Biology:PHI-base
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|---|---|
| Content | |
| Description | Pathogen-Host Interactions database |
| Data types captured | phenotypes of microbial mutants |
| Organisms | ~280 fungal, bacterial and protist pathogens of agronomic and medical importance tested on ~230 hosts |
| Contact | |
| Research centre | Rothamsted Research |
| Primary citation | PMID 31733065 |
| Release date | May 2005 |
| Access | |
| Data format | XML, FASTA |
| Website | phibase |
| Tools | |
| Web application | PHI-base Search
PHIB-BLAST PHI-Canto (Author curation) |
| Miscellaneous | |
| Software license | Creative Commons Attribution-NoDerivatives 4.0 International License |
| Software versioning | Yes |
| Data release frequency | 6 monthly |
| Version | 4.15 (May 2023) |
| Curation policy | Manual Curation |
The Pathogen-Host Interactions database (PHI-base) 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.[1][2][3][4] PHI-base has been part of the UK node of ELIXIR, the European life-science infrastructure for biological information, since 2016.[5]
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.[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
Version 4.15 (May 2, 2023) of PHI-base provides information on 9377 genes from 285 pathogens and 236 hosts and their impact on 20950 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.[5]
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.
Funding
PHI-base is a National Capability funded by the Biotechnology and Biological Sciences Research Council (BBSRC), a UK research council.[6]
References
- ↑ 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. PMID 16381911.
- ↑ 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.
- ↑ Winnenburg, R.; Urban, M.; Beacham, A.; Baldwin, T.K.; Holland, S.; Lindeberg, M.; Hansen, H.; Rawlings, C. et al. (2008). "PHI-base update: additions to the pathogen host interactions database". Nucleic Acids Research 36 (Database Issue): D572-576. doi:10.1093/nar/gkm858. PMID 17942425.
- ↑ 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. PMID 25414340.
- ↑ 5.0 5.1 Urban, Martin; Cuzick, Alayne; Seager, James; Wood, Valerie; Rutherford, Kim; Venkatesh, Shilpa Yagwakote; Sahu, Jashobanta; Iyer, S. Vijaylakshmi et al. (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. PMID 34788826.
- ↑ 6.0 6.1 Urban, M; Cuzick, A; Seager, J; Wood, V; Rutherford, K; Venkatesh, SY; De Silva, N; Martinez, MC et al. (8 January 2020). "PHI-base: the pathogen-host interactions database.". Nucleic Acids Research 48 (D1): D613–D620. doi:10.1093/nar/gkz904. PMID 31733065.
- ↑ 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. PMID 26468211.
- ↑ 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. PMID 26300902.
- ↑ Urban, M.; Cuzick, A.; Rutherford10.1093/nar/gkab103, K.; Irvine, A. G.; Pedro, H.; Pant, R.; Sadanadan, V.; Khamari, L. et al. (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. PMID 27915230.
- ↑ 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. PMID 27433158.
- ↑ Basenko, Evelina Y.; Pulman, Jane A.; Shanmugasundram, Achchuthan; Harb, Omar S.; Crouch, Kathryn; Starns, David; Warrenfeltz, Susanne; Aurrecoechea, Cristina et al. (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. PMID 30152809.
- ↑ 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. PMID 37401199.
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