Strategic area: Protecting Crops and the Environment, Rothamsted Research, Harpenden, United Kingdom.
Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
Elife. 2023 Jul 4;12:e84658. doi: 10.7554/eLife.84658.
The quantity and complexity of data being generated and published in biology has increased substantially, but few methods exist for capturing knowledge about phenotypes derived from molecular interactions between diverse groups of species, in such a way that is amenable to data-driven biology and research. To improve access to this knowledge, we have constructed a framework for the curation of the scientific literature studying interspecies interactions, using data curated for the Pathogen-Host Interactions database (PHI-base) as a case study. The framework provides a curation tool, phenotype ontology, and controlled vocabularies to curate pathogen-host interaction data, at the level of the host, pathogen, strain, gene, and genotype. The concept of a multispecies genotype, the 'metagenotype,' is introduced to facilitate capturing changes in the disease-causing abilities of pathogens, and host resistance or susceptibility, observed by gene alterations. We report on this framework and describe PHI-Canto, a community curation tool for use by publication authors.
生物学领域产生和发布的数据的数量和复杂性都大大增加，但很少有方法可以捕获关于不同物种群体之间分子相互作用衍生的表型的知识，而这些方法又适用于数据驱动的生物学和研究。为了更方便地获取这些知识，我们构建了一个框架，用于研究种间相互作用的科学文献的编目，使用了为病原体-宿主相互作用数据库（PHI-base）编目的数据作为案例研究。该框架提供了编目工具、表型本体和受控词汇表，可在宿主、病原体、菌株、基因和基因型等层面上编目病原体-宿主相互作用数据。我们引入了“多物种基因型”的概念，即“元基因型”，以促进捕获病原体致病能力的变化，以及宿主对基因改变导致的疾病的抗性或易感性。我们报告了这个框架，并描述了 PHI-Canto，这是一个供出版物作者使用的社区编目工具。
