Protein name tagging guidelines: lessons learned.
Protein name tagging guidelines: lessons learned.
复制标题
蛋白质名称标记指南：经验教训。
DOI：
10.1002/cfg.452
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发表时间：
2005
影响因子：
--
通讯作者：
Wu, CH
中科院分区：
文献类型：
--
作者：
Mani, I;Hu, ZZ;Jang, SB;Samuel, K;Krause, M;Phillips, O;Wu, CH
关键词：
对从生物医学文献中提取信息的兴趣是由于需要加速创建结构化数据库，这些数据库代表有关特定对象（如蛋白质和基因）的最新科学知识。针对目前蛋白质名称标注缺乏标准定义的问题进行了研究。我们描述的经验教训，在制定一套准则，并提出了第一套编码器间的结果，被视为系统性能的上限。程序员面临的问题包括：（a）既可指基因又可指蛋白质的名称含糊不清;（B）很难获得长蛋白质名称的确切范围;以及（c）准则的复杂性。这些问题是通过两种方式解决的：（a）将标记靶标定义为文献中用于描述蛋白质或蛋白质相关或相关对象的蛋白质命名实体，例如结构域、途径、表达或基因，以及（B）使用两种类型的标记，蛋白质标记和长形式标记，当名称边界难以确定时，后者用于可选地扩展蛋白质标签的边界。在300篇MEDLINE摘要中，三个注释器之间的蛋白质标签编码器间一致性为0.868 F-测量。指南和注释数据集以及自动工具沿着可用于研究。
Interest in information extraction from the biomedical literature is motivated by the need to speed up the creation of structured databases representing the latest scientific knowledge about specific objects, such as proteins and genes. This paper addresses the issue of a lack of standard definition of the problem of protein name tagging. We describe the lessons learned in developing a set of guidelines and present the first set of inter-coder results, viewed as an upper bound on system performance. Problems coders face include: (a) the ambiguity of names that can refer to either genes or proteins; (b) the difficulty of getting the exact extents of long protein names; and (c) the complexity of the guidelines. These problems have been addressed in two ways: (a) defining the tagging targets as protein named entities used in the literature to describe proteins or protein-associated or -related objects, such as domains, pathways, expression or genes, and (b) using two types of tags, protein tags and long-form tags, with the latter being used to optionally extend the boundaries of the protein tag when the name boundary is difficult to determine. Inter-coder consistency across three annotators on protein tags on 300 MEDLINE abstracts is 0.868 F-measure. The guidelines and annotated datasets, along with automatic tools, are available for research use.
影响因子：
14.9
作者：
Wu, CH;Yeh, LSL;Barker, WC
通讯作者：
Barker, WC
影响因子：
3.1
作者：
Hu, ZZ;Mani, I;Wu, CH
通讯作者：
Wu, CH
影响因子：
5.8
作者：
Kim, J-D;Ohta, T.;Tsujii, J.
通讯作者：
Tsujii, J.