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Building a pipeline to solicit expert knowledge from the community to aid gene summary curation.
Database: The Journal of Biological Databases and Curation ( IF 3.4 ) Pub Date : 2020-01-21 , DOI: 10.1093/database/baz152
Giulia Antonazzo 1 , Jose M Urbano 1 , Steven J Marygold 1 , Gillian H Millburn 1 , Nicholas H Brown 1
Affiliation  

Brief summaries describing the function of each gene's product(s) are of great value to the research community, especially when interpreting genome-wide studies that reveal changes to hundreds of genes. However, manually writing such summaries, even for a single species, is a daunting task; for example, the Drosophila melanogaster genome contains almost 14 000 protein-coding genes. One solution is to use computational methods to generate summaries, but this often fails to capture the key functions or express them eloquently. Here, we describe how we solicited help from the research community to generate manually written summaries of D. melanogaster gene function. Based on the data within the FlyBase database, we developed a computational pipeline to identify researchers who have worked extensively on each gene. We e-mailed these researchers to ask them to draft a brief summary of the main function(s) of the gene's product, which we edited for consistency to produce a 'gene snapshot'. This approach yielded 1800 gene snapshot submissions within a 3-month period. We discuss the general utility of this strategy for other databases that capture data from the research literature. Database URL: https://flybase.org/.

中文翻译:

建立一个渠道,向社区征求专家知识,以帮助基因摘要管理。

描述每个基因产物功能的简短摘要对于研究界具有很大价值,特别是在解释揭示数百个基因变化的全基因组研究时。然而,手动编写这样的摘要,即使是针对单个物种,也是一项艰巨的任务。例如,果蝇基因组包含近 14 000 个蛋白质编码基因。一种解决方案是使用计算方法生成摘要,但这通常无法捕获关键功能或雄辩地表达它们。在这里,我们描述了如何向研究界寻求帮助来生成黑腹果蝇基因功能的手写摘要。根据 FlyBase 数据库中的数据,我们开发了一个计算管道来识别对每个基因进行广泛研究的研究人员。我们给这些研究人员发了电子邮件,要求他们起草一份基因产物主要功能的简短摘要,我们对其进行了编辑以产生“基因快照”,以保持一致性。这种方法在 3 个月内提交了 1800 个基因快照。我们讨论了这种策略对于从研究文献中捕获数据的其他数据库的一般用途。数据库网址:https://flybase.org/。
更新日期:2020-04-17
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