PHI-base
{{Short description|Biological database}}
{{Infobox biodatabase
| title = PHI-base
| logo = alt=PHI-base logo
| description = Pathogen-Host Interactions database
| scope = phenotypes of microbial mutants
| organism = ~290 fungal, bacterial and protist pathogens of agronomic and medical importance tested on ~240 hosts
| center = Rothamsted Research
| laboratory =
| author =
| pmid = 39588765
| released = May 2005
| standard =
| format = XML, FASTA
| url = {{URL|phibase.org}}
| webservice =
| sql =
| webapp = PHI-base Search
PHIB-BLAST
PHI-Canto (Author curation)
| standalone =
| license = Creative Commons Attribution-NoDerivatives 4.0 International License
| versioning = Yes
| frequency = 6 monthly
| curation = Manual Curation
| bookmark =
| version = 4.17 (May 2024)
}}
The Pathogen-Host Interactions database (PHI-base){{cite journal|last1 = Urban|first1 = M.|last2 = Cuzick|first2 = A.|last3 = Seager|first3 = J.|last4 = Nonavinakere|first4 = N.|last5 = Sahoo|first5 = J.|last6 = Sahu|first6 = P.|last7 = Iyer|first7 = V. L.|last8 = Khamari|first8 = L.|last9 = Carbajo Martinez|first9 = M.|last10 = Hammond-Kosack|first10 = K.E.|year = 2025|title = PHI-base – the multi-species pathogen–host interaction database in 2025|journal = Nucleic Acids Research|issue = Database Issue|pages = D826-838|volume=53|doi = 10.1093/nar/gkae1084| pmid=39588765 |pmc= 11701570}} 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.
{{cite journal
|last1 = Winnenburg
|first1 = R.
|last2 = Baldwin
|first2 = T.K.
|last3 = Urban
|first3 = M.
|last4 = Rawlings
|first4 = C.
|last5 = Köhler
|first5 = J.
|last6 = Hammond-Kosack
|first6 = K.E.
|year = 2014
|title = PHI-base: a new database for pathogen host interactions
|journal = Nucleic Acids Research
|issue = Database Issue
|pages = D459-464
|doi = 10.1093/nar/gkj047
|pmc = 1347410
|pmid = 16381911
|volume=34
}}
{{cite journal
|last1 = Baldwin
|first1 = T.K.
|last2 = Winnenburg
|first2 = R.
|last3 = Urban
|first3 = M.
|last4 = Rawlings
|first4 = C.
|last5 = Köhler
|first5 = J.
|last6 = Hammond-Kosack
|first6 = K.E.
|year = 2006
|title = The pathogen-host interactions database (PHI-base) provides insights into generic and novel themes of pathogenicity
|journal = Molecular Plant-Microbe Interactions
|volume = 19
|issue = 12
|pages = 1451–1462
|doi = 10.1094/mpmi-19-1451
|pmid = 17153929
|doi-access = free
}}
{{cite journal
|last1 = Winnenburg
|first1 = R.
|last2 = Urban
|first2 = M.
|last3 = Beacham
|first3 = A.
|last4 = Baldwin
|first4 = T.K.
|last5 = Holland
|first5 = S.
|last6 = Lindeberg
|first6 = M.
|last7 = Hansen
|first7 = H.
|last8 = Rawlings
|first8 = C.
|last9 = Hammond-Kosack
|first9 = K.E.
|last10 = Köhler
|first10 = J.
|year = 2008
|title = PHI-base update: additions to the pathogen host interactions database
|journal = Nucleic Acids Research
|volume = 36
|issue = Database Issue
|pages = D572-576
|doi = 10.1093/nar/gkm858
|pmc = 2238852
|pmid = 17942425
}}
{{cite journal
|last1 = Urban
|first1 = M.
|last2 = Pant
|first2 = R.
|last3 = Raghunath
|first3 = A.
|last4 = Irvine
|first4 = A.G.
|last5 = Pedro
|first5 = H.
|last6 = Hammond-Kosack
|first6 = K.E.
|year = 2015
|title = The Pathogen-Host Interactions database (PHI-base): additions and future developments
|url= |journal = Nucleic Acids Research
|volume = 43
|pages = D645–D655
|pmid = 25414340
|pmc = 4383963
|issue = Database Issue
|doi = 10.1093/nar/gku1165
}}
PHI-base has been part of the UK node of ELIXIR, the European life-science infrastructure for biological information, since 2016.{{Cite journal |last1=Urban |first1=Martin |last2=Cuzick |first2=Alayne |last3=Seager |first3=James |last4=Wood |first4=Valerie |last5=Rutherford |first5=Kim |last6=Venkatesh |first6=Shilpa Yagwakote |last7=Sahu |first7=Jashobanta |last8=Iyer |first8=S. Vijaylakshmi |last9=Khamari |first9=Lokanath |last10=De Silva |first10=Nishadi |last11=Martinez |first11=Manuel Carbajo |last12=Pedro |first12=Helder |last13=Yates |first13=Andrew D. |last14=Hammond-Kosack |first14=Kim E. |date=2022-01-07 |title=PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions |journal=Nucleic Acids Research |volume=50 |issue=D1 |pages=D837–D847 |doi=10.1093/nar/gkab1037 |issn=1362-4962 |pmc=8728202 |pmid=34788826}}
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.{{cite journal |last1=Urban |first1=M |last2=Cuzick |first2=A |last3=Seager |first3=J |last4=Wood |first4=V |last5=Rutherford |first5=K |last6=Venkatesh |first6=SY |last7=De Silva |first7=N |last8=Martinez |first8=MC |last9=Pedro |first9=H |last10=Yates |first10=AD |last11=Hassani-Pak |first11=K |last12=Hammond-Kosack |first12=KE |title=PHI-base: the pathogen-host interactions database. |journal=Nucleic Acids Research |date=8 January 2020 |volume=48 |issue=D1 |pages=D613–D620 |doi=10.1093/nar/gkz904 |pmid=31733065|pmc=7145647 }}
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).
{{cite journal
|last1 = Brown
|first1 = N. A.
|last2 = Urban
|first2 = M.
|last3 = Hammond-Kosack
|first3 = K.E.
|year = 2016
|title = The trans-kingdom identification of negative regulators of pathogen hypervirulence
|journal = FEMS Microbiol Rev
|volume = 40
|issue = 1
|pages = 19–40
|pmid = 26468211
|pmc = 4703069
|doi = 10.1093/femsre/fuv042
}}
{{cite journal
|last1 = Urban
|first1 = M.
|last2 = Irvine
|first2 = A. G.
|last3 = Raghunath
|first3 = A.
|last4 = Cuzick
|first4 = A.
|last5 = Hammond-Kosack
|first5 = K.E.
|year = 2015
|title = Using the pathogen-host interactions database (PHI-base) to investigate plant pathogen genomes and genes implicated in virulence
|url= |journal = Front Plant Sci
|volume = 6
|pages = 605
|pmid = 26300902
|doi = 10.3389/fpls.2015.00605
|pmc=4526803
|doi-access = free
}}
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 4.17 (May 2024) of PHI-base provides information on 9973 genes from 296 pathogens and 249 hosts and their impact on 22415 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.
{{cite journal |last1=Urban |first1=M. |last2=Cuzick |first2=A. |last3=Rutherford |first3=K. |last4=Irvine |first4=A. G. |last5=Pedro |first5=H. |last6=Pant |first6=R. |last7=Sadanadan |first7=V. |last8=Khamari |first8=L. |last9=Billal |first9=S. |last10=Mohanty |first10=S. |last11=Hammond-Kosack |first11=K. |year=2017 |title=PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database |journal=Nucleic Acids Res |volume=45 |issue=D1 |pages=D604–D610 |doi=10.1093/nar/gkw1089 |pmc=5210566 |pmid=27915230}}
The database providers recently announced the launch of [https://phi5.phi-base.org/#/home PHI-base 5], a new gene-centric version of PHI-base, through a [https://www.rothamsted.ac.uk/news/pathogen-host-database-refocuses-genes press release] on the Rothamsted Research website. A summary of the improvements made is also [https://www.rothamsted.ac.uk/sites/default/files/Documents/PHI-base%205%20improvement%20summary.pdf available].
In 2016 the plant portion of PHI-base was used to establish a Semantic PHI-base search tool.{{cite journal | last1 = Rodriguez-Iglesias | first1 = A. | last2 = Rodriguez-Gonzalez | first2 = A. | last3 = Irvine | first3 = A.G. | last4 = Sesma | first4 = A. | last5 = Urban | first5 = M. | last6 = Hammond-Kosack | first6 = K.E. | last7 = Wilkinson | first7 = M.D. | year = 2016 | title = Publishing FAIR Data: An Exemplar Methodology Utilizing PHI-Base | journal = Front Plant Sci | volume = 7 | page = 641 | doi = 10.3389/fpls.2016.00641 | pmid = 27433158 | pmc = 4922217 | doi-access = free }}
PHI-base has been aligned with [http://ensemblgenomes.org/ Ensembl Genomes] since 2011, [https://fungidb.org/fungidb/ FungiDB] since 2016, and [https://www.globalbioticinteractions.org/ Global Biotic Interactions (GloBI)] since 2018.{{Cite journal |last1=Basenko |first1=Evelina Y. |last2=Pulman |first2=Jane A. |last3=Shanmugasundram |first3=Achchuthan |last4=Harb |first4=Omar S. |last5=Crouch |first5=Kathryn |last6=Starns |first6=David |last7=Warrenfeltz |first7=Susanne |last8=Aurrecoechea |first8=Cristina |last9=Stoeckert |first9=Christian J. |last10=Kissinger |first10=Jessica C. |last11=Roos |first11=David S. |last12=Hertz-Fowler |first12=Christiane |date=2018-03-20 |title=FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes |journal=Journal of Fungi |volume=4 |issue=1 |pages=39 |doi=10.3390/jof4010039 |issn=2309-608X |pmc=5872342 |pmid=30152809 |doi-access=free }} 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 900 peer-reviewed articles.
Since 2015, the website has linked to an online literature curation tool called [https://canto.phi-base.org/ PHI-Canto], enabling community-driven literature curation for various pathogenic species.{{Cite journal |last1=Cuzick |first1=Alayne |last2=Seager |first2=James |last3=Wood |first3=Valerie |last4=Urban |first4=Martin |last5=Rutherford |first5=Kim |last6=Hammond-Kosack |first6=Kim E |date=2023-07-04 |title=A framework for community curation of interspecies interactions literature |journal=eLife |volume=12 |doi=10.7554/elife.84658 |pmid=37401199 |issn=2050-084X|pmc=10319440 |doi-access=free }} 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 {{cite journal | vauthors = Rutherford KM, Lera-Ramírez M, Wood V | title = PomBase: a Global Core Biodata Resource-growth, collaboration, and sustainability | journal = Genetics | volume = 227 | issue = 1 | date = May 2024 | pmid = 38376816 | pmc = 11075564 | doi = 10.1093/genetics/iyae007 }} (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.
References
{{reflist|30em}}
External links
- [http://www.phi-base.org/ PHI-base]
{{Bioinformatics}}
Category:Biological interactions
Category:Genetics in the United Kingdom
Category:Plant pathogens and diseases