On the reproducibility of science: unique identification of research resources in the biomedical literature.
On the reproducibility of science: unique identification of research resources in the biomedical literature.
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作者：
Vasilevsky NA;Brush MH;Paddock H;Ponting L;Tripathy SJ;Larocca GM;Haendel MA
科学的可重复性一直是许多新闻报道的重点，有许多举措可以帮助解决这个问题。我们认为，一个贡献者只是缺乏特异性，这是必要的，使足够的研究重现性。特别是，无法唯一地识别研究资源，如抗体和模式生物，使得即使科学在其他方面是合理的，也很难或不可能复制实验。为了更好地了解这个问题的严重性，我们设计了一个实验，以确定在生物医学文献中的研究资源的“可识别性”。我们评估了神经科学，发育生物学，免疫学，细胞和分子生物学以及普通生物学领域的最新期刊文章，这些文章是根据期刊，出版商和实验方法报告指南的多种影响因素随机选择的。我们试图唯一地鉴定模型生物体（小鼠、大鼠、斑马鱼、蠕虫、苍蝇和酵母）、抗体、敲减试剂（吗啉代或RNAi）、构建体和细胞系。制定了具体的标准来确定资源是否是唯一可识别的，包括检查相关的储存库（如模式生物数据库和抗体登记）以及供应商网站。实验结果表明，无论领域、期刊影响因子或报告要求如何，54%的资源在出版物中不是唯一可识别的。例如，在许多情况下，无法鉴定进行实验的生物菌株或使用的抗体。我们的研究结果表明，可识别性是一个严重的问题的再现性。根据这些结果，我们向作者、审稿人、期刊编辑、供应商和出版商提供建议。科学的效率和可重复性取决于对当今科学中这一重大问题的研究范围的改进。
Scientific reproducibility has been at the forefront of many news stories and there exist numerous initiatives to help address this problem. We posit that a contributor is simply a lack of specificity that is required to enable adequate research reproducibility. In particular, the inability to uniquely identify research resources, such as antibodies and model organisms, makes it difficult or impossible to reproduce experiments even where the science is otherwise sound. In order to better understand the magnitude of this problem, we designed an experiment to ascertain the “identifiability” of research resources in the biomedical literature. We evaluated recent journal articles in the fields of Neuroscience, Developmental Biology, Immunology, Cell and Molecular Biology and General Biology, selected randomly based on a diversity of impact factors for the journals, publishers, and experimental method reporting guidelines. We attempted to uniquely identify model organisms (mouse, rat, zebrafish, worm, fly and yeast), antibodies, knockdown reagents (morpholinos or RNAi), constructs, and cell lines. Specific criteria were developed to determine if a resource was uniquely identifiable, and included examining relevant repositories (such as model organism databases, and the Antibody Registry), as well as vendor sites. The results of this experiment show that 54% of resources are not uniquely identifiable in publications, regardless of domain, journal impact factor, or reporting requirements. For example, in many cases the organism strain in which the experiment was performed or antibody that was used could not be identified. Our results show that identifiability is a serious problem for reproducibility. Based on these results, we provide recommendations to authors, reviewers, journal editors, vendors, and publishers. Scientific efficiency and reproducibility depend upon a research-wide improvement of this substantial problem in science today.
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影响因子：
3.7
作者：
Phuchareon J;Ohta Y;Woo JM;Eisele DW;Tetsu O
通讯作者：
Tetsu O
DOI：
10.1093/database/bat015
发表时间：
2013
期刊：
Database : the journal of biological databases and curation
影响因子：
--
作者：
Laulederkind SJ;Liu W;Smith JR;Hayman GT;Wang SJ;Nigam R;Petri V;Lowry TF;de Pons J;Dwinell MR;Shimoyama M
通讯作者：
Shimoyama M
影响因子：
14.9
作者：
Bradford Y;Conlin T;Dunn N;Fashena D;Frazer K;Howe DG;Knight J;Mani P;Martin R;Moxon SA;Paddock H;Pich C;Ramachandran S;Ruef BJ;Ruzicka L;Bauer Schaper H;Schaper K;Shao X;Singer A;Sprague J;Sprunger B;Van Slyke C;Westerfield M
通讯作者：
Westerfield M
影响因子：
1.9
作者：
Ciccarese P;Ocana M;Clark T
通讯作者：
Clark T
影响因子：
9.8
作者：
Haendel MA;Vasilevsky NA;Wirz JA
通讯作者：
Wirz JA