Integrative database management for mouse development: systems and concepts.
Cells in the developing embryo must integrate complex signals from the genome and environment to make decisions about their behavior or fate. The ability to understand the fundamental biology of the decision-making process, and how these decisions may go awry during abnormal development, requires a systems biology paradigm. Presently, the ability to build models with predictive capability in birth defects research is constrained by an incomplete understanding of the fundamental parameters underlying embryonic susceptibility, sensitivity, and vulnerability. Key developmental milestones must be parameterized in terms of system structure and dynamics, the relevant control methods, and the overall design logic of metabolic and regulatory networks. High-content data from genome-based studies provide some comprehensive coverage of these operational processes but a key research challenge is data integration. Analysis can be facilitated by data management resources and software to reveal the structure and function of bionetwork motifs potentially associated with an altered developmental phenotype. Borrowing from applied mathematics and artificial intelligence, we conceptualize a system that can help address the new challenges posed by the transformation of birth defects research into a data-driven science.
Singh
Amar V
AV
Department of Molecular, Cellular, and Craniofacial Biology, School of Dentistry, University of Louisville, Louisville, Kentucky 40202, USA.
Rouchka
Eric C
EC
Rempala
Greg A
GA
Bastian
Caleb D
CD
Knudsen
Thomas B
TB
D000818:Animals; D001185:Artificial Intelligence; D019295:Computational Biology; D003628:Database Management Systems; D047108:Embryonic Development; D005260:Female; D051188:Knowledge Bases; D008433:Mathematics; D051379:Mice / Q000002:abnormalities* / Q000196:embryology* / Q000235:genetics; D008954:Models, Biological; D011247:Pregnancy; D049490:Systems Biology; D043922:Toxicogenetics