47 research outputs found
Genetic characterisation of four genes in Arabidopsis required for a non salicylate dependent source of downy mildew resistance
No full textSIGLEAvailable from British Library Document Supply Centre- DSC:DXN056278 / BLDSC - British Library Document Supply CentreGBUnited Kingdo
PHI-base: the Pathogen-Host Interactions Database, version 5.0
No full text<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/" target="_blank" rel="noopener">Gene Ontology</a> (GO), <a href="https://pubmed.ncbi.nlm.nih.gov/21030441/" target="_blank" rel="noopener">Brenda Tissue Ontology</a> (BTO), and the <a href="https://obofoundry.org/ontology/phipo.html" target="_blank" rel="noopener">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" target="_blank" rel="noopener">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="../doi/10.5281/zenodo.5356870">https://zenodo.org/doi/10.5281/zenodo.5356870</a>. </p>
<h2>Data content</h2>
<ul>
<li>
<p><strong>phi-base_v5.0.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_v5.0.json</strong>: the PHI-base dataset in JSON format. This format is closer to the data format that is exported by PHI-Canto, the curation tool used by PHI-base. This format is primarily intended for programmatic usage and has additional data (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>
Textual Construction of Middle School Math Students as “Thinkers”
No full textThis paper investigates how the mathematical performance of a group of middle school students might be characterized when the text breaks from tradition and constructs students as members of the mathematical community. Firstly, I will consider how a current Canadian textbook presents The Locker Problem through a depersonalized, formalized style that promotes its authority over the student-reader (Rotman, 2006). Next I will argue that the presentation of the problem through a Problem-of-the-Week (POW) format promotes the author/ity (Povey et al, 1990) of the student- reader over the text. Finally, I will present a classroom episode where a small group of students explore The Locker Problem based on the POW format. While some have argued that one can infer the experience of the student-reader through a text’s choice of words (Herbel-Eisenmann & Wagner, 2007), I suggest that the student-reader’s style of performing mathematics might also be inferred based on the text’s presentation of a problem
Conserving "Big Stuff" – lessons learnt
No full textThis paper presents views formed by the author after the experience of conserving large technology objects and aims to encourage thought and discussion about some of the non-conservation aspects of large technology conservation projects. The topics discussed include the preconceived ideas that may affect your project (both your ideas and those of other people), dealing with specialists, contractors and volunteers and looking at the way you use time in a project
PHI-base/phipo: 2023-09-07 September 2023 release
No full textPHIPO September 2023 release
<p>This release contains the following changes since the previous release (3 August 2023).</p>
New terms
<ul>
<li>normal growth on amphotericin B (PHIPO:0001352) (#421)</li>
<li>normal growth on itraconazole (PHIPO:0001351) (#422)</li>
<li>resistance to triflumizole (PHIPO:0001342) (#419)</li>
<li>sensitive to triflumizole (PHIPO:0001343) (#419)</li>
<li>normal growth on triflumizole (PHIPO:0001344) (#419)</li>
<li>resistance to bitertanol (PHIPO:0001345) (#419)</li>
<li>sensitive to bitertanol (PHIPO:0001346) (#419)</li>
<li>normal growth on bitertanol (PHIPO:0001347) (#419)</li>
<li>resistance to pyrifenox (PHIPO:0001348) (#419)</li>
<li>sensitive to pyrifenox (PHIPO:0001349) (#419)</li>
<li>normal growth on pyrifenox (PHIPO:0001350) (#419)</li>
<li>normal growth on thiabendazole (PHIPO:0001341) (#418)</li>
<li>resistance to nocodazole (PHIPO:0001340) (#417)</li>
<li>sensitive to procymidone (PHIPO:0001339) (#415)</li>
<li>sensitive to thiram (PHIPO:0001338) (#414)</li>
<li>sensitive to fluazinam (PHIPO:0001337) (#413)</li>
<li>sensitive to myclobutanil (PHIPO:0001336) (#409)</li>
<li>resistance to myclobutanil (PHIPO:0001335) (#409)</li>
<li>resistance to fluazinam (PHIPO:0001334) (#413)</li>
<li>resistance to thiram (PHIPO:0001333) (#414)</li>
<li>resistance to procymidone (PHIPO:0001332) (#415)</li>
<li>normal growth on procymidone (PHIPO:0001331) (#415)</li>
<li>normal growth on thiram (PHIPO:0001330) (#414)</li>
<li>normal growth on fluazinam (PHIPO:0001329) (#413)</li>
<li>normal growth on myclobutanil (PHIPO:0001328) (#409)</li>
<li>normal growth on iprodione (PHIPO:0001327) (#410)</li>
<li>normal growth on prochloraz (PHIPO:0001326) (#411)</li>
<li>normal growth on tebuconazole (PHIPO:0001325) (#412)</li>
<li>normal growth on pyrimethanil (PHIPO:0001324) (#416)</li>
</ul>
<p><strong>Full Changelog</strong>: <a href="https://github.com/PHI-base/phipo/compare/v2023-08-03...v2023-09-07">https://github.com/PHI-base/phipo/compare/v2023-08-03...v2023-09-07</a></p>
PHI-base/phipo: 2024-01-31 January 2024 release
No full text<h1>PHIPO January 2024 release</h1>
<p>This release contains the following changes since the previous release (30 November 2023).</p>
<h2>New terms</h2>
<ul>
<li>resistance to pyrisoxazole (PHIPO:0001388) (#419)</li>
<li>sensitive to pyrisoxazole (PHIPO:0001389) (#419)</li>
<li>normal growth on pyrisoxazole (PHIPO:0001390) (#419)</li>
<li>resistance to metconazole (PHIPO:0001391) (#419)</li>
<li>sensitive to metconazole (PHIPO:0001392) (#419)</li>
<li>normal growth on metconazole (PHIPO:0001393) (#419)</li>
<li>resistance to trifloxystrobin (PHIPO:0001394) (#419)</li>
<li>sensitive to trifloxystrobin (PHIPO:0001395) (#419)</li>
<li>normal growth on trifloxystrobin (PHIPO:0001396) (#419)</li>
<li>sensitive to cell wall stress (PHIPO:0001397) (#427)</li>
<li>sensitive to oxidative stress (PHIPO:0001398) (#428)</li>
<li>resistance to flusilazole (PHIPO:0001399) (#419)</li>
<li>sensitive to flusilazole (PHIPO:0001400) (#419)</li>
<li>normal growth on flusilazole (PHIPO:0001401) (#419)</li>
<li>resistance to mandipropamid (PHIPO:0001402) (#419)</li>
<li>sensitive to mandipropamid (PHIPO:0001403) (#419)</li>
<li>normal growth on mandipropamid (PHIPO:0001404) (#419)</li>
<li>resistance to dimethomorph (PHIPO:0001405) (#419)</li>
<li>sensitive to dimethomorph (PHIPO:0001406) (#419)</li>
<li>normal growth on dimethomorph (PHIPO:0001407) (#419)</li>
<li>resistance to iprovalicarb (PHIPO:0001408) (#419)</li>
<li>sensitive to iprovalicarb (PHIPO:0001409) (#419)</li>
<li>normal growth on iprovalicarb (PHIPO:0001410) (#419)</li>
</ul>
<h2>Term hierarchy changes</h2>
<ul>
<li>'sensitive to congo red' (PHIPO:0001021) has an additional parent term: 'sensitive to stress' (PHIPO:0001397) (#427)</li>
<li>'sensitive to hydrogen peroxide' (PHIPO:0000943) has an additional parent term: 'sensitive to oxidative stress' (PHIPO:0001398) (#428)</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/PHI-base/phipo/compare/v2023-11-30...v2024-01-31</p>
PHI-base/phipo: 2023-10-11 October 2023 release
No full textPHIPO October 2023 release
<p>This release contains the following changes since the previous release (7 September 2023).</p>
New terms
<ul>
<li>resistance to prothioconazole (PHIPO:0001353) (#419)</li>
<li>sensitive to prothioconazole (PHIPO:0001354) (#419)</li>
<li>normal growth on prothioconazole (PHIPO:0001355) (#419)</li>
<li>resistance to fluopyram (PHIPO:0001356) (#419)</li>
<li>sensitive to fluopyram (PHIPO:0001357) (#419)</li>
<li>normal growth on fluopyram (PHIPO:0001358) (#419)</li>
<li>resistance to kresoxim-methyl (PHIPO:0001359) (#419)</li>
<li>sensitive to kresoxim-methyl (PHIPO:0001360) (#419)</li>
<li>normal growth on kresoxim-methyl (PHIPO:0001361) (#419)</li>
<li>resistance to isopyrazam (PHIPO:0001362) (#419)</li>
<li>sensitive to isopyrazam (PHIPO:0001363) (#419)</li>
<li>normal growth on isopyrazam (PHIPO:0001364) (#419)</li>
<li>resistance to bixafen (PHIPO:0001365) (#419)</li>
<li>sensitive to bixafen (PHIPO:0001366) (#419)</li>
<li>normal growth on bixafen (PHIPO:0001367) (#419)</li>
<li>normal growth on carboxin (PHIPO:0001368) (#419)</li>
<li>increased rate of hyphae formation (PHIPO:0001369) (#423)</li>
<li>resistance to pyrimorph (PHIPO:0001370) (#419)</li>
<li>sensitive to pyrimorph (PHIPO:0001371) (#419)</li>
<li>normal growth on pyrimorph (PHIPO:0001372) (#419)</li>
</ul>
<p><strong>Full Changelog</strong>: <a href="https://github.com/PHI-base/phipo/compare/v2023-09-07...v2023-10-11">https://github.com/PHI-base/phipo/compare/v2023-09-07...v2023-10-11</a></p>
PHI-base/phipo: 2023-07-06 July release
No full textPHIPO July 2023 release
<p>This release contains the following changes since the previous release (29 June 2023).</p>
New terms
<ul>
<li>resistance to salt stress (PHIPO:0001304) (#399)</li>
<li>resistance to non-ionic osmotic stress (PHIPO:0001305) (#399)</li>
<li>sensitive to salt stress (PHIPO:0001306) (#399)</li>
<li>sensitive to non-ionic osmotic stress (PHIPO:0001307) (#399)</li>
</ul>
<p><strong>Full Changelog</strong>: <a href="https://github.com/PHI-base/phipo/compare/v2023-06-29...v2023-07-06">https://github.com/PHI-base/phipo/compare/v2023-06-29...v2023-07-06</a></p>
PHI-base/phipo: 2023-06-19 June release
No full textPHIPO June 2023 release
<p>This release contains the following changes since the previous release (23 November 2022).</p>
New terms
<ul>
<li>normal growth on tolnaftate (PHIPO:0001287) (#391)</li>
<li>resistance to tolnaftate (PHIPO:0001288) (#392)</li>
<li>sensitive to tolnaftate (PHIPO:0001289) (#392)</li>
<li>normal growth on azoxystrobin (PHIPO:0001290) (#393)</li>
<li>resistance to fenpicoxamid (PHIPO:0001291) (#390)</li>
<li>sensitive to fenpicoxamid (PHIPO:0001292) (#394)</li>
<li>normal growth on fenpicoxamid (PHIPO:0001293) (#395)</li>
<li>inhibition of pathogen polygalacturonase by host present (PHIPO:0001294) (#384)</li>
<li>inhibition of pathogen polygalacturonase by host decreased (PHIPO:0001295) (#384)</li>
</ul>
<p><strong>Full Changelog:</strong> <a href="https://github.com/PHI-base/phipo/compare/v2022-11-23...v2023-06-19">https://github.com/PHI-base/phipo/compare/v2022-11-23...v2023-06-19</a></p>
PHI-base/phipo: 2023-06-22 June release 2
No full textPHIPO June 2023 release 2
<p>This release contains the following changes since the previous release (19 June 2023).</p>
New terms
<ul>
<li>inhibition of pathogen polygalacturonase by host present (PHIPO:0001294) (#384)</li>
<li>inhibition of pathogen polygalacturonase by host decreased (PHIPO:0001295) (#384)</li>
<li>resistance to arborcandin C (PHIPO:0001296) (#397)</li>
<li>sensitive to arborcandin C (PHIPO:0001297) (#397)</li>
<li>normal growth on arborcandin C (PHIPO:0001218) (#397)</li>
</ul>
<p><strong>Full Changelog</strong>: <a href="https://github.com/PHI-base/phipo/compare/v2023-06-19...v2023-06-22">https://github.com/PHI-base/phipo/compare/v2023-06-19...v2023-06-22</a></p>
