Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples.
Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples.
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DOI：
10.3897/zookeys.50.538
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发表时间：
2010-06-30
期刊：
影响因子：
1.3
通讯作者：
Erwin T
中科院分区：
文献类型：
--
作者：
Penev L;Agosti D;Georgiev T;Catapano T;Miller J;Blagoderov V;Roberts D;Smith VS;Brake I;Ryrcroft S;Scott B;Johnson NF;Morris RA;Sautter G;Chavan V;Robertson T;Remsen D;Stoev P;Parr C;Knapp S;Kress WJ;Thompson CF;Erwin T
本期 ZooKeys 上发表的四篇范例论文概述并说明了语义标记的概念及其对分类学论文进行语义增强的潜力。这四篇论文以不同的方式创建：（i）用 Microsoft Word 编写并作为无标签手稿提交（doi：10.3897/zookeys.50.504）； (ii) 从 Scratchpad 生成并作为 XML 标记的手稿提交（doi：10.3897/zookeys.50.505 和 doi：10.3897/zookeys.50.506）； (iii) 从作者的数据库（doi：10.3897/zookeys.50.485）生成并作为 XML 标记的手稿提交。 XML 标记和语义增强是在 ZooKeys 的编辑过程中使用专门为此目的设计的 Pensoft 标记工具 (PMT) 实现的。使用的 XML 模式是 TaxPub，它是美国国家医学图书馆期刊归档和交换标签套件 (NLM) 的文档类型定义 (DTD) 的扩展。在ZooKeys编辑工作流程中测试并实施了以下内容标记、布局、发布和传播的创新方法：（1）基于TaxPub的高度自动化、细粒度的XML标记； (2) 论文的最终 XML 输出根据 NLM DTD 进行验证，以便在 PubMedCentral 中存档； （3）通过XMP（可扩展元数据平台）嵌入PDF中的书目元数据； （4）出版后上传至生物多样性遗产图书馆（BHL）的PDF； (5) 通过 XML 向 Plazi 提供分类单元处理； (6) 论文的语义增强 HTML 版本，包含大量内部和外部链接和链接，例如： (i) 文本中主要标签元素的可视化（例如，分类单元名称、分类单元处理、地点等）； (ii) 论文章节、引文、参考文献、表格和图形之间的内部交叉链接； (iii) 整篇论文中或单独的分类单元处理中列出的地点的绘图； (v) 通过 Pensoft Taxon Profile (PTP) 自动标记、动态映射和链接到大型国际数据库服务和索引器的分类单元名称，例如全球生物多样性信息设施 (GBIF)、国家生物技术信息中心 (NCBI)、生命条形码 (BOLD)、生命百科全书 (EOL)、ZooBank、维基百科、维基物种、维基媒体等； (vi) 自动标记并链接到 NCBI 的 GenBank 登录号； (vii) 分类单元名称与 PubMed、Google Scholar、生物多样性遗产图书馆和其他来源参考文献的外部链接。随着工作示例的推出，ZooKeys 成为第一个提供完整的基于 XML 的编辑、出版和传播工作流程的分类学期刊，该工作流程作为常规且经济高效的实践实施。预计基于 XML 的工作流程也将很快通过 ZooKeys 即将出版的合作伙伴期刊 PhytoKeys 在植物学中实现。语义标记和增强预计将大大扩展和加速分类信息的发布、传播和使用方式。
The concept of semantic tagging and its potential for semantic enhancements to taxonomic papers is outlined and illustrated by four exemplar papers published in the present issue of ZooKeys. The four papers were created in different ways: (i) written in Microsoft Word and submitted as non-tagged manuscript (doi: 10.3897/zookeys.50.504); (ii) generated from Scratchpads and submitted as XML-tagged manuscripts (doi: 10.3897/zookeys.50.505 and doi: 10.3897/zookeys.50.506); (iii) generated from an author’s database (doi: 10.3897/zookeys.50.485) and submitted as XML-tagged manuscript. XML tagging and semantic enhancements were implemented during the editorial process of ZooKeys using the Pensoft Mark Up Tool (PMT), specially designed for this purpose. The XML schema used was TaxPub, an extension to the Document Type Definitions (DTD) of the US National Library of Medicine Journal Archiving and Interchange Tag Suite (NLM). The following innovative methods of tagging, layout, publishing and disseminating the content were tested and implemented within the ZooKeys editorial workflow: (1) highly automated, fine-grained XML tagging based on TaxPub; (2) final XML output of the paper validated against the NLM DTD for archiving in PubMedCentral; (3) bibliographic metadata embedded in the PDF through XMP (Extensible Metadata Platform); (4) PDF uploaded after publication to the Biodiversity Heritage Library (BHL); (5) taxon treatments supplied through XML to Plazi; (6) semantically enhanced HTML version of the paper encompassing numerous internal and external links and linkouts, such as: (i) vizualisation of main tag elements within the text (e.g., taxon names, taxon treatments, localities, etc.); (ii) internal cross-linking between paper sections, citations, references, tables, and figures; (iii) mapping of localities listed in the whole paper or within separate taxon treatments; (v) taxon names autotagged, dynamically mapped and linked through the Pensoft Taxon Profile (PTP) to large international database services and indexers such as Global Biodiversity Information Facility (GBIF), National Center for Biotechnology Information (NCBI), Barcode of Life (BOLD), Encyclopedia of Life (EOL), ZooBank, Wikipedia, Wikispecies, Wikimedia, and others; (vi) GenBank accession numbers autotagged and linked to NCBI; (vii) external links of taxon names to references in PubMed, Google Scholar, Biodiversity Heritage Library and other sources. With the launching of the working example, ZooKeys becomes the first taxonomic journal to provide a complete XML-based editorial, publication and dissemination workflow implemented as a routine and cost-efficient practice. It is anticipated that XML-based workflow will also soon be implemented in botany through PhytoKeys, a forthcoming partner journal of ZooKeys. The semantic markup and enhancements are expected to greatly extend and accelerate the way taxonomic information is published, disseminated and used.
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影响因子：
2.5
作者：
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