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Co-occurrence of Cell Lines, Basal Media and Supplementation in the Biomedical Research Literature
Journal of Data and Information Science Pub Date : 2020-07-03 , DOI: 10.2478/jdis-2020-0016
Jessica Cox 1 , Darin McBeath 1 , Corey Harper 1 , Ron Daniel 1
Affiliation  

Abstract Purpose The use of in vitro cell culture and experimentation is a cornerstone of biomedical research, however, more attention has recently been given to the potential consequences of using such artificial basal medias and undefined supplements. As a first step towards better understanding and measuring the impact these systems have on experimental results, we use text mining to capture typical research practices and trends around cell culture. Design/methodology/approach To measure the scale of in vitro cell culture use, we have analyzed a corpus of 94,695 research articles that appear in biomedical research journals published in ScienceDirect from 2000–2018. Central to our investigation is the observation that studies using cell culture describe conditions using the typical sentence structure of cell line, basal media, and supplemented compounds. Here we tag our corpus with a curated list of basal medias and the Cellosaurus ontology using the Aho-Corasick algorithm. We also processed the corpus with Stanford CoreNLP to find nouns that follow the basal media, in an attempt to identify supplements used. Findings Interestingly, we find that researchers frequently use DMEM even if a cell line's vendor recommends less concentrated media. We see long-tailed distributions for the usage of media and cell lines, with DMEM and RPMI dominating the media, and HEK293, HEK293T, and HeLa dominating cell lines used. Research limitations Our analysis was restricted to documents in ScienceDirect, and our text mining method achieved high recall but low precision and mandated manual inspection of many tokens. Practical implications Our findings document current cell culture practices in the biomedical research community, which can be used as a resource for future experimental design. Originality/value No other work has taken a text mining approach to surveying cell culture practices in biomedical research.

中文翻译:

生物医学研究文献中细胞系,基础培养基和补充剂的同时存在

摘要目的体外细胞培养和实验的使用是生物医学研究的基石,然而,近来,人们更加关注使用这种人工基础培养基和不确定的补充剂的潜在后果。作为更好地理解和衡量这些系统对实验结果的影响的第一步,我们使用文本挖掘来捕获典型的细胞培养研究实践和趋势。设计/方法/方法为了测量体外细胞培养的使用规模,我们分析了94,695篇研究论文的语料库,这些论文出现在2000-2018年间在ScienceDirect上发表的生物医学研究期刊中。我们调查的核心是观察到,使用细胞培养进行的研究使用细胞系,基础培养基,和补充的化合物。在这里,我们使用Aho-Corasick算法使用基础媒体和Cellosaurus本体的精选列表来标记我们的语料库。我们还使用Stanford CoreNLP处理了语料库,以找到遵循基础媒体的名词,以尝试识别所使用的补语。发现有趣的是,我们发现研究人员经常使用DMEM,即使细胞系的供应商建议使用不太集中的培养基。我们看到培养基和细胞系使用的长尾分布,其中以DMEM和RPMI为主,而以HEK293,HEK293T和HeLa为主的细胞系。研究局限性我们的分析仅限于ScienceDirect中的文档,并且我们的文本挖掘方法实现了较高的查全率,但精度较低,并要求对许多令牌进行手动检查。实际意义我们的发现记录了生物医学研究界当前的细胞培养实践,可以用作未来实验设计的资源。原创性/价值没有其他工作采用文本挖掘方法来调查生物医学研究中的细胞培养实践。
更新日期:2020-07-03
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