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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, Grondin CJ, Johnson RJ, Sciaky D, King BL, McMorran R, Wiegers J, Wiegers TC, Mattingly CJ. The Comparative Toxicogenomics Database: update 2017. Nucleic Acids Res. 2016 Sep 19;[Epub ahead of print]

To cite specific data:

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

Top ↑ Publications (38)

  1. Davis AP, Grondin CJ, Johnson RJ, Sciaky D, King BL, McMorran R, Wiegers J, Wiegers TC, Mattingly CJ.
    The Comparative Toxicogenomics Database: update 2017.
    Nucleic Acids Res. 2016 Sep 19;[Epub ahead of print] PMID:27651457
  2. Grondin CJ, Davis AP, Wiegers TC, King BL, Wiegers JA, Reif DM, Hoppin JA, Mattingly CJ.
    Advancing Exposure Science through Chemical Data Curation and Integration in the Comparative Toxicogenomics Database.
    Environ Health Perspect. 2016 May 12 PMID:27170236
  3. Davis AP, Wiegers TC, King BL, Wiegers J, Grondin CJ, Sciaky D, Johnson RJ, Mattingly CJ.
    Generating Gene Ontology-Disease Inferences to Explore Mechanisms of Human Disease at the Comparative Toxicogenomics Database.
    PLoS One. 2016 May 12;11(5):e0155530. PMID:27171405
  4. Pelletier D, Wiegers TC, Enayetallah A, Kibbey C, Gosink M, Koza-Taylor P, Mattingly CJ, Lawton M.
    ToxEvaluator: an integrated computational platform to aid the interpretation of toxicology study-related findings.
    Database (Oxford). 2016 May 9;2016. pii: baw062. PMID:27161010
  5. Li J, Sun Y, Johnson RJ, Sciaky D, Wei CH, Leaman R, Davis AP, Mattingly CJ, Wiegers TC, Lu Z.
    BioCreative V CDR task corpus: a resource for chemical disease relation extraction.
    Database (Oxford). 2016 May 9;2016. pii: baw068 PMID:27161011
  6. Wei CH, Peng Y, Leaman R, Davis AP, Mattingly CJ, Li J, Wiegers TC, Lu Z.
    Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task.
    Database (Oxford). 2016 Mar 19;2016. pii: baw032. PMID:26994911
  7. Mattingly CJ, Boyles R, Lawler CP, Haugen AC, Dearry A, Haendel M.
    Laying a Community-Based Foundation for Data-Driven Semantic Standards in Environmental Health Sciences.
    Environ Health Perspect. 2016 Feb 12. PMID:26871594
  8. Davis AP, Grondin CJ, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, King BL, Wiegers TC, Mattingly CJ.
    The Comparative Toxicogenomics Database's 10th year anniversary: update 2015.
    Nucleic Acids Res. 2015 Jan;43 (Database issue): D914-20. PMID:25326323
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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.
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. Mattingly CJ.
    NCI-Nature Pathway Interaction Database. doi:10.1038/pid.2011.2 (2011).
  27. 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
  28. 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
  29. 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
  30. Mattingly CJ, Hampton T, Brothers K, Griffin NE, Planchart AJ.
    Environ Health Perspect. 2009 Jun;117(6):981-7. PMID:19590694
  31. 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
  32. Mattingly CJ.
    Chemical databases for environmental health and clinical research.
    Toxicol Lett. 2009 Apr 10;186(1):62-5. PMID:18996453
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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. (47)

  1. Mattingly CJ, Grondin CJ, Johnson R, Sciaky D, King BL, Wiegers JA, Wiegers TC, Davis AP.
    The Comparative Toxicogenomics Database (CTD): Expanding Exposome and Phenotype Content to Elucidate Chemical-Disease Relationships.
    Society of Toxicology Annual Meeting. New Orleans, LA, USA. Mar 13-17, 2016.
  2. Grondin CJ, Davis AP, Wiegers TC, Wiegers JA, Mattingly CJ.
    The Comparative Toxicogenomics Database (CTD): Advancing understanding of molecular connections among chemicals, genes and diseases.
    American Chemical Society National Meeting. San Diego, CA, USA Mar 13-17, 2016.
  3. Collier G, Planchart A, Reif DM, Mattingly CJ.
    Elucidating Correlations between High-Throughput Chemical Screening and Curated Literature.
    Society of Toxicology Annual Meeting. New Orleans, LA, USA. Mar 13-17, 2016.
  4. Wiegers TC, Lu, Z.
    BioCreative V Track 3: Chemical-Disease Relation AND Disease Named Entity Recognition and Normalization.
    BioCreative V Challenge Workshop. cicCartuja, Sevilla, Spain. Sept 9-11, 2015.
  5. Grondin CJ, Davis AP, Wiegers JA, Wiegers TC, Mattingly CJ.
    Exposure Science Data and the Comparative Toxicogenomics Database.
    Society of Toxicology Annual Meeting. San Diego, CA, USA. Mar 22-26, 2015.
  6. Mattingly CJ, Grondin CJ, Lennon-Hopkins K, Saracini-Richards C, Sciaky D, Wiegers JA, McMorran R, King BL, Wiegers TC, Davis AP.
    The Comparative Toxicogenomics Database: Ten Years in the Making.
    Society of Toxicology Annual Meeting. San Diego, CA, USA. Mar 22-26, 2015.
  7. Grondin CJ, Davis AP, Mattingly CJ.
    Exposure data and the Comparative Toxicogenomics Database (CTD).
    Society of Toxicology Annual Meeting. Phoenix, AZ, USA. Mar 23-27, 2014.
  8. Davis AP, Mattingly CJ, Murphy CG, Lay JM, Lennon-Hopkins K, Sciaky D, Saracini-Richards C, King BL, Rosenstein MC, Wiegers TC.
    The Comparative Toxicogenomics Database.
    Society of Toxicology Annual Meeting. Phoenix, AZ, USA. Mar 23-27, 2014.
  9. Mattingly CJ.
    The Comparative Toxicogenomics Database (CTD): Facilitating Mechanistic Understanding of Chemical Effects.
    Society of Toxicology Annual Meeting. Phoenix, AZ, USA. Mar 23-27, 2014.
  10. Mattingly CJ.
    The Comparative Toxicogenomics Database (CTD): Leveraging Species Diversity to Understand Mechanisms of Toxicity.
    Society of Toxicology Annual Meeting. Phoenix, AZ, USA. Mar 23-27, 2014.
  11. Murphy CG, Mattingly CJ, Davis AP
    Exposure Data Curation for Integration into the Comparative Toxicogenomics Database (CTD).
    Society of Toxicology Annual Meeting. San Antonio, TX, USA. Mar 10-14, 2013.
  12. Mattingly CJ, Murphy CG, Johnson R, Lay JM, Lennon-Hopkins K, Saracini-Richards C, Sciaky D, King BL, Rosenstein MC, Wiegers TC, Davis AP.
    The Comparative Toxicogenomics Database.
    Society of Toxicology Annual Meeting. San Antonio, TX, USA. Mar 10-14, 2013.
  13. Wiegers TC
    BioCreative IV Track 3 CTD: Interoperability and Web Service-based NER
    BioCreative IV Conference. Bethesda, MD, USA. Oct 7-9, 2013.
  14. Wiegers TC
    BioC for NER Web Services-Based High Level Inter-process Communications
    BioCreative IV Conference. Bethesda, MD, USA. Oct 7-9, 2013.
  15. 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.
  16. Mattingly CJ, Davis AP, Murphy CG, Saraceni Richards CA, Mockus S, Rosenstein MC, Wiegers TC, King B.
    Predicting Mechanisms of Chemical Toxicity using the Comparative Toxicogenomics Database (CTD).
    Society of Toxicology Annual Meeting. San Francisco. CA, USA. Mar 11-15, 2012.
  17. Murphy CG, Davis AP, Saracini-Richards CA, Rosenstein MC, Wiegers TC, Mattingly CJ.
    Using CTD to discover and predict molecular connections between environmental chemicals and human health.
    Society of Toxicology Annual Meeting. San Francisco. CA, USA. Mar 11-15, 2012.
  18. 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.
  19. 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.
  20. 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.
  21. Davis AP, Murphy CG, Mattingly CJ.
    The Comparative Toxicogenomics Database.
    Society of Toxicology Annual Meeting. Washington, DC, USA. Mar 7-10, 2011.
  22. Davis AP.
    Using CTD to understand BPA.
    NIEHS BPA Grantee Research Update and Coordination Meeting. Research Triangle Park, NC, USA. Sep 21-22, 2010.
  23. Davis AP.
    The OpenHelix Blog. May 18, 2010.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. Mattingly CJ.
    The Comparative Toxicogenomics Database.
    Annual environmental health sciences core centers meeting. Philadelphia, PA, USA. Oct 2008.
  31. 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.
  32. 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.
  33. Mattingly CJ.
    The Comparative Toxicogenomics Database (CTD): Promoting understanding of chemical-gene-disease associations.
    NERC International Collaboration Initiative: Bioinformatics Workshop. Birmingham, UK. Mar 2008.
  34. 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.
  35. Davis AP, Murphy C, Rosenstein MC, Wiegers T, Forrest JN, Boyer JL, Mattingly CJ.
    Second International Biocuration Meeting. San Jose, CA, USA. Oct 2007.
  36. 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.
  37. Davis AP, Mattingly CJ, Rosenstein MC, Wiegers T, Forrest JN, Boyer JL.
    Society of Toxicology Annual Meeting. Charlotte, NC, USA. Mar 2007.
  38. 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.
  39. 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.
  40. 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.
  41. 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.
  42. Mattingly CJ.
    Cross-Species Comparative Approaches to Understanding Chemical-Gene Interactions.
    15th International Conference of Comparative Endocrinology. Boston, MA, USA. May 2005.
  43. Mattingly CJ.
    Comparative Approaches to Understanding Gene-Chemical Interactions.
    Northland Chapter of the Society of Toxicology Meeting. Minneapolis, MN, USA. Apr 2005.
  44. 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.
  45. Mattingly CJ.
    The Comparative Toxicogenomics Database (CTD): Comparative Molecular Approaches to Environmental Health Research.
    American Chemical Society National Meeting. Philadelphia, PA, USA. Aug 2004.
  46. Mattingly CJ.
    Comparative Approaches to Understanding Mechanisms of Toxicity: CTD.
    2004 World Congress on In Vitro Biology. San Francisco, CA, USA. May 2004.
  47. 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

  1. AlzBase: Alzheimer Database, an integrative database for gene dysregulation in Alzheimer disease.
  2. AutismKB: Evidence-based knowledgebase of autism spectrum disorder.
  3. BIAdb: Benzylisoquinoline Alkaloids Database.
  4. Bio2RDF: Linked data for the life sciences.
  5. BioGraph: Data integration and data mining platform for the exploration and discovery of biomedical information.
  6. BioXM: Biomax knowledge management system.
  7. BPA Genomics: Genomics data portal related to health effects of bisphenol A exposure.
  8. C2HI: Complete Chemical Information, a web service that ranks chemical-gene-disease associations among biomedical articles.
  9. CaGeDB: Calcium Gene Database, connecting calcium signaling and associated diseases.
  10. CancerResource: Cancer-relevant relationships of compounds and targets.
  11. CART: Chemical Annotation Retrieval Toolkit, retrieves annotations on biological effects of chemicals (part of Galaxy).
  12. Chem2Bio2RDF: Semantic framework for linking and data mining chemogenomic and systems chemical biology data.
  13. ChemIDplus: Chemical Identification dictionary and structure database.
  14. ChemiRs: Chemical Interactions with miRNAs.
  15. ChemProt: Annotated and predicted chemical-protein interactions.
  16. ChemSpider: Chemical structures and property predictions.
  17. dcGO: Domain Centric GO, database of domain-centric ontologies on functions, phenotypes, and diseases.
  18. DDMGD: Dragon Database for Methylated Genes and Diseases, provides associations between methylated genes and diseases.
  19. DDSS: Drug Discovery and Diagnostic Support System, ranks disease-associated genes in terms of causing less side-effects.
  20. DEER: Drug Environmental Effects and Regulation, explores the envrionmental effects on drug response.
  21. DID: Drug-Indication Database, a database of structured drug-indication relations.
  22. DIGEP-Pred: Drug-Induced Gene Expression Profile Predictor, drug-induced changes of gene expression based on chemical structural formula.
  23. DisGeNET: Disease Gene Network, discovery platform integrating information on gene-disease associations.
  24. DISQOVER: Semantic search platform that aggregates data from disparate sources.
  25. DisSim: Disease Similarity, explores similar diseases and discovers relationships among diseases and therapeutic chemicals.
  26. diXa: Data Infrastructure for Chemical Safety, a collection of high throughput toxicogenomics datasets produced by EU researchers.
  27. DNetDB: Disease Network Database, explores disease relationships to provide insights into disease taxonomy and etiology.
  28. drug2gene: Knowledgebase that combines compound/drug-gene/protein information from publicly available databases.
  29. Drug Voyager: Computational platform for exploring unintended drug action.
  30. DSigDB: Drug Signatures Database, a collection of annotated drug/compound gene sets.
  31. Ferret: A free extension for Chrome browsers that links to integrated CTD data.
  32. GAD: Genetic Association Database, genetic association data from complex diseases and disorders.
  33. Galaxy: A framework that makes advanced computational tools usable by non-experts.
  34. Ganfyd: Get A Note From Your Doctor, a collaborative medical wiki by medical professionals and invited non-medical experts.
  35. Gemma Phenocarta: Tools and database for meta-analysis of functional genomics data.
  36. GeneSetDB: Meta-database integrating public databases focusing on human disease and pharmacology.
  37. GeneWeaver: System for the integration of functional genomics experiments.
  38. GLADIATOR: Global Approach for Disease Associated Module Reconstruction, predicts disease modules by integrating knowledge of disease-related proteins and phenotypes across multiple diseases.
  39. GPSy: Gene Prioritization System, a cross-species system that prioritizes genes for follow-up functional analyses.
  40. GSKB: Gene Set KnowledgeBase, a comprehensive knowledgebase for pathway analysis in mouse.
  41. Harmonizome: Collection of processed datasets about genes and proteins.
  42. HerDing: Herb recommendation system to treat diseases using genes and chemicals.
  43. HExpoChem: Information on diverse sources of chemicals with the aim to explore human health risk from chemical exposure.
  44. HOMER: Human Organ-specific Molecular Electronic Repository, defining human organ-specific genes/proteins.
  45. iCTNet2: Integrated Complex Traits Networks, a Cytoscape app and database that builda networks by integrating biological interactions.
  46. LAERTES: Large-scale Adverse Effects Related to Treatment Evidence Standardization, assesses associations between drugs and health outcomes.
  47. Lmmd: Laboratory of Molecular Modeling and Design, a database of predicted chemical-gene-disease associations.
  48. Lynx: Database and knowledge extraction engine for integrative medicine.
  49. MBROLE: Metabolites Biological Role, analysis of functional annotations of chemical compounds compiled from public databases.
  50. MetaADEDB: Meta Adverse Drug Events Database, a comprehensive computer-available adverse drug events database.
  51. MetSigDis: Metabolic Signatures of Diseases.
  52. miRegulome: Integrated online repository that provides entire regulatory modules of a miRNA.
  53. MIRIAM: Provides a set of online services for the generation of unique and perennial identifiers for life science data.
  54. Monarch Initiative: Integrated platform of cross-species gene, disease, and phenotype data.
  55. MSeqDR: Mitochondrial disease Sequence Data Resource, collects and shares data for rare diseases, patients, and causative mutations.
  56. NCBI Gene: NCBI's integrated database of genes, their sequences, and information.
  57. NIF: Neuroscience Information Framework, supports neuroscience research into a collaborative framework.
  58. NPACT: Naturally occuring Plant-based Anticancerous Compound-Activity-Target Database, plant-derived natural compounds that exhibit anti-cancerous activity.
  59. NeruoMMSig: Neurodegenerative disease Multimodal Mechanistic Signatures, a web server for mechanism enrichment.
  60. PharmacoMicrobiomics: Explores interactions between human-associated microbes and drugs by building a knowledgebase.
  61. PharmDB-K: Bio-pharmacological network database, offers comprehensive traditional Korean medicine-associated compound, drug, disease, and protein information.
  62. PharmGKB: Pharmacogenomics Knowledgebase, curates information about drugs, diseases, and genes, including their variations and gene products.
  63. PhenoHM: Human-Mouse Comparative Phenomics Server, tool to mine human and mouse orthologous phenotypes.
  64. PHLeGrA: Pipeline for Hidden Variable Linked Graph Analytics, connects paths between drugs and adverse reactions.
  65. PPDB: Pathogenic Pathway Database for Periodontitis, manual collection of pathogenic pathways for periodontitis.
  66. PsyGeNET: Psychiatric Disorders Gene Association Network, resource for exploring psychiatric diseases and their associated genes.
  67. PubChem: NCBI's integrated database of the biological activities of small molecules.
  68. Reactome: Manually curated and peer-reviewed pathway database.
  69. RefGene: Indexes of genes and antibodies.
  70. RGD: Rat Genome Database, a premier site for genetic, genomic, phenotype, and disease data generated from rat research.
  71. SciCrunch: Researcher content management system designed for dynamic data.
  72. SIDD: Semantically Integrated Disease Database, establishes semantic associations among disease-related databases.
  73. SLAP: Semantic Link Association Prediction.
  74. STITCH: Search Tool for Interactions of Chemicals, a database of known and predicted interactions between chemicals and proteins.
  75. Surfaceome: Cancer-orientated database for genes encoding cell surface proteins.
  76. T3DB: Toxin and Toxin Target Database, a resource that combines detailed toxin data with comprehensive toxin target information.
  77. TarPred: Target Prediction, a web application for predicting therapeutic and side effect targets of chemical compounds.
  78. ToppGene: Suite of tools for gene list enrichment and prioritization based on functional annotations and protein interactions network.
  79. TOXPO: Toxicology Polymorphism Database.
  80. UniProt: Comprehensive, high-quality and freely accessible resource of protein sequence and functional information.
  81. WENDI: Web Engine for Non-obvious Drug Information.
  82. WhichGenes: Bioinformatics gene-set building tool.
  83. WITHDRAWN: Database of withdrawn and discontinued drugs that were pulled out of global markets due to safety concerns.