114 5 Survey of Ontologies in Bioinformatics
MIPS mips.gsf.de
The Munich Information Center for Protein Sequences provides protein se-
quence-related information based on whole-genome analysis (Mewes et al.
2004). The main focus of the work is directed toward the systematic organi-
zation of sequence-related attributes as gathered by a variety of algorithms
and primary information from experimental data together with information
compiled from the scientific literature.DIP dip.doe-mbi.ucla.edu
The Database of Interacting Proteins is a research tool for studying cellu-
lar networks of protein interactions (Salwinski et al. 2004). The DIP aims
to integrate the diverse body of experimental evidence on protein-protein
interactions into a single, easily accessible online database. Because the re-
liability of experimental evidence varies widely, methods of quality assess-
ment have been developed and utilized to identify the most reliable subset
of the interactions. This core set can be used as a reference when evaluating
the reliability of high-throughput protein-protein interaction data sets for de-
velopment of prediction methods, as well as in studies of the properties of
protein interaction networks.
Obtaining the DIP database requires registration. The database is available
in an XSD format called XIN, as well as in tab-delimited flat files and other
formats.SpiD http://genome.jouy.inra.fr/cgi-bin/spid/index.cgi
The Subtilis Protein interaction Database is a protein-protein interaction net-
work database centered on the replication machinery of the gram-positive
bacteriumBacillus subtilis(Hoebeke et al. 2001). This network was found by
using genome-wide yeast two-hybrid screening experiments and systematic
specificity assays (Noirot-Gros et al. 2002).MINT http://160.80.34.4/mint/
The Molecular INTeraction database is a relational database containing inter-
action data between biological molecules (Zanzoni et al. 2002). At present,
MINT centers on storing experimentally verified protein-protein interactions
with special emphasis on proteomes of mammalian organisms. MINT con-
sists of entries obtained from data mining of the scientific literature. The
database is available in either a text format or in XML.
HPID http://wilab.inha.ac.kr/hpid/
The Human Protein Interaction Database was designed for the following
purposes (Han et al. 2004):