Habitat-Lite: A GSC case study based on free text terms for environmental metadata

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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 ... continued below

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Kyrpides, Nikos; Hirschman, Lynette; Clark, Cheryl; Cohen, K. Bretonnel; Mardis, Scott; Luciano, Joanne et al. April 1, 2008.

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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 semi-automated 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 and invite the community's feedback on its further development in order to provide a minimum list of terms to capture high-level habitat information and to provide classification bins needed for future studies.

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  • Journal Name: OMICS A Journal of Integrative Biology

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  • Report No.: LBNL-282E
  • Grant Number: DE-AC02-05CH11231
  • Office of Scientific & Technical Information Report Number: 928961
  • Archival Resource Key: ark:/67531/metadc899503

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  • April 1, 2008

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  • Sept. 27, 2016, 1:39 a.m.

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  • Oct. 3, 2016, 4:19 p.m.

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Kyrpides, Nikos; Hirschman, Lynette; Clark, Cheryl; Cohen, K. Bretonnel; Mardis, Scott; Luciano, Joanne et al. Habitat-Lite: A GSC case study based on free text terms for environmental metadata, article, April 1, 2008; Berkeley, California. (digital.library.unt.edu/ark:/67531/metadc899503/: accessed October 20, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.