116 5 Survey of Ontologies in Bioinformatics
information on 1167 genes, 5537 transcription factor binding sites, 1714 reg-
ulatory regions, 14 locus control regions and 5335 expression patterns ob-
tained from 3898 scientific papers.
The TRRD is arranged in seven databases: TRRDGENES (general gene
description), TRRDLCR (locus control regions); TRRDUNITS (regulatory re-
gions: promoters, enhancers, silencers, etc.), TRRDSITES (transcription fac-
tor binding sites), TRRDFACTORS (transcription factors), TRRDEXP (expres-
sion patterns), and TRRDBIB (experimental publications). All of them are
relational databases, and the schema consists of a large number of table def-
initions. SRS is used as a basic tool for navigating and searching TRRD and
integrating it with external database and software resources.
COMPEL compel.bionet.nsc.ru
COMPEL is a database of composite regulatory elements, the basic struc-
tures of combinatorial regulation. Composite regulatory elements are two
closely situated binding sites for distinct transcription factors and represent
minimal functional units providing combinatorial transcriptional regulation.
Both specific factor DNA and factor-factor interactions contribute to the func-
tion of composite elements (CEs). Information about the structure of known
CEs and specific gene regulation achieved through such CEs appears to be
extremely useful for promoter prediction, for gene function prediction, and
for applied gene engineering as well.
Access to COMPEL requires registration, but it is free for noncommercial
use. The database consists of three relational database tables.
ooTFD http://www.ifti.org/ootfd
The purpose of ooTFD (object-oriented Transcription Factors Database) is to
capture information regarding the polypeptide interactions which constitute
and define the properties of transcription factors (Ghosh 2000). ooTFD is an
object-oriented successor to TFD (Ghosh 1993). The database is currently im-
plemented using ozone, a Java-based object-oriented database system. The
schema consists of nine primary Java data structures.5.6 Species-Specific Databases
SGD http://www.yeastgenome.org
TheSaccharomycesGenome Database is a database of the molecular biol-
ogy and genetics of the budding yeastSaccharomyces cerevisiae(Dwightetal.
2004). This database collects and organizes biological information about