On expert curation and scalability: UniProtKB/Swiss-Prot as a case study.
On expert curation and scalability: UniProtKB/Swiss-Prot as a case study.
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DOI：
10.1093/bioinformatics/btx439
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发表时间：
2017-11-01
期刊：
影响因子：
--
通讯作者：
UniProt Consortium T
中科院分区：
文献类型：
--
作者：
Poux S;Arighi CN;Magrane M;Bateman A;Wei CH;Lu Z;Boutet E;Bye-A-Jee H;Famiglietti ML;Roechert B;UniProt Consortium T
生物知识库，如UniProtKB/Swiss-Prot，是日常科学研究的一个重要组成部分，它提供专家管理员从文献中提取的经过提炼、总结和可计算的知识。虽然知识库在科学界发挥着越来越重要的作用，但它们跟上生物医学文献增长的能力正在受到审查。使用UniProtKB/Swiss-Prot作为案例研究，我们通过多种文献分类方法解决了这一问题。在PubTator文本挖掘工具的帮助下，我们标记了10000多篇文章，以评估与策展相关的论文比例。我们首先表明，策展人阅读和评估的论文比他们策划的要多得多，测量策划出版物的数量不足以提供一个完整的画面，这一事实表明，每年有8000- 10000篇论文在UniProt策划，而策展人每年评估50000 - 70000篇论文。我们发现，PubMed中90%的论文超出了UniProt的范围，每年在PubMed中索引的论文中最多有2-3%与UniProt策展相关，而且，尽管表面上看，UniProt中的专家策展是可扩展的。UniProt可在http://www.uniprot.org/上免费获得。 补充数据可在Bioinformatics在线获得。
Biological knowledgebases, such as UniProtKB/Swiss-Prot, constitute an essential component of daily scientific research by offering distilled, summarized and computable knowledge extracted from the literature by expert curators. While knowledgebases play an increasingly important role in the scientific community, their ability to keep up with the growth of biomedical literature is under scrutiny. Using UniProtKB/Swiss-Prot as a case study, we address this concern via multiple literature triage approaches. With the assistance of the PubTator text-mining tool, we tagged more than 10 000 articles to assess the ratio of papers relevant for curation. We first show that curators read and evaluate many more papers than they curate, and that measuring the number of curated publications is insufficient to provide a complete picture as demonstrated by the fact that 8000–10 000 papers are curated in UniProt each year while curators evaluate 50 000–70 000 papers per year. We show that 90% of the papers in PubMed are out of the scope of UniProt, that a maximum of 2–3% of the papers indexed in PubMed each year are relevant for UniProt curation, and that, despite appearances, expert curation in UniProt is scalable. UniProt is freely available at http://www.uniprot.org/. Supplementary data are available at Bioinformatics online.
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影响因子：
14.9
作者：
Wei CH;Kao HY;Lu Z
通讯作者：
Lu Z
影响因子：
64.8
作者：
Cuylen S;Blaukopf C;Politi AZ;Müller-Reichert T;Neumann B;Poser I;Ellenberg J;Hyman AA;Gerlich DW
通讯作者：
Gerlich DW
影响因子：
7.7
作者：
Sobecki M;Mrouj K;Camasses A;Parisis N;Nicolas E;Llères D;Gerbe F;Prieto S;Krasinska L;David A;Eguren M;Birling MC;Urbach S;Hem S;Déjardin J;Malumbres M;Jay P;Dulic V;Lafontaine DLj;Feil R;Fisher D
通讯作者：
Fisher D
影响因子：
158.5
作者：
Sleiman, Patrick M. A.;Flory, James;Hakonarson, Hakon
通讯作者：
Hakonarson, Hakon
影响因子：
--
作者：
Bandrowski, Anita;Brush, Matthew;Vasilevsky, Nicole
通讯作者：
Vasilevsky, Nicole