Article

The Comparative Toxicogenomics Database: A Cross-Species Resource for Building Chemical-Gene Interaction Networks

Department of Bioinformatics, Mount Desert Island Biological Laboratory, Salisbury Cove, Maine 04672, USA.
Toxicological Sciences (Impact Factor: 4.48). 09/2006; 92(2):587-95. DOI: 10.1093/toxsci/kfl008
Source: PubMed

ABSTRACT Chemicals in the environment play a critical role in the etiology of many human diseases. Despite their prevalence, the molecular mechanisms of action and the effects of chemicals on susceptibility to disease are not well understood. To promote understanding of these mechanisms, the Comparative Toxicogenomics Database (CTD; http://ctd.mdibl.org/) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. CTD integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. These comparisons will facilitate understanding of structure-function correlations and the genetic basis of susceptibility. Manual curation and integration of cross-species chemical-gene and chemical-protein interactions from the literature are now underway. These data will provide information for building complex interaction networks. New CTD features include (1) cross-species gene, rather than sequence, query and visualization capabilities; (2) integrated cross-links to microarray data from chemicals, genes, and sequences in CTD; (3) a reference set related to chemical-gene and protein interactions identified by an information retrieval system; and (4) a "Chemicals in the News" initiative that provides links from CTD chemicals to environmental health articles from the popular press. Here we describe these new features and our novel cross-species curation of chemical-gene and chemical-protein interactions.

Download full-text

Full-text

Available from: John N Forrest, Sep 27, 2014
0 Followers
 · 
98 Views
  • Source
    • "In order to elucidate molecular mechanisms of these environmental chemicals, a Database called comparative toxicogenomics database (CTD; http://ctd.mdibl.org/) has been created [29]. CTD presents scientifically reviewed and curated information on many aspects, such as chemicals, relevant genes and proteins, it also reveals their interactions in vertebrates (human, mice, rat, fish) and invertebrates (daphnids, Drosophila, nematode Caenorhabditis elegans) [28] [30]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: As nanotechnology industries increase production, increased release of engineered nanoparticles (NPs) to aquatic environments suggests a rising need for monitoring and evaluation of their potential toxicity. Based on previous and latest research results in the related field, this paper reviews methods, mechanisms, and typical bio-indicators of nanomaterials ecotoxicological research. It outlines detecting methods of NPs in ecotoxicologial studies, and discusses suspension methods of nanoparticles in this field. Proteomics and genomics technologies are predicted to be indispensable means in ecotoxicological studies of NPs. It also points out that biology of particle-induced oxidative stress is an important mechanistic paradigm, and so are solvent effects and the effects of NPs on other substances. Typical bio-indicators in aquatic systems are claimed to be determined to avoid unnecessary animal testing whenever possible and to reduce unnecessary testing costs. In ecotoxicological research of NPs, fish species are generally considered as preferred species; for nanoparticle ecotoxicity, suspension-feeding invertebrates may be a unique target group, therefore invertebrate testing is also very important; because of sensitivity to pollutants, phytoplankton testing should be strengthened. This paper also summarizes some conflicting results in current experiments, and gives some possible explanations. Finally, future research directions are proposed.
    CLEAN - Soil Air Water 04/2014; 42(4):377–385. DOI:10.1002/clen.201200559 · 1.84 Impact Factor
  • Source
    • "The CTD (http://ctdbase.org) is a publicly available resource that seeks to elucidate the mechanisms by which drugs and environmental chemicals influence the function of biological processes and human health (64, 65). The CTD curators manually curate peer-reviewed scientific articles to identify chemical–gene/protein interactions, chemical–disease relationships and gene–disease relationships (66). "
    [Show abstract] [Hide abstract]
    ABSTRACT: A vast amount of scientific information is encoded in natural language text, and the quantity of such text has become so great that it is no longer economically feasible to have a human as the first step in the search process. Natural language processing and text mining tools have become essential to facilitate the search for and extraction of information from text. This has led to vigorous research efforts to create useful tools and to create humanly labeled text corpora, which can be used to improve such tools. To encourage combining these efforts into larger, more powerful and more capable systems, a common interchange format to represent, store and exchange the data in a simple manner between different language processing systems and text mining tools is highly desirable. Here we propose a simple extensible mark-up language format to share text documents and annotations. The proposed annotation approach allows a large number of different annotations to be represented including sentences, tokens, parts of speech, named entities such as genes or diseases and relationships between named entities. In addition, we provide simple code to hold this data, read it from and write it back to extensible mark-up language files and perform some sample processing. We also describe completed as well as ongoing work to apply the approach in several directions. Code and data are available at http://bioc.sourceforge.net/.Database URL: http://bioc.sourceforge.net/
    Database The Journal of Biological Databases and Curation 01/2013; 2013:bat064. DOI:10.1093/database/bat064 · 4.46 Impact Factor
  • Source
    • "The CTD includes manually-curated, cross-species relations between chemicals and genes, proteins and mRNA transcripts (Fig. 1D; Mattingly et al., 2006). We downloaded the database (January 2012), spanning 219 618 direct relationships between 6079 unique environmental chemical factors and 21 267 genes and their products in 336 organisms, including humans. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Motivation: Complex diseases, such as Type 2 Diabetes Mellitus (T2D), result from the interplay of both environmental and genetic factors. However, most studies investigate either the genetics or the environment and there are a few that study their possible interaction in context of disease. One key challenge in documenting interactions between genes and environment includes choosing which of each to test jointly. Here, we attempt to address this challenge through a data-driven integration of epidemiological and toxicological studies. Specifically, we derive lists of candidate interacting genetic and environmental factors by integrating findings from genome-wide and environment-wide association studies. Next, we search for evidence of toxicological relationships between these genetic and environmental factors that may have an etiological role in the disease. We illustrate our method by selecting candidate interacting factors for T2D. Contact: abutte@stanford.edu
    Bioinformatics 06/2012; 28(12):i121-6. DOI:10.1093/bioinformatics/bts229 · 4.62 Impact Factor
Show more