鲁玛基因:从生物医学研究出版物的支持材料中大量挖掘基因组
Daniel J B Clarke1, Giacomo B Marino1, Eden Z Deng1
1Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
Communications biology
|April 20, 2024
概括
鲁玛基因使得生物医学研究中的数百万个基因组可以被搜索和重复使用. 这个工具解锁了以前无法访问的数据,用于高级分析和发现生物关系.
科学领域:
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
- 基因组学就是基因组学.
背景情况:
- 生物医学研究论文往往在补充表中包含有价值的基因组.
- 这些基因组通常无法用于大规模的搜索和重复使用.
- 发表的生物学数据的很大一部分仍然被埋藏和未得到充分利用.
研究的目的:
- 从生物医学文献中开发一个可搜索的哺乳动物基因组存储库.
- 通过使用已发表的基因组来实现新形式的数据分析和发现.
- 为访问和重用以前无法访问的生物数据集提供一个平台.
主要方法:
- 爬行PubMed中央识别和提取研究文章中的基因组.
- 开发Rummagene服务器来托管和服务数十万个基因组.
- 实施丰富分析,自由文本和表标题的搜索功能.
主要成果:
- 从5,448,589个扫描文章中成功识别出121,237篇文章,其中包含642,389个基因组.
- 证明了Rummagene在转录因子和激酶丰富分析中的实用性.
- 展示了通过相似性分析预测基因功能和发现新生物学关系的能力.
结论:
- 鲁玛基因显著提高了已公布的基因组数据的可访问性和可重复使用性.
- 该平台促进了先进的分析,包括基因功能预测和关系发现.
- Rummagene为研究界解锁了以前无法访问的生物医学数据集的庞大集合.
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