Genome Sequence Database (GSDB)
is an archival database of genome sequence data maintained at the
National Center for Genome Resources, Santa Fe.
The current version of GSDB, GSDB 2.0,
has also been developed with Sybase DBMS but without
using the OPM toolkit. For GSDB 2.0, an OPM interface,
including an OPM schema,
has been retrofitted on top of GSDB 2.0; this interface
allows accessing GSDB using the OPM query tools [6].
OPM schemas have also been retrofitted for preliminary versions
of the forthcoming GSDB 2.2.
GSDB 2.0 is structured around one main class of objects, Entry, whose objects represent DNA sequences and are identified by accession numbers. The actual sequences (strings) are represented by objects of another class, Sequence. GSDB 2.0 also contains objects representing various entities, including genes (class Gene), products (class Products), sources (class Source), and references (class Reference). These objects are commonly qualified as features (class Feature), that is, classes Gene, Products, Source, Reference, as well as other classes, are subclasses of Feature. The location of features on sequences is represented by location objects (class Location).
A subset of the GSDB 2.0 OPM schema is given in the Appendix.