118 5 Survey of Ontologies in Bioinformatics
clues regarding gene location, phenotype, and function. Synteny maps are
built based on the identification and mapping of conserved human-mouse
synteny regions. Comparative mapping is used to pinpoint unknown hu-
man homologs of known, mapped mouse genes.
GDB gdbwww.gdb.org
The GDB Human Genome Database is the main repository for all published
mapping information generated by the Human Genome Project. This data-
base is specific toHomo sapiens. The information stored in GDB includes
genetic maps, physical maps (clone, Sequence Tagged Site (STS), and Flu-
orescence In Situ Hybridization (FISH)-based), cytogenetic maps, physical
mapping reagents (clones, STSs), polymorphism information, and citations.
Pathbase http://www.pathbase.net
Pathbase is a mutant mouse pathology database that stores images of the
abnormal histology associated with spontaneous and induced mutations of
both embryonic and adult mice (Schofield et al. 2004). The database and the
images are publicly accessible and linked by anatomical site, gene, and other
identifiers to relevant databases. The database is structured around a novel
mouse pathology ontology, called MPATH, and provides high-resolution im-
ages of normal and diseased tissues that are searchable through orthogo-
nal taxonomies for pathology, developmental stage, anatomy, and gene at-
tributes. The database is annotated with GO terms, controlled vocabularies
for type of genetic manipulation or mutation, genotype, and free text for
mouse strain and additional attributes. The MPATH ontology is available in
DAG-Edit format.5.7 Specialized Protein Databases
ORDB senselab.med.yale.edu/senselab/ordb
The Olfactory Receptor Database is a central repository of olfactory recep-
tor (OR) and olfactory receptor-like gene and protein sequences (Crasto et al.
2002). The 2004 Nobel Prize in Physiology or Medicine was awarded jointly
to Richard Axel and Linda B. Buck for their discoveries of “odorant recep-
tors and the organization of the olfactory system.” Humans detect odorants
through ORs, which are located on the olfactory sensory neurons in the ol-
factory epithelium of the nose (Buck and Axel 1991; Buck 2000).
In building ORDB, relevant HTML files from GenBank and SWISS-PROT
and user-supplied text files are parsed to extract relevant data. Upon filter-