Wilkinson Mark D
Department of Medical Genetics, University of British Columbia and PI Bioinformatics, Heart + Lung Institute at St. Paul's Hospital, Vancouver, BC, Canada.
Methods Mol Biol. 2012;856:489-511. doi: 10.1007/978-1-61779-585-5_20.
The emergence of genomics tools for the evolutionary and comparative biology community led to a rapid explosion in the number of online resources targeted at this specialized community, including Web-based comparative genomics software, such as the Artemis Comparison Tool (WebACT); databases, such as PaleoDB, Global Biodiversity Information Facility, and TreeBase; and knowledge frameworks, such as the Evolution Ontology. Unfortunately, these providers are largely independent of one another and therefore the individual resources do not share any centralized plan for how the data or tools would or should be provided. As a result, there are a myriad of often incompatible technologies and frameworks being used by this community of providers. In this chapter, we explore approaches to online resource publication, both those already in use by the community, as well as new and emergent frameworks and standards. Exploration of the strengths and weaknesses of each approach, together with a brief exploration of the philosophy or informatics theory behind the varying approaches, will hopefully help readers as they navigate this data space. The discussion is constructed such that it lays the groundwork for exploration of a new global standard for data and knowledge representation--"The Semantic Web"--that holds promise of providing solutions to many of the complexities users face in their attempts to discover and integrate biodiversity data, and examples are provided.
面向进化生物学和比较生物学领域的基因组学工具的出现，使得针对这一专业领域的在线资源数量迅速激增，这些资源包括基于网络的比较基因组学软件，如阿耳忒弥斯比较工具（WebACT）；数据库，如古生物学数据库（PaleoDB）、全球生物多样性信息设施（Global Biodiversity Information Facility）和树库（TreeBase）；以及知识框架，如进化本体（Evolution Ontology）。不幸的是，这些资源提供者大多相互独立，因此各个资源之间没有关于如何提供数据或工具的任何统一计划。结果，这个资源提供者群体使用着大量通常互不兼容的技术和框架。在本章中，我们探讨在线资源发布的方法，包括该领域已经在使用的方法，以及新出现的框架和标准。探讨每种方法的优缺点，并简要探究不同方法背后的理念或信息学理论，希望能帮助读者在这个数据空间中导航。讨论内容的构建旨在为探索一种新的数据和知识表示全球标准——“语义网”——奠定基础，该标准有望为用户在发现和整合生物多样性数据时面临的许多复杂性问题提供解决方案，并给出了相关示例。
