Habitat-Lite: A GSC case study based on free text terms for environmental metadata
Habitat-Lite: A GSC case study based on free text terms for environmental metadata
复制标题
DOI：
10.1089/omi.2008.0016
复制
发表时间：
2008-06-01
影响因子：
3.3
通讯作者：
Field, Dawn
中科院分区：
文献类型：
--
作者：
Hirschman, Lynette;Clark, Cheryl;Field, Dawn
迫切需要捕获数量迅速增长的基因组、宏基因组和相关序列（如16 S核糖体基因）的元数据。这一需求是基因组标准协会（GSC）的主要关注点，而栖息地是拟议的“基因组序列最小信息”（MIGS）规范中的关键元数据描述符。这里描述的工作的目标是提供一个轻量级的，易于使用的（小）的术语集（“historat-Lite”），捕获有关栖息地的高层次信息，同时保留映射到最近推出的环境本体（EnvO）。我们构建MITRAT-Lite的动机是满足多个用户的需求，例如管理这些数据的注释者，托管数据的数据库提供商，以及需要在比较分析中搜索和使用这些数据的生物学家和生物信息学家。在这里，我们报告了一个案例研究的基础上半自动识别的术语从GenBank和黄金。我们估计，在最初版本的Repeat-Lite中的术语将提供有用的标签，超过60%的类型的信息中发现的GenBank隔离源字段，并在黄金栖息地字段中的85%左右的条款。我们提出了一个修订版的EnvO环境本体内定义的环境精简版，通过一个新的类别，EnvO-Lite-GSC。我们邀请社区对其进一步发展的反馈，以提供一个最低限度的术语列表，以获取高层次的栖息地信息，并提供未来研究所需的分类箱。
There is an urgent need to capture metadata on the rapidly growing number of genomic, metagenomic and related sequences, such as 16S ribosomal genes. This need is a major focus within the Genomic Standards Consortium (GSC), and Habitat is a key metadata descriptor in the proposed "Minimum Information about a Genome Sequence" (MIGS) specification. The goal of the work described here is to provide a light-weight, easy-to-use (small) set of terms ("Habitat-Lite") that captures high-level information about habitat while preserving a mapping to the recently launched Environment Ontology (EnvO). Our motivation for building Habitat-Lite is to meet the needs of multiple users, such as annotators curating these data, database providers hosting the data, and biologists and bioinformaticians alike who need to search and employ such data in comparative analyses. Here, we report a case study based on semiautomated identification of terms from GenBank and GOLD. We estimate that the terms in the initial version of Habitat-Lite would provide useful labels for over 60% of the kinds of information found in the GenBank isolation_source field, and around 85% of the terms in the GOLD habitat field. We present a revised version of Habitat-Lite defined within the EnvO Environmental Ontology through a new category, EnvO-Lite-GSC. We invite the community's feedback on its further development to provide a minimum list of terms to capture high-level habitat information and to provide classification bins needed for future studies.