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

Kottmann, Renzo; Gray, Tanya; Murphy, Sean D.; Kagan, Leonid; Kravitz, Saul; Lombardot, Thierry; Field, Dawn; Glöckner, Frank Oliver

doi:10.1089/omi.2008.0a10

Cited by 61 publications

(67 citation statements)

References 26 publications

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“…Furthermore, the huge amounts of data produced should be cataloged using detailed descriptors, like what is being created with the MIGS/MIMS initiative from the Genomics Standards Consortium. This initiative tries to establish guidelines to provide Minimum Information about a Metagenome Sequence (Kottmann et al, 2008), since biological interpretation of different datasets in a comparative manner is dependent on the quantity and quality of the contextual information.…”

Section: Discussionmentioning

confidence: 99%

Environmental microbiology through the lens of high-throughput DNA sequencing: Synopsis of current platforms and bioinformatics approaches

Logares

Haverkamp

Kumar

et al. 2012

Journal of Microbiological Methods

118

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Section: Discussionmentioning

confidence: 99%

Environmental microbiology through the lens of high-throughput DNA sequencing: Synopsis of current platforms and bioinformatics approaches

Logares

Haverkamp

Kumar

et al. 2012

Journal of Microbiological Methods

118

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“…The new version of Habitat-Lite will be supported in GCDML (Kottmann et al, 2008 These results indicate that it should be possible to produce a list of terms with good highlevel coverage for Habitat-Lite. We accept that candidate Habitat-Lite terms provide only very high-level information and that these terms may be an amalgamation of terms found in different branches of a future ontologies, or even among different orthogonal ontologies (e.g., for "organism-associated").…”

mentioning

confidence: 88%

“…This terms list will then be implemented in GCDML (Kottmann et al 2008) and used in the first instance to fill the "Habitat" field of the MIGS compliant Genome Catalogue database (http://gensc.org).…”

Section: Towards a Minimum Information List Of Habitat Terms For Use mentioning

confidence: 99%

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

Hirschman

Clark

Cohen

et al. 2008

OMICS: A Journal of Integrative Biology

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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-touse (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 HabitatLite 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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“…While there are several Laboratory Information Management Systems (LIMS) implementations available, these tools require development of semantic interoperable biodefense systems which reuse existing biomedical, metagenomic, and geographical ontologies and handle legacy data. [49][50][51] These efforts can reduce the current confusion and the lack of interoperability resulting from multiple BIOINFORMATICS FOR BIODEFENSE: CHALLENGES AND OPPORTUNITIES disjoint databases. Several obvious and dependent, or conditional, relationships that exist between attributes and elements can be reused and redefined from open source projects to accommodate integration while keeping biodefense-oriented implementations.…”

Section: Opportunitiesmentioning

confidence: 99%

Bioinformatics for Biodefense: Challenges and Opportunities

Valdivia-Granda¹

2010

Biosecurity and Bioterrorism: Biodefense Strategy, Practice, an

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The intentional release of traditional or combinatorial bioweapons remains one of the most important challenges that will continue to shape homeland security. The misuse of dual-use and how-to methods and techniques in the fields of molecular, synthetic, and computational biology can lessen the technical barriers for launching attacks, even for small groups or individuals. Bioinformatics is guiding the implementation of several biodefense countermeasures. However, existing algorithms have not effectively translated available pathogen genomic data into standardized diagnostics, rational vaccine development, or broad spectrum therapeutics. Despite its potential, bioinformatics has a limited impact on forensic and intelligence operations. More than 12 biodefense databases and information exchange architectures lack interoperability and a common layer that restricts scalability and the development of biodefense enterprises. Therefore, in order to use next-generation genome sequencing for medical intelligence, forensic operations, biothreat awareness, and mitigation, the attention has to be redirected toward the development of computational biology applications. This article debates some of the challenges that the bioinformatics field confronts in terms of biodefense problems and proposes potential opportunities to use pathogen genomic data. Issues related to the analysis of pathogen genomes and emerging methods including genomic barcoding, active curation, and knowledge management and their impact on intelligence, forensics, and policymaking are discussed.

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

Cited by 61 publications

References 26 publications

Environmental microbiology through the lens of high-throughput DNA sequencing: Synopsis of current platforms and bioinformatics approaches

Environmental microbiology through the lens of high-throughput DNA sequencing: Synopsis of current platforms and bioinformatics approaches

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

Bioinformatics for Biodefense: Challenges and Opportunities

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