A bioinformatics analysis of the cell line nomenclature
A bioinformatics analysis of the cell line nomenclature
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DOI：
10.1093/bioinformatics/btn502
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发表时间：
2008-12-01
期刊：
影响因子：
5.8
通讯作者：
States, David J.
中科院分区：
文献类型：
--
作者：
Sarntivijai, Sirarat;Ade, Alexander S.;States, David J.
动机：细胞系广泛用于生物医学研究，但描述细胞系的命名尚未标准化。这些问题既是语言问题，也是实验问题。已发表的文献中出现了许多模糊的细胞系名称。同一细胞系的用户可能以不同的方式引用它，并且细胞系可能在用户不知情的情况下发生突变或被污染。作为使这种命名合理化的第一步，我们创建了一个细胞系知识库（CLKB），其中包含体外培养细胞系的名称和描述性数据的结构良好的集合。这项工作的目标是：（i）帮助用户从生物医学文本中提取有用的信息，（ii）强调生物医学研究中细胞系名称标准化的重要性。该CLKB包含从ATCC、Hyper CLDB和MeSH编译的细胞系名称的广泛集合。除了名称之外，知识库还指定了细胞系之间的关系。我们分析了生物医学文本中细胞系名称的使用。问题包括名称含糊不清，名称使用的多态性以及一些细胞系名称也是常见的英语单词。语言模式与细胞系名称的发生进行了分析。应用这些模式来查找文献中的其他细胞系名称，只能识别出少量的其他名称。微阵列基因表达研究的注释被用作测试案例。CLKB有助于不同细胞系的数据探索和比较，以支持临床和实验研究。
Motivation: Cell lines are used extensively in biomedical research, but the nomenclature describing cell lines has not been standardized. The problems are both linguistic and experimental. Many ambiguous cell line names appear in the published literature. Users of the same cell line may refer to it in different ways, and cell lines may mutate or become contaminated without the knowledge of the user. As a first step towards rationalizing this nomenclature, we created a cell line knowledgebase (CLKB) with a well-structured collection of names and descriptive data for cell lines cultured in vitro. The objectives of this work are: (i) to assist users in extracting useful information from biomedical text and (ii) to highlight the importance of standardizing cell line names in biomedical research. This CLKB contains a broad collection of cell line names compiled from ATCC, Hyper CLDB and MeSH. In addition to names, the knowledgebase specifies relationships between cell lines. We analyze the use of cell line names in biomedical text. Issues include ambiguous names, polymorphisms in the use of names and the fact that some cell line names are also common English words. Linguistic patterns associated with the occurrence of cell line names are analyzed. Applying these patterns to find additional cell line names in the literature identifies only a small number of additional names. Annotation of microarray gene expression studies is used as a test case. The CLKB facilitates data exploration and comparison of different cell lines in support of clinical and experimental research.