Consistent re-modeling of signaling pathways and its implementation in the TRANSPATH database.
The data model of the signaling pathways database TRANSPATH has been re-engineered to a three-layer model comprising experimental evidences and summarized pathway information, both in a mechanistically detailed manner, and a "semantic" projection for the abstract overview. Each molecule is described in the context of a certain reaction in the multidimensional space of posttranslational modification, molecular family relationships, and the biological species of its origin. The new model makes the data better suitable for reconstructing signaling pathways and networks and mapping expression data, for instance from microarray experiments, onto regulatory networks.
Choi
Claudia
C
BIOBASE GmbH, Halchtersche Str.33, D-38304 Wolfenbüttel, Germany. cch@biobase.de
Crass
Torsten
T
Kel
Alexander
A
Kel-Margoulis
Olga
O
Krull
Mathias
M
Pistor
Susanne
S
Potapov
Anatolij
A
Voss
Nico
N
Wingender
Edgar
E
D000465:Algorithms; D001185:Artificial Intelligence; D016208:Databases, Factual; D005786:Gene Expression Regulation; D016247:Information Storage and Retrieval; D020411:Oligonucleotide Array Sequence Analysis; D015398:Signal Transduction; D012984:Software