Introducing Explorer of Taxon Concepts with a case study on spider measurement matrix building.
Introducing Explorer of Taxon Concepts with a case study on spider measurement matrix building.
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DOI：
10.1186/s12859-016-1352-7
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发表时间：
2016-11-17
影响因子：
3
通讯作者：
Koch NM
中科院分区：
文献类型：
--
作者：
Cui H;Xu D;Chong SS;Ramirez M;Rodenhausen T;Macklin JA;Ludäscher B;Morris RA;Soto EM;Koch NM
分类学描述传统上是用自然语言编写的，并以计算机无法直接使用的格式发布。探索分类概念（ETC）项目一直在开发一套基于网络的软件工具，将以电报风格发布的形态描述转换为可以重复使用和重新利用的字符数据。本文介绍了第一个半自动流水线，据我们所知，将形态描述转换为分类特征矩阵，以支持系统学和进化生物学研究。然后，我们演示和评估使用ETC输入创建-文本捕获-矩阵生成流水线从一组188蜘蛛形态描述中生成身体部位测量矩阵，并报告结果。从给定的蜘蛛分类出版物中，生成两个版本的输入（原始和标准化），并由ETC文本捕获和ETC矩阵生成工具使用。这些工具产生了两个相应的蜘蛛身体部位测量矩阵，并且发现来自归一化输入的矩阵与科学家共同作者手工策划的黄金标准矩阵更相似。原始描述中使用的特殊约定（例如，省略计量单位）是由于使用原始输入的性能较低。结果表明，描述文本的简单规范化大大提高了机器生成矩阵的质量，并减少了编辑工作。机器生成的矩阵还有助于确定黄金标准矩阵中的问题。ETC文本捕获和ETC矩阵生成是从蜘蛛分类描述中提取测量值的低障碍和有效工具，并且当描述是自包含的时更有效。使描述文本不那么独立的特殊约定对从生物多样性描述中自动提取数据提出了挑战，并阻碍了已发布知识的自动重用。将更新这些工具，以支持本案例研究中提出的新要求。本文的在线版本（doi：10.1186/s12859-016-1352-7）包含补充材料，可供授权用户使用。
Taxonomic descriptions are traditionally composed in natural language and published in a format that cannot be directly used by computers. The Exploring Taxon Concepts (ETC) project has been developing a set of web-based software tools that convert morphological descriptions published in telegraphic style to character data that can be reused and repurposed. This paper introduces the first semi-automated pipeline, to our knowledge, that converts morphological descriptions into taxon-character matrices to support systematics and evolutionary biology research. We then demonstrate and evaluate the use of the ETC Input Creation - Text Capture - Matrix Generation pipeline to generate body part measurement matrices from a set of 188 spider morphological descriptions and report the findings. From the given set of spider taxonomic publications, two versions of input (original and normalized) were generated and used by the ETC Text Capture and ETC Matrix Generation tools. The tools produced two corresponding spider body part measurement matrices, and the matrix from the normalized input was found to be much more similar to a gold standard matrix hand-curated by the scientist co-authors. Special conventions utilized in the original descriptions (e.g., the omission of measurement units) were attributed to the lower performance of using the original input. The results show that simple normalization of the description text greatly increased the quality of the machine-generated matrix and reduced edit effort. The machine-generated matrix also helped identify issues in the gold standard matrix. ETC Text Capture and ETC Matrix Generation are low-barrier and effective tools for extracting measurement values from spider taxonomic descriptions and are more effective when the descriptions are self-contained. Special conventions that make the description text less self-contained challenge automated extraction of data from biodiversity descriptions and hinder the automated reuse of the published knowledge. The tools will be updated to support new requirements revealed in this case study. The online version of this article (doi:10.1186/s12859-016-1352-7) contains supplementary material, which is available to authorized users.
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影响因子：
14.9
作者：
Blake JA;Bult CJ;Eppig JT;Kadin JA;Richardson JE;Mouse Genome Database Group
通讯作者：
Mouse Genome Database Group
影响因子：
14.9
作者：
Bowes JB;Snyder KA;Segerdell E;Gibb R;Jarabek C;Noumen E;Pollet N;Vize PD
通讯作者：
Vize PD
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：
0.9
作者：
Aisen, Santiago;Ramirez, Martin J.
通讯作者：
Ramirez, Martin J.
DOI：
10.1002/asi.21325
发表时间：
2010-06-01
影响因子：
--
作者：
Cui, Hong
通讯作者：
Cui, Hong