Genomic Database
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A Genomic Database is an Entity Database with Information about an Organism's DNA.
- Context:
- It can contain Gene Records.
- Example(s):
- See: Proteomic Database, Entity Database, Ontology.
References
- http://genome-www.stanford.edu/
- Hyperlinks to systematic analysis projects, resources, laboratories, and departments at Stanford University. Maintained by the Saccharomyces Genome Database within the Department of Genetics part of the School of Medicine.
- http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome
- The Genome database provides views for a variety of genomes, complete chromosomes, sequence maps with contigs, and integrated genetic and physical maps. The database is organized in six major organism groups: Archaea, Bacteria, Eukaryotae, Viruses, Viroids, and Plasmids and includes complete chromosomes, organelles and plasmids as well as draft genome assemblies.
- http://molecularbacteriology.com/database.aspx
- KEGG BRITE is a collection of hierarchical classifications representing our knowledge on various aspects of biological systems. In contrast to KEGG PATHWAY, which is limited to molecular interactions and reactions, KEGG BRITE incorporates many different types of relationships. Thus, the mapping of genomic and molecular data to KEGG BRITE (by the KO system shown below) supplements the KEGG PATHWAY mapping for inferring higher-order functions.
- http://www.eubios.info/HUGOHGD.htm
- For the purposes of this Statement on Human Genomic Databases, the HUGO Ethics Committee adopts the following definitions:
- A genomic database is a collection of data arranged in a systematic way so as to be searchable. Genomic data can include inter alia, nucleic acid and protein sequence variants (including neutral polymorphisms, susceptibility alleles to various phenotypes, pathogenic mutations), and polymorphic haplotypes. The work associated with a database includes collecting, annotating, curating, storing, validating and preparing specific sets for transmission.
- For the purposes of this Statement on Human Genomic Databases, the HUGO Ethics Committee adopts the following definitions:
- Nico M van Straalen, and Dick Roelofs. (2006). “An introduction to ecological genomics.
- http://books.google.com/books?id=tim5KQ6ivdMC&pg=PA34&lpg=PA34
- QUOTE: Without annotation, a genomic database is useless. Annotation is based on a system of gene ontology (GO): a controlled vocabulary used to describe...
- http://www.genome.jp/kegg/brite.html
- The genomic database contains isolates recovered from clinical samples submitted to the University of Minnesota Veterinary Diagnostic Laboratory. Isolates are genotyped using a repetitive element-based PCR (Rep-PCR) and added to the database. Genomic fingerprints are analyzed using the BioNumerics software and are included in a dendrogram, which also contains information regarding the date of isolation, genomic database ID, herd ID, geographical location, age of affected animals, lesions associated with isolation, serotyping, virulence markers, and antibiotic resistance profiles.
2009
- (Cusick et al., 2009) ⇒ Michael E Cusick, Haiyuan Yu, Alex Smolyar, Kavitha Venkatesan, Anne-Ruxandra Carvunis, Nicolas Simonis, Jean-François Rual, Heather Borick, Pascal Braun, Matija Dreze, Jean Vandenhaute, Mary Galli, Junshi Yazaki, David E Hill, Joseph R Ecker, Frederick P Roth, and Marc Vidal. (2009). “Literature-Curated Protein Interaction Datasets.” In: Nature Methods 6, 39 - 46 (2009)
- (Reeves et al., 2009) ⇒ Gabrielle A Reeves, David Talavera, and Janet M Thornton. (2009). “[dx.doi.org/10.1098/rsif.2008.0341|Genome and Proteome Annotation: Organization, Interpretation and Integration.].” In: J R Soc Interface, 6(31).