About: SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models

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About: SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models
Creator	Aziz, R Devoid, S Disz, T Edwards, R Henry, C
Source	PMC
abstract	The remarkable advance in sequencing technology and the rising interest in medical and environmental microbiology, biotechnology, and synthetic biology resulted in a deluge of published microbial genomes. Yet, genome annotation, comparison, and modeling remain a major bottleneck to the translation of sequence information into biological knowledge, hence computational analysis tools are continuously being developed for rapid genome annotation and interpretation. Among the earliest, most comprehensive resources for prokaryotic genome analysis, the SEED project, initiated in 2003 as an integration of genomic data and analysis tools, now contains >5,000 complete genomes, a constantly updated set of curated annotations embodied in a large and growing collection of encoded subsystems, a derived set of protein families, and hundreds of genome-scale metabolic models. Until recently, however, maintaining current copies of the SEED code and data at remote locations has been a pressing issue. To allow high-performance remote access to the SEED database, we developed the SEED Servers (http://www.theseed.org/servers): four network-based servers intended to expose the data in the underlying relational database, support basic annotation services, offer programmatic access to the capabilities of the RAST annotation server, and provide access to a growing collection of metabolic models that support flux balance analysis. The SEED servers offer open access to regularly updated data, the ability to annotate prokaryotic genomes, the ability to create metabolic reconstructions and detailed models of metabolism, and access to hundreds of existing metabolic models. This work offers and supports a framework upon which other groups can build independent research efforts. Large integrations of genomic data represent one of the major intellectual resources driving research in biology, and programmatic access to the SEED data will provide significant utility to a broad collection of potential users.
has issue date	2012-10-24(xsd:dateTime)
bibo:doi	10.1371/journal.pone.0048053
bibo:pmid	23110173
has license	cc0
sha1sum (hex)	ce05a808109c6307485aeda93945cd3b0e536623
schema:url	https://doi.org/10.1371/journal.pone.0048053
resource representing a document's title	SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models
has PubMed Central identifier	PMC3480482
has PubMed identifier	23110173
schema:publication	PLoS One
resource representing a document's body	covid:ce05a808109c6307485aeda93945cd3b0e536623#body_text
is schema:about of	named entity 'PERFORMANCE' named entity 'servers' named entity 'remote' named entity 'set' named entity 'support' named entity 'advance' named entity 'collection' named entity 'integrations' named entity 'Annotations' named entity 'ANNOTATIONS' named entity 'BIOLOGICAL' named entity 'GENOME ANALYSIS' named entity 'MODELS' named entity 'SEQUENCING TECHNOLOGY' named entity 'SEQUENCE' named entity 'MICROBIAL' named entity 'ADVANCE' named entity 'PRESSING' named entity 'REMOTE' named entity 'INTEGRATION' named entity 'ANALYSIS' named entity 'A MAJOR' named entity 'SCALE' named entity 'SYNTHETIC BIOLOGY' named entity 'INTENDED' named entity 'INDEPENDENT' named entity 'CREATE' named entity 'METABOLIC' named entity 'TRANSLATION' named entity 'ANNOTATIONS' named entity 'DATA' named entity 'BROAD' named entity 'NETWORK' named entity 'EXPOSE' named entity 'PERFORMANCE' named entity 'MEDICAL' named entity 'KNOWLEDGE' named entity 'CODE' named entity 'CURRENT' named entity 'OFFER' named entity 'BIOLOGY' named entity 'INTEREST' named entity 'COMPLETE' named entity 'COMPREHENSIVE' named entity 'COMPUTATIONAL ANALYSIS' named entity 'PROKARYOTIC' named entity 'RESEARCH' named entity 'COMPARISON' named entity 'COPIES' named entity 'COLLECTION' named entity 'BIOTECHNOLOGY' named entity 'DERIVED' named entity 'SUPPORT' named entity 'UNDERLYING' named entity 'RESOURCES' named entity 'MODELING' named entity 'MAINTAINING' named entity 'DETAILED' named entity 'RECENTLY' named entity 'PUBLISHED' named entity 'INFORMATION' named entity 'GENOME' named entity 'SERVERS' named entity 'DATABASE' named entity 'RAST' named entity 'LOCATIONS' named entity 'BASIC' named entity 'HIGH' named entity 'CONTAINS' named entity 'TOOLS' named entity 'POTENTIAL' named entity 'METABOLIC' named entity 'REPRESENT' named entity 'ACCESS' named entity 'WORK' named entity 'SERVERS' named entity 'GENOMES'

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