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

Scientific Journal Articles

EVS General

  1. 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]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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. Also cited as: Stud Health Technol Inform. 2004;107(Pt 1):33-7. [PubMed]
  9. Hartel F, Fragoso G, Ong K, Dionne R. Enhancing Quality of Retrieval Through Concept Edit History. AMIA Annu Symp Proc. 2003:279-83. [PubMed]
  10. 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.

Biomedical Applications

  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. Epub 2011 May 19. PubMed PMID: 21597104; PubMed Central PMCID: PMC3128396. [PubMed]
  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]
  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. Epub 2011 Aug 31. PubMed PMID: 21918596; PubMed Central PMCID: PMC3169352. [PubMed]
  4. Bertaud Gounot V, Donfack V, Lasbleiz J, Bourde A, Duvauferrier R. Creating an ontology driven rules base for an expert system for medical diagnosis. Stud Health Technol Inform. 2011;169:714-8. PubMed PMID: 21893840. [PubMed]
  5. Cuggia M, Bourde A, Turlin B, Vincendeau S, Bertaud V, Bohec C, Duvauferrier R. Automatic Definition of the Oncologic EHR Data Elements from NCIT in OWL. Stud Health Technol Inform. 2011;169:517-21. PubMed PMID: 21893803. [PubMed]
  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;1. pii: 9. PubMed PMID: 20805954; PubMed Central PMCID: PMC2929536. [PubMed]
  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]
  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]
  9. 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]
  10. Liu H, Li X, Yoon V, Clarke R. Annotating breast cancer microarray samples using ontologies. AMIA Annu Symp Proc. 2008 Nov 6:414-8. PubMed PMID: 18999108; PubMed Central PMCID: PMC2655965. [PubMed]
  11. 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. Epub 2007 Nov 7. PubMed PMID: 17989087; PubMed Central PMCID: PMC2238948. [PubMed]
  12. 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 11:508-12. PubMed PMID: 18693888; PubMed Central PMCID: PMC2655830. [PubMed]
  13. 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 11:85-9. PubMed PMID: 18693803. [PubMed]
  14. 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]
  15. 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]
  16. Deitzer JR, Payne PR, Starren JB. Coverage of clinical trials tasks in existing ontologies. AMIA Annu Symp Proc. 2006:903. PubMed PMID: 17238522; PubMed Central PMCID: PMC1839431. [PubMed]
  17. Bailey LO, Kennedy CH, Fritts MJ, Hartel FW. Development of a model for the representation of nanotechnology-specific terminology. AMIA Annu Symp Proc. 2006:849. PubMed PMID: 17238469; PubMed Central PMCID: PMC1839578. [PubMed]
  18. Shah NH, Rubin DL, Supekar KS, Musen MA. Ontology-based annotation and query of tissue microarray data. AMIA Annu Symp Proc. 2006:709-13. PubMed PMID: 17238433; PubMed Central PMCID: PMC1839511. [PubMed]
  19. Zhang S, Bodenreider O. Alignment of multiple ontologies of anatomy: deriving indirect mappings from direct mappings to a reference. AMIA Annu Symp Proc. 2005:864-8. PubMed PMID: 16779163; PubMed Central PMCID: PMC1560629. [PubMed]
  20. Bodenreider O, Hayamizu TF, Ringwald M, De Coronado S, Zhang S. Of mice and men: aligning mouse and human anatomies. AMIA Annu Symp Proc. 2005:61-5. PubMed PMID: 16779002; PubMed Central PMCID: PMC1560846. [PubMed]

caCORE and caBIG

  1. 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. Epub 2008 Dec 25. PubMed PMID: 19154797; PubMed Central PMCID: PMC2729758. [PubMed]
  2. 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. Epub 2008 Apr 24. PubMed PMID: 18436897; PubMed Central PMCID: PMC2442262. [PubMed]
  3. 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. Epub 2007 Apr 2. PubMed PMID: 17512259; PubMed Central PMCID: PMC2254758. [PubMed]
  4. 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. Chinese. PubMed PMID: 16617371. [PubMed]
  5. 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]

LexEVS

  1. 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]
  2. 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. Epub 2009 Mar 4. PubMed PMID: 19261933; PubMed Central PMCID: PMC2732233. [PubMed]

NLP

  1. Crowley RS, Tseytlin E, Jukic D. ReportTutor - an intelligent tutoring system that uses a natural language interface. AMIA Annu Symp Proc. 2005:171-5. PubMed PMID: 16779024; PubMed Central PMCID: PMC1560511. [PubMed]

Ontology and Semantics

  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]
  2. 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]
  3. Noy N, Tudorache T, de Coronado S, Musen M. Developing biomedical ontologies collaboratively. AMIA Annu Symp Proc. 2008:520-4. [Available online]
  4. Cohen B, Oren M, Min H, Perl Y, Halper M. Automated comparative auditing of NCIT genomic roles using NCBI. J Biomed Inform. 2008 Dec;41(6):904-13. Epub 2008 Mar 28. PubMed PMID: 18486558; PubMed Central PMCID: PMC2630966. [PubMed]
  5. Mougin F, Bodenreider O. Auditing the NCI thesaurus with semantic web technologies. AMIA Annu Symp Proc. 2008 Nov 6:500-4. PubMed PMID: 18999265; PubMed Central PMCID: PMC2655981. [PubMed]
  6. Detwiler LT, Suciu D, Brinkley JF. Regular paths in SparQL: querying the NCI Thesaurus. AMIA Annu Symp Proc. 2008 Nov 6:161-5. PubMed PMID: 18999137; PubMed Central PMCID: PMC2656016. [PubMed]
  7. 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]
  8. 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]
  9. Min H, Perl Y, Chen Y, Halper M, Geller J, Wang Y. Auditing as part of the terminology design life cycle. J Am Med Inform Assoc. 2006 Nov-Dec;13(6):676-90. Epub 2006 Aug 23. PubMed PMID: 16929044; PubMed Central PMCID: PMC1656963. [PubMed]
  10. 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]
  11. Cimino JJ, Zhu X. The practical impact of ontologies on biomedical informatics. Yearb Med Inform. 2006:124-35. Review. PubMed PMID: 17051306. [PubMed]
  12. 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]

Other Scientific Publications

  1. Ghazvinian A, Noy NF, Musen MA. From mappings to modules: Using mappings to identify domain-specific modules in large ontologies. (2011) KCAP 2011 - Proceedings of the 2011 Knowledge Capture Conference, pp. 33-40. [Scopus]
  2. Machado, C.M., Couto, F., Fernandes, A.R., Santos, S., Cardim, N., Freitas, A.T. Semantic characterization of hypertrophic cardiomyopathy disease (2010) 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010, art. no. 5703841, pp. 432-439. [Scopus]
  3. Hartung M, Gross A, Kirsten T, Rahm E. Discovering evolving regions in life science ontologies. (2010) Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 6254 LNBI, pp. 19-34. [Scopus]
  4. Sebastian A, Noy NF, Tudorache T, Musen MA. A generic ontology for collaborative ontology-development workflows. (2008) Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 5268 LNAI, pp. 318-328. Cited 1 time.[Scopus]
  5. Bernhard D. Automatic acquisition of semantic relationships from morphological relatedness. (2006) Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 4139 LNAI, pp. 121-132. [Scopus]
  6. Kumar A, Smith B. Oncology ontology in the NCI thesaurus. (2005) Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 3581 LNAI, pp. 213-220. Cited 3 times.[Scopus]

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