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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 the explicit use of EVS resources in support of cancer research and other scientific efforts. It does not include materials where EVS resources may play an important role but are not explicitly addressed, as often occurs, for example, when use has been made of NCI's semantic infrastructure and tooling, or of EVS supported terminologies and standards often maintained jointly with other NCI units, NIH institutes, federal agencies or other partners. {toc:minLevel=2} h2. Scientific Journal Articles h3. EVS General # Gonçalves RS, Parsia B, Sattler U. Analysing the evolution of the NCI thesaurus. ??Proceedings - IEEE Symposium on Computer-Based Medical Systems?? (2011) \[[At IEEE Xplore\|http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5999163&tag=1]\] * * 2009 # 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. \[[Available online\|http://www.sciencedirect.com/science/article/B6WHD-4VFC80H-4/2/42a20ff355ab427f4d674d96e913c63b]\] * * 2008 # 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. \[[Free PMC Article\|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2753293/?tool=pubmed]\] * * 2007 # 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. \[[Available online\|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655888/pdf/amia-0165-s2007.pdf]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/16697710]\] * * 2005 # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/15797001]\] * * 2004 # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/15360769]\] # 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. \[[Free PMC Article\|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447470/?tool=pubmed]\] * * 2003 # 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. # Hartel F, Fragoso G, Ong K, Dionne R. Enhancing Quality of Retrieval Through Concept Edit History. ??AMIA Annu Symp Proc.?? 2003:279-83. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/14728178]\] h3. Biomedical Applications # Liu H, Burkhart Q, Bell DSBertaud Gounot V, Donfack V, Lasbleiz J, Bourde A, Duvauferrier R. EvaluationCreating an ofontology thedriven NCPDPrules Structuredbase andfor Codifiedan Sigexpert Formatsystem for e-prescriptionsmedical diagnosis. ??JStud AmHealth MedTechnol Inform Assoc.??. 2011 Sep 1;18(5):645-51. Epub 2011 May 25. ;169:714-8. PubMed PMID: 21613642; PubMed Central PMCID: PMC316830121893840. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/2161364221893840]\] # PathakCuggia JM, WangBourde JA, KashyapTurlin SB, BasfordVincendeau MS, LiBertaud RV, MasysBohec DRC, ChuteDuvauferrier CGR. MappingAutomatic clinicalDefinition phenotypeof datathe elementsOncologic toEHR standardizedData metadataElements repositoriesfrom andNCIT controlled terminologies: the eMERGE Network experiencein OWL. ??JStud AmHealth MedTechnol Inform Assoc.?? 2011 Jul-Aug;18(4):376-86. Epub 2011 May 19. ;169:517-21. PubMed PMID: 21597104; PubMed Central PMCID: PMC312839621893803. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/2159710421893803]\] # ShermanLiu SH, ShatsBurkhart OQ, KetchamBell 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;10:83-91DS. Evaluation of the NCPDP Structured and Codified Sig Format for e-prescriptions. ??J Am Med Inform Assoc??. 2011 Sep 1;18(5):645-51. Epub 2011 May 25. PubMed PMID: 2155249421613642; PubMed Central PMCID: PMC3085425PMC3168301. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/2155249421613642]\] # ShermanOverton SJA, ShatsRomagnoli OC, FleissnerChhem 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;10:217-26R. Open biomedical ontologies applied to prostate cancer. ??Applied Ontology?? 2011;6(1):35-51. \[[Scopus\|http://www.scopus.com/inward/record.url?eid=2-s2.0-80052093434&partnerID=40&md5=e8ad9613fb41d3c802f7d09ae3db6c55]\] # 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 AugMay 3119. PubMed PMID: 2191859621597104; PubMed Central PMCID: PMC3169352PMC3128396. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/2191859621597104]\] # YongSherman MYS, Gonzalez-BeltranShats AO, BegentFleissner R. Establishing a knowledge trail from molecular experiments to clinical trials. ??N BiotechnolE, 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 Sep;28(5):464-80;10:217-26. Epub 2011 AprAug 531. PubMed PMID: 21473938 21918596; PubMed Central PMCID: PMC3169352. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/2147393821918596]\] # OvertonSherman JAS, RomagnoliShats CO, Chhem RKetcham 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. OpenPCCR: biomedicalPancreatic ontologiesCancer applied to prostate cancerCollaborative Registry. ??AppliedCancer OntologyInform.?? 2011;6(1):35-51. \[[Scopus Mar 23;10:83-91. PubMed PMID: 21552494; PubMed Central PMCID: PMC3085425. \[[PubMed\|http://www.scopus.com/inward/record.url?eid=2-s2.0-80052093434&partnerID=40&md5=e8ad9613fb41d3c802f7d09ae3db6c55ncbi.nlm.nih.gov/pubmed/21552494]\] # BertaudYong Gounot VMY, Donfack V, Lasbleiz J, Bourde Gonzalez-Beltran A, DuvauferrierBegent R. CreatingEstablishing ana ontologyknowledge driventrail rulesfrom basemolecular forexperiments anto expert system for medical diagnosisclinical trials. ??Stud Health Technol InformN Biotechnol.?? 2011;169:714-8 Sep;28(5):464-80. Epub 2011 Apr 5. PubMed PMID: 2189384021473938. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/2189384021473938]\] # Cuggia M, Bourde A, Turlin B, Vincendeau S, Bertaud V, Bohec C, Duvauferrier R. Automatic Definition of the Oncologic EHR Data Elements from NCIT in OWL. ??Stud Health Technol Inform.?? 2011;169:517-21* * 2010 # Crowley RS, Castine M, Mitchell K, Chavan G, McSherry T, Feldman M. caTIES: a grid based system for coding and retrieval of surgical pathology reports and tissue specimens in support of translational research. ??J Am Med Inform Assoc.?? 2010 May-Jun;17(3):253-64. PubMed PMID: 21893803.20442142; PubMed Central PMCID: PMC2995710. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/2189380320442142]\] h5. 2010 # Hirschfeld S, Songco D, Kramer BS, Guttmacher AE. National Children's Study: update in 2010. ??Mt Sinai J Med.?? 2011 Jan-Feb;78(1):119-25. doi: 10.1002/msj.20227. PubMed PMID: 21259268 \[[Full Text\|http://jamia.bmj.com/cgi/pmidlookup?view=long&pmid=20442142]\] # Deus HF, Veiga DF, Freire PR, Weinstein JN, Mills GB, Almeida JS. Exposing the cancer genome atlas as a SPARQL endpoint. ??J Biomed Inform??. 2010 Dec;43(6):998-1008. PubMed PMID: 20851208; PubMed Central PMCID: PMC3071752. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/2125926820851208]\] # CrowleyHirschfeld RSS, CastineSongco MD, MitchellKramer KBS, Chavan G, McSherry T, Feldman M. caTIES: a grid based system for coding and retrieval of surgical pathology reports and tissue specimens in support of translational researchGuttmacher AE. National Children's Study: update in 2010.* ??Mt Sinai J Am Med Inform Assoc.?? 20102011 MayJan-JunFeb;1778(31):253119-6425. PubMed PMIDdoi: 20442142;10.1002/msj.20227. PubMed Central PMCIDPMID: PMC299571021259268. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/2044214221259268]\] \[[Full Text\|http://jamia.bmj.com/cgi/pmidlookup?view=long&pmid=20442142]\] # 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 # Jiang G, Solbrig HR, Iberson-Hurst D, Kush RD, Chute CG. A Collaborative Framework for Representation and Harmonization of Clinical Study Data Elements Using Semantic MediaWiki. ??AMIA Summits Transl Sci Proc. 2010?? Mar 1;2010:11-5. PubMed PMID: 2080595421347136; PubMed Central PMCID: PMC2929536PMC3041544. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/2080595421347136]\] # DeusKang HFHP, VeigaBorromeo DFCD, FreireBerman PRJJ, WeinsteinBecich JN, Mills GB, Almeida JS. Exposing the cancer genome atlas as a SPARQL endpointMJ. The tissue microarray OWL schema: An open-source tool for sharing tissue microarray data.* ??J BiomedPathol Inform.??. 2010 Dec;43(6):998-1008Jul 13;1. pii: 9. PubMed PMID: 2085120820805954; PubMed Central PMCID: PMC3071752PMC2929536. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/2085120820805954]\] # ReedMartínez-Romero TLM, Kaufman-Rivi D. FDA adverse Event Problem Codes: standardizing the classification of device and patient problems associated with medical device useVázquez-Naya JM, Rabuñal JR, Pita-Fernández S, Macenlle R, Castro-Alvariño J, López-Roses L, Ulla JL, Martínez-Calvo AV, Vázquez S, Pereira J, Porto-Pazos AB, Dorado J, Pazos A, Munteanu CR. Artificial intelligence techniques for colorectal cancer drug metabolism: ontology and complex network.* ??BiomedCurr InstrumDrug Technol.Metab??. 2010 May-Jun;4411(34):248-56347-68. Review. PubMed PMID: 2071535920446907. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/2071535920446907]\] # JiangReed GTL, Solbrig HR, Iberson-Hurst D, Kush RD, Chute CGKaufman-Rivi D. AFDA adverse CollaborativeEvent FrameworkProblem forCodes: Representationstandardizing andthe Harmonizationclassification of device and Clinicalpatient Studyproblems Dataassociated Elementswith Usingmedical Semanticdevice MediaWikiuse. ??AMIABiomed Summits Transl Sci Proc. 2010Instrum Technol.?? Mar2010 1;2010:11-5May-Jun;44(3):248-56. PubMed PMID: 21347136; PubMed Central PMCID: PMC304154420715359. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/2134713620715359]\] # YipVázquez-Naya V, MeteJM, Martínez-Romero M, Porto-Pazos AB, Novoa F, Valladares-Ayerbes M, Topaloglu UPereira J, Munteanu CR, KockaraDorado SJ. Concept Discovery for Pathology Reports using an N-gram ModelOntologies of drug discovery and design for neurology, cardiology and oncology. ??AMIACurr Summits Transl Sci Proc.Pharm Des??. 2010 Mar 1;2010:43-7;16(24):2724-36. Review. PubMed PMID: 21347147; PubMed Central PMCID: PMC3041542. 20642429. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/2134714720642429]\] # Martínez-RomeroYip MV, Vázquez-NayaMete JMM, RabuñalTopaloglu JRU, Pita-FernándezKockara S,. Macenlle R, Castro-Alvariño J, López-Roses L, Ulla JL, Martínez-Calvo AV, Vázquez S, Pereira J, Porto-Pazos AB, Dorado J, Pazos A, Munteanu CR. Artificial intelligence techniques for colorectal cancer drug metabolism: ontology and complex network. ??Curr Drug Metab??. 2010 May;11(4):347-68. Review. PubMed PMID: 20446907. \ 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/2044690721347147]\] # Vázquez-Naya JM, Martínez-Romero Yong M, Porto-Pazos AB, Novoa F, Valladares-Ayerbes M, Pereira J, Munteanu CR, Dorado JBegent R. OntologiesBest use of drugexperimental discoverydata andin design for neurology, cardiology and oncologycancer informatics. ??Curr Pharm DesFuture Oncol.??. 2010;16(24):2724-36. Review. PubMed PMID: 20642429. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/20642429]\] # Yong M, Begent R. Best use of experimental data in cancer informatics. ??Future Oncol.?? 2010 2010 Oct;6(10):1551-62. Review. Erratum in: Future Oncol. 2011 Jan;7(1):154. PubMed PMID: 21062155. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/21062155]\] \[[PDF\|http://www.futuremedicine.com/doi/pdf/10.2217/fon.10.108]\] h5. 2009 # 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 \[[PDF\|http://www.futuremedicine.com/doi/pdf/10.2217/fon.10.108]\] * * 2009 # Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone SA, Sklyar N, Zhao M, Sarkans U, Brazma A. ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. ??Nucleic Acids Res.?? 2009 Jan;37(Database issue):D868-72. Epub 2008 Nov 10. PubMed PMID: 1920818419015125; PubMed Central PMCID: PMC2646250PMC2686529. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1920818419015125]\] # ParkinsonShah HNH, KapusheskyJonquet MC, KolesnikovChiang NAP, RusticiButte GAJ, ShojatalabChen MR, AbeygunawardenaMusen N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone SA, Sklyar N, Zhao M, Sarkans U, Brazma A. ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. ??Nucleic Acids Res.?? 2009 Jan;37(Database issue):D868-72. Epub 2008 Nov 10. PubMed PMID: 19015125; PubMed Central PMCID: PMC2686529. 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/19208184]\] # Yong M, Tolner B, Nagl S, Pedley RB, Chester K, Green AJ, Mayer A, Sharma S, Begent R. Data standards for minimum information collection for antibody therapy experiments. ??Protein Eng Des Sel.?? 2009 Mar;22(3):221-4. PubMed PMID: 19224941. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1901512519224941]\] # Yong M, Tolner B, Nagl S, Pedley RB, Chester K, Green AJ, Mayer A, Sharma S, Begent R. Data standards for minimum information collection for antibody therapy experiments \[[Oxford full text\|http://peds.oxfordjournals.org/content/22/3/221.long]\]  * 2008 # Kaefer CM, Milner JA. The role of herbs and spices in cancer prevention. ??ProteinJ EngNutr Des SelBiochem.?? 20092008 MarJun;2219(36):221-4347-61. Review. PubMed PMID: 1922494118499033; PubMed Central PMCID: PMC2771684. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1922494118499033]\] \[[OxfordPubMed full textCentral\|http://peds.oxfordjournals.org/content/22/3/221.longwww.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc-MS.gif]\] h5. 2008 # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/18999108]\] # Marinelli RJ, Montgomery K, Liu CL, Shah NH, Prapong W, Nitzberg M, Zachariah ZK, Sherlock GJ, Natkunam Y, West RB, van de Rijn M, Brown PO, Ball CA. The Stanford Tissue Microarray Database. ??Nucleic Acids Res.?? 2008 Jan;36(Database issue):D871-7. Epub 2007 Nov 7. PubMed PMID: 17989087; PubMed Central PMCID: PMC2238948. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/17989087]\] * * 2007 # KaeferBurgun CMA, MilnerBodenreider JAO. TheIssues rolein ofintegrating herbsepidemiology and spicesresearch information in cancer prevention oncology: experience with ICD-O3 and the NCI Thesaurus. ??JAMIA Annu NutrSymp BiochemProc.?? 2008 Jun;19(6):347-61. Review. PubMed PMID: 18499033; PubMed Central PMCID: PMC2771684. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/18499033]\]2007 Oct 11:85-9. PubMed PMID: 18693803. \[[PubMed Central\|http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc-MS.gifpubmed/18693803]\] h5. 2007 # MarquetFrey GLJ, DameronMaojo OV, Mitchell Saikali S, Mosser J, Burgun A. Grading glioma tumors using OWL-DL and NCI Thesaurus. ??AMIA Annu Symp ProcJA. Bioinformatics linkage of heterogeneous clinical and genomic information in support of personalized medicine. ??Yearb Med Inform.?? 2007 Oct 11:50898-12105. PubMedErratum PMIDin: 18693888;Yearb Med Inform. 2008:19. PubMed Central PMCIDPMID: PMC265583017700912. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1869388817700912]\] # BurgunMarquet AG, BodenreiderDameron O., Issues in integrating epidemiology and research information in oncology: experience with ICD-O3 and theSaikali S, Mosser J, Burgun A. Grading glioma tumors using OWL-DL and NCI Thesaurus.* ??AMIA Annu Symp Proc.?? 2007 Oct 11:85508-912. PubMed PMID: 1869380318693888; PubMed Central PMCID: PMC2655830. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1869380318693888]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/17686183]\] h5. 2006 * * 2006 # TobiasDeitzer JJR, ChilukuriPayne RPR, Komatsoulis GA, Mohanty S, Sioutos N, Warzel DB, Wright LW, Crowley RSStarren JB. The CAP Cancer Protocols -- A Case Study Coverage of caCOREclinical Basedtrials Datatasks Standardsin Implementation to Integrate with the Cancer Biomedical Informatics Gridexisting ontologies. ??BMCAMIA MedicalAnnu Informatics Decision Making??, 20; 6:25, 2006Symp Proc.?? 2006:903. PubMed PMID: 17238522; PubMed Central PMCID: PMC1839431. \[[Free PMC ArticlePubMed\|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1524939/?tool=pubmedpubmed/17238522]\] # Shah NH, DeitzerRubin JRDL, PayneSupekar PRKS, StarrenMusen JBMA. CoverageOntology-based ofannotation clinicaland trialsquery tasksof intissue existingmicroarray ontologiesdata. ??AMIA Annu Symp Proc.?? 2006:903709-13. PubMed PMID: 1723852217238433; PubMed Central PMCID: PMC1839431PMC1839511. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1723852217238433]\] # Shah NH, Rubin DL, Supekar KS, Musen MA. Ontology-based annotation and query of tissue microarray data 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.* ??AMIABMC Medical AnnuInformatics SympDecision Proc.Making?? 2006:709-13. PubMed PMID: 17238433; PubMed Central PMCID: PMC1839511, 20; 6:25, 2006. \[[PubMedFree PMC Article\|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1524939/?tool=pubmed/17238433]\] h5. 2005 # Zhang* * 2005 # Bodenreider O, Hayamizu TF, Ringwald M, De Coronado S, BodenreiderZhang OS. AlignmentOf ofmice multiple ontologies of anatomyand men: derivingaligning indirectmouse mappingsand from direct mappings to a referencehuman anatomies. ??AMIA Annu Symp Proc.?? 2005:86461-85. PubMed PMID: 1677916316779002; PubMed Central PMCID: PMC1560629PMC1560846. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1677916316779002]\] # BodenreiderZhang OS, HayamizuBodenreider TF, Ringwald M, De Coronado S, Zhang S. Of mice and men: aligning mouse and human anatomiesO. Alignment of multiple ontologies of anatomy: deriving indirect mappings from direct mappings to a reference.* ??AMIA Annu Symp Proc.?? 2005:61864-58. PubMed PMID: 1677900216779163; PubMed Central PMCID: PMC1560846PMC1560629. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1677900216779163]\] h3. caCORE and caBIG # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/19154797]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/17512259]\] # Gao Q, Zhang YL, Xie ZY, Zhang QP, Hu ZZ. caCORE: core architecture of bioinformation on cancer research in America. ??Beijing Da Xue Xue Bao.?? 2006 Apr 18;38(2):218-21. Chinese. PubMed PMID: 16617371. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/16617371]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/14668224]\] h3. LexEVS # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/20962136]\] # Tao C, Pathak J, Solbrig HR, Wei WQ, Chute CG. LexRDF Model: An RDF-based Unified Model for Heterogeneous Biomedical Ontologies. ??CEUR Workshop Proc??. 2009 Oct 26;521:3. PubMed PMID: 21804785; PubMed Central PMCID: PMC3146261. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/21804785]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/19261933]\] # Pathak J, Jiang G, Dwarkanath SO, Buntrock JD, Chute CG. LexValueSets: an approach for context-driven value sets extraction. ??AMIA Annu Symp Proc??. 2008 Nov 6:556-60. PubMed PMID: 18998955; PubMed Central PMCID: PMC2656093. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/18998955]\] # Jiang G, Peterson KJ, Johnson TM, Celik C, Jakob R, Chute CG. Representing the ClaML-based ICD10 in LexGrid terminology model. ??AMIA Annu Symp Proc??. 2008 Nov 6:992. PubMed PMID: 18998953. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/18998953]\] # Pathak J, Jiang G, Dwarkanath SO, Buntrock JD, Chute CG. Adopting Graph Traversal Techniques for Context-Driven Value Sets Extraction from Biomedical Knowledge Sources. ??Proc IEEE Int Conf Semant Comput??. 2008 Aug 12;2008:460-467. PubMed PMID: 21625412; PubMed Central PMCID: PMC3101576. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/21625412]\] h3. Nanotechnology # Thomas DG, Klaessig F, Harper SL, Fritts M, Hoover MD, Gaheen S, Stokes TH, Reznik-Zellen R, Freund ET, Klemm JD, Paik DS, Baker NA. Informatics and standards for nanomedicine technology. ??Wiley Interdiscip Rev Nanomed Nanobiotechnol??. 2011 Jun 30. doi: 10.1002/wnan.152. Epub ahead of print. PubMed PMID: 21721140. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/21721140]\] # Thomas DG, Pappu RV, Baker NA. NanoParticle Ontology for cancer nanotechnology research. J Biomed Inform. 2011 Feb;44(1):59-74. Epub 2010 Mar 6. PubMed PMID: 20211274; PubMed Central PMCID: PMC3042056. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/20211274]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/17238469]\] h3. NLP # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/1677902417238469]\] h3. Ontology, Semantics and SemanticsNLP # Payne PR, Borlawsky TB, Lele O, James S, Greaves AW. The TOKEn project: knowledge synthesis for in silico science. ??J Am Med Inform Assoc.?? 2011 Oct 7. [Epub ahead of print] PubMed PMID: 21984589. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/21984589]\] # Jonquet C, LePendu P, Falconer S, Coulet A, Noy NF, Musen MA, Shah NH NCBO Resource Index: Ontology-based search and mining of biomedical resources ??Web Semantics: Science, Services and Agents on the World Wide Web??, Volume 9, Issue 3, September 2011, Pages 316-324, ISSN 1570-8268, 10.1016/j.websem.2011.06.005. \[[ScienceDirect\|http://www.sciencedirect.com/science/article/pii/S1570826811000485]\] # McCusker JP, Luciano JS, McGuinness DL. Towards an Ontology for Conceptual Modeling. ??Proc. of the International Conference on Biomedical Ontology, 2011.?? \[[Online\|http://tw.rpi.edu/web/doc/towardscmo]\] * * 2010 # Payne PR, Borlawsky TB, Stephens W, Barrett MC, Nguyen-Pham T, Greaves AW. The TRITON Project: Design and Implementation of an Integrative Translational Research Information Management Platform. ??AMIA Annu Symp Proc.?? 2010 Nov 13;2010:617-21. PubMed PMID: 21347052; PubMed Central PMCID: PMC3041280. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/21347052]\] \[[Full Text\|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041280/?tool=pubmed]\] # 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). \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/21057720]\] # Martinez-Romero M, Vazquez-Naya J, Munteanu CR, Pereira J, Pazos A. An approach for the automatic recommendation of ontologies using collaborative knowledge. ??Proceedings of the 14th international conference on Knowledge-based and intelligent information and engineering systems: Part II (KES\'10)??, Rossitza Setchi, Ivan Jordanov, Robert J. Howlett, and Lakhmi C. Jain (Eds.). Springer-Verlag, Berlin, Heidelberg, 74-81. # Jonquet C, Musen MA, Shah NH. Building a biomedical ontology recommender web service. ??J Biomed Semantics.?? 2010 Jun 22;1 Suppl 1:S1. PubMed PMID: 20626921; PubMed Central PMCID: PMC2903720. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/20626921]\] \[[PDF\|http://www.jbiomedsem.com/content/pdf/2041-1480-1-S1-S1.pdf]\] # Parai GK, Jonquet C, Xu R, Musen MA, Shah NH. The Lexicon Builder Web service: Building Custom Lexicons from two hundred Biomedical Ontologies. ??AMIA Annu Symp Proc.?? 2010 Nov 13;2010:587-91. PubMed PMID: 21347046; PubMed Central PMCID: PMC3041331. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/21347046]\] \[[PDF\|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041331/pdf/amia-2010_sympproc_0587.pdf]\] # Sun P, Zhang S. Identifying Granularity Differences between Large Biomedical Ontologies through Rules. ??AMIA Annu Symp Proc. 2010?? Nov 13;2010:927-31. PubMed PMID: 21347114; PubMed Central PMCID: PMC3041335. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/21347114]\] \[[Full Text\|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041335/?tool=pubmed]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/21347074]\] * * 2009 # McCusker JP, Phillips JA, González Beltrán A, Finkelstein A, Krauthammer M. Semantic web data warehousing for caGrid. ??BMC Bioinformatics.?? 2009 Oct 1;10 Suppl 10:S2. PubMed PMID: 19796399; PubMed Central PMCID: PMC2755823. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/19796399]\] # Kementsietsidis A, Lim L, Wang M. Profile-based retrieval of records in medical databases. ??AMIA Annu Symp Proc.?? 2009 Nov 14;2009:312-6. PubMed PMID: 20351871; PubMed Central PMCID: PMC2815445. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/20351871]\] # Shah NH, Bhatia N, Jonquet C, Rubin D, Chiang AP, Musen MA. Comparison of concept recognizers for building the Open Biomedical Annotator. ??BMC Bioinformatics.?? 2009 Sep 17;10 Suppl 9:S14. PubMed PMID: 19761568; PubMed Central PMCID: PMC2745685. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/19761568]\] \[[Full Text\|http://www.biomedcentral.com/1471-2105/10/S9/S14]\] # Jonquet C, Shah NH, Musen MA. The open biomedical annotator. ??Summit on Translat Bioinforma.?? 2009 Mar 1;2009:56-60. PubMed PMID: 21347171; PubMed Central PMCID: PMC3041576. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/21347171]\] \[[Full Text\|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041576/?tool=pubmed]\] * * 2008 # Noy N, Tudorache T, de Coronado S, Musen M. Developing biomedical ontologies collaboratively. ??AMIA Annu Symp Proc.?? 2008:520-4. \[[Available online\|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656043/pdf/amia-0520-s2008.pdf]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/18999137]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/19221606]\] # Bodenreider O. Comparing SNOMED CT and the NCI Thesaurus through Semantic Web technologies. ??Proceedings of the Third International Conference on Knowledge Representation in Medicine (KR-MED 2008),?? 2008: p. 37-43. \[[PDF\|http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-410/Paper07.pdf]\] # Kementsietsidis A, Lim L, Wang M. Supporting ontology-based keyword search over medical databases. ??AMIA Annu Symp Proc.?? 2008 Nov 6:409-13. PubMed PMID: 18998839; PubMed Central PMCID: PMC2656038. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/18998839]\] # Rubin DL, Shah NH, Noy NF. Biomedical ontologies: a functional perspective. ??Brief Bioinform.?? 2008 Jan;9(1):75-90. Epub 2007 Dec 12. Review. PubMed PMID: 18077472. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/18077472]\] # Shah NH, Muse MA. UMLS-Query: a perl module for querying the UMLS. ??AMIA Annu Symp Proc.?? 2008 Nov 6:652-6. PubMed PMID: 18998805; PubMed Central PMCID: PMC2656020. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/18998805]\] \[[Full Text\|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656020/?tool=pubmed]\] * * 2007 # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/18974854]\] * * 2006 # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/16929044]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/17051306]\] # Cuenca Grau B, Parsia B, Sirin E, Kalyanpur A. Modularity and web ontologies. ??Proc. of KR-06??, 2006. \[[PDF\|http://www.aaai.org/Papers/KR/2006/KR06-022.pdf]\] * * 2005 # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/16779024]\] # 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. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/16342916]\] h2. Other Scientific Publications # Ghazvinian A, Noy NF, Musen MA. From mappings to modules: Using mappings to identify domain-specific modules in large ontologies. (2011) ??KCAP 2011 - Proceedings of the 2011 Knowledge Capture Conference??, pp. 33-40. \[[Scopus\|http://www.scopus.com/inward/record.url?eid=2-s2.0-79960276657&partnerID=40&md5=89ee8ee5dc29c216c12b55745959a1c4]\] # Tudorache T, Musen MA. Collaborative Development of Large-Scale Biomedical Ontologies. (2011) ??Collaborative Computational Technologies for Biomedical Research?? (eds S. Ekins, M. A. Z. Hupcey and A. J. Williams), John Wiley & Sons, Inc., Hoboken, NJ, USA. pp. 179-200. doi: 10.1002/9781118026038.ch12 * * 2010 # Amin W, Kang HP, Becich MJ. Data Management, Databases, and Warehousing. ??Biomedical Informatics for Cancer Research.?? (M.F. Ochs, J.T. Casagrande, R.V. Davuluri, eds). DOI 10.1007/978-1-4419-5714-6_3, © Springer Science+Business Media, LLC 2010. pp.39-71. # Machado CM, Couto F, Fernandes AR, Santos S, Cardim N, Freitas AT. Semantic characterization of hypertrophic cardiomyopathy disease (2010) ??2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010??, art. no. 5703841, pp. 432-439. \[[Scopus\|http://www.scopus.com/inward/record.url?eid=2-s2.0-79952014366&partnerID=40&md5=4f5d6e004bbea4a8237ebf583a16ac2a]\] # Hartung M, Gross A, Kirsten T, Rahm E. Discovering evolving regions in life science ontologies. (2010) ??Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)??, 6254 LNBI, pp. 19-34. \[[Scopus\|http://www.scopus.com/inward/record.url?eid=2-s2.0-78049425046&partnerID=40&md5=b75edf974601dc0257eb0cb8999f3292]\] * * 2009 # Jonquet C, Shah NH, Musen MA. Prototyping a Biomedical Ontology Recommender Service. ??Bio-Ontologies: Knowledge in Biology??, Stockholm, Sweden (2009). # Hastings S, Oster S, Langella S, Melean C, Borlawsky T, Dhavel R, Payne P. Adoption and Adaptation of caGrid for CTSA. ??Summit on Translat Bioinforma. 2009?? Mar 1;2009:44-8. PubMed PMID: 21347169; PubMed Central PMCID: PMC3041578. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/21347169]\] \[[Full Text\|http://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21347169/?tool=pubmed]\] # Borlawsky TB, Dhaval R, Hastings SL, Payne PR. Development of an agile knowledge engineering framework in support of multi-disciplinary translational research. ??Summit on Translat Bioinforma. 2009?? Mar 1;2009:14-8. PubMed PMID: 21347164; PubMed Central PMCID: PMC3041563. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/21347164]\] * * 2008 # Sebastian A, Noy NF, Tudorache T, Musen MA. A generic ontology for collaborative ontology-development workflows. (2008) ??Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)??, 5268 LNAI, pp. 318-328. \[[Scopus\|http://www.scopus.com/inward/record.url?eid=2-s2.0-56649105039&partnerID=40&md5=3ee1963c5952f19952e28d3e049f3dd4]\] # Bodenreider O. Biomedical ontologies in action: role in knowledge management, data integration and decision support. ??Yearbook of Medical Informatics?? (2008) pp.67-79. # Allemang D, Hendler J. ??Semantic Web for the Working Ontologist: Effective Modeling in RDFS and OWL.?? Elsevier, 2008. # Payne PR, Borlawsky TB, Kwok A, Dhaval R, Greaves AW. Ontology-anchored Approaches to Conceptual Knowledge Discovery in a Multi-dimensional Research Data Repository. ??Summit on Translat Bioinforma. 2008?? Mar 1;2008:85-9. PubMed PMID: 21347129; PubMed Central PMCID: PMC3041525. \[[PubMed\|http://www.ncbi.nlm.nih.gov/pubmed/21347129]\] * * 2007 # Arvanitis TN, Taweel A, Zhao L, et al. Supporting E-Trials Over Distributed Networks: A tool for capturing randomised control trials (RCT) eligibility criteria using the National Cancer Institute's (NCI) Enterprise Vocabulary Services (EVS) ??Technol Health Care?? 2007;15:298-299. # Dmitrieva J, Bei Y, Verbeek FJ. Ontological context visualization. ??OWLED 2007 Workshop on OWL: Volume 258 of CEUR Workshop Proceedings.?? eds Golbreich C, Kalyanpur A, Parsia B. CEUR-WS.org (2007). * * 2006 # Noy NF, Chugh A, Liu W, Musen MA. A Framework for Ontology Evolution in Collaborative Environments. ??The Semantic Web - ISWC 2006.?? Lecture Notes in Computer Science 4273 pp.544-558, DOI: 10.1007/11926078_39 \[[Springer\|http://dx.doi.org/10.1007/11926078_39]\] \[[PDF\|http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.106.3290&rep=rep1&type=pdf]\] # Bernhard D. Automatic acquisition of semantic relationships from morphological relatedness. (2006) ??Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)??, 4139 LNAI, pp. 121-132. \[[Scopus\|http://www.scopus.com/inward/record.url?eid=2-s2.0-33749651005&partnerID=40&md5=2e5894b13afc2c73efb96498815c4f52]\] * * 2005 # Kumar A, Smith B. Oncology ontology in the NCI thesaurus. (2005) ??Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)??, 3581 LNAI, pp. 213-220. \[[Scopus\|http://www.scopus.com/inward/record.url?eid=2-s2.0-26944456307&partnerID=40&md5=358b2f8fdf0f5d81fab0e6e30fd08157]\] # Lintern R, Storey M. Jambalaya Express: Ontology Visualization-On-Demand. In ??8th Protege Conference??, Madrid, Spain, July 18-21, 2005. \[[PDF\|http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.129.3252&rep=rep1&type=pdf]\] * * 2002 # Hartel FW, de Coronado S. Information Standards Within the National Cancer Institute. (2002) ??Cancer Informatics: Essential Technologies for Clinical Trials?? JS Silva, et al., eds. Springer-Verlag, pp. 135-156. {multi-excerpt} {scrollbar:icons=false}

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{multi-excerpt:name=Bibliography}Below is a preliminary bibliography of scientific literature on EVS and the explicit use of EVS resources in support of cancer research and other scientific efforts.  It does not include materials where EVS resources may play an important role but are not explicitly addressed, as often occurs, for example, when use has been made of NCI's semantic infrastructure and tooling, or of EVS supported terminologies and standards often maintained jointly with other NCI units, NIH institutes, federal agencies or other partners.

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h2. Scientific Journal Articles

h3. EVS General

# Gonçalves RS, Parsia B, Sattler U. 
*Analysing the evolution of the NCI thesaurus.*
??Proceedings - IEEE Symposium on Computer-Based Medical Systems?? (2011) \[[At IEEE Xplore|http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5999163&tag=1]\]
*&nbsp;*
*2009*
# 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. \[[Available online|http://www.sciencedirect.com/science/article/B6WHD-4VFC80H-4/2/42a20ff355ab427f4d674d96e913c63b]\]
*&nbsp;*
*2008*
# 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. \[[Free PMC Article|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2753293/?tool=pubmed]\]
*&nbsp;*
*2007*
# 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. \[[Available online|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655888/pdf/amia-0165-s2007.pdf]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/16697710]\]
*&nbsp;*
*2005*
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/15797001]\]
*&nbsp;*
*2004*
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/15360769]\]
# 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. \[[Free PMC Article|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447470/?tool=pubmed]\]
*&nbsp;*
*2003*
# 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.
# Hartel F, Fragoso G, Ong K, Dionne R. 
*Enhancing Quality of Retrieval Through Concept Edit History.* 
??AMIA Annu Symp Proc.?? 2003:279-83. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/14728178]\]

h3. Biomedical Applications

# Liu H, Burkhart Q, Bell DSBertaud Gounot V, Donfack V, Lasbleiz J, Bourde A, Duvauferrier R. 
*EvaluationCreating an ofontology thedriven NCPDPrules Structuredbase andfor Codifiedan Sigexpert Formatsystem for e-prescriptionsmedical diagnosis.* 
??JStud AmHealth MedTechnol Inform Assoc.??. 2011 Sep 1;18(5):645-51. Epub 2011 May 25. ;169:714-8. PubMed PMID: 21613642; PubMed Central PMCID: PMC316830121893840. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/2161364221893840]\]
# PathakCuggia JM, WangBourde JA, KashyapTurlin SB, BasfordVincendeau MS, LiBertaud RV, MasysBohec DRC, ChuteDuvauferrier CGR. 
*MappingAutomatic clinicalDefinition phenotypeof datathe elementsOncologic toEHR standardizedData metadataElements repositoriesfrom andNCIT controlled terminologies: the eMERGE Network experiencein OWL.* 
??JStud AmHealth MedTechnol Inform Assoc.??  2011 Jul-Aug;18(4):376-86. Epub 2011 May 19. ;169:517-21. PubMed PMID: 21597104; PubMed Central PMCID: PMC312839621893803. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/2159710421893803]\]
# ShermanLiu SH, ShatsBurkhart OQ, KetchamBell 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;10:83-91DS. 
*Evaluation of the NCPDP Structured and Codified Sig Format for e-prescriptions.* 
??J Am Med Inform Assoc??. 2011 Sep 1;18(5):645-51. Epub 2011 May 25. PubMed PMID: 2155249421613642; PubMed Central PMCID: PMC3085425PMC3168301. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/2155249421613642]\]
# ShermanOverton SJA, ShatsRomagnoli OC, FleissnerChhem 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;10:217-26R. 
*Open biomedical ontologies applied to prostate cancer.* 
??Applied Ontology?? 2011;6(1):35-51.  \[[Scopus|http://www.scopus.com/inward/record.url?eid=2-s2.0-80052093434&partnerID=40&md5=e8ad9613fb41d3c802f7d09ae3db6c55]\]
# 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 AugMay 3119. PubMed PMID: 2191859621597104; PubMed Central PMCID: PMC3169352PMC3128396. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/2191859621597104]\]
# YongSherman MYS, Gonzalez-BeltranShats AO, BegentFleissner R. 
*Establishing a knowledge trail from molecular experiments to clinical trials.* 
??N BiotechnolE, 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 Sep;28(5):464-80;10:217-26. Epub 2011 AprAug 531. PubMed PMID: 21473938 21918596; PubMed Central PMCID: PMC3169352.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/2147393821918596]\]
# OvertonSherman JAS, RomagnoliShats CO, Chhem RKetcham 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. 
*OpenPCCR: biomedicalPancreatic ontologiesCancer applied to prostate cancerCollaborative Registry.* 
??AppliedCancer OntologyInform.?? 2011;6(1):35-51.  \[[Scopus Mar 23;10:83-91. PubMed PMID: 21552494; PubMed Central PMCID: PMC3085425. \[[PubMed|http://www.scopus.com/inward/record.url?eid=2-s2.0-80052093434&partnerID=40&md5=e8ad9613fb41d3c802f7d09ae3db6c55ncbi.nlm.nih.gov/pubmed/21552494]\]
# BertaudYong Gounot VMY, Donfack V, Lasbleiz J, Bourde Gonzalez-Beltran A, DuvauferrierBegent R. 
*CreatingEstablishing ana ontologyknowledge driventrail rulesfrom basemolecular forexperiments anto expert system for medical diagnosisclinical trials.* 
??Stud Health Technol InformN Biotechnol.?? 2011;169:714-8 Sep;28(5):464-80. Epub 2011 Apr 5. PubMed PMID: 2189384021473938.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/2189384021473938]\]
# Cuggia M, Bourde A, Turlin B, Vincendeau S, Bertaud V, Bohec C, Duvauferrier R. 
*Automatic Definition of the Oncologic EHR Data Elements from NCIT in OWL.* 
??Stud Health Technol Inform.?? 2011;169:517-21*&nbsp;*
*2010*
# Crowley RS, Castine M, Mitchell K, Chavan G, McSherry T, Feldman M.
*caTIES: a grid based system for coding and retrieval of surgical pathology reports and tissue specimens in support of translational research.*
??J Am Med Inform Assoc.?? 2010 May-Jun;17(3):253-64. PubMed PMID: 21893803.20442142; PubMed Central PMCID: PMC2995710.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/2189380320442142]\]
h5. 2010
# Hirschfeld S, Songco D, Kramer BS, Guttmacher AE. 
*National Children's Study: update in 2010.*
??Mt Sinai J Med.?? 2011 Jan-Feb;78(1):119-25. doi: 10.1002/msj.20227. PubMed PMID: 21259268 \[[Full Text|http://jamia.bmj.com/cgi/pmidlookup?view=long&pmid=20442142]\]
# Deus HF, Veiga DF, Freire PR, Weinstein JN, Mills GB, Almeida JS. 
*Exposing the cancer genome atlas as a SPARQL endpoint.* 
??J Biomed Inform??. 2010 Dec;43(6):998-1008. PubMed PMID: 20851208; PubMed Central PMCID: PMC3071752. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/2125926820851208]\]
# CrowleyHirschfeld RSS, CastineSongco MD, MitchellKramer KBS, Chavan G, McSherry T, Feldman M.
*caTIES: a grid based system for coding and retrieval of surgical pathology reports and tissue specimens in support of translational researchGuttmacher AE. 
*National Children's Study: update in 2010.*
??Mt Sinai J Am Med Inform Assoc.?? 20102011 MayJan-JunFeb;1778(31):253119-6425. PubMed PMIDdoi: 20442142;10.1002/msj.20227. PubMed Central PMCIDPMID: PMC299571021259268.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/2044214221259268]\] \[[Full Text|http://jamia.bmj.com/cgi/pmidlookup?view=long&pmid=20442142]\]
# 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
# Jiang G, Solbrig HR, Iberson-Hurst D, Kush RD, Chute CG. 
*A Collaborative Framework for Representation and Harmonization of Clinical Study Data Elements Using Semantic MediaWiki.*
??AMIA Summits Transl Sci Proc. 2010?? Mar 1;2010:11-5. PubMed PMID: 2080595421347136; PubMed Central PMCID: PMC2929536PMC3041544. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/2080595421347136]\]
# DeusKang HFHP, VeigaBorromeo DFCD, FreireBerman PRJJ, WeinsteinBecich JN, Mills GB, Almeida JS. 
*Exposing the cancer genome atlas as a SPARQL endpointMJ. 
*The tissue microarray OWL schema: An open-source tool for sharing tissue microarray data.* 
??J BiomedPathol Inform.??. 2010 Dec;43(6):998-1008Jul 13;1. pii: 9. PubMed PMID: 2085120820805954; PubMed Central PMCID: PMC3071752PMC2929536. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/2085120820805954]\]
# ReedMartínez-Romero TLM, Kaufman-Rivi D. 
*FDA adverse Event Problem Codes: standardizing the classification of device and patient problems associated with medical device useVázquez-Naya JM, Rabuñal JR, Pita-Fernández S, Macenlle R, Castro-Alvariño J, López-Roses L, Ulla JL, Martínez-Calvo AV, Vázquez S, Pereira J, Porto-Pazos AB, Dorado J, Pazos A, Munteanu CR. 
*Artificial intelligence techniques for colorectal cancer drug metabolism: ontology and complex network.* 
??BiomedCurr InstrumDrug Technol.Metab??. 2010 May-Jun;4411(34):248-56347-68. Review. PubMed PMID: 2071535920446907.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/2071535920446907]\]
# JiangReed GTL, Solbrig HR, Iberson-Hurst D, Kush RD, Chute CGKaufman-Rivi D. 
*AFDA adverse CollaborativeEvent FrameworkProblem forCodes: Representationstandardizing andthe Harmonizationclassification of device and Clinicalpatient Studyproblems Dataassociated Elementswith Usingmedical Semanticdevice MediaWikiuse.* 
??AMIABiomed Summits Transl Sci Proc. 2010Instrum Technol.?? Mar2010 1;2010:11-5May-Jun;44(3):248-56. PubMed PMID: 21347136; PubMed Central PMCID: PMC304154420715359. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/2134713620715359]\]
# YipVázquez-Naya V, MeteJM, Martínez-Romero M, Porto-Pazos AB, Novoa F, Valladares-Ayerbes M, Topaloglu UPereira J, Munteanu CR, KockaraDorado SJ. 
*Concept Discovery for Pathology Reports using an N-gram ModelOntologies of drug discovery and design for neurology, cardiology and oncology.* 
??AMIACurr Summits Transl Sci Proc.Pharm Des??. 2010 Mar 1;2010:43-7;16(24):2724-36. Review. PubMed PMID: 21347147; PubMed Central PMCID: PMC3041542. 20642429.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/2134714720642429]\]
# Martínez-RomeroYip MV, Vázquez-NayaMete JMM, RabuñalTopaloglu JRU, Pita-FernándezKockara S,. Macenlle R, Castro-Alvariño J, López-Roses L, Ulla JL, Martínez-Calvo AV, Vázquez S, Pereira J, Porto-Pazos AB, Dorado J, Pazos A, Munteanu CR. 
*Artificial intelligence techniques for colorectal cancer drug metabolism: ontology and complex network.* 
??Curr Drug Metab??. 2010 May;11(4):347-68. Review. PubMed PMID: 20446907.  \
*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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/2044690721347147]\]
# Vázquez-Naya JM, Martínez-Romero Yong M, Porto-Pazos AB, Novoa F, Valladares-Ayerbes M, Pereira J, Munteanu CR, Dorado JBegent R. 
*OntologiesBest use of drugexperimental discoverydata andin design for neurology, cardiology and oncologycancer informatics.* 
??Curr Pharm DesFuture Oncol.??. 2010;16(24):2724-36. Review. PubMed PMID: 20642429.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/20642429]\]
# Yong M, Begent R. 
*Best use of experimental data in cancer informatics.* 
??Future Oncol.?? 2010  2010 Oct;6(10):1551-62. Review. Erratum in: Future Oncol. 2011 Jan;7(1):154. PubMed PMID: 21062155.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/21062155]\] \[[PDF|http://www.futuremedicine.com/doi/pdf/10.2217/fon.10.108]\]
h5. 2009
# 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 \[[PDF|http://www.futuremedicine.com/doi/pdf/10.2217/fon.10.108]\]
*&nbsp;*
*2009*
# Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone SA, Sklyar N, Zhao M, Sarkans U, Brazma A. 
*ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression.* 
??Nucleic Acids Res.?? 2009 Jan;37(Database issue):D868-72. Epub 2008 Nov 10. PubMed PMID: 1920818419015125; PubMed Central PMCID: PMC2646250PMC2686529. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1920818419015125]\]
# ParkinsonShah HNH, KapusheskyJonquet MC, KolesnikovChiang NAP, RusticiButte GAJ, ShojatalabChen MR, AbeygunawardenaMusen N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone SA, Sklyar N, Zhao M, Sarkans U, Brazma A. 
*ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression.* 
??Nucleic Acids Res.?? 2009 Jan;37(Database issue):D868-72. Epub 2008 Nov 10. PubMed PMID: 19015125; PubMed Central PMCID: PMC2686529. 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/19208184]\]
# Yong M, Tolner B, Nagl S, Pedley RB, Chester K, Green AJ, Mayer A, Sharma S, Begent R. 
*Data standards for minimum information collection for antibody therapy experiments.* 
??Protein Eng Des Sel.?? 2009 Mar;22(3):221-4. PubMed PMID: 19224941.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1901512519224941]\]
# Yong M, Tolner B, Nagl S, Pedley RB, Chester K, Green AJ, Mayer A, Sharma S, Begent R. 
*Data standards for minimum information collection for antibody therapy experiments \[[Oxford full text|http://peds.oxfordjournals.org/content/22/3/221.long]\]
*&nbsp;*
*2008*
# Kaefer CM, Milner JA. 
*The role of herbs and spices in cancer prevention.* 
??ProteinJ EngNutr Des SelBiochem.?? 20092008 MarJun;2219(36):221-4347-61. Review. PubMed PMID: 1922494118499033; PubMed Central PMCID: PMC2771684.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1922494118499033]\] \[[OxfordPubMed full textCentral|http://peds.oxfordjournals.org/content/22/3/221.longwww.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc-MS.gif]\]
h5. 2008
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/18999108]\]
# Marinelli RJ, Montgomery K, Liu CL, Shah NH, Prapong W, Nitzberg M, Zachariah ZK, Sherlock GJ, Natkunam Y, West RB, van de Rijn M, Brown PO, Ball CA. 
*The Stanford Tissue Microarray Database.* 
??Nucleic Acids Res.?? 2008 Jan;36(Database issue):D871-7. Epub 2007 Nov 7. PubMed PMID: 17989087; PubMed Central PMCID: PMC2238948. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/17989087]\]
*&nbsp;*
*2007*
# KaeferBurgun CMA, MilnerBodenreider JAO. 
*TheIssues rolein ofintegrating herbsepidemiology and spicesresearch information in cancer prevention oncology: experience with ICD-O3 and the NCI Thesaurus.* 
??JAMIA Annu NutrSymp BiochemProc.?? 2008 Jun;19(6):347-61. Review. PubMed PMID: 18499033; PubMed Central PMCID: PMC2771684. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/18499033]\]2007 Oct 11:85-9. PubMed PMID: 18693803. \[[PubMed Central|http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc-MS.gifpubmed/18693803]\]
h5. 2007
# MarquetFrey GLJ, DameronMaojo OV, Mitchell Saikali S, Mosser J, Burgun A. 
*Grading glioma tumors using OWL-DL and NCI Thesaurus.* 
??AMIA Annu Symp ProcJA. 
*Bioinformatics linkage of heterogeneous clinical and genomic information in support of personalized medicine.*
??Yearb Med Inform.?? 2007 Oct 11:50898-12105. PubMedErratum PMIDin: 18693888;Yearb Med Inform. 2008:19. PubMed Central PMCIDPMID: PMC265583017700912. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1869388817700912]\]
# BurgunMarquet AG, BodenreiderDameron O., 
*Issues in integrating epidemiology and research information in oncology: experience with ICD-O3 and theSaikali S, Mosser J, Burgun A. 
*Grading glioma tumors using OWL-DL and NCI Thesaurus.* 
??AMIA Annu Symp Proc.?? 2007 Oct 11:85508-912. PubMed PMID: 1869380318693888; PubMed Central PMCID: PMC2655830. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1869380318693888]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/17686183]\]
h5. 2006
*&nbsp;*
*2006*
# TobiasDeitzer JJR, ChilukuriPayne RPR, Komatsoulis GA, Mohanty S, Sioutos N, Warzel DB, Wright LW, Crowley RSStarren JB. 
*The CAP Cancer Protocols -- A Case Study Coverage of caCOREclinical Basedtrials Datatasks Standardsin Implementation to Integrate with the Cancer Biomedical Informatics Gridexisting ontologies.* 
??BMCAMIA MedicalAnnu Informatics Decision Making??, 20; 6:25, 2006Symp Proc.?? 2006:903. PubMed PMID: 17238522; PubMed Central PMCID: PMC1839431. \[[Free PMC ArticlePubMed|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1524939/?tool=pubmedpubmed/17238522]\]
# Shah NH, DeitzerRubin JRDL, PayneSupekar PRKS, StarrenMusen JBMA. 
*CoverageOntology-based ofannotation clinicaland trialsquery tasksof intissue existingmicroarray ontologiesdata.* 
??AMIA Annu Symp Proc.?? 2006:903709-13. PubMed PMID: 1723852217238433; PubMed Central PMCID: PMC1839431PMC1839511. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1723852217238433]\]
# Shah NH, Rubin DL, Supekar KS, Musen MA. 
*Ontology-based annotation and query of tissue microarray data 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.* 
??AMIABMC Medical AnnuInformatics SympDecision Proc.Making?? 2006:709-13. PubMed PMID: 17238433; PubMed Central PMCID: PMC1839511, 20; 6:25, 2006. \[[PubMedFree PMC Article|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1524939/?tool=pubmed/17238433]\]
h5. 2005
# Zhang*&nbsp;*
*2005*
# Bodenreider O, Hayamizu TF, Ringwald M, De Coronado S, BodenreiderZhang OS. 
*AlignmentOf ofmice multiple ontologies of anatomyand men: derivingaligning indirectmouse mappingsand from direct mappings to a referencehuman anatomies.* 
??AMIA Annu Symp Proc.??  2005:86461-85. PubMed PMID: 1677916316779002; PubMed Central PMCID: PMC1560629PMC1560846. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1677916316779002]\]
# BodenreiderZhang OS, HayamizuBodenreider TF, Ringwald M, De Coronado S, Zhang S. 
*Of mice and men: aligning mouse and human anatomiesO. 
*Alignment of multiple ontologies of anatomy: deriving indirect mappings from direct mappings to a reference.* 
??AMIA Annu Symp Proc.??  2005:61864-58. PubMed PMID: 1677900216779163; PubMed Central PMCID: PMC1560846PMC1560629. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1677900216779163]\]

h3. caCORE and caBIG

# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/19154797]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/17512259]\]
# Gao Q, Zhang YL, Xie ZY, Zhang QP, Hu ZZ. 
*caCORE: core architecture of bioinformation on cancer research in America.* 
??Beijing Da Xue Xue Bao.?? 2006 Apr 18;38(2):218-21. Chinese. PubMed PMID: 16617371. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/16617371]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/14668224]\]

h3. LexEVS

# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/20962136]\]
# Tao C, Pathak J, Solbrig HR, Wei WQ, Chute CG. 
*LexRDF Model: An RDF-based Unified Model for Heterogeneous Biomedical Ontologies.* 
??CEUR Workshop Proc??. 2009 Oct 26;521:3. PubMed PMID: 21804785; PubMed Central PMCID: PMC3146261.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/21804785]\]
# 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.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/19261933]\]
# Pathak J, Jiang G, Dwarkanath SO, Buntrock JD, Chute CG. 
*LexValueSets: an approach for context-driven value sets extraction.* 
??AMIA Annu Symp Proc??. 2008 Nov 6:556-60. PubMed PMID: 18998955; PubMed Central PMCID: PMC2656093.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/18998955]\]
# Jiang G, Peterson KJ, Johnson TM, Celik C, Jakob R, Chute CG. 
*Representing the ClaML-based ICD10 in LexGrid terminology model.* 
??AMIA Annu Symp Proc??. 2008 Nov 6:992. PubMed PMID: 18998953.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/18998953]\]
# Pathak J, Jiang G, Dwarkanath SO, Buntrock JD, Chute CG. 
*Adopting Graph Traversal Techniques for Context-Driven Value Sets Extraction from Biomedical Knowledge Sources.* 
??Proc IEEE Int Conf Semant Comput??. 2008 Aug 12;2008:460-467.  PubMed PMID: 21625412; PubMed Central PMCID: PMC3101576.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/21625412]\]

h3. Nanotechnology

# Thomas DG, Klaessig F, Harper SL, Fritts M, Hoover MD, Gaheen S, Stokes TH, Reznik-Zellen R, Freund ET, Klemm JD, Paik DS, Baker NA. 
*Informatics and standards for nanomedicine technology.* 
??Wiley Interdiscip Rev Nanomed Nanobiotechnol??. 2011 Jun 30. doi: 10.1002/wnan.152. Epub ahead of print. PubMed PMID: 21721140.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/21721140]\]
# Thomas DG, Pappu RV, Baker NA. 
*NanoParticle Ontology for cancer nanotechnology research.* J Biomed Inform. 2011 Feb;44(1):59-74. Epub 2010 Mar 6. PubMed PMID: 20211274; PubMed Central PMCID: PMC3042056.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/20211274]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/17238469]\]

h3. NLP

# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/1677902417238469]\]

h3. Ontology, Semantics and SemanticsNLP

# Payne PR, Borlawsky TB, Lele O, James S, Greaves AW.
*The TOKEn project: knowledge synthesis for in silico science.*
??J Am Med Inform Assoc.?? 2011 Oct 7.  [Epub ahead of print] PubMed PMID: 21984589.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/21984589]\]
# Jonquet C, LePendu P, Falconer S, Coulet A, Noy NF, Musen MA, Shah NH
*NCBO Resource Index: Ontology-based search and mining of biomedical resources*
??Web Semantics: Science, Services and Agents on the World Wide Web??, Volume 9, Issue 3, September 2011, Pages 316-324, ISSN 1570-8268, 10.1016/j.websem.2011.06.005. \[[ScienceDirect|http://www.sciencedirect.com/science/article/pii/S1570826811000485]\]
# McCusker JP, Luciano JS, McGuinness DL.
*Towards an Ontology for Conceptual Modeling.*
??Proc. of the International Conference on Biomedical Ontology, 2011.?? \[[Online|http://tw.rpi.edu/web/doc/towardscmo]\]
*&nbsp;*
*2010*
# Payne PR, Borlawsky TB, Stephens W, Barrett MC, Nguyen-Pham T, Greaves AW.
*The TRITON Project: Design and Implementation of an Integrative Translational Research Information Management Platform.*
??AMIA Annu Symp Proc.?? 2010 Nov 13;2010:617-21. PubMed PMID: 21347052; PubMed Central PMCID: PMC3041280.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/21347052]\] \[[Full Text|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041280/?tool=pubmed]\]
# 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). \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/21057720]\]
# Martinez-Romero M, Vazquez-Naya J, Munteanu CR, Pereira J, Pazos A.
*An approach for the automatic recommendation of ontologies using collaborative knowledge.* 
??Proceedings of the 14th international conference on Knowledge-based and intelligent information and engineering systems: Part II (KES\'10)??, Rossitza Setchi, Ivan Jordanov, Robert J. Howlett, and Lakhmi C. Jain (Eds.). Springer-Verlag, Berlin, Heidelberg, 74-81.
# Jonquet C, Musen MA, Shah NH. 
*Building a biomedical ontology recommender web service.*
??J Biomed Semantics.?? 2010 Jun 22;1 Suppl 1:S1. PubMed PMID: 20626921; PubMed Central PMCID: PMC2903720.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/20626921]\] \[[PDF|http://www.jbiomedsem.com/content/pdf/2041-1480-1-S1-S1.pdf]\] 
# Parai GK, Jonquet C, Xu R, Musen MA, Shah NH. 
*The Lexicon Builder Web service: Building Custom Lexicons from two hundred Biomedical Ontologies.*
??AMIA Annu Symp Proc.?? 2010 Nov 13;2010:587-91. PubMed PMID: 21347046; PubMed Central PMCID: PMC3041331. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/21347046]\] \[[PDF|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041331/pdf/amia-2010_sympproc_0587.pdf]\]
# Sun P, Zhang S. 
*Identifying Granularity Differences between Large Biomedical Ontologies through Rules.*
??AMIA Annu Symp Proc. 2010?? Nov 13;2010:927-31. PubMed PMID: 21347114; PubMed Central PMCID: PMC3041335. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/21347114]\] \[[Full Text|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041335/?tool=pubmed]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/21347074]\]
*&nbsp;*
*2009*
# McCusker JP, Phillips JA, González Beltrán A, Finkelstein A, Krauthammer M.
*Semantic web data warehousing for caGrid.*
??BMC Bioinformatics.?? 2009 Oct 1;10 Suppl 10:S2. PubMed PMID: 19796399; PubMed Central PMCID: PMC2755823. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/19796399]\]
# Kementsietsidis A, Lim L, Wang M. 
*Profile-based retrieval of records in medical databases.*
??AMIA Annu Symp Proc.?? 2009 Nov 14;2009:312-6. PubMed PMID: 20351871; PubMed Central PMCID: PMC2815445.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/20351871]\]
# Shah NH, Bhatia N, Jonquet C, Rubin D, Chiang AP, Musen MA. 
*Comparison of concept recognizers for building the Open Biomedical Annotator.*
??BMC Bioinformatics.?? 2009 Sep 17;10 Suppl 9:S14. PubMed PMID: 19761568; PubMed Central PMCID: PMC2745685.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/19761568]\] \[[Full Text|http://www.biomedcentral.com/1471-2105/10/S9/S14]\] 
# Jonquet C, Shah NH, Musen MA. 
*The open biomedical annotator.*
??Summit on Translat Bioinforma.?? 2009 Mar 1;2009:56-60. PubMed PMID: 21347171; PubMed Central PMCID: PMC3041576.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/21347171]\] \[[Full Text|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041576/?tool=pubmed]\] 
*&nbsp;*
*2008*
# Noy N, Tudorache T, de Coronado S, Musen M. 
*Developing biomedical ontologies collaboratively.* 
??AMIA Annu Symp Proc.?? 2008:520-4. \[[Available online|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656043/pdf/amia-0520-s2008.pdf]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/18999137]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/19221606]\]
# Bodenreider O. 
*Comparing SNOMED CT and the NCI Thesaurus through Semantic Web technologies.* 
??Proceedings of the Third International Conference on Knowledge Representation in Medicine (KR-MED 2008),?? 2008: p. 37-43.  \[[PDF|http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-410/Paper07.pdf]\]
# Kementsietsidis A, Lim L, Wang M. 
*Supporting ontology-based keyword search over medical databases.*
??AMIA Annu Symp Proc.?? 2008 Nov 6:409-13. PubMed PMID: 18998839; PubMed Central PMCID: PMC2656038.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/18998839]\]
# Rubin DL, Shah NH, Noy NF. 
*Biomedical ontologies: a functional perspective.*
??Brief Bioinform.?? 2008 Jan;9(1):75-90. Epub 2007 Dec 12. Review. PubMed PMID: 18077472.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/18077472]\]
# Shah NH, Muse MA.
*UMLS-Query: a perl module for querying the UMLS.*
??AMIA Annu Symp Proc.?? 2008 Nov 6:652-6. PubMed PMID: 18998805; PubMed Central PMCID: PMC2656020.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/18998805]\] \[[Full Text|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656020/?tool=pubmed]\]
*&nbsp;*
*2007*
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/18974854]\]
*&nbsp;*
*2006*
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/16929044]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/17051306]\]
# Cuenca Grau B, Parsia B, Sirin E, Kalyanpur A. 
*Modularity and web ontologies.* 
??Proc. of KR-06??, 2006.  \[[PDF|http://www.aaai.org/Papers/KR/2006/KR06-022.pdf]\]
*&nbsp;*
*2005*
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/16779024]\]
# 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. \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/16342916]\]

h2. Other Scientific Publications

# Ghazvinian A, Noy NF, Musen MA. 
*From mappings to modules: Using mappings to identify domain-specific modules in large ontologies.* (2011) 
??KCAP 2011 - Proceedings of the 2011 Knowledge Capture Conference??, pp. 33-40. \[[Scopus|http://www.scopus.com/inward/record.url?eid=2-s2.0-79960276657&partnerID=40&md5=89ee8ee5dc29c216c12b55745959a1c4]\]
# Tudorache T, Musen MA. 
*Collaborative Development of Large-Scale Biomedical Ontologies.* (2011) 
??Collaborative Computational Technologies for Biomedical Research?? (eds S. Ekins, M. A. Z. Hupcey and A. J. Williams), John Wiley & Sons, Inc., Hoboken, NJ, USA. pp. 179-200. doi: 10.1002/9781118026038.ch12
*&nbsp;*
*2010*
# Amin W, Kang HP, Becich MJ.
*Data Management, Databases, and Warehousing.*
??Biomedical Informatics for Cancer Research.?? (M.F. Ochs, J.T. Casagrande, R.V. Davuluri, eds). DOI 10.1007/978-1-4419-5714-6_3, © Springer Science+Business Media, LLC 2010. pp.39-71.
# Machado CM, Couto F, Fernandes AR, Santos S, Cardim N, Freitas AT. 
*Semantic characterization of hypertrophic cardiomyopathy disease* (2010) 
??2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010??, art. no. 5703841, pp. 432-439. \[[Scopus|http://www.scopus.com/inward/record.url?eid=2-s2.0-79952014366&partnerID=40&md5=4f5d6e004bbea4a8237ebf583a16ac2a]\]
# Hartung M, Gross A, Kirsten T, Rahm E. 
*Discovering evolving regions in life science ontologies.* (2010) 
??Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)??, 6254 LNBI, pp. 19-34. \[[Scopus|http://www.scopus.com/inward/record.url?eid=2-s2.0-78049425046&partnerID=40&md5=b75edf974601dc0257eb0cb8999f3292]\]
*&nbsp;*
*2009*
# Jonquet C, Shah NH, Musen MA.
*Prototyping a Biomedical Ontology Recommender Service.*
??Bio-Ontologies: Knowledge in Biology??, Stockholm, Sweden (2009).
# Hastings S, Oster S, Langella S, Melean C, Borlawsky T, Dhavel R, Payne P.
*Adoption and Adaptation of caGrid for CTSA.*
??Summit on Translat Bioinforma. 2009?? Mar 1;2009:44-8. PubMed PMID: 21347169; PubMed Central PMCID: PMC3041578.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/21347169]\] \[[Full Text|http://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21347169/?tool=pubmed]\]
# Borlawsky TB, Dhaval R, Hastings SL, Payne PR.
*Development of an agile knowledge engineering framework in support of multi-disciplinary translational research.*
??Summit on Translat Bioinforma. 2009?? Mar 1;2009:14-8. PubMed PMID: 21347164; PubMed Central PMCID: PMC3041563.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/21347164]\]
*&nbsp;*
*2008*
# Sebastian A, Noy NF, Tudorache T, Musen MA. 
*A generic ontology for collaborative ontology-development workflows.* (2008) 
??Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)??, 5268 LNAI, pp. 318-328. \[[Scopus|http://www.scopus.com/inward/record.url?eid=2-s2.0-56649105039&partnerID=40&md5=3ee1963c5952f19952e28d3e049f3dd4]\]
# Bodenreider O. 
*Biomedical ontologies in action: role in knowledge management, data integration and decision support.* 
??Yearbook of Medical Informatics?? (2008) pp.67-79.
# Allemang D, Hendler J. 
??Semantic Web for the Working Ontologist: Effective Modeling in RDFS and OWL.??
Elsevier, 2008.
# Payne PR, Borlawsky TB, Kwok A, Dhaval R, Greaves AW.
*Ontology-anchored Approaches to Conceptual Knowledge Discovery in a Multi-dimensional Research Data Repository.*
??Summit on Translat Bioinforma. 2008?? Mar 1;2008:85-9. PubMed PMID: 21347129; PubMed Central PMCID: PMC3041525.  \[[PubMed|http://www.ncbi.nlm.nih.gov/pubmed/21347129]\]
*&nbsp;*
*2007*
# Arvanitis TN, Taweel A, Zhao L, et al. 
*Supporting E-Trials Over Distributed Networks: A tool for capturing randomised control trials (RCT) eligibility criteria using the National Cancer Institute's (NCI) Enterprise Vocabulary Services (EVS)* 
??Technol Health Care?? 2007;15:298-299.
# Dmitrieva J, Bei Y, Verbeek FJ. 
*Ontological context visualization.* 
??OWLED 2007 Workshop on OWL: Volume 258 of CEUR Workshop Proceedings.?? eds Golbreich C, Kalyanpur A, Parsia B. CEUR-WS.org (2007).
*&nbsp;*
*2006*
# Noy NF, Chugh A, Liu W, Musen MA.
*A Framework for Ontology Evolution in Collaborative Environments.*
??The Semantic Web - ISWC 2006.?? Lecture Notes in Computer Science 4273 pp.544-558, DOI: 10.1007/11926078_39 \[[Springer|http://dx.doi.org/10.1007/11926078_39]\] \[[PDF|http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.106.3290&rep=rep1&type=pdf]\]
# Bernhard D. 
*Automatic acquisition of semantic relationships from morphological relatedness.* (2006) 
??Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)??, 4139 LNAI, pp. 121-132. \[[Scopus|http://www.scopus.com/inward/record.url?eid=2-s2.0-33749651005&partnerID=40&md5=2e5894b13afc2c73efb96498815c4f52]\]
*&nbsp;*
*2005*
# Kumar A, Smith B. 
*Oncology ontology in the NCI thesaurus.* (2005) 
??Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)??, 3581 LNAI, pp. 213-220. \[[Scopus|http://www.scopus.com/inward/record.url?eid=2-s2.0-26944456307&partnerID=40&md5=358b2f8fdf0f5d81fab0e6e30fd08157]\]
# Lintern R, Storey M. 
*Jambalaya Express: Ontology Visualization-On-Demand.* In 
??8th Protege Conference??, Madrid, Spain, July 18-21, 2005. \[[PDF|http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.129.3252&rep=rep1&type=pdf]\]
*&nbsp;*
*2002*
# Hartel FW, de Coronado S. 
*Information Standards Within the National Cancer Institute.* (2002) 
??Cancer Informatics: Essential Technologies for Clinical Trials?? JS Silva, et al., eds. Springer-Verlag, pp. 135-156. 

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