View source for PHI-base

{{Short description|Biological database}}
{{Infobox biodatabase
| title = PHI-base
| logo = [[File:PHI-base 01.jpg|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 = 34788826
| 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 = 4.16 (Nov 2023)
}}
The '''Pathogen-Host Interactions database''' ('''PHI-base''') <ref name="Urban2022" /> is a biological database that contains manually curated information on genes experimentally proven to affect the outcome of [[Host–pathogen interaction|pathogen-host interactions]]. The database has been maintained by researchers at [[Rothamsted Experimental Station|Rothamsted Research]] and external collaborators since 2005.<ref name="pmid16381911">
{{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
}}
</ref><ref name="pmid17153929">
{{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
}}
</ref><ref name="pmid17942425">
{{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
}}
</ref><ref name="pmid25414340">
{{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
}}
</ref>
PHI-base has been part of the UK node of [[ELIXIR]], the European life-science infrastructure for biological information, since 2016.<ref name="Urban2022">{{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}}</ref>
== Background ==
The [[Pathogen]]-[[Host (biology)|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.<ref name=":1">{{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 }}</ref>
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 ([[fungicide]]s).<ref name="pmid26468211">
{{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
}}
</ref><ref name="pmid26300902">
{{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
}}
</ref>
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, [[Enzyme Commission number|EC Numbers]], etc.), and links to other external data sources such as [[UniProt]], [[EMBL]], and the [[National Center for Biotechnology Information|NCBI]] taxonomy services.
== Current developments ==
Version 4.17 (May 2024) of PHI-base <ref name="Urban2022" /> provides information on 9973 genes from 296 pathogens and 249 hosts and their impact on 22408 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 (biotechnology)|BLAST]] algorithm to compare a user's sequence against the sequences available from PHI-base.<ref name="pmid27915230">
{{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}}
</ref>
In 2016 the plant portion of PHI-base was used to establish a Semantic PHI-base search tool.<ref>{{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 }}</ref>
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.<ref>{{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 }}</ref> 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.<ref name="Urban2022" />
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.<ref>{{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 }}</ref> 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 <ref>Rutherford, K. M., Lera-Ramírez, M. & Wood, V. PomBase: a Global Core Biodata Resource-growth, collaboration, and sustainability. Genetics (2024), PMID  38376816
</ref> (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.<ref name=":1" />
== References ==
{{reflist|30em}}
== External links ==
* [http://www.phi-base.org/ PHI-base]
{{Bioinformatics}}
[[Category:Biological interactions]]
[[Category:Genetics databases]]
[[Category:Genetics in the United Kingdom]]
[[Category:Genomics]]
[[Category:Online databases]]
[[Category:Pathogenic microbes]]
[[Category:Plant pathogens and diseases]]
[[Category:Rothamsted Experimental Station]]
[[Category:Science and technology in Hertfordshire]]