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1.

The curation paradigm and application tool used for manual curation of the scientific literature at the Comparative Toxicogenomics Database.

Davis AP, Wiegers TC, Rosenstein MC, Murphy CG, Mattingly CJ.

Database (Oxford). 2011 Sep 20;2011:bar034. doi: 10.1093/database/bar034. Print 2011. Erratum in: Database (Oxford). 2012;2012:bas012. Rosenstein, Michael C [added].

2.

MEDIC: a practical disease vocabulary used at the Comparative Toxicogenomics Database.

Davis AP, Wiegers TC, Rosenstein MC, Mattingly CJ.

Database (Oxford). 2012 Mar 20;2012:bar065. doi: 10.1093/database/bar065. Print 2012.

3.

Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks.

Davis AP, Murphy CG, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Mattingly CJ.

Nucleic Acids Res. 2009 Jan;37(Database issue):D786-92. doi: 10.1093/nar/gkn580. Epub 2008 Sep 9.

4.

Text mining effectively scores and ranks the literature for improving chemical-gene-disease curation at the comparative toxicogenomics database.

Davis AP, Wiegers TC, Johnson RJ, Lay JM, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, Murphy CG, Mattingly CJ.

PLoS One. 2013 Apr 17;8(4):e58201. doi: 10.1371/journal.pone.0058201. Print 2013.

5.

A CTD-Pfizer collaboration: manual curation of 88,000 scientific articles text mined for drug-disease and drug-phenotype interactions.

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.

Database (Oxford). 2013 Nov 28;2013:bat080. doi: 10.1093/database/bat080. Print 2013.

6.

Targeted journal curation as a method to improve data currency at the Comparative Toxicogenomics Database.

Davis AP, Johnson RJ, Lennon-Hopkins K, Sciaky D, Rosenstein MC, Wiegers TC, Mattingly CJ.

Database (Oxford). 2012 Dec 6;2012:bas051. doi: 10.1093/database/bas051. Print 2012.

7.

Text mining and manual curation of chemical-gene-disease networks for the comparative toxicogenomics database (CTD).

Wiegers TC, Davis AP, Cohen KB, Hirschman L, Mattingly CJ.

BMC Bioinformatics. 2009 Oct 8;10:326. doi: 10.1186/1471-2105-10-326.

8.

The Comparative Toxicogenomics Database: update 2011.

Davis AP, King BL, Mockus S, Murphy CG, Saraceni-Richards C, Rosenstein M, Wiegers T, Mattingly CJ.

Nucleic Acids Res. 2011 Jan;39(Database issue):D1067-72. doi: 10.1093/nar/gkq813. Epub 2010 Sep 22.

9.

The comparative toxicogenomics database: a cross-species resource for building chemical-gene interaction networks.

Mattingly CJ, Rosenstein MC, Davis AP, Colby GT, Forrest JN Jr, Boyer JL.

Toxicol Sci. 2006 Aug;92(2):587-95. Epub 2006 May 4.

10.

Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information.

Kim S, Kim W, Wei CH, Lu Z, Wilbur WJ.

Database (Oxford). 2012 Nov 17;2012:bas042. doi: 10.1093/database/bas042. Print 2012.

11.

The Comparative Toxicogenomics Database's 10th year anniversary: update 2015.

Davis AP, Grondin CJ, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, King BL, Wiegers TC, Mattingly CJ.

Nucleic Acids Res. 2015 Jan;43(Database issue):D914-20. doi: 10.1093/nar/gku935. Epub 2014 Oct 17.

12.

The Comparative Toxicogenomics Database: update 2013.

Davis AP, Murphy CG, Johnson R, Lay JM, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, King BL, Rosenstein MC, Wiegers TC, Mattingly CJ.

Nucleic Acids Res. 2013 Jan;41(Database issue):D1104-14. doi: 10.1093/nar/gks994. Epub 2012 Oct 23.

13.

GeneComps and ChemComps: a new CTD metric to identify genes and chemicals with shared toxicogenomic profiles.

Davis AP, Murphy CG, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Hampton TH, Mattingly CJ.

Bioinformation. 2009 Oct 15;4(4):173-4.

14.

The Comparative Toxicogenomics Database facilitates identification and understanding of chemical-gene-disease associations: arsenic as a case study.

Davis AP, Murphy CG, Rosenstein MC, Wiegers TC, Mattingly CJ.

BMC Med Genomics. 2008 Oct 9;1:48. doi: 10.1186/1755-8794-1-48.

15.

Ranking transitive chemical-disease inferences using local network topology in the comparative toxicogenomics database.

King BL, Davis AP, Rosenstein MC, Wiegers TC, Mattingly CJ.

PLoS One. 2012;7(11):e46524. doi: 10.1371/journal.pone.0046524. Epub 2012 Nov 7.

16.

Web services-based text-mining demonstrates broad impacts for interoperability and process simplification.

Wiegers TC, Davis AP, Mattingly CJ.

Database (Oxford). 2014 Jun 10;2014. pii: bau050. doi: 10.1093/database/bau050. Print 2014.

17.

Collaborative biocuration--text-mining development task for document prioritization for curation.

Wiegers TC, Davis AP, Mattingly CJ.

Database (Oxford). 2012 Nov 22;2012:bas037. doi: 10.1093/database/bas037. Print 2012.

18.

Disease model curation improvements at Mouse Genome Informatics.

Bello SM, Richardson JE, Davis AP, Wiegers TC, Mattingly CJ, Dolan ME, Smith CL, Blake JA, Eppig JT.

Database (Oxford). 2012 Mar 20;2012:bar063. doi: 10.1093/database/bar063. Print 2012.

19.

DiseaseComps: a metric that discovers similar diseases based upon common toxicogenomic profiles at CTD.

Davis AP, Rosenstein MC, Wiegers TC, Mattingly CJ.

Bioinformation. 2011;7(4):154-6. Epub 2011 Oct 14.

20.

Building an efficient curation workflow for the Arabidopsis literature corpus.

Li D, Berardini TZ, Muller RJ, Huala E.

Database (Oxford). 2012 Dec 6;2012:bas047. doi: 10.1093/database/bas047. Print 2012.

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