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"isni" } ], "name": "Rothamsted Research" } ], "person_or_org": { "family_name": "Urban", "given_name": "Martin", "identifiers": [ { "identifier": "0000-0003-2440-4352", "scheme": "orcid" } ], "name": "Urban, Martin", "type": "personal" }, "role": { "id": "datamanager", "title": { "de": "DatenmanagerIn", "en": "Data manager" } } }, { "affiliations": [ { "name": "Rothamsted Research" } ], "person_or_org": { "family_name": "Hammond-Kosack", "given_name": "Kim", "identifiers": [ { "identifier": "0000-0002-9699-485X", "scheme": "orcid" } ], "name": "Hammond-Kosack, Kim", "type": "personal" }, "role": { "id": "projectleader", "title": { "de": "ProjektleiterIn", "en": "Project leader" } } } ], "description": "

Download the dataset here: phi-base_v5.5.zip

\n

The Pathogen–Host Interactions Database (PHI-base) is an online database that catalogues experimentally-verified pathogenicity, virulence and effector genes from fungal, oomycete, and bacterial pathogens, which infect animal, plant, fungal, and insect hosts. PHI-base is a valuable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention.

\n

Information in PHI-base is manually curated by domain experts and is supported by strong experimental evidence (for example, gene disruption and gene complementation experiments), as well as references to the literature in which the original experiments are described. Annotations are made using terms from ontologies and controlled vocabularies, including the Gene Ontology (GO), Brenda Tissue Ontology (BTO), and the Pathogen–Host Interaction Phenotype Ontology (PHIPO).

\n

PHI-base 5 includes data that was curated using a new curation process described in Cuzick et. al (2023). Data releases for PHI-base 5 do not use the same schema as data releases from PHI-base 4, but all data records from PHI-base 4 that can be made compatible with the new schema are included with this release. Data releases from PHI-base 4 and PHI-base 5 will occur in parallel until such time that all data from PHI-base 4 can be migrated to PHI-base 5. The PHI-base 4 data releases are available on Zenodo at https://zenodo.org/doi/10.5281/zenodo.5356870.

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For more information about the planned transition from PHI-base 4 to PHI-base 5, see the Help and Announcements page on the PHI-base 5 website.

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Release statistics

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This version of the PHI-base 5 dataset contains the following types of information:

\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Data typeCount
Genes11316
Interactions36736
Pathogen species336
Host species259
Diseases360
References (publications)5719
Annotations 
Pathogen-host interaction phenotype21828
Gene-for-gene phenotype590
Pathogen phenotype14037
Host phenotype25
GO biological process1838
GO cellular component205
GO molecular function300
Post-translational modification16
Physical interaction230
WT RNA expression102
WT protein expression4
\n

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