A framework for community curation of interspecies interactions literature
A framework for community curation of interspecies interactions literature
复制标题
种间相互作用文献的社区管理框架
DOI：
10.1101/2022.12.15.520601
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发表时间：
2022
期刊：
影响因子：
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通讯作者：
Cuzick A
中科院分区：
文献类型：
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作者：
Cuzick A
在生物学中生成和发布的数据的数量和复杂性大幅增加，但很少有方法可以捕获有关来自不同物种群体之间分子相互作用的表型的知识，以这种方式适合数据驱动的生物学和研究。为了改善对这些知识的获取，我们构建了一个研究物种间相互作用的科学文献的管理框架，并使用病原体-宿主相互作用数据库（PHI-base）管理的数据作为案例研究。该框架提供了一个策展工具，表型本体，和控制词汇，以策展病原体-宿主相互作用的数据，在主机，病原体，菌株，基因和基因型的水平。引入多物种基因型的概念，即“元基因型”，以便于捕捉病原体致病能力的变化，以及通过基因改变观察到的宿主抗性或易感性。我们报告这个框架，并描述PHI-Canto，一个社区策展工具，供出版物作者使用。
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.