic species. 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[11].
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.

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

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" (https://pubmed.ncbi.nlm.nih.gov/34788826). Nucleic Acids Research. 50
(D1): D837–D847. doi:10.1093/nar/gkab1037 (https://doi.org/10.1093%2Fnar%2Fgkab103
7). ISSN 1362-4962 (https://www.worldcat.org/issn/1362-4962). PMC 8728202 (https://www.
ncbi.nlm.nih.gov/pmc/articles/PMC8728202). PMID 34788826 (https://pubmed.ncbi.nlm.nih.
gov/34788826).
2. 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" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210566). Nucleic Acids Res. 45
(D1): D604–D610. doi:10.1093/nar/gkw1089 (https://doi.org/10.1093%2Fnar%2Fgkw1089).
PMC 5210566 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210566). PMID 27915230
(https://pubmed.ncbi.nlm.nih.gov/27915230).
3. 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" (https://www.ncbi.nlm.nih.
gov/pmc/articles/PMC1347410). Nucleic Acids Research. 34 (Database Issue): D459-464.
doi:10.1093/nar/gkj047 (https://doi.org/10.1093%2Fnar%2Fgkj047). PMC 1347410 (https://w
ww.ncbi.nlm.nih.gov/pmc/articles/PMC1347410). PMID 16381911 (https://pubmed.ncbi.nlm.
nih.gov/16381911).
4. 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" (https://doi.org/10.1094%2Fmpmi-19-1451). Molecular
Plant-Microbe Interactions. 19 (12): 1451–1462. doi:10.1094/mpmi-19-1451 (https://doi.org/1
0.1094%2Fmpmi-19-1451). PMID 17153929 (https://pubmed.ncbi.nlm.nih.gov/17153929).
5. 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" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC22
38852). Nucleic Acids Research. 36 (Database Issue): D572-576. doi:10.1093/nar/gkm858
(https://doi.org/10.1093%2Fnar%2Fgkm858). PMC 2238852 (https://www.ncbi.nlm.nih.gov/p
mc/articles/PMC2238852). PMID 17942425 (https://pubmed.ncbi.nlm.nih.gov/17942425).
6. 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"
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383963). Nucleic Acids Research. 43
(Database Issue): D645–D655. doi:10.1093/nar/gku1165 (https://doi.org/10.1093%2Fnar%2
Fgku1165). PMC 4383963 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383963).
PMID 25414340 (https://pubmed.ncbi.nlm.nih.gov/25414340).
7. 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" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC452680
3). Front Plant Sci. 6: 605. doi:10.3389/fpls.2015.00605 (https://doi.org/10.3389%2Ffpls.201
5.00605). PMC 4526803 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4526803).
PMID 26300902 (https://pubmed.ncbi.nlm.nih.gov/26300902).
8. Brown, N. A.; Urban, M.; Hammond-Kosack, K.E. (2016). "The trans-kingdom identification of
negative regulators of pathogen hypervirulence" (https://www.ncbi.nlm.nih.gov/pmc/articles/
PMC4703069). FEMS Microbiol Rev. 40 (1): 19–40. doi:10.1093/femsre/fuv042 (https://doi.o
rg/10.1093%2Ffemsre%2Ffuv042). PMC 4703069 (https://www.ncbi.nlm.nih.gov/pmc/article
s/PMC4703069). PMID 26468211 (https://pubmed.ncbi.nlm.nih.gov/26468211).
 9. 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" (https://www.ncbi.nlm.nih.gov/p
mc/articles/PMC7145647). Nucleic Acids Research. 48 (D1): D613–D620.
doi:10.1093/nar/gkz904 (https://doi.org/10.1093%2Fnar%2Fgkz904). PMC 7145647 (https://
www.ncbi.nlm.nih.gov/pmc/articles/PMC7145647). PMID 31733065 (https://pubmed.ncbi.nl
m.nih.gov/31733065).
10. 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" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4922217).
Front Plant Sci. 7: 641. doi:10.3389/fpls.2016.00641 (https://doi.org/10.3389%2Ffpls.2016.0
0641). PMC 4922217 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4922217).
PMID 27433158 (https://pubmed.ncbi.nlm.nih.gov/27433158).
11. 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" (https://dx.doi.org/10.7554/elife.84658). eLife. 12.
doi:10.7554/elife.84658 (https://doi.org/10.7554%2Felife.84658). ISSN 2050-084X (https://w
ww.worldcat.org/issn/2050-084X).

External links
PHI-base (http://www.phi-base.org/)

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