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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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/21597104]\] # 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. \[[Free PMC Article\|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1524939/?tool=pubmed]\] h3. LexEVS h3. NLP h3. Ontologies # 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). \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/21057720]\] # Noy N, Tudorache T, de Coronado S, Musen M. Developing biomedical ontologies collaboratively. ??AMIA Annu Symp Proc.?? 2008:520-4. \[[Available online\|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656043/pdf/amia-0520-s2008.pdf]\] h2. Pending Processing h3. PubMed records # PathakSherman JS, WangShats JO, KashyapKetcham SMA, BasfordAnderson MMA, LiWhitcomb RDC, MasysLynch DRHT, ChuteGhiorzo CG.P, MappingRubinstein clinicalWS, phenotypeSasson dataAR, elementsGrizzle toWE, standardizedHaynatzki metadataG, repositoriesFeng andJ, controlledSherman terminologies:A, theKinarsky eMERGEL, NetworkBrand experienceRE. JPCCR: AmPancreatic MedCancer InformCollaborative AssocRegistry. 2011 Jul-Aug; 18 (4) :376-86??Cancer Inform.?? 2011 Mar 23;10:83-91. PubMed PMID:21597104 21552494; PubMed Central PMCID: PMC3128396PMC3085425. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/2159710421552494]\] # Sherman S, Shats O, KetchamFleissner MAE, AndersonBascom MAG, WhitcombYiee DCK, LynchCopur HTM, GhiorzoCrow PK, RubinsteinRooney WSJ, SassonMateen ARZ, Grizzle WE, Haynatzki GKetcham MA, Feng J, Sherman A, Gleason M, Kinarsky L, Brand RE. PCCR: Pancreatic Cancer Collaborative Registry. Silva-Lopez E, Edney J, Reed E, Berger A, Cowan K. Multicenter breast cancer collaborative registry. ??Cancer Inform.?? 2011 Mar 23; 10:83-91217-26. Epub 2011 Aug 31. PubMed PMID:21552494 21918596; PubMed Central PMCID: PMC3085425PMC3169352. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/2155249421918596]\] # ShermanBertaud Gounot SV, ShatsDonfack OV, FleissnerLasbleiz EJ, BascomBourde GA, YieeDuvauferrier K,R. CopurCreating M,an Crowontology K,driven Rooneyrules J,base Mateenfor Z,an Ketchamexpert MA,system Fengfor J,medical 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 Citationdiagnosis. ??Stud Health Technol Inform.?? 2011;169:714-8. PubMed PMID: 21893840. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/2191859621893840]\] # SchulzCuggia SM, SchoberBourdÃ© DA, TudoseTurlin IB, StenzhornVincendeau H.S, TheBertaud PitfallsV, ofBohec ThesaurusC, OntologizationDuvauferrier -R. theAutomatic CaseDefinition of the NCI Thesaurus. AMIA Annu Symp Proc. 2010 Nov 13; 2010:727-31Oncologic EHR Data Elements from NCIT in OWL. ??Stud Health Technol Inform.?? 2011;169:517-21. PubMed PMID:21347074; PubMed Central PMCID: PMC3041372 21893803. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/2134707421893803]\] # PathakSchulz JS, PetersSchober LD, ChuteTudose CGI, BodenreiderStenzhorn OH. ComparingThe andPitfalls evaluatingof terminologyThesaurus servicesOntologization application- programmingthe interfaces:Case RxNav,of UMLSKSthe andNCI LexBIGThesaurus. J??AMIA AmAnnu MedSymp Inform AssocProc.?? 2010 Nov-Dec; 17 (6) :714-9 13;2010:727-31. PubMed PMID:20962136 21347074; PubMed Central PMCID: PMC3000749PMC3041372. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/2096213621347074]\] # KangLiu HPK, BorromeoChapman CDWW, BermanSavova JJG, BecichChute MJ.CG, TheSioutos tissueN, microarrayCrowley OWLRS. schema:Effectiveness Anof openLexico-sourcesyntactic Pattern toolMatching for sharing tissue microarray data. J Pathol Inform. 2010 Jul 13; 1PubMed PMID:20805954 Ontology Enrichment with Clinical Documents. ??Methods Inf Med.?? 2010 Nov 8;49(6). PubMed PMID: 21057720; PubMed Central PMCID: PMC3125434. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/21057720]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/20962136]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/21347147]\] #: 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. ??J Biomed Inform.?? 2009 Jun;42(3):530-9. PubMed PMID: 19475726. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/19475726]\] #: 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/19154797]\] #: 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/19261933]\] #: Bitar D, Goubar A, Desenclos JC. International travels and fever screening during epidemics: a literature review on the effectiveness and potential use of non-contact infrared thermometers. ??Euro Surveill.?? 2009 Feb 12;14(6). pii: 19115. Review. PubMed PMID: 19215720. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/19215720]\] #: 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/19208184]\] #: 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/18486558]\] #: 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/18999265]\] #: 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/18999137]\] #: Liu H, Li X, Yoon V, Clarke R. Annotating breast cancer microarray samples using ontologies. ??AMIA Annu Symp Proc.?? 2008 Nov 6:414-8. PubMed PMID: 18999108; PubMed Central PMCID: PMC2655965. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/18999108]\] #: Noy NF, Tudorache T, de Coronado S, Musen MA. Developing biomedical ontologies collaboratively. ??AMIA Annu Symp Proc.?? 2008 Nov 6:520-4. PubMed PMID: 18998901; PubMed Central PMCID: PMC2656043. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/18998901]\] #: 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/18436897]\] #: 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/17512259]\] #: 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. PubMed PMID: 19789731; PubMed Central PMCID: PMC2753293. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/19789731]\] #: 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/19221606]\] #: 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: PMC2929536PMC2238948. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/2080595417989087]\] #: ReedMarquet TLG, 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 CitationDameron 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/2071535918693888]\] # 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: 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 Oct 11:165-70. PubMed PMID:21347147 18693819; PubMed Central PMCID: PMC3041542PMC2655888. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/2134714718693819]\] # Cimino JJ, Hayamizu TF: Burgun A, Bodenreider O, Davis B, Stafford GA, Ringwald M. The caBIG terminology review process. J Biomed Inform. 2009 Jun; 42 (3) :571-80. 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:19154797; PubMed Central PMCID: PMC2729758. [PubMed Citation18693803. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1915479718693803]\] #: PathakShah JNH, SolbrigRubin HRDL, BuntrockEspinosa JDI, JohnsonMontgomery TMK, ChuteMusen CGMA. LexGrid:Annotation aand frameworkquery forof representing,tissue storing,microarray anddata queryingusing biomedicalthe terminologies from simple to sublime. J Am Med Inform Assoc. 2009 May-Jun; 16 (3) :305-15NCI Thesaurus. ??BMC Bioinformatics.?? 2007 Aug 8;8:296. PubMed PMID:19261933 17686183; PubMed Central PMCID: PMC2732233PMC1988837. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/1926193317686183]\] #: ShahYang NHHJ, JonquetLay CYL, ChiangTsao APWY, ButteLiou AJYC, ChenLin R,CK. MusenImpact MA. Ontology-driven indexing of public datasets for translational bioinformatics. BMC Bioinformatics. 2009 Feb 5; 10 Suppl 2:S1of language anxiety and self-efficacy on accessing Internet sites. ??Cyberpsychol Behav.?? 2007 Apr;10(2):226-33. PubMed PMID:19208184; PubMed Central PMCID: PMC2646250 17474840. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/1920818417474840]\] # Mougin F, Bodenreider O. Auditing the NCI thesaurus with semantic web technologies. AMIA Annu Symp Proc. 2008 Nov 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. ??J Biomed Inform.?? 2007 Feb;40(1):30-43. Epub 2006 Mar 15. PubMed PMID:18999265; PubMed Central PMCID: PMC2655981 16697710. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/1899926516697710]\] #: DetwilerZhang LTS, Suciu D, Brinkley JF. Regular paths in SparQL: querying the NCI Thesaurus. AMIA Annu Symp Proc. 2008 Nov 6;Bodenreider O. Experience in Aligning Anatomical Ontologies. ??Int J Semant Web Inf Syst.?? 2007;3(2):1-26. PubMed PMID:18999137 18974854; PubMed Central PMCID: PMC2656016PMC2575410. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/1899913718974854]\] #: LiuMin H, Li X, Yoon V, Clarke R. Annotating breast cancer microarray samples using ontologies. AMIA Annu Symp Proc. 2008 Nov 6;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:18999108 16929044; PubMed Central PMCID: PMC2655965PMC1656963. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/1899910816929044]\] # 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: 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:18436897; PubMed Central PMCID: PMC2442262 16617371. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/1843689716617371]\] #: KomatsoulisDeitzer GAJR, WarzelPayne 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) :106-23PR, Starren JB. Coverage of clinical trials tasks in existing ontologies. ??AMIA Annu Symp Proc.?? 2006:903. PubMed PMID:17512259 17238522; PubMed Central PMCID: PMC2254758PMC1839431. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/17512259] # Marinelli RJ, Montgomery K, Liu CL, Shah NH, Prapong W, Nitzberg M, Zachariah ZK, Sherlock GJ, Natkunam Y, West RB, van de Rijn M, Brown PO, Ball CA. The Stanford Tissue Microarray Database. Nucleic Acids Res. 2008 Jan; 36 (Database issue) :D871-717238522]\] #: 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:17989087 17238469; PubMed Central PMCID: PMC2238948PMC1839578. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/1798908717238469]\] #: MinShah HNH, CohenRubin BDL, HalperSupekar MKS, Oren M, Perl Y. Detecting role errors in the gene hierarchy of the NCI Thesaurus. Cancer Inform. 2008; 6:293-313Musen MA. Ontology-based annotation and query of tissue microarray data. ??AMIA Annu Symp Proc.?? 2006:709-13. PubMed PMID:19221606 17238433; PubMed Central PMCID: PMC2623310PMC1839511. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/1922160617238433]\] #: TrottiNadkarni APM, ColevasBrandt AD,CA. SetserThe A,Common BaschData 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 CitationElements for cancer research: remarks on functions and structure. ??Methods Inf Med.?? 2006;45(6):594-601. PubMed PMID: 17149500; PubMed Central PMCID: PMC2980785. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1799193117149500]\] #: MarquetCimino GJJ, Dameron O, Saikali S, Mosser J, Burgun A. Grading glioma tumors using OWL-DL and NCI Thesaurus. AMIA Annu Symp Proc. 2007 Oct 11;Zhu X. The practical impact of ontologies on biomedical informatics. ??Yearb Med Inform.?? 2006:124-35. Review. PubMed PMID:18693888; PubMed Central PMCID: PMC2655830 17051306. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/1869388817051306]\] #: Burgun A, Bodenreider OWang MH. IssuesExtension inneural integratingnetwork-type epidemiology2 and research information in oncology: experience with ICD-O3 and the NCI Thesaurus. AMIA Annu Symp Proc. 2007 Oct 11;its applications. ??IEEE Trans Neural Netw.?? 2005 Nov;16(6):1352-61. PubMed PMID:18693803 16342480. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/1869380316342480]\] # 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: 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:17686183; PubMed Central PMCID: PMC1988837 15947476. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/1768618315947476]\] # Zhang: Hartel FW, de Coronado S, Bodenreider O. Experience in Aligning Anatomical Ontologies. Int J Semant Web Inf Syst. 2007; 3 (2) :1-26Dionne R, Fragoso G, Golbeck J. Modeling a description logic vocabulary for cancer research. ??J Biomed Inform.?? 2005 Apr;38(2):114-29. PubMed PMID:18974854; PubMed Central PMCID: PMC2575410 15797001. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/1897485415797001]\] # Gao: Q, Zhang YLS, XieBodenreider ZY,O. Zhang QP, Hu ZZ. [caCORE: core architectureAlignment of multiple ontologies of bioinformationanatomy: onderiving cancerindirect researchmappings infrom America].direct Beijingmappings Dato Xuea Xue Baoreference. 2006??AMIA AprAnnu 18; 38 (2) :218-21Symp Proc.?? 2005:864-8. PubMed PMID:16617371 16779163; PubMed Central PMCID: PMC1560629. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/1661737116779163]\] # Deitzer JR, Payne PR, Starren JB. Coverage of clinical trials tasks in existing ontologies. : Crowley RS, Tseytlin E, Jukic D. ReportTutor - an intelligent tutoring system that uses a natural language interface. ??AMIA Annu Symp Proc. 2006;?? 2005:171-5. PubMed PMID:17238522 16779024; PubMed Central PMCID: PMC1839431PMC1560511. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/1723852216779024]\] # Bailey LO: Bodenreider O, Hayamizu TF, KennedyRingwald CHM, De FrittsCoronado MJS, HartelZhang FWS. Development ofOf amice modeland formen: thealigning representationmouse ofand nanotechnology-specifichuman terminologyanatomies. ??AMIA Annu Symp Proc. 2006;?? 2005:61-5. PubMed PMID:17238469 16779002; PubMed Central PMCID: PMC1839578PMC1560846. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/1723846916779002]\] #: ShahCeusters NHW, RubinSmith DLB, Supekar KS, Musen MA. Ontology-based annotation and queryGoldberg L. A terminological and ontological analysis of tissuethe microarrayNCI dataThesaurus. AMIA Annu??Methods SympInf ProcMed.?? 2006;2005;44(4):498-507. PubMed PMID:17238433; PubMed Central PMCID: PMC1839511 16342916. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/1723843316342916]\] #: NadkarniSung PMWP, BrandtMatzen CA.VC, TheShih CommonMH. DataTime Elementsdomain forsystem canceridentification research:of remarksunknown oninitial functions and structure. Methods Inf Med. 2006; 45 (6) :594-601conditions. ??J Zhejiang Univ Sci.?? 2004 Sep;5(9):1035-44. PubMed PMID:17149500; PubMed Central PMCID: PMC2980785 15322997. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/1714950015322997]\] # Cimino JJ, Zhu X. The practical impact of ontologies on biomedical informatics. Yearb Med Inform. 2006; PubMed PMID:17051306. [PubMed Citation: Fragoso G, de Coronado S, Haber M, Hartel F, Wright L. Overview and utilization of the NCI thesaurus. ??Comp Funct Genomics.?? 2004;5(8):648-54. PubMed PMID: 18629178; PubMed Central PMCID: PMC2447470. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1705130618629178]\] #: de ZhangCoronado 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 CitationHaber 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1677916315360769]\] # Crowley RS: Covitz PA, Hartel F, TseytlinSchaefer EC, 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 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1677902414668224]\] #: Bodenreider O, Hayamizu TF, Ringwald MSung WP, DeShih Coronado SMH, ZhangChen SKS. OfAnalytical method micefor andpromoting men:process aligningcapability mouseof andshock humanabsorption anatomiessteel. AMIA??J AnnuZhejiang SympUniv ProcSci. 2005;?? 2003 Jul-Aug;4(4):388-92. PubMed PMID:16779002; PubMed Central PMCID: PMC1560846 12861612. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/1677900212861612]\] # Ceusters W, Smith B: Wang MH, GoldbergHung LCP. AExtension neural terminologicalnetwork and ontologicalits analysis of the NCI Thesaurus. Methods Inf Med. 2005; 44 (4) :498-507applications. ??Neural Netw.?? 2003 Jun-Jul;16(5-6):779-84. PubMed PMID:16342916 12850034. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/1634291612850034]\] # Covitz PA, Hartel F, Schaefer C, De Coronado S: Hartel FW, Fragoso G, SahniOng HKL, Gustafson S, Buetow KHDionne R. caCORE:Enhancing aquality commonof infrastructureretrieval forthrough cancerconcept informatics.edit Bioinformaticshistory. 2003??AMIA DecAnnu 12; 19 (18) :2404-12Symp Proc.?? 2003:279-83. PubMed PMID:14668224 14728178; PubMed Central PMCID: PMC1480320. \[[PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/1466822414728178]\] {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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/21597104]\]
# 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. \[[Free PMC Article|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1524939/?tool=pubmed]\]

h3. LexEVS

h3. NLP

h3. Ontologies

# 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). \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/21057720]\]
# Noy N, Tudorache T, de Coronado S, Musen M. Developing biomedical ontologies collaboratively. ??AMIA Annu Symp Proc.?? 2008:520-4. \[[Available online|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656043/pdf/amia-0520-s2008.pdf]\]


h2. Pending Processing

h3. PubMed records

# PathakSherman JS, WangShats JO, KashyapKetcham SMA, BasfordAnderson MMA, LiWhitcomb RDC, MasysLynch DRHT, ChuteGhiorzo CG.P, MappingRubinstein clinicalWS, phenotypeSasson dataAR, elementsGrizzle toWE, standardizedHaynatzki metadataG, repositoriesFeng andJ, controlledSherman terminologies:A, theKinarsky eMERGEL, NetworkBrand experienceRE. JPCCR: AmPancreatic MedCancer InformCollaborative AssocRegistry. 2011 Jul-Aug; 18 (4) :376-86??Cancer Inform.?? 2011 Mar 23;10:83-91. PubMed PMID:21597104 21552494; PubMed Central PMCID: PMC3128396PMC3085425. \[[PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/2159710421552494]\]
# Sherman S, Shats O, KetchamFleissner MAE, AndersonBascom MAG, WhitcombYiee DCK, LynchCopur HTM, GhiorzoCrow PK, RubinsteinRooney WSJ, SassonMateen ARZ, Grizzle WE, Haynatzki GKetcham MA, Feng J, Sherman A, Gleason M, Kinarsky L, Brand RE. PCCR: Pancreatic Cancer Collaborative Registry. Silva-Lopez E, Edney J, Reed E, Berger A, Cowan K. Multicenter breast cancer collaborative registry. ??Cancer Inform.?? 2011 Mar 23; 10:83-91217-26. Epub 2011 Aug 31. PubMed PMID:21552494 21918596; PubMed Central PMCID: PMC3085425PMC3169352. \[[PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/2155249421918596]\]
# ShermanBertaud Gounot SV, ShatsDonfack OV, FleissnerLasbleiz EJ, BascomBourde GA, YieeDuvauferrier K,R. CopurCreating M,an Crowontology K,driven Rooneyrules J,base Mateenfor Z,an Ketchamexpert MA,system Fengfor J,medical 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 Citationdiagnosis. ??Stud Health Technol Inform.?? 2011;169:714-8. PubMed PMID: 21893840. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/2191859621893840]\]
# SchulzCuggia SM, SchoberBourdÃ© DA, TudoseTurlin IB, StenzhornVincendeau H.S, TheBertaud PitfallsV, ofBohec ThesaurusC, OntologizationDuvauferrier -R. theAutomatic CaseDefinition of the NCI Thesaurus. AMIA Annu Symp Proc. 2010 Nov 13; 2010:727-31Oncologic EHR Data Elements from NCIT in OWL. ??Stud Health Technol Inform.?? 2011;169:517-21. PubMed PMID:21347074; PubMed Central PMCID: PMC3041372 21893803. \[[PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/2134707421893803]\]
# PathakSchulz JS, PetersSchober LD, ChuteTudose CGI, BodenreiderStenzhorn OH. ComparingThe andPitfalls evaluatingof terminologyThesaurus servicesOntologization application- programmingthe interfaces:Case RxNav,of UMLSKSthe andNCI LexBIGThesaurus. J??AMIA AmAnnu MedSymp Inform AssocProc.?? 2010 Nov-Dec; 17 (6) :714-9 13;2010:727-31. PubMed PMID:20962136 21347074; PubMed Central PMCID: PMC3000749PMC3041372. \[[PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/2096213621347074]\]
# KangLiu HPK, BorromeoChapman CDWW, BermanSavova JJG, BecichChute MJ.CG, TheSioutos tissueN, microarrayCrowley OWLRS. schema:Effectiveness Anof openLexico-sourcesyntactic Pattern toolMatching for sharing tissue microarray data. J Pathol Inform. 2010 Jul 13; 1PubMed PMID:20805954 Ontology Enrichment with Clinical Documents. ??Methods Inf Med.?? 2010 Nov 8;49(6). PubMed PMID: 21057720; PubMed Central PMCID: PMC3125434. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/21057720]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/20962136]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/21347147]\]
#: 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. ??J Biomed Inform.?? 2009 Jun;42(3):530-9. PubMed PMID: 19475726. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/19475726]\]
#: 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/19154797]\]
#: 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/19261933]\]
#: Bitar D, Goubar A, Desenclos JC. International travels and fever screening during epidemics: a literature review on the effectiveness and potential use of non-contact infrared thermometers. ??Euro Surveill.?? 2009 Feb 12;14(6). pii: 19115.  Review. PubMed PMID: 19215720. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/19215720]\]
#: 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/19208184]\]
#: 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/18486558]\]
#: 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/18999265]\]
#: 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/18999137]\]
#: Liu H, Li X, Yoon V, Clarke R. Annotating breast cancer microarray samples using ontologies. ??AMIA Annu Symp Proc.?? 2008 Nov 6:414-8. PubMed PMID: 18999108; PubMed Central PMCID: PMC2655965. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/18999108]\]
#: Noy NF, Tudorache T, de Coronado S, Musen MA. Developing biomedical ontologies collaboratively. ??AMIA Annu Symp Proc.?? 2008 Nov 6:520-4. PubMed PMID: 18998901; PubMed Central PMCID: PMC2656043. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/18998901]\]
#: 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/18436897]\]
#: 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/17512259]\]
#: 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. PubMed PMID: 19789731; PubMed Central PMCID: PMC2753293. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/19789731]\]
#: 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/19221606]\]
#: 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: PMC2929536PMC2238948. \[[PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/2080595417989087]\]
#: ReedMarquet TLG, 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 CitationDameron 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/2071535918693888]\]
# 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: 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 Oct 11:165-70. PubMed PMID:21347147 18693819; PubMed Central PMCID: PMC3041542PMC2655888. \[[PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/2134714718693819]\]
# Cimino JJ, Hayamizu TF: Burgun A, Bodenreider O, Davis B, Stafford GA, Ringwald M. The caBIG terminology review process. J Biomed Inform. 2009 Jun; 42 (3) :571-80. 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:19154797; PubMed Central PMCID: PMC2729758. [PubMed Citation18693803. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1915479718693803]\]
#: PathakShah JNH, SolbrigRubin HRDL, BuntrockEspinosa JDI, JohnsonMontgomery TMK, ChuteMusen CGMA. LexGrid:Annotation aand frameworkquery forof representing,tissue storing,microarray anddata queryingusing biomedicalthe terminologies from simple to sublime. J Am Med Inform Assoc. 2009 May-Jun; 16 (3) :305-15NCI Thesaurus. ??BMC Bioinformatics.?? 2007 Aug 8;8:296. PubMed PMID:19261933 17686183; PubMed Central PMCID: PMC2732233PMC1988837. \[[PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/1926193317686183]\]
#: ShahYang NHHJ, JonquetLay CYL, ChiangTsao APWY, ButteLiou AJYC, ChenLin R,CK. MusenImpact MA. Ontology-driven indexing of public datasets for translational bioinformatics. BMC Bioinformatics. 2009 Feb 5; 10 Suppl 2:S1of language anxiety and self-efficacy on accessing Internet sites. ??Cyberpsychol Behav.?? 2007 Apr;10(2):226-33. PubMed PMID:19208184; PubMed Central PMCID: PMC2646250 17474840. \[[PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/1920818417474840]\]
# Mougin F, Bodenreider O. Auditing the NCI thesaurus with semantic web technologies. AMIA Annu Symp Proc. 2008 Nov 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. ??J Biomed Inform.?? 2007 Feb;40(1):30-43. Epub 2006 Mar 15. PubMed PMID:18999265; PubMed Central PMCID: PMC2655981 16697710. \[[PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/1899926516697710]\]
#: DetwilerZhang LTS, Suciu D, Brinkley JF. Regular paths in SparQL: querying the NCI Thesaurus. AMIA Annu Symp Proc. 2008 Nov 6;Bodenreider O. Experience in Aligning Anatomical Ontologies. ??Int J Semant Web Inf Syst.?? 2007;3(2):1-26. PubMed PMID:18999137 18974854; PubMed Central PMCID: PMC2656016PMC2575410. \[[PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/1899913718974854]\]
#: LiuMin H, Li X, Yoon V, Clarke R. Annotating breast cancer microarray samples using ontologies. AMIA Annu Symp Proc. 2008 Nov 6;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:18999108 16929044; PubMed Central PMCID: PMC2655965PMC1656963. \[[PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/1899910816929044]\]
# 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: 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:18436897; PubMed Central PMCID: PMC2442262 16617371. \[[PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/1843689716617371]\]
#: KomatsoulisDeitzer GAJR, WarzelPayne 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) :106-23PR, Starren JB. Coverage of clinical trials tasks in existing ontologies. ??AMIA Annu Symp Proc.?? 2006:903. PubMed PMID:17512259 17238522; PubMed Central PMCID: PMC2254758PMC1839431. \[[PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/17512259]
# Marinelli RJ, Montgomery K, Liu CL, Shah NH, Prapong W, Nitzberg M, Zachariah ZK, Sherlock GJ, Natkunam Y, West RB, van de Rijn M, Brown PO, Ball CA. The Stanford Tissue Microarray Database. Nucleic Acids Res. 2008 Jan; 36 (Database issue) :D871-717238522]\]
#: 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:17989087 17238469; PubMed Central PMCID: PMC2238948PMC1839578. \[[PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/1798908717238469]\]
#: MinShah HNH, CohenRubin BDL, HalperSupekar MKS, Oren M, Perl Y. Detecting role errors in the gene hierarchy of the NCI Thesaurus. Cancer Inform. 2008; 6:293-313Musen MA. Ontology-based annotation and query of tissue microarray data. ??AMIA Annu Symp Proc.?? 2006:709-13. PubMed PMID:19221606 17238433; PubMed Central PMCID: PMC2623310PMC1839511. \[[PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/1922160617238433]\]
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