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OMeta: an ontology-based, data-driven metadata tracking system.

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PubMed ID: 30612540

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Singh I, Kuscuoglu M, Harkins DM, Sutton G, Fouts DE, Nelson KE

BMC Bioinformatics. Jan 2019. doi: 10.1186/s12859-018-2580-9

COMMENT: Ometa is a data-driven web application designed for the management and tracking of contextual metadata (specimen, spatial-temporal, phenotypic characteristics) that facilitate the organization, administration, curation, sharing and consulting of data in microbial and metagenomic NGS-based OMICs studies.

A data-driven web application, OMeta, has been developed for use by researchers consisting of a browser-based interface, a command-line interface (CLI), and server-side components that provide an intuitive platform for configuring, capturing, viewing, and sharing metadata. Project and sample metadata can be set based on existing standards or based on projects goals. Recorded information includes details on the biological samples, procedures, protocols, and experimental technologies, etc. This information can be organized based on events, including sample collection, sample quantification, sequencing assay, and analysis results. OMeta enables configuration in various presentation types: checkbox, file, drop-box, ontology, and fields can be configured to use the National Center for Biomedical Ontology (NCBO), a biomedical ontology server.

OMeta has been used in important projects:

  • GSCID/GCID
  • JCVI Human Microbiome Project (HMP)
  • Data Processing and Coordinating Center (DPCC) of the NIAID Centers of Excellence for Influenza Research and Surveillance (CEIRS)

OMeta is an open source tool built on an open source infrastructure.

The OMeta project home page is: https://github.com/JCVenterInstitute/OMeta-Public

Contributor

Raquel Tobes