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

Area of Science:

• Genomics and Bioinformatics
• Environmental Science
• Data Curation

Background:

• Growing genomic and metagenomic data require standardized metadata.
• The Genomic Standards Consortium (GSC) focuses on metadata standards like Minimum Information about a Genome Sequence (MIGS).
• Habitat is a crucial descriptor within MIGS for genomic data.

Purpose of the Study:

• To develop a lightweight, user-friendly metadata term set (Habitat-Lite) for high-level habitat information.
• To ensure Habitat-Lite maps to the Environment Ontology (EnvO) for interoperability.
• To meet the needs of data annotators, database providers, and researchers for searching and analyzing genomic data.

Main Methods:

• Semiautomated identification of habitat terms from GenBank and GOLD databases.
• Development of Habitat-Lite as a simplified metadata descriptor.
• Integration of Habitat-Lite within the EnvO framework as EnvO-Lite-GSC.

Main Results:

• Initial Habitat-Lite terms effectively label over 60% of GenBank isolation_source fields.
• Habitat-Lite terms cover approximately 85% of GOLD habitat fields.
• A revised Habitat-Lite is presented, integrated into EnvO as EnvO-Lite-GSC.

Conclusions:

• Habitat-Lite provides a valuable, high-level habitat metadata standard for genomic sequences.
• The EnvO-Lite-GSC category enhances the utility of EnvO for genomic data.
• Community feedback is invited for further refinement of Habitat-Lite for future studies.