Tuesday, October 20, 2009
Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical–gene–disease networks.
Authors: Allan Peter Davis, Cynthia G. Murphy, Cynthia A. Saraceni-Richards,Michael C. Rosenstein, Thomas C. Wiegers and Carolyn J. Mattingly
In this paper, the authors discuss the comparative toxicogenomics database (CTD). The authors have developed the CTD http://ctd.mdibl.org/ as a unique tool to provide connections between chemicals, genes/proteins and diseases and to provide the basis for testable hypotheses about the mechanisms underlying the etiology of environmental diseases. CTD is a curated database that promotes understanding about the effects of environmental chemicals on human health. Biocurators at CTD manually curate chemical-gene interactions, chemical-disease relationships and gene-disease relationships from the literature.
CTD is distinct from these databases in three ways: (1) it focuses on environmental chemicals; (2) it integrates curated and imported data, allowing users to explore connections between chemicals, genes, and diseases; and (3) it function not only as a repository for information, but also as a resource for generating novel hypotheses about environmental diseases and chemical actions. Environmental chemicals can affect genes in multiple ways, including mutagenesis, altered methylation, physical interaction and influencing gene expression or protein function so CTD focuses its manual curation effort on environmental chemicals (e.g. arsenic, heavy metals and dioxins), how those chemicals interact with genes or proteins in different species and how they relate to human diseases. CTD biocurators capture three types of core data from the literature: chemical-gene interactions, chemical-disease relationship and gene-disease relationships. These data are curated in a structured format using controlled vocabularies and are integrated to establish a triad of chemicals, genes and diseases. CTD enhances its core data pages with links to the external resources. A powerful feature of CTD is the integration of curated chemical, gene and disease core data from the literature to generate new, putative discoveries. For example, if chemical a interacts with gene B (via a curated chemical-gene interaction) and independently gene B is associated with disease C (via a curated gene-disease relationship), then it may be relationship with disease C (inferred via gene B). This approach was recently supported by analyzing the CTD arsenic data set, wherein CTD correctly predicted types of diseases that may be associated with arsenic exposure and set of genes that may be involved in modulating arsenic-relate disease, such as lung cancer and diabetes.
Future development of CTD will aim to further expand the depth of its curated data and enhance the data query and visualization capabilities.
In this paper, the authors discuss the comparative toxicogenomics database (CTD). The authors have developed the CTD http://ctd.mdibl.org/ as a unique tool to provide connections between chemicals, genes/proteins and diseases and to provide the basis for testable hypotheses about the mechanisms underlying the etiology of environmental diseases. CTD is a curated database that promotes understanding about the effects of environmental chemicals on human health. Biocurators at CTD manually curate chemical-gene interactions, chemical-disease relationships and gene-disease relationships from the literature.
CTD is distinct from these databases in three ways: (1) it focuses on environmental chemicals; (2) it integrates curated and imported data, allowing users to explore connections between chemicals, genes, and diseases; and (3) it function not only as a repository for information, but also as a resource for generating novel hypotheses about environmental diseases and chemical actions. Environmental chemicals can affect genes in multiple ways, including mutagenesis, altered methylation, physical interaction and influencing gene expression or protein function so CTD focuses its manual curation effort on environmental chemicals (e.g. arsenic, heavy metals and dioxins), how those chemicals interact with genes or proteins in different species and how they relate to human diseases. CTD biocurators capture three types of core data from the literature: chemical-gene interactions, chemical-disease relationship and gene-disease relationships. These data are curated in a structured format using controlled vocabularies and are integrated to establish a triad of chemicals, genes and diseases. CTD enhances its core data pages with links to the external resources. A powerful feature of CTD is the integration of curated chemical, gene and disease core data from the literature to generate new, putative discoveries. For example, if chemical a interacts with gene B (via a curated chemical-gene interaction) and independently gene B is associated with disease C (via a curated gene-disease relationship), then it may be relationship with disease C (inferred via gene B). This approach was recently supported by analyzing the CTD arsenic data set, wherein CTD correctly predicted types of diseases that may be associated with arsenic exposure and set of genes that may be involved in modulating arsenic-relate disease, such as lung cancer and diabetes.
Future development of CTD will aim to further expand the depth of its curated data and enhance the data query and visualization capabilities.
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