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PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions.

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cam.depositDate2022-01-27
cam.issuedOnline2021-11-12
dc.contributor.authorUrban, Martin
dc.contributor.authorCuzick, Alayne
dc.contributor.authorSeager, James
dc.contributor.authorWood, Valerie
dc.contributor.authorRutherford, Kim
dc.contributor.authorVenkatesh, Shilpa Yagwakote
dc.contributor.authorSahu, Jashobanta
dc.contributor.authorIyer, S Vijaylakshmi
dc.contributor.authorKhamari, Lokanath
dc.contributor.authorDe Silva, Nishadi
dc.contributor.authorMartinez, Manuel Carbajo
dc.contributor.authorPedro, Helder
dc.contributor.authorYates, Andrew D
dc.contributor.authorHammond-Kosack, Kim E
dc.contributor.orcidUrban, Martin [0000-0003-2440-4352]
dc.contributor.orcidCuzick, Alayne [0000-0001-8941-3984]
dc.contributor.orcidSeager, James [0000-0001-7487-610X]
dc.contributor.orcidWood, Valerie [0000-0001-6330-7526]
dc.contributor.orcidRutherford, Kim [0000-0001-6277-726X]
dc.contributor.orcidDe Silva, Nishadi [0000-0003-4802-2375]
dc.contributor.orcidPedro, Helder [0000-0001-7582-1565]
dc.contributor.orcidYates, Andrew D [0000-0002-8886-4772]
dc.contributor.orcidHammond-Kosack, Kim E [0000-0002-9699-485X]
dc.date.accessioned2022-01-28T00:31:30Z
dc.date.available2022-01-28T00:31:30Z
dc.date.issued2022-01-07
dc.date.updated2022-01-27T14:00:18Z
dc.description.abstractSince 2005, the Pathogen-Host Interactions Database (PHI-base) has manually curated experimentally verified pathogenicity, virulence and effector genes from fungal, bacterial and protist pathogens, which infect animal, plant, fish, insect and/or fungal hosts. PHI-base (www.phi-base.org) is devoted to the identification and presentation of phenotype information on pathogenicity and effector genes and their host interactions. Specific gene alterations that did not alter the in host interaction phenotype are also presented. PHI-base is invaluable for comparative analyses and for the discovery of candidate targets in medically and agronomically important species for intervention. Version 4.12 (September 2021) contains 4387 references, and provides information on 8411 genes from 279 pathogens, tested on 228 hosts in 18, 190 interactions. This provides a 24% increase in gene content since Version 4.8 (September 2019). Bacterial and fungal pathogens represent the majority of the interaction data, with a 54:46 split of entries, whilst protists, protozoa, nematodes and insects represent 3.6% of entries. Host species consist of approximately 54% plants and 46% others of medical, veterinary and/or environmental importance. PHI-base data is disseminated to UniProtKB, FungiDB and Ensembl Genomes. PHI-base will migrate to a new gene-centric version (version 5.0) in early 2022. This major development is briefly described.
dc.format.mediumPrint
dc.identifier.doi10.17863/CAM.80408
dc.identifier.eissn1362-4962
dc.identifier.issn0305-1048
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/332984
dc.language.isoeng
dc.publisherOxford University Press (OUP)
dc.publisher.departmentDepartment of Biochemistry
dc.publisher.urlhttp://dx.doi.org/10.1093/nar/gkab1037
dc.rightsAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectAnimals
dc.subjectApicomplexa
dc.subjectBacteria
dc.subjectDatabases, Factual
dc.subjectDiplomonadida
dc.subjectFungi
dc.subjectHost-Pathogen Interactions
dc.subjectInsecta
dc.subjectInternet
dc.subjectNematoda
dc.subjectPhenotype
dc.subjectPhylogeny
dc.subjectPlants
dc.subjectUser-Computer Interface
dc.subjectVirulence
dc.titlePHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions.
dc.typeArticle
dcterms.dateAccepted2021-11-08
prism.endingPageD847
prism.issueIdentifierD1
prism.publicationDate2022
prism.publicationNameNucleic Acids Res
prism.startingPageD837
prism.volume50
pubs.funder-project-idBiotechnology and Biological Sciences Research Council (BB/S020098/1)
pubs.licence-display-nameApollo Repository Deposit Licence Agreement
pubs.licence-identifierapollo-deposit-licence-2-1
rioxxterms.typeJournal Article/Review
rioxxterms.versionVoR
rioxxterms.versionofrecord10.1093/nar/gkab1037

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