The Genome Database (GDB) is an archival database of genomic mapping
data maintained at Johns Hopkins School of Medicine,
Baltimore [10].
The new version of GDB, GDB 6.0,
is developed with the Sybase database management system (DBMS),
using the OPM toolkit [4].
GDB 6.0 consists of a federation of three distinct databases:
Human Genome Database (HGD), Citation Database and
Registry Database.
GDB contains accessioned objects representing entities of interest. All accessioned objects in GDB belong to class DBObject and are classified in subclasses of DBObject, organized in a class hierarchy. The main subclasses of this class hierarchy contain objects representing genomic data, literature references, and information on people and organizations.
Biological function information is represented by objects of class BiologicalObject, whose subclasses include Expression, GeneFamily, GeneProduct and Organism.
Data for representing and displaying maps are represented by objects of class MappingObject, whose subclasses include Map, GenomicSegment, and MapElement. Map contains objects representing the information regarding a resolved map and its subclasses include ContentContigMap, CytogeneticMap, IntegratedMap, LinkageMap, and RadiationHybridMap.
GenomicSegment contains objects representing any named region or set of regions of a genome, and its subclasses include Clone, CellLine, Chromosome, Contig, and CytogeneticMarker.
Maps are constructed by placing genomic segments on maps. Objects of class MapElement represent location information for genomic segments on specific maps.
Literature references are represented by objects of class Citations, whose subclasses include JournalArticle, ConferencePaper, PersonalCommunication, and Book.
GDB provides links to external databases. Such links are represented by objects of class ExternalLink. Subclasses of ExternalLink include Enzyme, Phenotype, and Sequence.
A subset of the GDB 6.0 OPM schema is given in the Appendix.