{"title":"GEM: Genome Editing Meta-database, a dataset of genome editing related metadata systematically extracted from PubMed literatures","authors":"Takayuki Suzuki , Hidemasa Bono","doi":"10.1016/j.ggedit.2022.100024","DOIUrl":null,"url":null,"abstract":"<div><p>Genome editing is a widely used tool for making precise genomic changes. However, no specialized databases which are sufficiently comprehensive are available with consolidated data on genome editing. Therefore, we have developed a genome editing meta-database (GEM, web interface: https://bonohu.hiroshima-u.ac.jp/gem/) that aims to collect an exhaustive dataset of metadata related to genome editing. The GEM is systematically extracted via specialized text-mining from PubMed and PubMed Central (PMC) literatures that contain experiments involving the use of the seven types of genome editing tools. We constructed a dataset consisting of 50,162 entries of metadata based on 15,952 studies with 1,088 species that users can search and retrieve graphically in the GEM web interface. GEM, therefore, allows bioscientists to easily obtain information about genome editing and apply it to their respective research.</p></div>","PeriodicalId":73137,"journal":{"name":"Gene and genome editing","volume":"5 ","pages":"Article 100024"},"PeriodicalIF":0.0000,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Gene and genome editing","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2666388022000144","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0
Abstract
Genome editing is a widely used tool for making precise genomic changes. However, no specialized databases which are sufficiently comprehensive are available with consolidated data on genome editing. Therefore, we have developed a genome editing meta-database (GEM, web interface: https://bonohu.hiroshima-u.ac.jp/gem/) that aims to collect an exhaustive dataset of metadata related to genome editing. The GEM is systematically extracted via specialized text-mining from PubMed and PubMed Central (PMC) literatures that contain experiments involving the use of the seven types of genome editing tools. We constructed a dataset consisting of 50,162 entries of metadata based on 15,952 studies with 1,088 species that users can search and retrieve graphically in the GEM web interface. GEM, therefore, allows bioscientists to easily obtain information about genome editing and apply it to their respective research.
GEM:Genome Editing Meta database，一个从PubMed文献中系统提取的基因组编辑相关元数据的数据集
基因组编辑是一种广泛使用的工具，用于进行精确的基因组改变。然而，没有足够全面的专门数据库可以获得关于基因组编辑的综合数据。因此，我们开发了一个基因组编辑元数据库(GEM, web界面:https://bonohu.hiroshima-u.ac.jp/gem/)，旨在收集与基因组编辑相关的元数据的详尽数据集。GEM通过专门的文本挖掘从PubMed和PubMed Central (PMC)文献中系统地提取，这些文献包含涉及使用七种基因组编辑工具的实验。我们构建了一个包含50,162个元数据条目的数据集，该数据集基于15,952项研究，涉及1,088个物种，用户可以在GEM web界面上以图形方式搜索和检索。因此，GEM使生物科学家能够轻松获取有关基因组编辑的信息，并将其应用于各自的研究。
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