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{{Short description|Biological database}}
{{Infobox biodatabase
{{Infobox biodatabase
|title = PHI-base
| title = PHI-base
|logo = [[File:PHI-base 01.jpg|alt=PHI-base logo]]
| logo = [[File:PHI-base 01.jpg|alt=PHI-base logo]]
|description = Pathogen-Host Interactions database
| description = Pathogen-Host Interactions database
|scope = phenotypes of microbial mutants
| scope = phenotypes of microbial mutants
|organism = ~276 fungal, bacterial and protist pathogens of agronomic and medical importance tested on ~224 hosts
| organism = ~290 fungal, bacterial and protist pathogens of agronomic and medical importance tested on ~240 hosts
|center = Rothamsted Research
| center = Rothamsted Research
|laboratory =
| laboratory =
|author =
| author =
|pmid = 31733065
| pmid = 34788826
|released = May 2005
| released = May 2005
|standard =
| standard =
|format = XML, FASTA
| format = XML, FASTA
|url = [http://www.phibase.org PHI-base]
| url = {{URL|phibase.org}}
|webservice =
| webservice =
|sql =
| sql =
|webapp = PHI-base Search
| webapp = PHI-base Search
PHIB-BLAST
PHIB-BLAST
PHI-Canto (Author curation)
PHI-Canto (Author curation)
|standalone =
| standalone =
|license = Creative Commons Attribution-NoDerivatives 4.0 International License
| license = Creative Commons Attribution-NoDerivatives 4.0 International License
|versioning = Yes
| versioning = Yes
|frequency = 6 monthly
| frequency = 6 monthly
|curation = Manual Curation
| curation = Manual Curation
|bookmark =
| bookmark =
|version = 4.11 (May 2021)
| version = 4.16 (Nov 2023)
}}
}}


The '''Pathogen-Host Interactions database''' ('''PHI-base''') is a biological database that contains curated information on genes experimentally proven to affect the outcome of [[Host–pathogen interaction|pathogen-host interactions]]. The database is maintained by researchers at [[Rothamsted Experimental Station|Rothamsted Research]], together with external collaborators since 2005.<ref name="pmid27915230">
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 = 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.
|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
⚫
|pmid = 27915230
⚫
|pmc = 5210566
⚫
|doi = 10.1093/nar/gkw1089
⚫
|year = 2017
⚫
}}
</ref><ref name="pmid16381911">
{{cite journal
{{cite journal
|last1 = Winnenburg
|last1 = Winnenburg
Line 164: Line 131:
|issue = Database Issue
|issue = Database Issue
|doi = 10.1093/nar/gku1165
|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">
</ref><ref name="pmid26300902">
Line 187: Line 178:
|doi-access = free
|doi-access = free
}}
}}
</ref>
</ref><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> Since April 2017 PHI-base is part of [[ELIXIR]], the European life-science infrastructure for biological information via its ELIXIR-UK node.


⚫
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.
⚫
== Background ==
⚫
The [[Pathogen]]-[[Host (biology)|Host]] Interactions database was developed to utilise effectively the growing number of verified genes that mediate an organism's ability to cause disease and / or to trigger host responses.<ref>{{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>


⚫
== Current developments ==
⚫
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 is the first on-line resource devoted to the identification and presentation of information on fungal and oomycete pathogenicity genes and their host interactions. As such, PHI-base is a valuable 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).{{cn}}
⚫
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>
⚫
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 4.11 (May 5th, 2021) of PHI-base provides information on 8070 genes from 276 pathogens and 224 hosts and their impact on 17060 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 2015 the web-site includes an online literature curation tool called PHI-Canto for community literature curation of various pathogenic species. 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".<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 is 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 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 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:
PHI-base is a resource for many applications including:
Line 231: Line 203:
› The rapid cross-checking of phenotypic differences between pathogenic species when writing articles for peer review
› 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.
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
Several specific improvements to PHI-base are currently supported. The [[PhytoPath]] project develops a bioinformatics resource that integrates genome-scale data from important plant pathogen species with the phenotypes captured in PHI-base. Using the Ensembl Genomes browser, PhytoPath provides access to complete genome assemblies and gene models of priority crop and model-fungal and oomycete phytopathogens. An advanced PhytoPath BioMart search tool allows searches across different species of plant pathogens.
</ref> (https://www.pombase.org), the model organism database for fission yeast.


== Funding ==
== Funding ==
PHI-base is a National Capability funded by the [[Biotechnology and Biological Sciences Research Council]] (BBSRC), a UK research council.
PHI-base is a National Capability funded by the [[Biotechnology and Biological Sciences Research Council]] (BBSRC), a UK research council.<ref name=":1" />


== References ==
== References ==

Latest revision as of 02:35, 31 July 2024

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.[1]

Background

[edit]

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.[6]

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).[7][8]

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

[edit]

Version 4.17 (May 2024) of PHI-base [1] 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 algorithm to compare a user's sequence against the sequences available from PHI-base.[9]

In 2016 the plant portion of PHI-base was used to establish a Semantic PHI-base search tool.[10]

PHI-base has been aligned with Ensembl Genomes since 2011, FungiDB since 2016, and Global Biotic Interactions (GloBI) since 2018.[11] 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.[1]

Since 2015, the website has linked to an online literature curation tool called PHI-Canto, enabling community-driven literature curation for various pathogenic species.[12] 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 [13] (https://www.pombase.org), the model organism database for fission yeast.

Funding

[edit]

PHI-base is a National Capability funded by the Biotechnology and Biological Sciences Research Council (BBSRC), a UK research council.[6]

References

[edit]
  1. ^ a b c d 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, 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.
  7. ^ 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.
  8. ^ 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.
  9. ^ Urban, M.; Cuzick, A.; Rutherford, 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.
  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". Front Plant Sci. 7: 641. doi:10.3389/fpls.2016.00641. PMC 4922217. PMID 27433158.
  11. ^ 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.
  12. ^ 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.
  13. ^ 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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