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Below is a preliminary bibliography of scientific literature on EVS and its use.

Journal Articles Co-Authored by EVS Staff

  1. Liu K, Chapman WW, Savova G, Chute CG, Sioutos N, Crowley RS. Effectiveness of Lexico-syntactic Pattern Matching for Ontology Enrichment with Clinical Documents. Methods Inf Med. 2010: 8;49(6). PubMed Citation
  2. De Coronado S, Wright LW, Fragoso G, Haber MW, Hahn-Dantona EA, Hartel FW, Quan SL, Safran T, Thomas N, Whiteman L. The NCI Thesaurus Quality Assurance Life Cycle. Journal of Biomedical Informatics 2009 June;42(3):530-539. Available online
  3. Noy N, Tudorache T, de Coronado S, Musen M. Developing biomedical ontologies collaboratively. AMIA Annu Symp Proc. 2008:520-4. Available online
  4. Noy NF, de Coronado S, Solbrig H, Fragoso G, Hartel FW, Musen MA. Representing the NCI Thesaurus in OWL DL: Modeling tools help modeling languages. Appl Ontol. 2008 Jan 1;3(3):173-190. Free PMC Article
  5. Haber MW, Kisler BW, Lenzen M, Wright LW. Controlled Terminology for Clinical Research: A Collaboration between CDISC and NCI Enterprise Vocabulary Services. Drug Information Journal 2007;41(3):405-412. Available online
  6. Sioutos N, De Coronado S, Haber MW, Hartel FW, Shaiu WL, Wright LW. NCI Thesaurus: A Semantic Model Integrating Cancer-Related Clinical and Molecular Information. Journal of Biomedical Informatics 2007 Feb;40(1):30-43. Epub 2006 Mar 15. PubMed Citation
  7. De Coronado S, Tuttle MS, Solbrig HR. Using the UMLS Semantic Network to Validate NCI Thesaurus Structure and Analyze its Alignment with the OBO Relations Ontology. AMIA Annu Symp Proc. 2007:165-70. Available online
  8. Tobias J, Chilukuri R, Komatsoulis GA, Mohanty S, Sioutos N, Warzel DB, Wright LW, Crowley RS. The CAP Cancer Protocols – A Case Study of caCORE Based Data Standards Implementation to Integrate with the Cancer Biomedical Informatics Grid. BMC Medical Informatics Decision Making, 20; 6:25, 2006. Free PMC Article
  9. Hartel FW, De Coronado S, Dionne R, Fragoso G, Golbeck J. Modeling a description logic vocabulary for cancer research. Journal of Biomedical Informatics, 2005; 38(2):114-129. PubMed Citation
  10. Fragoso G, De Coronado S, Haber MW, Hartel FW, Wright LW. Overview and Utilization of the NCI Thesaurus. Comparative and Functional Genomics (Dec. 2004) 5(8):648-654. Free PMC Article
  11. De Coronado S, Haber MW, Sioutos N, Tuttle MS, Wright LW. NCI Thesaurus: Using Science-Based Terminology to Integrate Cancer Research Results. Proceedings of the 11th World Congress on Medical Informatics (Medinfo 2004) Amsterdam: IOS Press 2004, pp. 33-37. PubMed Citation
  12. Hartel F, Fragoso G, Ong K, Dionne R. Enhancing Quality of Retrieval Through Concept Edit History. AMIA Annu Symp Proc. 2003:279-83. PubMed Citation
  13. Goldbeck J, Fragoso G, Hartel F, Hendler J, Oberthaler J, Parsia B. The National Cancer Institute's Thesaurus and Ontology. Journal of Web Semantics (2003) 1:75-80.

Journal Articles by Others on EVS and Its Use

[under construction – some initial raw PubMed records below]

  1. Pathak J, Wang J, Kashyap S, Basford M, Li R, Masys DR, Chute CG. Mapping clinical phenotype data elements to standardized metadata repositories and controlled terminologies: the eMERGE Network experience. J Am Med Inform Assoc. 2011 Jul-Aug; 18 (4) :376-86. PubMed PMID:21597104; PubMed Central PMCID: PMC3128396. PubMed Citation
  2. Sherman S, Shats O, Ketcham MA, Anderson MA, Whitcomb DC, Lynch HT, Ghiorzo P, Rubinstein WS, Sasson AR, Grizzle WE, Haynatzki G, Feng J, Sherman A, Kinarsky L, Brand RE. PCCR: Pancreatic Cancer Collaborative Registry. Cancer Inform. 2011 Mar 23; 10:83-91. PubMed PMID:21552494; PubMed Central PMCID: PMC3085425. PubMed Citation
  3. Sherman S, Shats O, Fleissner E, Bascom G, Yiee K, Copur M, Crow K, Rooney J, Mateen Z, Ketcham MA, Feng J, Sherman A, Gleason M, Kinarsky L, Silva-Lopez E, Edney J, Reed E, Berger A, Cowan K. Multicenter breast cancer collaborative registry. Cancer Inform. 2011; 10:217-26. PubMed PMID:21918596. PubMed Citation
  4. Schulz S, Schober D, Tudose I, Stenzhorn H. The Pitfalls of Thesaurus Ontologization - the Case of the NCI Thesaurus. AMIA Annu Symp Proc. 2010 Nov 13; 2010:727-31. PubMed PMID:21347074; PubMed Central PMCID: PMC3041372. PubMed Citation
  5. Pathak J, Peters L, Chute CG, Bodenreider O. Comparing and evaluating terminology services application programming interfaces: RxNav, UMLSKS and LexBIG. J Am Med Inform Assoc. 2010 Nov-Dec; 17 (6) :714-9. PubMed PMID:20962136; PubMed Central PMCID: PMC3000749. PubMed Citation
  6. Kang HP, Borromeo CD, Berman JJ, Becich MJ. The tissue microarray OWL schema: An open-source tool for sharing tissue microarray data. J Pathol Inform. 2010 Jul 13; 1PubMed PMID:20805954; PubMed Central PMCID: PMC2929536. PubMed Citation
  7. Reed TL, Kaufman-Rivi D. FDA adverse Event Problem Codes: standardizing the classification of device and patient problems associated with medical device use. Biomed Instrum Technol. 2010 May-Jun; 44 (3) :248-56. PubMed PMID:20715359. PubMed Citation
  8. Yip V, Mete M, Topaloglu U, Kockara S. Concept Discovery for Pathology Reports using an N-gram Model. AMIA Summits Transl Sci Proc. 2010 Mar 1; 2010:43-7. PubMed PMID:21347147; PubMed Central PMCID: PMC3041542. PubMed Citation
  9. Cimino JJ, Hayamizu TF, Bodenreider O, Davis B, Stafford GA, Ringwald M. The caBIG terminology review process. J Biomed Inform. 2009 Jun; 42 (3) :571-80. PubMed PMID:19154797; PubMed Central PMCID: PMC2729758. PubMed Citation
  10. Pathak J, Solbrig HR, Buntrock JD, Johnson TM, Chute CG. LexGrid: a framework for representing, storing, and querying biomedical terminologies from simple to sublime. J Am Med Inform Assoc. 2009 May-Jun; 16 (3) :305-15. PubMed PMID:19261933; PubMed Central PMCID: PMC2732233. PubMed Citation
  11. Shah NH, Jonquet C, Chiang AP, Butte AJ, Chen R, Musen MA. Ontology-driven indexing of public datasets for translational bioinformatics. BMC Bioinformatics. 2009 Feb 5; 10 Suppl 2:S1. PubMed PMID:19208184; PubMed Central PMCID: PMC2646250. PubMed Citation
  12. Mougin F, Bodenreider O. Auditing the NCI thesaurus with semantic web technologies. AMIA Annu Symp Proc. 2008 Nov 6; PubMed PMID:18999265; PubMed Central PMCID: PMC2655981. PubMed Citation
  13. Detwiler LT, Suciu D, Brinkley JF. Regular paths in SparQL: querying the NCI Thesaurus. AMIA Annu Symp Proc. 2008 Nov 6; PubMed PMID:18999137; PubMed Central PMCID: PMC2656016. PubMed Citation
  14. Liu H, Li X, Yoon V, Clarke R. Annotating breast cancer microarray samples using ontologies. AMIA Annu Symp Proc. 2008 Nov 6; PubMed PMID:18999108; PubMed Central PMCID: PMC2655965. PubMed Citation
  15. Shironoshita EP, Jean-Mary YR, Bradley RM, Kabuka MR. semCDI: a query formulation for semantic data integration in caBIG. J Am Med Inform Assoc. 2008 Jul-Aug; 15 (4) :559-68. PubMed PMID:18436897; PubMed Central PMCID: PMC2442262. PubMed Citation
  16. Komatsoulis GA, Warzel DB, Hartel FW, Shanbhag K, Chilukuri R, Fragoso G, Coronado S, Reeves DM, Hadfield JB, Ludet C, Covitz PA. caCORE version 3: Implementation of a model driven, service-oriented architecture for semantic interoperability. J Biomed Inform. 2008 Feb; 41 (1) :106-23. PubMed PMID:17512259; PubMed Central PMCID: PMC2254758. PubMed Citation
  17. Marinelli RJ, Montgomery K, Liu CL, Shah NH, Prapong W, Nitzberg M, Zachariah ZK, Sherlock GJ, Natkunam Y, West RB, van de Rijn M, Brown PO, Ball CA. The Stanford Tissue Microarray Database. Nucleic Acids Res. 2008 Jan; 36 (Database issue) :D871-7. PubMed PMID:17989087; PubMed Central PMCID: PMC2238948. PubMed Citation
  18. Min H, Cohen B, Halper M, Oren M, Perl Y. Detecting role errors in the gene hierarchy of the NCI Thesaurus. Cancer Inform. 2008; 6:293-313. PubMed PMID:19221606; PubMed Central PMCID: PMC2623310. PubMed Citation
  19. Trotti A, Colevas AD, Setser A, Basch E. Patient-reported outcomes and the evolution of adverse event reporting in oncology. J Clin Oncol. 2007 Nov 10; 25 (32) :5121-7. PubMed PMID:17991931. PubMed Citation
  20. Marquet G, Dameron O, Saikali S, Mosser J, Burgun A. Grading glioma tumors using OWL-DL and NCI Thesaurus. AMIA Annu Symp Proc. 2007 Oct 11; PubMed PMID:18693888; PubMed Central PMCID: PMC2655830. PubMed Citation
  21. Burgun A, Bodenreider O. Issues in integrating epidemiology and research information in oncology: experience with ICD-O3 and the NCI Thesaurus. AMIA Annu Symp Proc. 2007 Oct 11; PubMed PMID:18693803. PubMed Citation
  22. Shah NH, Rubin DL, Espinosa I, Montgomery K, Musen MA. Annotation and query of tissue microarray data using the NCI Thesaurus. BMC Bioinformatics. 2007 Aug 8; 8:296. PubMed PMID:17686183; PubMed Central PMCID: PMC1988837. PubMed Citation
  23. Zhang S, Bodenreider O. Experience in Aligning Anatomical Ontologies. Int J Semant Web Inf Syst. 2007; 3 (2) :1-26. PubMed PMID:18974854; PubMed Central PMCID: PMC2575410. PubMed Citation
  24. Gao Q, Zhang YL, Xie ZY, Zhang QP, Hu ZZ. [caCORE: core architecture of bioinformation on cancer research in America]. Beijing Da Xue Xue Bao. 2006 Apr 18; 38 (2) :218-21. PubMed PMID:16617371. PubMed Citation
  25. Deitzer JR, Payne PR, Starren JB. Coverage of clinical trials tasks in existing ontologies. AMIA Annu Symp Proc. 2006; PubMed PMID:17238522; PubMed Central PMCID: PMC1839431. PubMed Citation
  26. Bailey LO, Kennedy CH, Fritts MJ, Hartel FW. Development of a model for the representation of nanotechnology-specific terminology. AMIA Annu Symp Proc. 2006; PubMed PMID:17238469; PubMed Central PMCID: PMC1839578. PubMed Citation
  27. Shah NH, Rubin DL, Supekar KS, Musen MA. Ontology-based annotation and query of tissue microarray data. AMIA Annu Symp Proc. 2006; PubMed PMID:17238433; PubMed Central PMCID: PMC1839511. PubMed Citation
  28. Nadkarni PM, Brandt CA. The Common Data Elements for cancer research: remarks on functions and structure. Methods Inf Med. 2006; 45 (6) :594-601. PubMed PMID:17149500; PubMed Central PMCID: PMC2980785. PubMed Citation
  29. Cimino JJ, Zhu X. The practical impact of ontologies on biomedical informatics. Yearb Med Inform. 2006; PubMed PMID:17051306. PubMed Citation
  30. Zhang S, Bodenreider O. Alignment of multiple ontologies of anatomy: deriving indirect mappings from direct mappings to a reference. AMIA Annu Symp Proc. 2005; PubMed PMID:16779163; PubMed Central PMCID: PMC1560629. PubMed Citation
  31. Crowley RS, Tseytlin E, Jukic D. ReportTutor - an intelligent tutoring system that uses a natural language interface. AMIA Annu Symp Proc. 2005; PubMed PMID:16779024; PubMed Central PMCID: PMC1560511. PubMed Citation
  32. Bodenreider O, Hayamizu TF, Ringwald M, De Coronado S, Zhang S. Of mice and men: aligning mouse and human anatomies. AMIA Annu Symp Proc. 2005; PubMed PMID:16779002; PubMed Central PMCID: PMC1560846. PubMed Citation
  33. Ceusters W, Smith B, Goldberg L. A terminological and ontological analysis of the NCI Thesaurus. Methods Inf Med. 2005; 44 (4) :498-507. PubMed PMID:16342916. PubMed Citation
  34. de Coronado S, Haber MW, Sioutos N, Tuttle MS, Wright LW. NCI Thesaurus: using science-based terminology to integrate cancer research results. Stud Health Technol Inform. 2004; 107 (Pt 1) :33-7. PubMed PMID:15360769. PubMed Citation
  35. Covitz PA, Hartel F, Schaefer C, De Coronado S, Fragoso G, Sahni H, Gustafson S, Buetow KH. caCORE: a common infrastructure for cancer informatics. Bioinformatics. 2003 Dec 12; 19 (18) :2404-12. PubMed PMID:14668224. PubMed Citation
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