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How Can We Use Bioinformatics to Predict Which Agents Will Cause Birth Defects?
SINGH, A. V. AND T. B. KNUDSEN. How Can We Use Bioinformatics to Predict Which Agents Will Cause Birth Defects? Second Edition, Chapter 19, Barbara Hales; Anthony Scialli; Melissa S. Tassinari (ed.), Teratology Primer. John Wiley & Sons Incorporated, New York, NY, 1(2):51-53, (2010).
The U.S. National Library of Medicine’s Pubmed site includes 19 million citations and abstracts and continues to grow. The BDSM team is now working on assembling the literature’s unstructured data into a structured database and linking it to BDSM within a system that can then be used for testing and generating new hypotheses. This effort will generate data bases of entities (such as genes, proteins, metabolites, gene ontology processes) linked to PubMed identifiers/abstracts and providing information on the relationships between them. The end result will be an online/standalone tool that will help researchers to focus on the papers most relevant to their query and uncover hidden connections and obvious information gaps.
The availability of genomic sequences from a growing number of human and model organisms has provided an explosion of data, information, and knowledge regarding biological systems and disease processes. High-throughput technologies such as DNA and protein microarray biochips are now standard tools for probing the cellular state and determining important cellular behaviors at the genomic/proteomic levels. While these newer technologies are beginning to provide important information on cellular reactions to toxicant exposure (toxicogenomics), a major challenge that remains is the formulation of a strategy to integrate transcript, protein, metabolite, and toxicity data. This integration will require new concepts and tools in bioinformatics.