Research Article
Open access
Published Online: 19 June 2008

A Standard MIGS/MIMS Compliant XML Schema: Toward the Development of the Genomic Contextual Data Markup Language (GCDML)

Publication: OMICS A Journal of Integrative Biology
Volume 12, Issue Number 2

Abstract

The Genomic Contextual Data Markup Language (GCDML) is a core project of the Genomic Standards Consortium (GSC) that implements the “Minimum Information about a Genome Sequence” (MIGS) specification and its extension, the “Minimum Information about a Metagenome Sequence” (MIMS). GCDML is an XML Schema for generating MIGS/MIMS compliant reports for data entry, exchange, and storage. When mature, this sample-centric, strongly-typed schema will provide a diverse set of descriptors for describing the exact origin and processing of a biological sample, from sampling to sequencing, and subsequent analysis. Here we describe the need for such a project, outline design principles required to support the project, and make an open call for participation in defining the future content of GCDML. GCDML is freely available, and can be downloaded, along with documentation, from the GSC Web site (http://gensc.org).

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cover image OMICS: A Journal of Integrative Biology
OMICS A Journal of Integrative Biology
Volume 12Issue Number 2June 2008
Pages: 115 - 121
PubMed: 18479204

History

Published online: 19 June 2008
Published in print: June 2008
Published ahead of print: 14 May 2008

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Renzo Kottmann
Microbial Genomics Group, Max Planck Institute for Marine Microbiology and Jacobs University Bremen, 28359 Bremen, Germany.
Tanya Gray
NERC Centre for Ecology and Hydrology, Mansfield Road, Oxford, Oxfordshire, United Kingdom.
Sean Murphy
J. Craig Venter Institute, Rockville Maryland.
Leonid Kagan
J. Craig Venter Institute, Rockville Maryland.
Saul Kravitz
J. Craig Venter Institute, Rockville Maryland.
Thierry Lombardot
Microbial Genomics Group, Max Planck Institute for Marine Microbiology and Jacobs University Bremen, 28359 Bremen, Germany.
Dawn Field
NERC Centre for Ecology and Hydrology, Mansfield Road, Oxford, Oxfordshire, United Kingdom.
Frank Oliver Glöckner
Microbial Genomics Group, Max Planck Institute for Marine Microbiology and Jacobs University Bremen, 28359 Bremen, Germany.
and the Genomic Standards Consortium

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