1. Главная
  2. Ресурсы
  3. Библиотечный поиск
Habitat-Lite: A GSCCase Study Based onFree Text Terms forEnvironmentalMetadata Lynette HirschmanCheryl ClarkKevin Bretonnel Cohen2008 год

Habitat-Lite: A GSC Case Study Based on Free Text Terms for Environmental Metadata
статья из журнала

Полный текстСтраница публикацииПубликация в OpenAlex
Аннотация: 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.
Год издания: 2008
Авторы: Lynette Hirschman, Cheryl Clark, Kevin Bretonnel Cohen, Scott Mardis, Joanne Luciano, Renzo Kottmann, James H. Cole, Victor Markowitz, Nikos C. Kyrpides, Norman Morrison, Lynn M. Schriml, Dawn Field
Издательство: Mary Ann Liebert, Inc.
Источник: OMICS A Journal of Integrative Biology
Ключевые слова: Environmental DNA in Biodiversity Studies, Genomics and Phylogenetic Studies, Microbial Community Ecology and Physiology
Другие ссылки: OMICS A Journal of Integrative Biology (HTML)
University of North Texas Digital Library (University of North Texas) (PDF)
University of North Texas Digital Library (University of North Texas) (HTML)
eScholarship (California Digital Library) (PDF)
eScholarship (California Digital Library) (HTML)
MPG.PuRe (Max Planck Society) (PDF)
MPG.PuRe (Max Planck Society) (HTML)
OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (HTML)
PubMed (HTML)