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{scrollbar:icons=false} h1. {page-info:title} {multi-excerpt:name=Bibliography}Below is a preliminary bibliography of scientific literature on EVS and its use. {toc:minLevel=2} h2. Scientific Journal Articles h3. EVS General # 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. \[[Available online\|http://www.sciencedirect.com/science/article/B6WHD-4VFC80H-4/2/42a20ff355ab427f4d674d96e913c63b]\] # 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. \[[Free PMC Article\|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2753293/?tool=pubmed]\] # 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. \[[Available online\|http://www.nxtbook.com/nxtbooks/dia/druginformationjournal0507/index.php?startpage=142]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/16697710]\] # 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. \[[Available online\|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655888/pdf/amia-0165-s2007.pdf]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/15797001]\] # 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. \[[Free PMC Article\|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447470/?tool=pubmed]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/15360769]\] # Hartel F, Fragoso G, Ong K, Dionne R. Enhancing Quality of Retrieval Through Concept Edit History. ??AMIA Annu Symp Proc.?? 2003:279-83. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/14728178]\] # 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. h3. Biomedical Applications # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/21597104]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/21552494]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/21918596]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/21893840]\] # Cuggia M, BourdÃ© 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/21893803]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/20805954]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/20715359]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/21347147]\] # TobiasShah JNH, ChilukuriJonquet RC, KomatsoulisChiang GAAP, MohantyButte SAJ, SioutosChen NR, WarzelMusen 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 ArticleMA. 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1524939/?tool=pubmedpubmed/19208184]\] h3. caCORE and caBIG # CiminoLiu JJH, HayamizuLi TFX, BodenreiderYoon OV, DavisClarke B,R. StaffordAnnotating GA,breast Ringwaldcancer M.microarray Thesamples caBIG terminology review processusing ontologies. ??JAMIA Annu BiomedSymp InformProc.?? 2009 Jun;42(3):571-80. Epub 2008 Dec 25. 2008 Nov 6:414-8. PubMed PMID: 1915479718999108; PubMed Central PMCID: PMC2729758PMC2655965. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1915479718999108]\] # ShironoshitaMarinelli EPRJ, Jean-MaryMontgomery YRK, BradleyLiu RMCL, KabukaShah MR. semCDI: a query formulation for semantic data integration in caBIG. ??J Am Med Inform AssocNH, 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 Jul-AugJan;1536(4Database issue):559D871-687. Epub 20082007 AprNov 247. PubMed PMID: 1843689717989087; PubMed Central PMCID: PMC2442262PMC2238948. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1843689717989087]\] # KomatsoulisMarquet GAG, WarzelDameron DBO, HartelSaikali FWS, ShanbhagMosser KJ, ChilukuriBurgun R,A. FragosoGrading G,glioma Coronadotumors 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 using OWL-DL and NCI Thesaurus. ??AMIA Annu Symp Proc.?? 2007 Oct 11:508-12. PubMed PMID: 18693888; PubMed Central PMCID: PMC2254758PMC2655830. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1751225918693888]\] # GaoBurgun QA, ZhangBodenreider YL,O. XieIssues ZY,in Zhangintegrating QP,epidemiology Huand ZZ.research caCORE:information corein architectureoncology: ofexperience bioinformationwith onICD-O3 cancerand researchthe inNCI AmericaThesaurus. ??BeijingAMIA DaAnnu XueSymp Xue BaoProc.?? 20062007 Apr 18;38(2):218-21. Chinese. Oct 11:85-9. PubMed PMID: 1661737118693803. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1661737118693803]\] # CovitzShah PANH, HartelRubin FDL, SchaeferEspinosa CI, DeMontgomery Coronado SK, FragosoMusen G,MA. SahniAnnotation H,and Gustafsonquery S,of Buetowtissue KH.microarray caCORE:data ausing commonthe infrastructure for cancer informaticsNCI Thesaurus. ??BMC Bioinformatics.?? 20032007 DecAug 12;19(18):2404-128;8:296. PubMed PMID: 1466822417686183; PubMed Central PMCID: PMC1988837. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1466822417686183]\] h3. LexEVS # PathakTobias J, PetersChilukuri LR, ChuteKomatsoulis CGGA, BodenreiderMohanty O.S, ComparingSioutos andN, evaluatingWarzel terminologyDB, servicesWright applicationLW, programmingCrowley interfaces: RxNav, UMLSKS and LexBIG. ??J Am Med Inform Assoc.?? 2010 Nov-Dec;17(6):714-9. PubMed PMID: 20962136; PubMed Central PMCID: PMC3000749. \[[PubMedRS. 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. \[[Free PMC Article\|http://www.ncbi.nlm.nih.gov/pubmed/20962136pmc/articles/PMC1524939/?tool=pubmed]\] h3. caCORE and caBIG # PathakCimino JJJ, SolbrigHayamizu HRTF, BuntrockBodenreider JDO, JohnsonDavis TMB, Chute CG. LexGrid: a framework for representing, storing, and querying biomedical terminologies from simple to sublimeStafford GA, Ringwald M. The caBIG terminology review process. ??J AmBiomed Med Inform Assoc.?? 2009 May-Jun;1642(3):305571-1580. Epub 20092008 MarDec 425. PubMed PMID: 1926193319154797; PubMed Central PMCID: PMC2732233PMC2729758. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1926193319154797]\] h3. NLP # CrowleyShironoshita RSEP, TseytlinJean-Mary EYR, JukicBradley D.RM, ReportTutorKabuka -MR. ansemCDI: intelligenta tutoringquery systemformulation thatfor usessemantic adata naturalintegration languagein interfacecaBIG. ??AMIAJ Am AnnuMed SympInform ProcAssoc.?? 2005:171-5 2008 Jul-Aug;15(4):559-68. Epub 2008 Apr 24. PubMed PMID: 1677902418436897; PubMed Central PMCID: PMC1560511PMC2442262. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1677902418436897]\] h3. Ontologies # LiuKomatsoulis KGA, ChapmanWarzel WWDB, 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)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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/2105772017512259]\] # SchulzGao SQ, SchoberZhang DYL, TudoseXie IZY, StenzhornZhang H.QP, TheHu PitfallsZZ. ofcaCORE: Thesauruscore Ontologizationarchitecture -of thebioinformation Caseon ofcancer theresearch NCIin ThesaurusAmerica. ??AMIABeijing AnnuDa SympXue ProcXue Bao.?? 20102006 NovApr 13;2010:727-3118;38(2):218-21. Chinese. PubMed PMID: 21347074; PubMed Central PMCID: PMC304137216617371. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/2134707416617371]\] # Noy N Covitz PA, Hartel F, TudoracheSchaefer TC, deDe Coronado S, Musen M. Developing biomedical ontologies collaboratively. ??AMIA Annu Symp Proc.?? 2008:520-4Fragoso 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. \[[Available onlinePubMed\|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656043/pdf/amia-0520-s2008.pdfpubmed/14668224]\] h3. LexEVS # CiminoPathak JJJ, ZhuPeters X.L, TheChute practicalCG, impact of ontologies on biomedical informaticsBodenreider O. Comparing and evaluating terminology services application programming interfaces: RxNav, UMLSKS and LexBIG. ??YearbJ Am Med Inform Assoc.?? 2006:124-35. Review. PubMed PMID: 170513062010 Nov-Dec;17(6):714-9. PubMed PMID: 20962136; PubMed Central PMCID: PMC3000749. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1705130620962136]\] # CeustersPathak WJ, SmithSolbrig BHR, GoldbergBuntrock L.JD, A terminological and ontological analysis of the NCI ThesaurusJohnson TM, Chute CG. LexGrid: a framework for representing, storing, and querying biomedical terminologies from simple to sublime. ??MethodsJ InfAm Med Inform Assoc.?? 2009 2005May-Jun;4416(43):498-507.305-15. Epub 2009 Mar 4. PubMed PMID: 19261933; PubMed Central PMCID: 16342916PMC2732233. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1634291619261933]\] h2h3. Pending ProcessingNLP h3. PubMed records # ShahCrowley NHRS, JonquetTseytlin CE, ChiangJukic AP,D. ButteReportTutor AJ,- Chenan R,intelligent Musentutoring MA. Ontology-driven indexing of public datasets for translational bioinformaticssystem that uses a natural language interface. ??BMC BioinformaticsAMIA Annu Symp Proc.?? 2009 Feb 5;10 Suppl 2:S1. PubMed PMID: 19208184; PubMed 2005:171-5. PubMed PMID: 16779024; PubMed Central PMCID: PMC2646250PMC1560511. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1920818416779024]\] h3. Ontologies # Cohen BLiu K, Chapman WW, OrenSavova MG, MinChute HCG, PerlSioutos YN, HalperCrowley MRS. Automated comparative auditing of NCIT genomic roles using NCBIEffectiveness of Lexico-syntactic Pattern Matching for Ontology Enrichment with Clinical Documents. ??JMethods BiomedInf InformMed.?? 20082010: Dec8;4149(6):904-13. Epub 2008 Mar 28. PubMed PMID: 18486558; PubMed Central PMCID: PMC2630966. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1848655821057720]\] # Mougin FSchulz S, Schober D, Tudose I, BodenreiderStenzhorn OH. Auditing The Pitfalls of Thesaurus Ontologization - the NCICase thesaurusof withthe semanticNCI web technologiesThesaurus. ??AMIA Annu Symp Proc.?? 20082010 Nov 613;2010:500727-431. PubMed PMID: 1899926521347074; PubMed Central PMCID: PMC2655981PMC3041372. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1899926521347074]\] # DetwilerNoy LTN, SuciuTudorache DT, Brinkleyde JF.Coronado RegularS, pathsMusen inM. SparQL:Developing queryingbiomedical theontologies NCI Thesauruscollaboratively. ??AMIA Annu Symp Proc.?? 2008 Nov 6:161520-54. PubMed PMID: 18999137; PubMed Central PMCID: PMC2656016. \[[PubMedAvailable online\|http://www.ncbi.nlm.nih.gov/pubmed/18999137]\] # Liu H, Li X, Yoon V, Clarke R. Annotating breast cancer microarray samples using ontologies. ??AMIA Annu Symp Procpmc/articles/PMC2656043/pdf/amia-0520-s2008.pdf]\] # Cohen B, Oren M, Min H, Perl Y, Halper M. Automated comparative auditing of NCIT genomic roles using NCBI. ??J Biomed Inform.?? 2008 Nov 6:414-8Dec;41(6):904-13. Epub 2008 Mar 28. PubMed PMID: 1899910818486558; PubMed Central PMCID: PMC2655965PMC2630966. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1899910818486558]\] # MinMougin HF, Cohen B, Halper M, Oren M, Perl Y. Detecting role errors in the gene hierarchy of the NCI Thesaurus. ??Cancer InformBodenreider O. Auditing the NCI thesaurus with semantic web technologies. ??AMIA Annu Symp Proc.?? 2008; Nov 6:293500-3134. PubMed PMID: 1922160618999265; PubMed Central PMCID: PMC2623310PMC2655981. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1922160618999265]\] # MarinelliDetwiler RJLT, MontgomerySuciu KD, LiuBrinkley CL,JF. ShahRegular NH,paths Prapongin W,SparQL: Nitzbergquerying M,the 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 7NCI Thesaurus. ??AMIA Annu Symp Proc.?? 2008 Nov 6:161-5. PubMed PMID: 1798908718999137; PubMed Central PMCID: PMC2238948PMC2656016. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1798908718999137]\] # MarquetMin GH, DameronCohen OB, SaikaliHalper SM, MosserOren JM, BurgunPerl AY. Grading glioma tumors using OWL-DL andDetecting role errors in the gene hierarchy of the NCI Thesaurus. ??AMIA Annu Symp ProcCancer Inform.?? 2007 Oct 11:508-122008;6:293-313. PubMed PMID: 1869388819221606; PubMed Central PMCID: PMC2655830PMC2623310. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1869388819221606]\] # BurgunCimino AJJ, BodenreiderZhu OX. IssuesThe inpractical integratingimpact epidemiologyof andontologies researchon information in oncology: experience with ICD-O3 and the NCI Thesaurusbiomedical informatics. ??AMIAYearb AnnuMed Symp ProcInform.?? 2007 Oct 11:85-92006:124-35. Review. PubMed PMID: 1869380317051306. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1869380317051306]\] # Shah NH, Rubin DL, Espinosa I, Montgomery K, Musen MA. Annotation and query of tissue microarray data using # Ceusters W, Smith B, Goldberg L. A terminological and ontological analysis of the NCI Thesaurus. ??BMCMethods Inf BioinformaticsMed.?? 2007 Aug 8;8:2962005;44(4):498-507. PubMed PMID: 17686183; PubMed Central PMCID: PMC198883716342916. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1768618316342916]\] h2. Pending Processing h3. PubMed records # Yang HJ, Lay YL, Tsao WY, Liou YC, Lin CK. Impact of language anxiety and self-efficacy on accessing Internet sites. ??Cyberpsychol Behav.?? 2007 Apr;10(2):226-33. PubMed PMID: 17474840. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/17474840]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/18974854]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/16929044]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/17238522]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/17238469]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/17238433]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/17149500]\] # Cimino JJ, Zhu X. The practical impact of ontologies on biomedical informatics. ??Yearb Med Inform.?? 2006:124-35. Review. PubMed PMID: 17051306. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/17051306]\] # Wang MH. Extension neural network-type 2 and its applications. ??IEEE Trans Neural Netw.?? 2005 Nov;16(6):1352-61. PubMed PMID: 16342480. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/16342480]\] # Ahrazem O, IbÃ¡Ã±ez MD, LÃ³pez-TorrejÃ³n G, SÃ¡nchez-Monge R, Sastre J, Lombardero M, Barber D, Salcedo G. Lipid transfer proteins and allergy to oranges. ??Int Arch Allergy Immunol.?? 2005 Jul;137(3):201-10. Epub 2005 Jun 9. PubMed PMID: 15947476. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/15947476]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/16779163]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/16779024]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/16779002]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/16342916]\] # Sung WP, Matzen VC, Shih MH. Time domain system identification of unknown initial conditions. ??J Zhejiang Univ Sci.?? 2004 Sep;5(9):1035-44. PubMed PMID: 15322997. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/15322997]\] # Sung WP, Shih MH, Chen KS. Analytical method for promoting process capability of shock absorption steel. ??J Zhejiang Univ Sci.?? 2003 Jul-Aug;4(4):388-92. PubMed PMID: 12861612. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/12861612]\] # Wang MH, Hung CP. Extension neural network and its applications. ??Neural Netw.?? 2003 Jun-Jul;16(5-6):779-84. PubMed PMID: 12850034. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/12850034]\] {multi-excerpt} {scrollbar:icons=false}

Wiki Markup

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h1. {page-info:title}

{multi-excerpt:name=Bibliography}Below is a preliminary bibliography of scientific literature on EVS and its use.

{toc:minLevel=2}

h2. Scientific Journal Articles

h3. EVS General

# 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. \[[Available online|http://www.sciencedirect.com/science/article/B6WHD-4VFC80H-4/2/42a20ff355ab427f4d674d96e913c63b]\]
# 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. \[[Free PMC Article|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2753293/?tool=pubmed]\]
# 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. \[[Available online|http://www.nxtbook.com/nxtbooks/dia/druginformationjournal0507/index.php?startpage=142]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/16697710]\]
# 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. \[[Available online|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655888/pdf/amia-0165-s2007.pdf]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/15797001]\]
# 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. \[[Free PMC Article|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447470/?tool=pubmed]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/15360769]\]
# Hartel F, Fragoso G, Ong K, Dionne R. Enhancing Quality of Retrieval Through Concept Edit History. ??AMIA Annu Symp Proc.?? 2003:279-83. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/14728178]\]
# 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.

h3. Biomedical Applications

# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/21597104]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/21552494]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/21918596]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/21893840]\]
# Cuggia M, BourdÃ© 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/21893803]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/20805954]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/20715359]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/21347147]\]
# TobiasShah JNH, ChilukuriJonquet RC, KomatsoulisChiang GAAP, MohantyButte SAJ, SioutosChen NR, WarzelMusen 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 ArticleMA. 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1524939/?tool=pubmedpubmed/19208184]\]

h3. caCORE and caBIG

# CiminoLiu JJH, HayamizuLi TFX, BodenreiderYoon OV, DavisClarke B,R. StaffordAnnotating GA,breast Ringwaldcancer M.microarray Thesamples caBIG terminology review processusing ontologies. ??JAMIA Annu BiomedSymp InformProc.?? 2009 Jun;42(3):571-80. Epub 2008 Dec 25. 2008 Nov 6:414-8. PubMed PMID: 1915479718999108; PubMed Central PMCID: PMC2729758PMC2655965. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1915479718999108]\]
# ShironoshitaMarinelli EPRJ, Jean-MaryMontgomery YRK, BradleyLiu RMCL, KabukaShah MR. semCDI: a query formulation for semantic data integration in caBIG. ??J Am Med Inform AssocNH, 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 Jul-AugJan;1536(4Database issue):559D871-687. Epub 20082007 AprNov 247. PubMed PMID: 1843689717989087; PubMed Central PMCID: PMC2442262PMC2238948. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1843689717989087]\]
# KomatsoulisMarquet GAG, WarzelDameron DBO, HartelSaikali FWS, ShanbhagMosser KJ, ChilukuriBurgun R,A. FragosoGrading G,glioma Coronadotumors 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 using OWL-DL and NCI Thesaurus. ??AMIA Annu Symp Proc.?? 2007 Oct 11:508-12. PubMed PMID: 18693888; PubMed Central PMCID: PMC2254758PMC2655830. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1751225918693888]\]
# GaoBurgun QA, ZhangBodenreider YL,O. XieIssues ZY,in Zhangintegrating QP,epidemiology Huand ZZ.research caCORE:information corein architectureoncology: ofexperience bioinformationwith onICD-O3 cancerand researchthe inNCI AmericaThesaurus. ??BeijingAMIA DaAnnu XueSymp Xue BaoProc.?? 20062007 Apr 18;38(2):218-21. Chinese. Oct 11:85-9. PubMed PMID: 1661737118693803. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1661737118693803]\]
# CovitzShah PANH, HartelRubin FDL, SchaeferEspinosa CI, DeMontgomery Coronado SK, FragosoMusen G,MA. SahniAnnotation H,and Gustafsonquery S,of Buetowtissue KH.microarray caCORE:data ausing commonthe infrastructure for cancer informaticsNCI Thesaurus. ??BMC Bioinformatics.?? 20032007 DecAug 12;19(18):2404-128;8:296. PubMed PMID: 1466822417686183; PubMed Central PMCID: PMC1988837. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1466822417686183]\]

h3. LexEVS

# PathakTobias J, PetersChilukuri LR, ChuteKomatsoulis CGGA, BodenreiderMohanty O.S, ComparingSioutos andN, evaluatingWarzel terminologyDB, servicesWright applicationLW, programmingCrowley interfaces: RxNav, UMLSKS and LexBIG. ??J Am Med Inform Assoc.?? 2010 Nov-Dec;17(6):714-9. PubMed PMID: 20962136; PubMed Central PMCID: PMC3000749. \[[PubMedRS. 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. \[[Free PMC Article|http://www.ncbi.nlm.nih.gov/pubmed/20962136pmc/articles/PMC1524939/?tool=pubmed]\]

h3. caCORE and caBIG

# PathakCimino JJJ, SolbrigHayamizu HRTF, BuntrockBodenreider JDO, JohnsonDavis TMB, Chute CG. LexGrid: a framework for representing, storing, and querying biomedical terminologies from simple to sublimeStafford GA, Ringwald M. The caBIG terminology review process. ??J AmBiomed Med Inform Assoc.?? 2009 May-Jun;1642(3):305571-1580. Epub 20092008 MarDec 425.  PubMed PMID: 1926193319154797; PubMed Central PMCID: PMC2732233PMC2729758. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1926193319154797]\]

h3. NLP

# CrowleyShironoshita RSEP, TseytlinJean-Mary EYR, JukicBradley D.RM, ReportTutorKabuka -MR. ansemCDI: intelligenta tutoringquery systemformulation thatfor usessemantic adata naturalintegration languagein interfacecaBIG. ??AMIAJ Am AnnuMed SympInform ProcAssoc.?? 2005:171-5 2008 Jul-Aug;15(4):559-68. Epub 2008 Apr 24. PubMed PMID: 1677902418436897; PubMed Central PMCID: PMC1560511PMC2442262. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1677902418436897]\]

h3. Ontologies

# LiuKomatsoulis KGA, ChapmanWarzel WWDB, 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)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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/2105772017512259]\]
# SchulzGao SQ, SchoberZhang DYL, TudoseXie IZY, StenzhornZhang H.QP, TheHu PitfallsZZ. ofcaCORE: Thesauruscore Ontologizationarchitecture -of thebioinformation Caseon ofcancer theresearch NCIin ThesaurusAmerica. ??AMIABeijing AnnuDa SympXue ProcXue Bao.?? 20102006 NovApr 13;2010:727-3118;38(2):218-21. Chinese. PubMed PMID: 21347074; PubMed Central PMCID: PMC304137216617371. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/2134707416617371]\]
# Noy N Covitz PA, Hartel F, TudoracheSchaefer TC, deDe Coronado S, Musen M. Developing biomedical ontologies collaboratively. ??AMIA Annu Symp Proc.?? 2008:520-4Fragoso 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. \[[Available onlinePubMed|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656043/pdf/amia-0520-s2008.pdfpubmed/14668224]\]

h3. LexEVS

# CiminoPathak JJJ, ZhuPeters X.L, TheChute practicalCG, impact of ontologies on biomedical informaticsBodenreider O. Comparing and evaluating terminology services application programming interfaces: RxNav, UMLSKS and LexBIG. ??YearbJ Am Med Inform Assoc.?? 2006:124-35. Review. PubMed PMID: 170513062010 Nov-Dec;17(6):714-9. PubMed PMID: 20962136; PubMed Central PMCID: PMC3000749. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1705130620962136]\]
# CeustersPathak WJ, SmithSolbrig BHR, GoldbergBuntrock L.JD, A terminological and ontological analysis of the NCI ThesaurusJohnson TM, Chute CG. LexGrid: a framework for representing, storing, and querying biomedical terminologies from simple to sublime. ??MethodsJ InfAm Med Inform Assoc.?? 2009 2005May-Jun;4416(43):498-507.305-15. Epub 2009 Mar 4.  PubMed PMID: 19261933; PubMed Central PMCID: 16342916PMC2732233. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1634291619261933]\]


h2h3. Pending ProcessingNLP

h3. PubMed records

# ShahCrowley NHRS, JonquetTseytlin CE, ChiangJukic AP,D. ButteReportTutor AJ,- Chenan R,intelligent Musentutoring MA. Ontology-driven indexing of public datasets for translational bioinformaticssystem that uses a natural language interface. ??BMC BioinformaticsAMIA Annu Symp Proc.??  2009 Feb 5;10 Suppl 2:S1. PubMed PMID: 19208184; PubMed 2005:171-5. PubMed PMID: 16779024; PubMed Central PMCID: PMC2646250PMC1560511. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1920818416779024]\]

h3. Ontologies

# Cohen BLiu K, Chapman WW, OrenSavova MG, MinChute HCG, PerlSioutos YN, HalperCrowley MRS. Automated comparative auditing of NCIT genomic roles using NCBIEffectiveness of Lexico-syntactic Pattern Matching for Ontology Enrichment with Clinical Documents. ??JMethods BiomedInf InformMed.?? 20082010: Dec8;4149(6):904-13. Epub 2008 Mar 28. PubMed PMID: 18486558; PubMed Central PMCID: PMC2630966. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1848655821057720]\]
# Mougin FSchulz S, Schober D, Tudose I, BodenreiderStenzhorn OH. Auditing The Pitfalls of Thesaurus Ontologization - the NCICase thesaurusof withthe semanticNCI web technologiesThesaurus. ??AMIA Annu Symp Proc.?? 20082010 Nov 613;2010:500727-431. PubMed PMID: 1899926521347074; PubMed Central PMCID: PMC2655981PMC3041372. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1899926521347074]\]
# DetwilerNoy LTN, SuciuTudorache DT, Brinkleyde JF.Coronado RegularS, pathsMusen inM. SparQL:Developing queryingbiomedical theontologies NCI Thesauruscollaboratively. ??AMIA Annu Symp Proc.?? 2008 Nov 6:161520-54. PubMed PMID: 18999137; PubMed Central PMCID: PMC2656016. \[[PubMedAvailable online|http://www.ncbi.nlm.nih.gov/pubmed/18999137]\]
# Liu H, Li X, Yoon V, Clarke R. Annotating breast cancer microarray samples using ontologies. ??AMIA Annu Symp Procpmc/articles/PMC2656043/pdf/amia-0520-s2008.pdf]\]
# Cohen B, Oren M, Min H, Perl Y, Halper M. Automated comparative auditing of NCIT genomic roles using NCBI. ??J Biomed Inform.?? 2008 Nov 6:414-8Dec;41(6):904-13. Epub 2008 Mar 28. PubMed PMID: 1899910818486558; PubMed Central PMCID: PMC2655965PMC2630966. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1899910818486558]\]
# MinMougin HF, Cohen B, Halper M, Oren M, Perl Y. Detecting role errors in the gene hierarchy of the NCI Thesaurus. ??Cancer InformBodenreider O. Auditing the NCI thesaurus with semantic web technologies. ??AMIA Annu Symp Proc.?? 2008; Nov 6:293500-3134. PubMed PMID: 1922160618999265; PubMed Central PMCID: PMC2623310PMC2655981. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1922160618999265]\]
# MarinelliDetwiler RJLT, MontgomerySuciu KD, LiuBrinkley CL,JF. ShahRegular NH,paths Prapongin W,SparQL: Nitzbergquerying M,the 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 7NCI Thesaurus. ??AMIA Annu Symp Proc.?? 2008 Nov 6:161-5. PubMed PMID: 1798908718999137; PubMed Central PMCID: PMC2238948PMC2656016. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1798908718999137]\]
# MarquetMin GH, DameronCohen OB, SaikaliHalper SM, MosserOren JM, BurgunPerl AY. Grading glioma tumors using OWL-DL andDetecting role errors in the gene hierarchy of the NCI Thesaurus. ??AMIA Annu Symp ProcCancer Inform.?? 2007 Oct 11:508-122008;6:293-313. PubMed PMID: 1869388819221606; PubMed Central PMCID: PMC2655830PMC2623310. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1869388819221606]\]
# BurgunCimino AJJ, BodenreiderZhu OX. IssuesThe inpractical integratingimpact epidemiologyof andontologies researchon information in oncology: experience with ICD-O3 and the NCI Thesaurusbiomedical informatics. ??AMIAYearb AnnuMed Symp ProcInform.?? 2007 Oct 11:85-92006:124-35. Review. PubMed PMID: 1869380317051306. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1869380317051306]\]
# Shah NH, Rubin DL, Espinosa I, Montgomery K, Musen MA. Annotation and query of tissue microarray data using # Ceusters W, Smith B, Goldberg L. A terminological and ontological analysis of the NCI Thesaurus. ??BMCMethods Inf BioinformaticsMed.?? 2007 Aug 8;8:2962005;44(4):498-507. PubMed PMID: 17686183; PubMed Central PMCID: PMC198883716342916. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1768618316342916]\]


h2. Pending Processing

h3. PubMed records

# Yang HJ, Lay YL, Tsao WY, Liou YC, Lin CK. Impact of language anxiety and self-efficacy on accessing Internet sites. ??Cyberpsychol Behav.?? 2007 Apr;10(2):226-33. PubMed PMID: 17474840. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/17474840]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/18974854]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/16929044]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/17238522]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/17238469]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/17238433]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/17149500]\]
# Cimino JJ, Zhu X. The practical impact of ontologies on biomedical informatics. ??Yearb Med Inform.?? 2006:124-35. Review. PubMed PMID: 17051306. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/17051306]\]
# Wang MH. Extension neural network-type 2 and its applications. ??IEEE Trans Neural Netw.?? 2005 Nov;16(6):1352-61. PubMed PMID: 16342480. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/16342480]\]
# Ahrazem O, IbÃ¡Ã±ez MD, LÃ³pez-TorrejÃ³n G, SÃ¡nchez-Monge R, Sastre J, Lombardero M, Barber D, Salcedo G. Lipid transfer proteins and allergy to oranges. ??Int Arch Allergy Immunol.?? 2005 Jul;137(3):201-10. Epub 2005 Jun 9. PubMed PMID: 15947476. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/15947476]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/16779163]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/16779024]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/16779002]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/16342916]\]
# Sung WP, Matzen VC, Shih MH. Time domain system identification of unknown initial conditions. ??J Zhejiang Univ Sci.?? 2004 Sep;5(9):1035-44. PubMed PMID: 15322997. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/15322997]\]
# Sung WP, Shih MH, Chen KS. Analytical method for promoting process capability of shock absorption steel. ??J Zhejiang Univ Sci.?? 2003 Jul-Aug;4(4):388-92. PubMed PMID: 12861612. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/12861612]\]
# Wang MH, Hung CP. Extension neural network and its applications. ??Neural Netw.??  2003 Jun-Jul;16(5-6):779-84. PubMed PMID: 12850034. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/12850034]\]

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