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2 results for “PHI-base”
PHI-base: the Pathogen-Host Interactions Database, version 5.1
<p><strong>Download the dataset here: <a title="Download PHI-base 5.1" href="https://zenodo.org/records/16738930/files/phi-base_v5.1.zip?download=1">phi-base_v5.1.zip</a></strong></p> <p>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.</p> <p>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 <a href="https://www.geneontology.org/">Gene Ontology</a> (GO), <a href="https://pubmed.ncbi.nlm.nih.gov/21030441/">Brenda Tissue Ontology</a> (BTO), and the <a href="https://obofoundry.org/ontology/phipo.html">Pathogen–Host Interaction Phenotype Ontology</a> (PHIPO).</p> <p>PHI-base 5 includes data that was curated using a new curation process described in <a href="https://doi.org/10.7554/eLife.84658">Cuzick et. al</a> (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 <a href="https://zenodo.org/doi/10.5281/zenodo.5356870">https://zenodo.org/doi/10.5281/zenodo.5356870</a>.</p> <p>For more information about the planned transition from PHI-base 4 to PHI-base 5, see the <a href="https://phi5.phi-base.org/#/help">Help</a> and <a href="https://phi5.phi-base.org/#/announcements">Announcements</a> page on the PHI-base 5 website.</p> <h2>Release statistics</h2> <p>This version of the PHI-base 5 dataset contains the following types of information:</p> <table style="border-collapse: collapse; border-width: 1px; width: 40.2168%; height: 362.8px;"> <thead> <tr style="height: 19.6px;"> <th style="border-width: 1px; width: 84.846%; height: 19.6px;">Data type</th> <th style="border-width: 1px; width: 15.4054%; height: 19.6px;">Count</th> </tr> </thead> <tbody> <tr style="height: 19.6px;"> <td style="border-width: 1px; width: 84.846%; height: 19.6px;">Genes</td> <td style="border-width: 1px; width: 15.4054%; height: 19.6px;">9457</td> </tr> <tr style="height: 19.6px;"> <td style="border-width: 1px; width: 84.846%; height: 19.6px;">Interactions</td> <td style="border-width: 1px; width: 15.4054%; height: 19.6px;">31094</td> </tr> <tr style="height: 19.6px;"> <td style="border-width: 1px; width: 84.846%; height: 19.6px;">Pathogen species</td> <td style="border-width: 1px; width: 15.4054%; height: 19.6px;">303</td> </tr> <tr style="height: 19.6px;"> <td style="border-width: 1px; width: 84.846%; height: 19.6px;">Host species</td> <td style="border-width: 1px; width: 15.4054%; height: 19.6px;">237</td> </tr> <tr style="height: 19.6px;"> <td style="border-width: 1px; width: 84.846%; height: 19.6px;">Diseases</td> <td style="border-width: 1px; width: 15.4054%; height: 19.6px;">343</td> </tr> <tr style="height: 19.6px;"> <td style="border-width: 1px; width: 84.846%; height: 19.6px;">References</td> <td style="border-width: 1px; width: 15.4054%; height: 19.6px;">5202</td> </tr> <tr style="height: 19.6px;"> <td style="border-width: 1px; width: 84.846%; height: 19.6px;"><strong>Annotations</strong></td> <td style="border-width: 1px; width: 15.4054%; height: 19.6px;"> </td> </tr> <tr style="height: 10px;"> <td style="border-width: 1px; width: 84.846%; height: 10px;">Pathogen-host interaction phenotype</td> <td style="border-width: 1px; width: 15.4054%; height: 10px;">18260</td> </tr> <tr style="height: 19.6px;"> <td style="border-width: 1px; width: 84.846%; height: 19.6px;">Gene-for-gene phenotype</td> <td style="border-width: 1px; width: 15.4054%; height: 19.6px;">452</td> </tr> <tr style="height: 19.6px;"> <td style="border-width: 1px; width: 84.846%; height: 19.6px;">Pathogen phenotype</td> <td style="border-width: 1px; width: 15.4054%; height: 19.6px;">9413</td> </tr> <tr style="height: 19.6px;"> <td style="border-width: 1px; width: 84.846%; height: 19.6px;">Host phenotype</td> <td style="border-width: 1px; width: 15.4054%; height: 19.6px;">14</td> </tr> <tr style="height: 19.6px;"> <td style="border-width: 1px; width: 84.846%; height: 19.6px;">GO biological process</td> <td style="border-width: 1px; width: 15.4054%; height: 19.6px;">1453</td> </tr> <tr style="height: 19.6px;"> <td style="border-width: 1px; width: 84.846%; height: 19.6px;">GO cellular component</td> <td style="border-width: 1px; width: 15.4054%; height: 19.6px;">85</td> </tr> <tr style="height: 19.6px;"> <td style="border-width: 1px; width: 84.846%; height: 19.6px;">GO molecular function</td> <td style="border-width: 1px; width: 15.4054%; height: 19.6px;">152</td> </tr> <tr style="height: 19.6px;"> <td style="border-width: 1px; width: 84.846%; height: 19.6px;">Post-translational modification</td> <td style="border-width: 1px; width: 15.4054%; height: 19.6px;">6</td> </tr> <tr style="height: 19.6px;"> <td style="border-width: 1px; width: 84.846%; height: 19.6px;">Physical interaction</td> <td style="border-width: 1px; width: 15.4054%; height: 19.6px;">53</td> </tr> <tr style="height: 19.6px;"> <td style="border-width: 1px; width: 84.846%; height: 19.6px;">WT RNA expression</td> <td style="border-width: 1px; width: 15.4054%; height: 19.6px;">36</td> </tr> <tr style="height: 19.6px;"> <td style="border-width: 1px; width: 84.846%; height: 19.6px;">WT protein expression</td> <td style="border-width: 1px; width: 15.4054%; height: 19.6px;">2</td> </tr> </tbody> </table> <h2>File contents</h2> <ul> <li> <p><strong>phi-base_v5.1.xlsx</strong>: the PHI-base dataset as an Excel spreadsheet. This format follows the layout of the PHI-base 5 website, with sheets corresponding to the sections of gene pages on the website. This format is designed for use by non-technical users.</p> </li> <li> <p><strong>phi-base_v5.1.json</strong>: the PHI-base dataset in JSON format. This is modelled on the export format used by PHI-Canto, the curation tool used by PHI-base. This format is primarily intended for programmatic usage and has additional information (e.g. metadata for curation sessions) that is not included in the spreadsheet format.</p> </li> <li> <p><strong>phi-base.schema.json</strong>: a <a href="https://json-schema.org/">JSON Schema</a> file for the JSON format of the dataset. This is included as documentation for the fields in the JSON file, but can also be used to validate the dataset.</p> </li> </ul>
PHI-base 5 web display issue tracker Nov 2021 to Sept 2024 with closed issues
<p>Closed GitHub issues are listed for the PHI-base 5 web display for the period 08/11/2021 to 17/09/2024.</p>
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