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Citing CTD/Publications/Use

Contents

  1. Citing CTD
  2. Publications
  3. Presentations, Posters, Etc.
  4. Users of CTD Data

Top ↑ Citing CTD

To cite CTD in your publications:

Davis AP, Murphy CG, Johnson R, Lay JM, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, King BL, Rosenstein MC, Wiegers TC, Mattingly CJ. The Comparative Toxicogenomics Database: update 2013. Nucleic Acids Res. 2013 Jan 1;41(D1):D1104-14.

To cite specific data:

Curated [chemical–gene interactions|chemical–disease|gene–disease] data were retrieved from the Comparative Toxicogenomics Database (CTD), North Carolina State University, Raleigh, NC and Mount Desert Island Biological Laboratory, Salisbury Cove, Maine. World Wide Web (URL: http://ctdbase.org/). [Month, year of data retrieval].

See also: CTD logos.

Top ↑ Publications (30)

  1. Wiegers TC, Davis AP, Mattingly CJ.
    Web services-based text-mining demonstrates broad impacts for interoperability and process simplification.
    Database (Oxford). 2014 Jun 10:bau050. PMID:24919658
  2. Comeau DC, Batista-Navarro RT, Dai HJ, Dogan RI, Yepes AJ, Khare R, Lu Z, Marques H, Mattingly CJ, Neves M, Peng Y, Rak R, Rinaldi F, Tsai RT, Verspoor K, Wiegers TC, Wu CH, Wilbur WJ.
    BioC interoperability track overview.
    Database (Oxford). 2014 Jun 30:bau053. PMID:24980129
  3. Arighi CN, Wu CH, Cohen KB, Hirschman L, Krallinger M, Valencia A, Lu Z, Wilbur JW, Wiegers TC
    BioCreative-IV virtual issue.
    Database (Oxford). 2014 May 22:bau039. PMID:24852177
  4. Davis AP, Wiegers TC, Roberts PM, King BL, Lay JM, Lennon-Hopkins K, Sciaky D, Johnson R, Keating H, Greene N, Hernandez R, McConnell KJ, Enayetallah AE, Mattingly CJ.
    A CTD-Pfizer collaboration: manual curation of 88,000 scientific articles text mined for drug-disease and drug-phenotype interactions.
    Database (Oxford). 2013 Nov 28:bat080. PMID:24288140
  5. Wiegers TC, Davis AP, Mattingly CJ.
    Web services-based text-mining demonstrates broad impacts for interoperability and process simplification.
    Proceedings of the Fourth BioCreative Evaluation Workshop 1: 69-84.
  6. Comeau DC, Islamaj DR, Ciccarese P, Cohen KB, Krallinger M, Leitner F, Lu Z, Peng Y, Rinaldi F, Torii M, Valencia A, Verspoor K, Wiegers TC, Wu CH, Wilbur WJ.
    BioC: a minimalist approach to interoperability for biomedical text processing.
    Database (Oxford). 2013 Sep 18:bat064. PMID:24048470
  7. Davis AP, Wiegers TC, Johnson RJ, Lay JM, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, Murphy CG, Mattingly CJ.
    Text mining effectively scores and ranks the literature for improving chemical-gene-disease curation at the Comparative Toxicogenomics Database.
    PLoS One. 2013 Apr 17;8(4):e58201. PMID:23613709
  8. Davis AP, Murphy CG, Johnson R, Lay JM, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, King BL, Rosenstein MC, Wiegers TC, Mattingly CJ.
    The Comparative Toxicogenomics Database: update 2013.
    Nucleic Acids Res. 2013 Jan 1;41(D1):D1104-14. PMID:23093600
  9. Davis AP, Johnson RJ, Lennon-Hopkins K, Sciaky D, Rosenstein MC, Wiegers TC, Mattingly CJ.
    Targeted journal curation as a method to improve data currency at the Comparative Toxicogenomics Database.
    Database (Oxford). 2012 Dec 6;2012:bas051. PMID:23221299
  10. Wiegers TC, Davis AP, Mattingly CJ.
    Collaborative biocuration--text-mining development task for document prioritization for curation.
    Database (Oxford). 2012 Nov 22;2012:bas037. PMID:23180769
  11. King BL, Davis AP, Rosenstein MC, Wiegers TC, Mattingly CJ.
    Ranking Transitive Chemical-Disease Inferences Using Local Network Topology in the Comparative Toxicogenomics Database.
    PLoS One. 2012;7(11):e46524. PMID:23144783
  12. Hirschman L, Burns GA, Krallinger M, Arighi C, Cohen KB, Valencia A, Wu CH, Chatr-Aryamontri A, Dowell KG, Huala E, Lourenço A, Nash R, Veuthey AL, Wiegers T, Winter AG.
    Text mining for the biocuration workflow.
    Database (Oxford). 2012 Apr 18;2012:bas020. PMID:22513129
  13. Bello SM, Richardson JE, Davis AP, Wiegers TC, Mattingly CJ, Dolan ME, Smith CL, Blake JA, Eppig JT.
    Disease model curation improvements at Mouse Genome Informatics.
    Database (Oxford). 2012 Mar 20;2012:bar063. PMID:22434831
  14. Davis AP, Wiegers TC, Rosenstein MC, Mattingly CJ.
    MEDIC: a practical disease vocabulary used at the Comparative Toxicogenomics Database.
    Database (Oxford). 2012 Mar 20;2012:bar065. PMID:22434833
  15. Mattingly CJ, McKone TE, Callahan MA, Blake JA, Cohen Hubal EA.
    Providing the Missing Link: the Exposure Science Ontology ExO.
    Environ Sci Technol. 2012 Mar 20;46(6):3046-53. PMID:22324457
  16. Davis AP, Rosenstein MC, Wiegers TC, Mattingly CJ.
    DiseaseComps: a metric that discovers similar diseases based upon common toxicogenomic profiles at CTD.
    Bioinformation. 2011 Oct 14;7(4):154-6. PMID:22125387
  17. Davis AP, Wiegers TC, Rosenstein MC, Murphy CG, Mattingly CJ.
    The curation paradigm and application tool used for manual curation of the scientific literature at the Comparative Toxicogenomics Database.
    Database (Oxford). 2011 Sep 20;2011:bar034. PMID:21933848
  18. Mattingly CJ.
    NCI-Nature Pathway Interaction Database. doi:10.1038/pid.2011.2 (2011).
  19. Davis AP, King BL, Mockus S, Murphy CG, Saraceni-Richards C, Rosenstein M, Wiegers T, Mattingly CJ.
    The Comparative Toxicogenomics Database: update 2011.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D1067-72. PMID:20864448
  20. Davis AP, Murphy CG, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Hampton TH, Mattingly CJ.
    GeneComps and ChemComps: a new CTD metric to identify genes and chemicals with shared toxicogenomic profiles.
    Bioinformation. 2009 Oct 15;4(4):173-4. PMID:20198196
  21. Wiegers TC, Davis AP, Cohen KB, Hirschman L, Mattingly CJ.
    Text mining and manual curation of chemical-gene-disease networks for the Comparative Toxicogenomics Database (CTD).
    BMC Bioinformatics. 2009 Oct 8;10(1):326. PMID:19814812
  22. Mattingly CJ, Hampton T, Brothers K, Griffin NE, Planchart AJ.
    Environ Health Perspect. 2009 Jun;117(6):981-7. PMID:19590694
  23. Gohlke JM, Thomas R, Zhang Y, Rosenstein MC, Davis AP, Murphy C, Becker KG, Mattingly CJ, Portier CJ.
    Genetic and environmental pathways to complex diseases.
    BMC Syst Biol. 2009 May 5;3(1):46. PMID:19416532
  24. Mattingly CJ.
    Chemical databases for environmental health and clinical research.
    Toxicol Lett. 2009 Apr 10;186(1):62-5. PMID:18996453
  25. Davis AP, Murphy CG, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Mattingly CJ.
    Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D786-92. PMID:18782832
  26. Davis AP, Murphy CG, Rosenstein MC, Wiegers TC, Mattingly CJ.
    The Comparative Toxicogenomics Database facilitates identification and understanding of chemical-gene-disease associations: arsenic as a case study.
    BMC Med Genomics. 2008 Oct 9;1(1):48. PMID:18845002
  27. Mattingly CJ, Colby GT, Rosenstein MC, Forrest JN, Boyer JL.
    The Comparative Toxicogenomics Database (CTD): a resource for comparative toxicological studies.
    J Exp Zoolog A Comp Exp Biol. 2006 Sep 1;305(9):689-92. PMID:16902965
  28. Mattingly CJ, Rosenstein MC, Davis AP, Colby GT, Forrest JN, Boyer JL.
    The Comparative Toxicogenomics Database: a cross-species resource for building chemical-gene interaction networks.
    Toxicol Sci. 2006 Aug;92(2):587-95. PMID:16675512
  29. Mattingly CJ, Colby GT, Rosenstein MC, Forrest JN, Boyer JL.
    Promoting comparative molecular studies in environmental health research: an overview of the comparative toxicogenomics database (CTD).
    Pharmacogenomics J. 2004;4(1):5-8. PMID:14735110
  30. Mattingly CJ, Colby GT, Forrest JN, Boyer JL.
    The Comparative Toxicogenomics Database (CTD).
    Environ Health Perspect. 2003 May;111(6):793-5. PMID:12760826

Top ↑ Presentations, Posters, Etc. (32)

  1. Wiegers TC, Davis AP, Mattingly CJ.
    Web services-based text-mining demonstrates broad impacts for interoperability and process simplification.
    BioCreative IV Workshop. Bethesda, MD, USA. Oct 6-8, 2013.
  2. Wiegers TC, Davis AP, Mattingly CJ.
    Collaborative Biocuration--Text Mining Development Task for Document Prioritization for Curation.
    BioCreative Workshop 2012. Georgetown University, Washington, DC, USA. Apr 4-5, 2012.
  3. Bello SM, Davis AP, Wiegers TC, Dolan ME, Smith C, Richardson J, Blake J, Eppig JT, Mattingly CJ.
    Waiting for a robust Disease Ontology: a merger of OMIM and MeSH as a practical interim solution.
    International Conference on Biomedical Ontology, University at Buffalo, NY, USA. Jul 26-30, 2011.
  4. Rosenstein MC, Wiegers TC, McMorran RA.
    Oracle to PostgreSQL: CTD's Path to Database Happiness.
    Mouse Genome Informatics Group Meeting. The Jackson Laboratory. Bar Harbor, ME, USA. Jun 8, 2011.
  5. Davis AP, Murphy CG, Saraceni-Richards CA, Mockus S, Rosenstein MC, Wiegers TC, King B, Mattingly CJ.
    Environmental chemicals and human health: uncovering the connections with CTD.
    Society of Toxicology Annual Meeting. Washington, DC, USA. Mar 7-10, 2011.
  6. Davis AP, Murphy CG, Mattingly CJ.
    The Comparative Toxicogenomics Database.
    Society of Toxicology Annual Meeting. Washington, DC, USA. Mar 7-10, 2011.
  7. Davis AP.
    Using CTD to understand BPA.
    NIEHS BPA Grantee Research Update and Coordination Meeting. Research Triangle Park, NC, USA. Sep 21-22, 2010.
  8. Davis AP.
    The OpenHelix Blog. May 18, 2010.
  9. Murphy CG.
    Use and development of ontologies in the Comparative Toxicogenomics Database (CTD).
    Protein Ontology 3rd Annual Meeting. University of Delaware, Newark, DE, USA. Apr 26-27, 2010.
  10. Davis AP, Murphy CG, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Mattingly CJ.
    CTD: exploring over 1,000,000 chemical-gene-disease interactions.
    Society of Toxicology Annual Meeting. Salt Lake City, UT, USA. Mar 7-11, 2010.
  11. Davis AP.
    Mapping OMIM to MeSH: a disease hierarchy for CTD.
    Mouse Genome Informatics Group Meeting. The Jackson Laboratory. Bar Harbor, ME, USA. Feb 23, 2010.
  12. Wiegers TC, Murphy C, Saraceni-Richards CA, Rosenstein MC, Davis AP, Mattingly CJ.
    The Comparative Toxicogenomics Database (CTD) Text Mining Study.
    3rd International Biocuration Conference. Berlin, Germany. Apr 2009.
  13. Mattingly CJ, Murphy C, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Davis AP.
    The Comparative Toxicogenomics Database (CTD): A discovery tool for identifying chemical-gene-disease networks.
    Society of Toxicology Annual Meeting. Baltimore, MD, USA. Mar 2009.
  14. Mattingly CJ, Murphy C, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Davis AP.
    Using the Comparative Toxicogenomics Database (CTD) to identify chemical-gene-disease associations.
    Society of Experimental Toxicology and Chemistry. Tampa, FL, USA. Nov 2008.
  15. Mattingly CJ.
    The Comparative Toxicogenomics Database.
    Annual environmental health sciences core centers meeting. Philadelphia, PA, USA. Oct 2008.
  16. Davis AP, Murphy CG, Rosenstein MC, Wiegers TC, Boyer JL, Mattingly CJ.
    Using CTD to discover chemical-gene-disease associations: arsenic as a case study.
    Mechanisms of Toxicity, Gordon Research Conference, Bates College, Lewiston, ME, USA. Jul 27-Aug 1, 2008.
  17. Mattingly CJ.
    Using the Comparative Toxicogenomics Database (CTD) to Explore Chemical-Gene-Disease Connections.
    University of Maine Graduate School of Biomedical Sciences Symposium. Orono, ME, USA. May 2008.
  18. Mattingly CJ.
    The Comparative Toxicogenomics Database (CTD): Promoting understanding of chemical-gene-disease associations.
    NERC International Collaboration Initiative: Bioinformatics Workshop. Birmingham, UK. Mar 2008.
  19. Mattingly CJ, Davis AP, Rosenstein MC, Wiegers T, Forrest JN, Boyer JL.
    Using the Comparative Toxicogenomics Database to identify chemical-gene-disease associations: arsenic as a case study.
    Society of Toxicology Annual Meeting. Seattle, WA, USA. Mar 2008.
  20. Davis AP, Murphy C, Rosenstein MC, Wiegers T, Forrest JN, Boyer JL, Mattingly CJ.
    Second International Biocuration Meeting. San Jose, CA, USA. Oct 2007.
  21. Mattingly CJ.
    The Comparative Toxicogenomics Database: Promoting Understanding About the Mechanisms of Chemical Actions. Toxicology Division of the American Society for Pharmacology and Experimental Therapeutics (ASPET).
    "Toxicogenomics Approaches for Evaluating Drug and Chemical Toxicity" Symposium at the Experimental Biology Annual Meeting. Washington, DC, USA. Apr 2007.
  22. Davis AP, Mattingly CJ, Rosenstein MC, Wiegers T, Forrest JN, Boyer JL.
    Society of Toxicology Annual Meeting. Charlotte, NC, USA. Mar 2007.
  23. Mattingly CJ, Rosenstein MC, Davis AP, Colby GC, Forrest JN, Boyer JL.
    Comparative Toxicogenomics Database (CTD): Promoting Understanding of Chemical-Gene Interactions.
    Keystone: the Molecular and Integrative Basis for Toxic Responses. Victoria, BC. May 2006.
  24. Davis AP, Mattingly CJ, Rosenstein MC, Forrest JN, Boyer JL.
    The Comparative Toxicogenomics Database: A Public Resource for Chemical-Gene and Chemical-Protein Interactions.
    EPA Science Forum 2006, U.S Environmental Protection Agency, Washington, DC, USA. May 2006.
  25. Mattingly CJ, Rosenstein MC, Davis AP, Forrest JN, Boyer JL.
    The Comparative Toxicogenomics Database (CTD).
    Society of Toxicology Annual Meeting. San Diego, CA, USA. Mar 2006.
  26. Colby GT, Mattingly CJ, Rosenstein, MC, Forrest JN, Boyer JL.
    Data Integration in the Comparative Toxicogenomics Database (CTD).
    Annual meeting of the International Society for Computational Biology. Detroit, MI, USA. Jun 2005.
  27. Mattingly CJ.
    Cross-Species Comparative Approaches to Understanding Chemical-Gene Interactions.
    15th International Conference of Comparative Endocrinology. Boston, MA, USA. May 2005.
  28. Mattingly CJ.
    Comparative Approaches to Understanding Gene-Chemical Interactions.
    Northland Chapter of the Society of Toxicology Meeting. Minneapolis, MN, USA. Apr 2005.
  29. Mattingly CJ, Colby GT, Rosenstein MC, Forrest JN, Boyer JL.
    The Comparative Toxicogenomics Database (CTD).
    Society of Toxicology Annual Meeting. New Orleans, LA, USA. Mar 2005.
  30. Mattingly CJ.
    The Comparative Toxicogenomics Database (CTD): Comparative Molecular Approaches to Environmental Health Research.
    American Chemical Society National Meeting. Philadelphia, PA, USA. Aug 2004.
  31. Mattingly CJ.
    Comparative Approaches to Understanding Mechanisms of Toxicity: CTD.
    2004 World Congress on In Vitro Biology. San Francisco, CA, USA. May 2004.
  32. Mattingly CJ, Colby GT, Rosenstein MC, Forrest JN, Boyer JL.
    The Comparative Toxicogenomics Database (CTD).
    Society of Toxicology Annual Meeting. Salt Lake City, UT, USA. Mar 2004.

Top ↑ Users of CTD Data (53)

  1. AutismKB: Evidence-based knowledgebase of autism spectrum disorder.
  2. BIAdb: A database for Benzylisoquinoline Alkaloids.
  3. Bio2RDF: Linked data for the life sciences.
  4. BioGraph: Biomedical knowledge discovery server.
  5. BioXM: A fully customizable knowledge management solution for better integrated and knowledge-based drug discovery and development.
  6. Bisphenol A Genomics Data Portal: A database of genomics datasets related to health effects of Bisphenol A exposure.
  7. C2HI: A complete chemical information decision system.
  8. CancerResource: Explores the drug target interaction space for applying personalized medicine.
  9. chem2bio2rdf: A semantic framework for linking and data mining chemogenomic and systems chemical biology data.
  10. ChemIDplus®: A resource providing access to structure and nomenclature information for the identification of chemical substances cited in NLM® databases.
  11. ChemProt: Annotated and predicted chemical-protein interactions.
  12. ChemSpider: Links together compound information across the web, providing free text and structure search access of millions of chemical structures.
  13. dcGO: Domain Centric GO, provides associations between ontologies and protein domains at superfamily and family levels.
  14. DDSS (Drug Discovery and Diagnostic Support System).
  15. DEER (Drug, Environmental Effects and Regulation): Explores the envrionmental effects on drug response.
  16. DIGEP-Pred: A web service for in silico prediction of drug-induced changes of gene expression profiles based on structural formula.
  17. DisGeNET: A gene-disease database integrating gene-disease associations from several public, expert, curated data sources and text mining derived associations.
  18. drug2gene: Reports relations between genes/proteins and drugs/compounds.
  19. GAD (Genetic Association Database): An archive of human genetic association studies of complex diseases and disorders. GAD's goal is to allow the user to identify medically relevant polymorphisms from the large volume of polymorphism and mutational data, in the context of standardized nomenclature.
  20. Galaxy: An analysis workflow system (CTD data is available under "Human Genome Variation").
  21. Ganfyd: Get a Note from Your Doctor: a collaborative medical reference wiki by medical professionals and invited non-medical experts.
  22. GeneSetDB: Meta-database integrating public databases focusing on human disease and pharmacology.
  23. GeneWeaver: A system for the integration of functional genomics experiments.
  24. GPSy: Gene Prioritization System: a cross-species system that prioritizes genes for follow-up functional analyses
  25. Harvester Portal: Crosslinks search engines, scientific sites, and Mio documents.
  26. HExpoChem: Contains information on diverse sources of chemicals with the aim to explore human health risk from chemical exposure.
  27. Homer: Human Organ-specific Molecular Electronic Repository: can be used to analyze, identify, and characterize organ-specific biomarkers in association with disease-organ and disease-protein relationships.
  28. InterMine: InterMOD consortium's data warehouse system to integrate data from key model organisms to improve cross-species research (uses CTD's MEDIC).
  29. Lmmd (Laboratory of Molecular Modeling and Design): A database of predicted chemical-gene-disease associations.
  30. MetaADEDB: A database of averse drug effects.
  31. MIRIAM Registry: This application enables users to search collections of curated models with precision, quickly identify the biological phenomena that a given curated model or model constituent represents, and facilitates model reuse, model composition into large subcellular models, and format conversion.
  32. NCBI Gene: A database of genes from RefSeq genomes, defined by sequence and/or located in the NCBI Map Viewer.
  33. Neurocarta: Aggregates disease-gene relations for the neurosciences (extension of Gemma).
  34. NeuroLex: A dynamic lexicon of neuroscience terms.
  35. NPACT (Naturally occuring Plant based Anticancerous Compound-Activity-Target DataBase): A curated database of Plant-derived natural compounds that exhibit anti-cancerous activity.
  36. PharmDB: Tripartite pharmacological network database.
  37. PharmGKB: Curates information that establishes knowledge about the relationships among drugs, diseases, and genes, including their variations and gene products.
  38. PhenoHM: Human-Mouse Comparative Phenomics Server.
  39. PPDB (Pathogenic Pathway Database for Periodontitis): A manual collection of pathogenic pathways for periodontitis.
  40. PubChem: Provides information on the biological activities of small molecules.
  41. Reactome: A manually curated and peer-reviewed pathway database.
  42. RefGene: Indexes of genes and antibodies.
  43. RGD (Rat Genome Database): A resource that curates and integrates rat genetic and genomic data and provides access to this data to support research using the rat as a genetic model for the study of human disease.
  44. SIDD: Establishes semantic associations among disease-related databases, and integrates them to provide disease global view at biological levels.
  45. STITCH: A resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases, and the literature.
  46. Surfaceome: A cancer-orientated database for genes encoding cell surface proteins.
  47. T3DB (Toxin and Toxin Target Database): A resource that combines detailed toxin data with comprehensive toxin target information.
  48. ToppGene: A portal for gene list enrichment analysis and candidate gene prioritization based on functional annotations and protein interactions network.
  49. TOXPO (TOXicology POlymorphism Database).
  50. UCSC Genome Browser: Contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides a portal to the ENCODE project.
  51. UniProt: A comprehensive catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and PIR.
  52. WENDI: A tool for finding non-obvious associations between compounds and biology.
  53. WhichGenes: A tool for building gene sets to use for further experiments.