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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 Co-Authored by h3. EVS StaffGeneral # LiuDe Coronado KS, ChapmanWright WWLW, SavovaFragoso G, ChuteHaber CGMW, SioutosHahn-Dantona NEA, CrowleyHartel RS.FW, EffectivenessQuan of Lexico-syntactic Pattern Matching for Ontology Enrichment with Clinical Documents. _Methods Inf Med._ 2010: 8;49(6). [PubMed CitationSL, 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.ncbi.nlm.nih.gov/pubmed/21057720sciencedirect.com/science/article/B6WHD-4VFC80H-4/2/42a20ff355ab427f4d674d96e913c63b] # De Noy NF, de Coronado S, WrightSolbrig LWH, Fragoso G, HaberHartel MWFW, 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 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.sciencedirectnih.comgov/sciencepmc/article/B6WHD-4VFC80H-4/2/42a20ff355ab427f4d674d96e913c63barticles/PMC2753293/?tool=pubmed] # NoyHaber NMW, TudoracheKisler TBW, deLenzen Coronado SM, MusenWright MLW. DevelopingControlled biomedicalTerminology ontologiesfor collaboratively. _AMIA Annu Symp Proc._ 2008:520-4. Clinical Research: A Collaboration between CDISC and NCI Enterprise Vocabulary Services. _Drug Information Journal_ 2007;41(3):405-412. [Available online\|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656043/pdf/amia-0520-s2008.pdfnxtbook.com/nxtbooks/dia/druginformationjournal0507/index.php?startpage=142] # NoySioutos NFN, deDe Coronado S, SolbrigHaber HMW, Fragoso G, Hartel FW, MusenShaiu MA.WL, RepresentingWright theLW. NCI Thesaurus: inA Semantic OWLModel DL: Modeling tools help modeling languages. _Appl Ontol._ 2008 Jan 1;3(3):173-190. [Free PMC ArticleIntegrating Cancer-Related Clinical and Molecular Information. _Journal of Biomedical Informatics_ 2007 Feb;40(1):30-43. Epub 2006 Mar 15. [PubMed Citation\|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2753293/?tool=pubmedpubmed/16697710] # HaberDe MW, Kisler BWCoronado S, LenzenTuttle MMS, WrightSolbrig LWHR. Using Controlledthe TerminologyUMLS forSemantic ClinicalNetwork Research:to AValidate CollaborationNCI betweenThesaurus CDISCStructure and NCI Enterprise Vocabulary Services Analyze its Alignment with the OBO Relations Ontology. _DrugAMIA Annu InformationSymp JournalProc._ 2007;41(3):405-412:165-70. [Available online\|http://www.nxtbook.com/nxtbooks/dia/druginformationjournal0507/index.php?startpage=142ncbi.nlm.nih.gov/pmc/articles/PMC2655888/pdf/amia-0165-s2007.pdf] # SioutosHartel NFW, De Coronado S, HaberDionne MWR, HartelFragoso FWG, ShaiuGolbeck WL,J. WrightModeling LW.a NCIdescription Thesaurus:logic Avocabulary Semanticfor Model Integrating Cancer-Related Clinical and Molecular Informationcancer research. _Journal of Biomedical Informatics_, 2007 Feb;40(12005; 38(2):30-43. Epub 2006 Mar 15114-129. [PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/1669771015797001] # Fragoso G, De Coronado S, TuttleHaber MSMW, SolbrigHartel HR.FW, UsingWright theLW. UMLSOverview Semanticand NetworkUtilization toof Validatethe NCI Thesaurus. Structure_Comparative and AnalyzeFunctional its Alignment with the OBO Relations Ontology. _AMIA Annu Symp Proc._ 2007:165-70. [Available onlineGenomics_ (Dec. 2004) 5(8):648-654. [Free PMC Article\|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655888/pdf/amia-0165-s2007.pdfPMC2447470/?tool=pubmed] # TobiasDe Coronado JS, ChilukuriHaber RMW, KomatsoulisSioutos GAN, Mohanty S, Sioutos N, Warzel DB, Tuttle MS, Wright LW, Crowley RS. TheNCI CAPThesaurus: CancerUsing Protocols Science--Based ATerminology Caseto StudyIntegrate ofCancer caCOREResearch BasedResults. Data_Proceedings Standardsof Implementationthe to11th IntegrateWorld withCongress theon Cancer BiomedicalMedical Informatics Grid.(Medinfo 2004)_BMC Medical Informatics Decision Making_, 20; 6:25, 2006. [Free PMC ArticleAmsterdam: IOS Press 2004, pp. 33-37. Also cited as: _Stud Health Technol Inform._ 2004;107(Pt 1):33-7. [PubMed Citation\|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1524939/?tool=pubmedpubmed/15360769] # Hartel FWF, DeFragoso Coronado SG, DionneOng RK, Fragoso G, Golbeck JDionne R. ModelingEnhancing aQuality descriptionof logicRetrieval vocabularyThrough forConcept cancerEdit researchHistory. _JournalAMIA ofAnnu BiomedicalSymp InformaticsProc._, 2005; 38(2):114-129 2003:279-83. [PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/1579700114728178] # Goldbeck J, Fragoso G, DeHartel Coronado SF, HaberHendler MWJ, HartelOberthaler FWJ, WrightParsia LWB. OverviewThe andNational UtilizationCancer ofInstitute's theThesaurus NCIand ThesaurusOntology. _ComparativeJournal andof FunctionalWeb GenomicsSemantics_ (Dec. 20042003) 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 Citation1:75-80. 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1536076921597104]\] # HartelTobias FJ, FragosoChilukuri GR, OngKomatsoulis KGA, DionneMohanty R.S, EnhancingSioutos QualityN, ofWarzel RetrievalDB, ThroughWright ConceptLW, EditCrowley HistoryRS. _AMIAThe AnnuCAP SympCancer Proc._ 2003:279-83. [PubMed Citation\|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. h2. Journal Articles by Others on EVS and Its Use \[under construction -- some initial raw PubMed records below\]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 Citation\|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 # Pathak J, Wang J, Kashyap S, Basford M, Li R, Masys DR, Chute CG. Mapping clinical phenotype data elements to standardized metadata repositories and controlled terminologies: the eMERGE Network experience. J Am Med Inform Assoc. 2011 Jul-Aug; 18 (4) :376-86. PubMed PMID:21597104; PubMed Central PMCID: PMC3128396. [PubMed Citation\|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 Citation\|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. PubMed PMID:21918596. [PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/21918596] # Schulz S, Schober D, Tudose I, Stenzhorn H. The Pitfalls of Thesaurus Ontologization - the Case of the NCI Thesaurus. AMIA Annu Symp Proc. 2010 Nov 13; 2010:727-31. PubMed PMID:21347074; PubMed Central PMCID: PMC3041372. [PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/21347074] # Pathak J, Peters L, Chute CG, Bodenreider O. Comparing and evaluating terminology services application programming interfaces: RxNav, UMLSKS and LexBIG. J Am Med Inform Assoc. 2010 Nov-Dec; 17 (6) :714-9. PubMed PMID:20962136; PubMed Central PMCID: PMC3000749. [PubMed Citation\|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; 1PubMed PMID:20805954; PubMed Central PMCID: PMC2929536. [PubMed Citation\|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 Citation\|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 Citation\|http://www.ncbi.nlm.nih.gov/pubmed/21347147] # Cimino JJ, Hayamizu TF, Bodenreider O, Davis B, Stafford GA, Ringwald M. The caBIG terminology review process. J Biomed Inform. 2009 Jun; 42 (3) :571-80. PubMed PMID:19154797; PubMed Central PMCID: PMC2729758. [PubMed Citation\|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. PubMed PMID:19261933; PubMed Central PMCID: PMC2732233. [PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/19261933] # Shah NH, Jonquet C, Chiang AP, Butte AJ, Chen R, Musen MA. Ontology-driven indexing of public datasets for translational bioinformatics. BMC Bioinformatics. 2009 Feb 5; 10 Suppl 2:S1. PubMed PMID:19208184; PubMed Central PMCID: PMC2646250. [PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/19208184] # Mougin F, Bodenreider O. Auditing the NCI thesaurus with semantic web technologies. AMIA Annu Symp Proc. 2008 Nov 6; PubMed PMID:18999265; PubMed Central PMCID: PMC2655981. [PubMed Citation\|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; PubMed PMID:18999137; PubMed Central PMCID: PMC2656016. [PubMed Citation\|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; PubMed PMID:18999108; PubMed Central PMCID: PMC2655965. [PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/18999108] # Shironoshita EP, Jean-Mary YR, Bradley RM, Kabuka MR. semCDI: a query formulation for semantic data integration in caBIG. J Am Med Inform Assoc. 2008 Jul-Aug; 15 (4) :559-68. PubMed PMID:18436897; PubMed Central PMCID: PMC2442262. [PubMed Citation\|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. PubMed PMID:17512259; PubMed Central PMCID: PMC2254758. [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) :D871-7. PubMed PMID:17989087; PubMed Central PMCID: PMC2238948. [PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/17989087] # Min H, Cohen B, Halper M, Oren M, Perl Y. Detecting role errors in the gene hierarchy of the NCI Thesaurus. Cancer Inform. 2008; 6:293-313. PubMed PMID:19221606; PubMed Central PMCID: PMC2623310. [PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/19221606] # Trotti A, Colevas AD, Setser A, Basch E. Patient-reported outcomes and the evolution of adverse event reporting in oncology. J Clin Oncol. 2007 Nov 10; 25 (32) :5121-7. PubMed PMID:17991931. [PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/17991931] # Marquet G, Dameron O, Saikali S, Mosser J, Burgun A. Grading glioma tumors using OWL-DL and NCI Thesaurus. AMIA Annu Symp Proc. 2007 Oct 11; PubMed PMID:18693888; PubMed Central PMCID: PMC2655830. [PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/18693888] # Burgun A, Bodenreider O. Issues in integrating epidemiology and research information in oncology: experience with ICD-O3 and the NCI Thesaurus. AMIA Annu Symp Proc. 2007 Oct 11; PubMed PMID:18693803. [PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/18693803] # Shah NH, Rubin DL, Espinosa I, Montgomery K, Musen MA. Annotation and query of tissue microarray data using the NCI Thesaurus. BMC Bioinformatics. 2007 Aug 8; 8:296. PubMed PMID:17686183; PubMed Central PMCID: PMC1988837. [PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/17686183] # Zhang S, Bodenreider O. Experience in Aligning Anatomical Ontologies. Int J Semant Web Inf Syst. 2007; 3 (2) :1-26. PubMed PMID:18974854; PubMed Central PMCID: PMC2575410. [PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/18974854] # Gao Q, Zhang YL, Xie ZY, Zhang QP, Hu ZZ. [caCORE: core architecture of bioinformation on cancer research in America]. Beijing Da Xue Xue Bao. 2006 Apr 18; 38 (2) :218-21. PubMed PMID:16617371. [PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/16617371] # Deitzer JR, Payne PR, Starren JB. Coverage of clinical trials tasks in existing ontologies. AMIA Annu Symp Proc. 2006; PubMed PMID:17238522; PubMed Central PMCID: PMC1839431. [PubMed Citation\|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; PubMed PMID:17238469; PubMed Central PMCID: PMC1839578. [PubMed Citation\|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; PubMed PMID:17238433; PubMed Central PMCID: PMC1839511. [PubMed Citation\|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 Citation\|http://www.ncbi.nlm.nih.gov/pubmed/17149500] # Cimino JJ, Zhu X. The practical impact of ontologies on biomedical informatics. Yearb Med Inform. 2006; PubMed PMID:17051306. [PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/17051306] # Zhang S, Bodenreider O. Alignment of multiple ontologies of anatomy: deriving indirect mappings from direct mappings to a reference. AMIA Annu Symp Proc. 2005; PubMed PMID:16779163; PubMed Central PMCID: PMC1560629. [PubMed Citation\|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; PubMed PMID:16779024; PubMed Central PMCID: PMC1560511. [PubMed Citation\|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; PubMed PMID:16779002; PubMed Central PMCID: PMC1560846. [PubMed Citation\|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 Citation\|http://www.ncbi.nlm.nih.gov/pubmed/16342916] # Covitz PA, Hartel F, Schaefer C, De Coronado S, Fragoso G, Sahni H, Gustafson S, Buetow KH. caCORE: a common infrastructure for cancer informatics. Bioinformatics. 2003 Dec 12; 19 (18) :2404-12. PubMed PMID:14668224. [PubMed Citation\|http://www.ncbi.nlm.nih.gov/pubmed/14668224] {multi-excerpt} {scrollbar:icons=false}

Wiki Markup

{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 Co-Authored by 

h3. EVS StaffGeneral

# LiuDe Coronado KS, ChapmanWright WWLW, SavovaFragoso G, ChuteHaber CGMW, SioutosHahn-Dantona NEA, CrowleyHartel RS.FW, EffectivenessQuan of Lexico-syntactic Pattern Matching for Ontology Enrichment with Clinical Documents. _Methods Inf Med._ 2010: 8;49(6). [PubMed CitationSL, 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.ncbi.nlm.nih.gov/pubmed/21057720sciencedirect.com/science/article/B6WHD-4VFC80H-4/2/42a20ff355ab427f4d674d96e913c63b]
# De Noy NF, de Coronado S, WrightSolbrig LWH, Fragoso G, HaberHartel MWFW, 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 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.sciencedirectnih.comgov/sciencepmc/article/B6WHD-4VFC80H-4/2/42a20ff355ab427f4d674d96e913c63barticles/PMC2753293/?tool=pubmed]
# NoyHaber NMW, TudoracheKisler TBW, deLenzen Coronado SM, MusenWright MLW. DevelopingControlled biomedicalTerminology ontologiesfor collaboratively. _AMIA Annu Symp Proc._ 2008:520-4. Clinical Research: A Collaboration between CDISC and NCI Enterprise Vocabulary Services. _Drug Information Journal_ 2007;41(3):405-412. [Available online|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656043/pdf/amia-0520-s2008.pdfnxtbook.com/nxtbooks/dia/druginformationjournal0507/index.php?startpage=142]
# NoySioutos NFN, deDe Coronado S, SolbrigHaber HMW, Fragoso G, Hartel FW, MusenShaiu MA.WL, RepresentingWright theLW. NCI Thesaurus: inA Semantic OWLModel DL: Modeling tools help modeling languages. _Appl Ontol._ 2008 Jan 1;3(3):173-190. [Free PMC ArticleIntegrating Cancer-Related Clinical and Molecular Information. _Journal of Biomedical Informatics_ 2007 Feb;40(1):30-43. Epub 2006 Mar 15. [PubMed Citation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2753293/?tool=pubmedpubmed/16697710]
# HaberDe MW, Kisler BWCoronado S, LenzenTuttle MMS, WrightSolbrig LWHR. Using Controlledthe TerminologyUMLS forSemantic ClinicalNetwork Research:to AValidate CollaborationNCI betweenThesaurus CDISCStructure and NCI Enterprise Vocabulary Services Analyze its Alignment with the OBO Relations Ontology. _DrugAMIA Annu InformationSymp JournalProc._ 2007;41(3):405-412:165-70. [Available online|http://www.nxtbook.com/nxtbooks/dia/druginformationjournal0507/index.php?startpage=142ncbi.nlm.nih.gov/pmc/articles/PMC2655888/pdf/amia-0165-s2007.pdf]
# SioutosHartel NFW, De Coronado S, HaberDionne MWR, HartelFragoso FWG, ShaiuGolbeck WL,J. WrightModeling LW.a NCIdescription Thesaurus:logic Avocabulary Semanticfor Model Integrating Cancer-Related Clinical and Molecular Informationcancer research. _Journal of Biomedical Informatics_, 2007 Feb;40(12005; 38(2):30-43. Epub 2006 Mar 15114-129. [PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/1669771015797001]
# Fragoso G, De Coronado S, TuttleHaber MSMW, SolbrigHartel HR.FW, UsingWright theLW. UMLSOverview Semanticand NetworkUtilization toof Validatethe NCI Thesaurus. Structure_Comparative and AnalyzeFunctional its Alignment with the OBO Relations Ontology. _AMIA Annu Symp Proc._ 2007:165-70. [Available onlineGenomics_ (Dec. 2004) 5(8):648-654. [Free PMC Article|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655888/pdf/amia-0165-s2007.pdfPMC2447470/?tool=pubmed]
# TobiasDe Coronado JS, ChilukuriHaber RMW, KomatsoulisSioutos GAN, Mohanty S, Sioutos N, Warzel DB, Tuttle MS, Wright LW, Crowley RS. TheNCI CAPThesaurus: CancerUsing Protocols Science--Based ATerminology Caseto StudyIntegrate ofCancer caCOREResearch BasedResults. Data_Proceedings Standardsof Implementationthe to11th IntegrateWorld withCongress theon Cancer BiomedicalMedical Informatics Grid.(Medinfo 2004)_BMC Medical Informatics Decision Making_, 20; 6:25, 2006. [Free PMC ArticleAmsterdam: IOS Press 2004, pp. 33-37. Also cited as: _Stud Health Technol Inform._ 2004;107(Pt 1):33-7. [PubMed Citation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1524939/?tool=pubmedpubmed/15360769]
# Hartel FWF, DeFragoso Coronado SG, DionneOng RK, Fragoso G, Golbeck JDionne R. ModelingEnhancing aQuality descriptionof logicRetrieval vocabularyThrough forConcept cancerEdit researchHistory. _JournalAMIA ofAnnu BiomedicalSymp InformaticsProc._, 2005; 38(2):114-129 2003:279-83. [PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/1579700114728178]
# Goldbeck J, Fragoso G, DeHartel Coronado SF, HaberHendler MWJ, HartelOberthaler FWJ, WrightParsia LWB. OverviewThe andNational UtilizationCancer ofInstitute's theThesaurus NCIand ThesaurusOntology. _ComparativeJournal andof FunctionalWeb GenomicsSemantics_ (Dec. 20042003) 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 Citation1:75-80.

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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1536076921597104]\]
# HartelTobias FJ, FragosoChilukuri GR, OngKomatsoulis KGA, DionneMohanty R.S, EnhancingSioutos QualityN, ofWarzel RetrievalDB, ThroughWright ConceptLW, EditCrowley HistoryRS. _AMIAThe AnnuCAP SympCancer Proc._ 2003:279-83. [PubMed Citation|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.


h2. Journal Articles by Others on EVS and Its Use

\[under construction -- some initial raw PubMed records below\]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 Citation|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

# Pathak J, Wang J, Kashyap S, Basford M, Li R, Masys DR, Chute CG. Mapping clinical phenotype data elements to standardized metadata repositories and controlled terminologies: the eMERGE Network experience. J Am Med Inform Assoc. 2011 Jul-Aug; 18 (4) :376-86. PubMed PMID:21597104; PubMed Central PMCID: PMC3128396. [PubMed Citation|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 Citation|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. PubMed PMID:21918596. [PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/21918596]
# Schulz S, Schober D, Tudose I, Stenzhorn H. The Pitfalls of Thesaurus Ontologization - the Case of the NCI Thesaurus. AMIA Annu Symp Proc. 2010 Nov 13; 2010:727-31. PubMed PMID:21347074; PubMed Central PMCID: PMC3041372. [PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/21347074]
# Pathak J, Peters L, Chute CG, Bodenreider O. Comparing and evaluating terminology services application programming interfaces: RxNav, UMLSKS and LexBIG. J Am Med Inform Assoc. 2010 Nov-Dec; 17 (6) :714-9. PubMed PMID:20962136; PubMed Central PMCID: PMC3000749. [PubMed Citation|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; 1PubMed PMID:20805954; PubMed Central PMCID: PMC2929536. [PubMed Citation|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 Citation|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 Citation|http://www.ncbi.nlm.nih.gov/pubmed/21347147]
# Cimino JJ, Hayamizu TF, Bodenreider O, Davis B, Stafford GA, Ringwald M. The caBIG terminology review process. J Biomed Inform. 2009 Jun; 42 (3) :571-80. PubMed PMID:19154797; PubMed Central PMCID: PMC2729758. [PubMed Citation|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. PubMed PMID:19261933; PubMed Central PMCID: PMC2732233. [PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/19261933]
# Shah NH, Jonquet C, Chiang AP, Butte AJ, Chen R, Musen MA. Ontology-driven indexing of public datasets for translational bioinformatics. BMC Bioinformatics. 2009 Feb 5; 10 Suppl 2:S1. PubMed PMID:19208184; PubMed Central PMCID: PMC2646250. [PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/19208184]
# Mougin F, Bodenreider O. Auditing the NCI thesaurus with semantic web technologies. AMIA Annu Symp Proc. 2008 Nov 6; PubMed PMID:18999265; PubMed Central PMCID: PMC2655981. [PubMed Citation|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; PubMed PMID:18999137; PubMed Central PMCID: PMC2656016. [PubMed Citation|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; PubMed PMID:18999108; PubMed Central PMCID: PMC2655965. [PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/18999108]
# Shironoshita EP, Jean-Mary YR, Bradley RM, Kabuka MR. semCDI: a query formulation for semantic data integration in caBIG. J Am Med Inform Assoc. 2008 Jul-Aug; 15 (4) :559-68. PubMed PMID:18436897; PubMed Central PMCID: PMC2442262. [PubMed Citation|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. PubMed PMID:17512259; PubMed Central PMCID: PMC2254758. [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) :D871-7. PubMed PMID:17989087; PubMed Central PMCID: PMC2238948. [PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/17989087]
# Min H, Cohen B, Halper M, Oren M, Perl Y. Detecting role errors in the gene hierarchy of the NCI Thesaurus. Cancer Inform. 2008; 6:293-313. PubMed PMID:19221606; PubMed Central PMCID: PMC2623310. [PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/19221606]
# Trotti A, Colevas AD, Setser A, Basch E. Patient-reported outcomes and the evolution of adverse event reporting in oncology. J Clin Oncol. 2007 Nov 10; 25 (32) :5121-7. PubMed PMID:17991931. [PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/17991931]
# Marquet G, Dameron O, Saikali S, Mosser J, Burgun A. Grading glioma tumors using OWL-DL and NCI Thesaurus. AMIA Annu Symp Proc. 2007 Oct 11; PubMed PMID:18693888; PubMed Central PMCID: PMC2655830. [PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/18693888]
# Burgun A, Bodenreider O. Issues in integrating epidemiology and research information in oncology: experience with ICD-O3 and the NCI Thesaurus. AMIA Annu Symp Proc. 2007 Oct 11; PubMed PMID:18693803. [PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/18693803]
# Shah NH, Rubin DL, Espinosa I, Montgomery K, Musen MA. Annotation and query of tissue microarray data using the NCI Thesaurus. BMC Bioinformatics. 2007 Aug 8; 8:296. PubMed PMID:17686183; PubMed Central PMCID: PMC1988837. [PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/17686183]
# Zhang S, Bodenreider O. Experience in Aligning Anatomical Ontologies. Int J Semant Web Inf Syst. 2007; 3 (2) :1-26. PubMed PMID:18974854; PubMed Central PMCID: PMC2575410. [PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/18974854]
# Gao Q, Zhang YL, Xie ZY, Zhang QP, Hu ZZ. [caCORE: core architecture of bioinformation on cancer research in America]. Beijing Da Xue Xue Bao. 2006 Apr 18; 38 (2) :218-21. PubMed PMID:16617371. [PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/16617371]
# Deitzer JR, Payne PR, Starren JB. Coverage of clinical trials tasks in existing ontologies. AMIA Annu Symp Proc. 2006; PubMed PMID:17238522; PubMed Central PMCID: PMC1839431. [PubMed Citation|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; PubMed PMID:17238469; PubMed Central PMCID: PMC1839578. [PubMed Citation|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; PubMed PMID:17238433; PubMed Central PMCID: PMC1839511. [PubMed Citation|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 Citation|http://www.ncbi.nlm.nih.gov/pubmed/17149500]
# Cimino JJ, Zhu X. The practical impact of ontologies on biomedical informatics. Yearb Med Inform. 2006; PubMed PMID:17051306. [PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/17051306]
# Zhang S, Bodenreider O. Alignment of multiple ontologies of anatomy: deriving indirect mappings from direct mappings to a reference. AMIA Annu Symp Proc. 2005; PubMed PMID:16779163; PubMed Central PMCID: PMC1560629. [PubMed Citation|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; PubMed PMID:16779024; PubMed Central PMCID: PMC1560511. [PubMed Citation|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; PubMed PMID:16779002; PubMed Central PMCID: PMC1560846. [PubMed Citation|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 Citation|http://www.ncbi.nlm.nih.gov/pubmed/16342916]
# Covitz PA, Hartel F, Schaefer C, De Coronado S, Fragoso G, Sahni H, Gustafson S, Buetow KH. caCORE: a common infrastructure for cancer informatics. Bioinformatics. 2003 Dec 12; 19 (18) :2404-12. PubMed PMID:14668224.  [PubMed Citation|http://www.ncbi.nlm.nih.gov/pubmed/14668224]

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