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PHI-base: a new database for pathogen host interactions

R. Winnenburg
2006 Nucleic Acids Research  
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  ...  All authors are grateful to Gavin Harrison and the Rothamsted Computing Services group for efficient provision and support with the computational infrastructure for PHI-base.  ... 
doi:10.1093/nar/gkj047 pmid:16381911 pmcid:PMC1347410 fatcat:ksqrzpewafhmfhxvmd56nyxwam

PHI-base: a new interface and further additions for the multi-species pathogen–host interactions database

Martin Urban, Alayne Cuzick, Kim Rutherford, Alistair Irvine, Helder Pedro, Rashmi Pant, Vidyendra Sadanadan, Lokanath Khamari, Santoshkumar Billal, Sagar Mohanty, Kim E. Hammond-Kosack
2016 Nucleic Acids Research  
The pathogen-host interactions database (PHI-base) is available at www.phi-base.org.  ...  A PHIB-BLAST search function is provided and a link to PHI-Canto, a tool for authors to directly curate their own published data into PHI-base.  ...  ACKNOWLEDGEMENTS We thank all the species experts who contributed database annotations from their field of expertise into PHI-base.  ... 
doi:10.1093/nar/gkw1089 pmid:27915230 pmcid:PMC5210566 fatcat:wlgkt2ppprfexkharj4ej5axem

PHI-base: the pathogen-host interactions database

2019 Nucleic Acids Research  
The pathogen-host interactions database (PHI-base) is available at www.phi-base.org.  ...  In this article, we describe the increased data content of PHI-base, plus new database features and further integration with complementary databases.  ...  ACKNOWLEDGEMENTS We thank all the species experts who contributed database annotations from their field of expertise into PHI-base.  ... 
doi:10.1093/nar/gkz904 pmid:31733065 pmcid:PMC7145647 fatcat:lytif2lhgbdahfxn2vhvcfi4ry

PHI-base update: additions to the pathogen host interaction database

R. Winnenburg, M. Urban, A. Beacham, T. K. Baldwin, S. Holland, M. Lindeberg, H. Hansen, C. Rawlings, K. E. Hammond-Kosack, J. Kohler
2007 Nucleic Acids Research  
The pathogen-host interaction database (PHI-base) is a web-accessible database that catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and Oomycete pathogens  ...  PHI-base is therefore an invaluable resource for the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention.  ...  ACKNOWLEDGEMENTS The authors would like to thank the FRAC team for allowing inclusion of their data on fungicides and the PAMGO group for compiling a useful ontology on microbe-host interactions.  ... 
doi:10.1093/nar/gkm858 pmid:17942425 pmcid:PMC2238852 fatcat:3icb7nv7zrgvlpanwr3gy7ycee

The Pathogen-Host Interactions database (PHI-base): additions and future developments

Martin Urban, Rashmi Pant, Arathi Raghunath, Alistair G. Irvine, Helder Pedro, Kim E. Hammond-Kosack
2014 Nucleic Acids Research  
The Pathogen-Host Interactions database (PHI-base) catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and protist pathogens.  ...  Future plans for PHI-base include development of tools facilitating community-led curation and inclusion of the corresponding host target(s).  ...  Dr Jan Taubert (formerly Rothamsted Research) is thanked for his expert support in maintaining the PHI-base parser.  ... 
doi:10.1093/nar/gku1165 pmid:25414340 pmcid:PMC4383963 fatcat:fum357rupbcxjcujwuvfnivbg4

Publishing FAIR Data: An Exemplar Methodology Utilizing PHI-Base

Alejandro Rodríguez-Iglesias, Alejandro Rodríguez-González, Alistair G. Irvine, Ane Sesma, Martin Urban, Kim E. Hammond-Kosack, Mark D. Wilkinson
2016 Frontiers in Plant Science  
In this work, we describe the process of migrating a database of notable relevance to the plant sciences-the Pathogen-Host Interaction Database (PHI-base)-to a form that conforms to each of the FAIR Principles  ...  Query 1: Retrieve an overview of the interactions in Semantic PHI-base.  ...  PHI-base is funded by the UK Biotechnology and Biological Sciences Research Council (BBSRC) (BB/I/001077/1, BB/K020056/1) and receives additional support from the BBSRC as a National Capability (BB/J/004383  ... 
doi:10.3389/fpls.2016.00641 pmid:27433158 pmcid:PMC4922217 fatcat:aq2r3jg77fa2xevr267uyt7qw4

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

Martin Urban, Alayne Cuzick, James Seager, Valerie Wood, Kim Rutherford, Shilpa Yagwakote Venkatesh, Jashobanta Sahu, S Vijaylakshmi Iyer, Lokanath Khamari, Nishadi De Silva, Manuel Carbajo Martinez, Helder Pedro (+2 others)
2021 Nucleic Acids Research  
Since 2005, the PathogenHost Interactions Database (PHI-base) has manually curated experimentally verified pathogenicity, virulence and effector genes from fungal, bacterial and protist pathogens, which  ...  PHI-base will migrate to a new gene-centric version (version 5.0) in early 2022. This major development is briefly described.  ...  Dr Keywan Hassani-Pak and Dan Smith are thanked for integrating PHI-base data into Knetminer for specific plant pathogenic species.  ... 
doi:10.1093/nar/gkab1037 pmid:34788826 pmcid:PMC8728202 fatcat:adlzgqq65neinmskzurgpegie4

Using the pathogen-host interactions database (PHI-base) to investigate plant pathogen genomes and genes implicated in virulence

Martin Urban, Alistair G. Irvine, Alayne Cuzick, Kim E. Hammond-Kosack
2015 Frontiers in Plant Science  
Citation: Urban M, Irvine AG, Cuzick A and Hammond-Kosack KE (2015) Using the pathogen-host interactions database (PHI-base) to investigate plant pathogen genomes and genes implicated in virulence.  ...  PHI-base is a multi-species manually curated database combining peer-reviewed published phenotype data from plant and animal pathogens and gene/protein information in a single database.  ...  Acknowledgments The authors would like to thank all contributing scientists, who provided expert knowledge by reviewing PHI-base data and suggesting articles for curation.  ... 
doi:10.3389/fpls.2015.00605 pmid:26300902 pmcid:PMC4526803 fatcat:vkj2ps7fsjgsbgfygq5v3c2gcy

The Pathogen-Host Interactions Database (PHI-base) Provides Insights into Generic and Novel Themes of Pathogenicity

Thomas K. Baldwin, Rainer Winnenburg, Martin Urban, Chris Rawlings, Jacob Koehler, Kim E. Hammond-Kosack
2006 Molecular Plant-Microbe Interactions  
In this report, we describe the Pathogen-Host Interactions database (PHI-base), which systematically compiles such pathogenicity genes involved in pathogen-host interactions.  ...  We further discuss the utilization of PHI-base for the computational identification of pathogenicity genes through comparative genomics.  ...  Harrison and the Rothamsted Computing Services group for efficient provision and support with the computational infrastructure for PHI-base.  ... 
doi:10.1094/mpmi-19-1451 pmid:17153929 fatcat:mnzj7yuz4vcqvojcm43r336s4q

PhytoPath: an integrative resource for plant pathogen genomics

Helder Pedro, Uma Maheswari, Martin Urban, Alistair George Irvine, Alayne Cuzick, Mark D. McDowall, Daniel M. Staines, Eugene Kulesha, Kim Elizabeth Hammond-Kosack, Paul Julian Kersey
2015 Nucleic Acids Research  
PhytoPath (www.phytopathdb.org) is a resource for genomic and phenotypic data from plant pathogen species, that integrates phenotypic data for genes from PHI-base, an expertly curated catalog of genes  ...  Genes with associated PHI-base data can be easily identified across all plant pathogen species using a BioMart-based query tool and visualized in their genomic context on the Ensembl genome browser.  ...  ACKNOWLEDGEMENTS The authors would like to thank all the species experts who contributed additional database entries from their field of expertise into PHI-base; and the members of our Scientific Advisory  ... 
doi:10.1093/nar/gkv1052 pmid:26476449 pmcid:PMC4702788 fatcat:rr4yqb22afefzhena2rdm27mo4

Saving plants from disease

KIM HAMMOND-KOSACK
2019 Futurum Careers  
We realised there wasn't a database available for the type of gene function we were interested in, so in 2003, the Excel sheet turned into the database called PHI-base.  ...  The PomBase team is helping to develop a new tool -PHI-Canto -to allow scientists to enter new information in PHI-base.  ... 
doi:10.33424/futurum12 fatcat:ejljgis5dbhzfp2oyk7naona4m

PHI-Nets: A Network Resource for Ascomycete Fungal Pathogens to Annotate and Identify Putative Virulence Interacting Proteins and siRNA Targets

Elzbieta I. Janowska-Sejda, Artem Lysenko, Martin Urban, Chris Rawlings, Sophia Tsoka, Kim E. Hammond-Kosack
2019 Frontiers in Microbiology  
All 15 networks have been made accessible for download at www.phi-base.org providing a rich resource for major crop plant pathogens.  ...  The F. graminearum phenotypic network analysis implicates eight B. cinerea targets and 35 F. graminearum predicted interacting proteins as prime candidate virulence genes for further testing.  ...  Integration of PHI-Base Annotation Pathogen-host interactions database is a unique resource that focuses on genes involved in pathogen-host interactions, and gene functions that are experimentally verified  ... 
doi:10.3389/fmicb.2019.02721 pmid:31866958 pmcid:PMC6908471 fatcat:ll5oi2ki6neq7btr3vmgdwlhr4

Pathogenomics and Management of Fusarium Diseases in Plants

Sephra N. Rampersad
2020 Pathogens  
interactions that lead to disease.  ...  metabolism; (ii) comparison of such genes among related pathogens; (iii) identification of potential genetic targets for chemical control; and (iv) better characterization of the complex dynamics of host–microbe  ...  Database and Website Usage Reference PHI-base -Pathogen-Host Interaction database http://www.phi-base.org/ PHI-base is a web-accessible database that catalogues experimentally verified pathogenicity, virulence  ... 
doi:10.3390/pathogens9050340 pmid:32369942 pmcid:PMC7281180 fatcat:lq3xceamqnayjav32jrmxn65cm

Searching for Novel Targets to Control Wheat Head Blight Disease—I-Protein Identification, 3D Modeling and Virtual Screening

Natália F. Martins, Emmanuel Bresso, Roberto C. Togawa, Martin Urban, John Antoniw, Bernard Maigret, Kim Hammond-Kosack
2016 Advances in microbiology  
Fusarium head blight (FHB) is a destructive disease of wheat and other cereals.  ...  In this article, we provide the strategic steps for the specific target selection for the phytopathogen system wheat-How to cite this paper: Martins  ...  Acknowledgements The authors gratefully acknowledge CNPq (funding grant 400432/2012-9) EMBRAPA The authors would also thank the funding resources of PHI-base, the UK Biotechnology and Biological Sciences  ... 
doi:10.4236/aim.2016.611079 fatcat:vuuukinyjbf6nbjtrpcrhput7y

Victors: a web-based knowledge base of virulence factors in human and animal pathogens

Samantha Sayers, Li Li, Edison Ong, Shunzhou Deng, Guanghua Fu, Yu Lin, Brian Yang, Shelley Zhang, Zhenzong Fa, Bin Zhao, Zuoshuang Xiang, Yongqing Li (+4 others)
2018 Nucleic Acids Research  
These VFs and their interactions with the host are represented in a machine-readable Ontology of Host-Pathogen Interactions.  ...  Virulence factors (VFs) are molecules that allow microbial pathogens to overcome host defense mechanisms and cause disease in a host.  ...  Another database, PHI-base (http://www.phi-base.org/) contains genes involved in host-pathogen interactions.  ... 
doi:10.1093/nar/gky999 pmid:30365026 fatcat:peptxl6wx5gfjhwsymcwrep7gy
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