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This bibliography includes journal articles and other scientific literature about 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 is made of NCI's semantic infrastructure and tooling), or of EVS supported terminologies and standards (such as CTCAE, SPL, ICSR, and SDTM) often maintained jointly with other NCI units, NIH institutes, federal agencies and other partners.

EVS General

  1. Elkin PL, Tuttle MS, Rallins M, Trajkovski J, Lumakovska E, Brown SH.
    Implementations of Terminology.
    In Elkin PL, ed. Terminology and Terminological Systems, Ch.8 pp.125-175, Springer London, 2012. [Springer]
     
    2011
  2. 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]
  3. Gonçalves RS, Parsia B, Sattler U.
    Analysing Multiple Versions of an Ontology: A Study of the NCI Thesaurus.
    Proceedings of the 24th International Workshop on Description Logics (DL 2011), Barcelona, Spain, July 13-16, 2011. [PDF (CEUR Workshop Procs. v.745)]
     
    2009
  4. 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]
     
    2008
  5. 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]
     
    2007
  6. 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]
  7. 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]
  8. 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]
     
    2005
  9. 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]
     
    2004
  10. 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]
  11. 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]
     
    2003
  12. 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.
  13. Hartel F, Fragoso G, Ong K, Dionne R.
    Enhancing Quality of Retrieval Through Concept Edit History.
    AMIA Annu Symp Proc. 2003:279-83. [PubMed]

    EVS Origins

    2002
  14. Hartel FW, de Coronado S.
    Information Standards Within the National Cancer Institute.
    Cancer Informatics: Essential Technologies for Clinical Trials JS Silva, et al., eds. Springer-Verlag; 2002 Jan 8. pp. 135-156.
     
    2001
  15. Gwaltney K, Chute C, Hageman D, Kibbe W, McCormick K, Reeves D, Wright L.
    An assessment of cancer clinical trials vocabulary and IT infrastructure in the U.S.
    Proc AMIA Symp. 2001:224-8. PubMed PMID: 11825185; PubMed Central PMCID: PMC2243595. [PubMed] [Free PMC Article]
  16. Hubbard SL.
    Information systems in oncology.
    Cancer: Principles & Practice of Oncology, 6th ed. Devita VT, Hellman S, Rosenberg SA, eds. Philadelphia: Lippincott Williams & Wilkins; 2001. pp. 3135–46.
  17. Hubbard SM, Setser A.
    The Cancer Informatics Infrastructure: a new initiative of the National Cancer Institute.
    Semin Oncol Nurs. 2001 Feb;17(1):55-61. Review. PubMed PMID: 11236366. [PubMed] [Full Text]
  18. Silva JS, Ball MJ, Douglas JV.
    The Cancer Informatics Infrastructure (CII): An Architecture for Translating Clinical Research into Patient Care.
    Proceedings of the 10th World Congress on Medical Informatics (Medinfo 2001) Amsterdam: IOS Press 2001, pp. 114-117. Also cited as: Stud Health Technol Inform. 2001;84(Pt 1):114-7. PubMed PMID: 11604717. [PubMed]
     
    1999
  19. Silva J, Wittes R.
    Role of clinical trials informatics in the NCI's cancer informatics infrastructure.
    Proc AMIA Symp. 1999:950-4. PubMed PMID: 10566501; PubMed Central PMCID: PMC2232686. [PubMed] [Free PMC Article]
     

    Biomedical Applications

     
  20. Cuggia M, Dufour J-C, Zekri O, Gibaud I, Garde C, Bohec C, Duvauferrier R, Fieschi D, Besana P, Charlois L, Bourde A, Garcelon N, Laurent J, Fieschi M, Dameron O.
    Système sémantiquement interopérable de sélection semi-automatique des patients éligibles aux essais thérapeutiques en cancérologie [ASTEC: Automatic selection of clinical trials based on eligibility criteria].
    IRBM, 2012. In Press. Available online 6 March 2012. [http://dx.doi.org/10.1016/j.irbm.2012.02.001]
  21. Elkin PL.
    Springer Terminology Related Standards Development.
    In Elkin PL, ed. Terminology and Terminological Systems, Ch.7 pp.107-123, Springer London, 2012. [Springer]
  22. Groza T, Hunter J, Zankl A.
    The Bone Dysplasia Ontology: Integrating genotype and phenotype information in the skeletal dysplasia domain.
    BMC Bioinformatics. 2012 Mar 26;13(1):50. [Epub ahead of print] PubMed PMID: 22449239. [PubMed]
  23. Hayamizu TF, de Coronado S, Fragoso G, Sioutos N, Kadin JA, Ringwald M.
    The mouse-human anatomy ontology mapping project.
    Database (Oxford). 2012 Mar 20;2012:bar066. Print 2012. PubMed PMID: 22434834. [PubMed] [Full Text]
  24. Ho Sui SJ, Begley K, Reilly D, Chapman B, McGovern R, Rocca-Sera P, Maguire E, Altschuler GM, Hansen TA, Sompallae R, Krivtsov A, Shivdasani RA, Armstrong SA, Culhane AC, Correll M, Sansone SA, Hofmann O, Hide W.
    The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D984-91. Epub 2011 Nov 24. PubMed PMID: 22121217; PubMed Central PMCID: PMC3245064. [PubMed]
  25. McCullough CE, Reed TL, Kaufman-Rivi D.
    A Tool to Analyze Medical Device Problems: The Food and Drug Administration Device Problem Codes.
    J Clinical Engineering. 2012 Apr/Jun;37(2):56–62. doi: 10.1097/JCE.0b013e31824c99f1 [Online]
  26. Parikh PP, Minning TA, Nguyen V, Lalithsena S, Asiaee AH, Sahoo SS, Doshi P, Tarleton R, Sheth AP.
    A Semantic Problem Solving Environment for Integrative Parasite Research: Identification of Intervention Targets for Trypanosoma cruzi.
    PLoS Negl Trop Dis. 2012 Jan;6(1):e1458. Epub 2012 Jan 17. PubMed PMID: 22272365; PubMed Central PMCID: PMC3260319. [PubMed]
  27. Schriml LM, Arze C, Nadendla S, Chang YW, Mazaitis M, Felix V, Feng G, Kibbe WA.
    Disease Ontology: a backbone for disease semantic integration.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D940-6. Epub 2011 Nov 12. PubMed PMID: 22080554; PubMed Central PMCID: PMC3245088. [PubMed]
  28. Wang H, Yatawara M, Huang S, Dudley K, Szekely C, Holden S, Piantadosi S.
    The Integrated Proactive Surveillance System for Prostate Cancer.
    Open Med Inform J. 2012;6:1-8. Epub 2012 Mar 2. PubMed PMID: 22505956. [PubMed] [PDF]
     
    2011
  29. Adams N, Hoehndorf R, Gkoutos GV, Hansen G, Hennig C.
    PIDO: The Primary Immunodeficiency Disease Ontology.
    Bioinformatics. 2011 Sep 22. [Epub ahead of print] PubMed PMID: 21949270. [PubMed]
  30. Bertaud-Gounot V, Donfack V, Lasbleiz J, Bourde A, Duvauferrier R.
    Creating an ontology driven rules base for an expert system for medical diagnosis.
    Stud Health Technol Inform. 2011;169:714-8. PubMed PMID: 21893840. [PubMed]
  31. Chen S, Hsu C.
    The TCR Cancer Registry Repository for Annotating Cancer Data.
    Emergency Management and Management Sciences (ICEMMS), 2011 2nd IEEE International Conference on, 2011 Aug 8-10:297-300. [IEEE]
  32. Chute CG, Pathak J, Savova GK, Bailey KR, Schor MI, Hart LA, Beebe CE, Huff SM.
    The SHARPn project on secondary use of Electronic Medical Record data: progress, plans, and possibilities.
    AMIA Annu Symp Proc. 2011;2011:248-56. Epub 2011 Oct 22. PubMed PMID: 22195076; PubMed Central PMCID: PMC3243296. [PubMed]
  33. Cuggia M, Bourde A, Turlin B, Vincendeau S, Bertaud V, Bohec C, Duvauferrier R.
    Automatic Definition of the Oncologic EHR Data Elements from NCIT in OWL.
    Stud Health Technol Inform. 2011;169:517-21. PubMed PMID: 21893803. [PubMed]
  34. Hu H, Correll M, Kvecher L, Osmond M, Clark J, Bekhash A, Schwab G, Gao D, Gao J, Kubatin V, Shriver CD, Hooke JA, Maxwell LG, Kovatich AJ, Sheldon JG, Liebman MN, Mural RJ.
    DW4TR: A Data Warehouse for Translational Research.
    J Biomed Inform. 2011 Dec;44(6):1004-19. PubMed PMID: 21872681. [PubMed]
  35. Kush RD.
    Interoperability for the Learning Health System.
    Digital Infrastructure for the Learning Health System: The Foundation for Continuous Improvement in Health and Health Care: Workshop Series Summary. Grossmann C, Powers B, McGinnis JM eds. Institute of Medicine (2011) pp.108-114. [Online]
  36. Lasbleiz J, Brillet E, Decaux O, Duvauferrier R, Bertaud-Gounot V.
    Staging disease with Protégé 4: Example of multiple myeloma.
    IRBM, 2011 32(6):329-331. Available online 21 November 2011, doi:10.1016/j.irbm.2011.10.003
  37. Li X, Wang Q, Zheng Y, Lv S, Ning S, Sun J, Huang T, Zheng Q, Ren H, Xu J, Wang X, Li Y.
    Prioritizing human cancer microRNAs based on genes' functional consistency between microRNA and cancer.
    Nucleic Acids Res. 2011 Dec;39(22):e153. Epub 2011 Oct 5. PubMed PMID: 21976726; PubMed Central PMCID: PMC3239203. [PubMed]
  38. Liu H, Burkhart Q, Bell DS.
    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: 21613642; PubMed Central PMCID: PMC3168301. [PubMed]
  39. Moser RP, Hesse BW, Shaikh AR, Courtney P, Morgan G, Augustson E, Kobrin S, Levin KY, Helba C, Garner D, Dunn M, Coa K.
    Grid-enabled measures: using Science 2.0 to standardize measures and share data.
    Am J Prev Med. 2011 May;40(5 Suppl 2):S134-43. PubMed PMID: 21521586; PubMed Central PMCID: PMC3088871. [PubMed]
  40. Overton JA, Romagnoli C, Chhem R.
    Open biomedical ontologies applied to prostate cancer.
    Applied Ontology 2011;6(1):35-51. [ACM DL]
  41. 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]
  42. Schad PA, Mobley LR, Hamilton CM.
    Building a biomedical cyberinfrastructure for collaborative research.
    Am J Prev Med. 2011 May;40(5 Suppl 2):S144-50. PubMed PMID: 21521587. [PubMed]
  43. Sherman S, Shats O, Fleissner E, Bascom G, Yiee K, Copur M, Crow K, Rooney J, Mateen Z, Ketcham MA, Feng J, Sherman A, Gleason M, Kinarsky L, Silva-Lopez E, Edney J, Reed E, Berger A, Cowan K.
    Multicenter breast cancer collaborative registry.
    Cancer Inform. 2011;10:217-26. Epub 2011 Aug 31. PubMed PMID: 21918596; PubMed Central PMCID: PMC3169352. [PubMed]
  44. 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]
  45. Warden GI, Lacson R, Khorasani R.
    Leveraging Terminologies for Retrieval of Radiology Reports with Critical Imaging Findings.
    AMIA Annu Symp Proc. 2011 Oct;2011:1481-8. Epub 2011 Oct 22. PubMed PMID: 22195212; PubMed Central PMCID: PMC3243125. [PubMed]
  46. Yong MY, Gonzalez-Beltran A, Begent R.
    Establishing a knowledge trail from molecular experiments to clinical trials.
    N Biotechnol. 2011 Sep;28(5):464-80. Epub 2011 Apr 5. PubMed PMID: 21473938. [PubMed]
     
    2010
  47. 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: 20442142; PubMed Central PMCID: PMC2995710. [PubMed] [Full Text]
  48. 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]
  49. 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. [PubMed]
  50. 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: 21347136; PubMed Central PMCID: PMC3041544. [PubMed]
  51. Kang HP, Borromeo CD, Berman JJ, Becich MJ.
    The tissue microarray OWL schema: An open-source tool for sharing tissue microarray data.
    J Pathol Inform. 2010 Jul 13;1. pii: 9. PubMed PMID: 20805954; PubMed Central PMCID: PMC2929536. [PubMed]
  52. Lu R.
    Biomedical data retrieval utilizing textual data in a gene expression database by Richard Lu, MD.
    Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2010. [URI]
  53. Machado CM, Couto F, Fernandes AR, Santos S, Cardim N, Freitas AT.
    Semantic characterization of hypertrophic cardiomyopathy disease
    2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010, art. no. 5703841, 2010, pp. 432-439. [Scopus]
  54. Martínez-Romero M, Vázquez-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.
    Curr Drug Metab. 2010 May;11(4):347-68. Review. PubMed PMID: 20446907. [PubMed]
  55. 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]
  56. Sim I, Carini S, Tu S, Wynden R, Pollock BH, Mollah SA, Gabriel D, Hagler HK, Scheuermann RH, Lehmann HP, Wittkowski KM, Nahm M, Bakken S.
    The Human Studies Database Project: Federating Human Studies Design Data Using the Ontology of Clinical Research.
    AMIA Summits Transl Sci Proc. 2010: 51–55. [Online]
  57. Vázquez-Naya JM, Martínez-Romero M, Porto-Pazos AB, Novoa F, Valladares-Ayerbes M, Pereira J, Munteanu CR, Dorado J.
    Ontologies of drug discovery and design for neurology, cardiology and oncology.
    Curr Pharm Des. 2010;16(24):2724-36. Review. PubMed PMID: 20642429. [PubMed]
  58. 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]
  59. Yong M, Begent R.
    Best use of experimental data in cancer informatics.
    Future Oncol. 2010 Oct;6(10):1551-62. Review. Erratum in: Future Oncol. 2011 Jan;7(1):154. PubMed PMID: 21062155. [PubMed] [PDF]
     
    2009
  60. 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: 19015125; PubMed Central PMCID: PMC2686529. [PubMed]
  61. 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]
  62. 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] [Oxford full text]
     
    2008
  63. Kaefer CM, Milner JA.
    The role of herbs and spices in cancer prevention.
    J Nutr Biochem. 2008 Jun;19(6):347-61. Review. PubMed PMID: 18499033; PubMed Central PMCID: PMC2771684. [PubMed] [PubMed Central]
  64. 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]
  65. 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]
     
    2007
  66. 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.
  67. Burgun A, Bodenreider O.
    Issues in integrating epidemiology and research information in oncology: experience with ICD-O3 and the NCI Thesaurus.
    AMIA Annu Symp Proc. 2007 Oct 11:85-9. PubMed PMID: 18693803. [PubMed]
  68. Frey LJ, Maojo V, Mitchell JA.
    Bioinformatics linkage of heterogeneous clinical and genomic information in support of personalized medicine.
    Yearb Med Inform. 2007:98-105. Erratum in: Yearb Med Inform. 2008:19. PubMed PMID: 17700912. [PubMed]
  69. Marquet G, Dameron O, Saikali S, Mosser J, Burgun A.
    Grading glioma tumors using OWL-DL and NCI Thesaurus.
    AMIA Annu Symp Proc. 2007 Oct 11:508-12. PubMed PMID: 18693888; PubMed Central PMCID: PMC2655830. [PubMed]
  70. Richesson RL, Krischer J.
    Data standards in clinical research: gaps, overlaps, challenges and future directions.
    J Am Med Inform Assoc. 2007 Nov-Dec;14(6):687-96. Epub 2007 Aug 21. Erratum in: J Am Med Inform Assoc. 2008. [PubMed]
    Mar-Apr;15(2):265. PubMed PMID: 17712081; PubMed Central PMCID: PMC2213488.
  71. 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]
  72. Shifman MA, Li Y, Colangelo CM, Stone KL, Wu TL, Cheung KH, Miller PL, Williams KR.
    YPED: a web-accessible database system for protein expression analysis.
    J Proteome Res. 2007 Oct;6(10):4019-24. Epub 2007 Sep 15. PubMed PMID: 17867667. [PubMed]
     
    2006
  73. Deitzer JR, Payne PR, Starren JB.
    Coverage of clinical trials tasks in existing ontologies.
    AMIA Annu Symp Proc. 2006:903. PubMed PMID: 17238522; PubMed Central PMCID: PMC1839431. [PubMed]
  74. Shah NH, Rubin DL, Supekar KS, Musen MA.
    Ontology-based annotation and query of tissue microarray data.
    AMIA Annu Symp Proc. 2006:709-13. PubMed PMID: 17238433; PubMed Central PMCID: PMC1839511. [PubMed]
  75. Tobias J, Chilukuri R, Komatsoulis GA, Mohanty S, Sioutos N, Warzel DB, Wright LW, Crowley RS.
    The CAP Cancer Protocols – A Case Study of caCORE Based Data Standards Implementation to Integrate with the Cancer Biomedical Informatics Grid.
    BMC Medical Informatics Decision Making, 20; 6:25, 2006. [Free PMC Article]
     
    2005
  76. Bodenreider O, Hayamizu TF, Ringwald M, De Coronado S, Zhang S.
    Of mice and men: aligning mouse and human anatomies.
    AMIA Annu Symp Proc. 2005:61-5. PubMed PMID: 16779002; PubMed Central PMCID: PMC1560846. [PubMed]
  77. Zhang S, Bodenreider O.
    Alignment of multiple ontologies of anatomy: deriving indirect mappings from direct mappings to a reference.
    AMIA Annu Symp Proc. 2005:864-8. PubMed PMID: 16779163; PubMed Central PMCID: PMC1560629. [PubMed]
     
    2003
  78. Chute CG, Carter JS, Tuttle MS, Haber MW, Brown SH.
    Integrating pharmacokinetics knowledge into a drug ontology as an extension to support pharmacogenomics.
    AMIA Annu Symp Proc. 2003:170-4. PubMed PMID: 14728156; PubMed Central PMCID: PMC1480302. [PubMed] [Free PMC Article]
     
    2002
  79. Kogan SC, Ward JM, Anver MR, Berman JJ, Brayton C, Cardiff RD, Carter JS, de Coronado S, Downing JR, Fredrickson TN, Haines DC, Harris AW, Harris NL, Hiai H, Jaffe ES, MacLennan IC, Pandolfi PP, Pattengale PK, Perkins AS, Simpson RM, Tuttle MS, Wong JF, Morse HC 3rd; Hematopathology subcommittee of the Mouse Models of Human Cancers Consortium.
    Bethesda proposals for classification of nonlymphoid hematopoietic neoplasms in mice.
    Blood. 2002 Jul 1;100(1):238-45. PubMed PMID: 12070033. [PubMed]
     

    caCORE, caGrid and caBIG

     
  80. Boyd LB, Hunicke-Smith SP, Stafford GA, Freund ET, Ehlman M, Chandran U, Dennis R, Fernandez AT, Goldstein S, Steffen D, Tycko B, Klemm JD.
    The caBIG® Life Science Business Architecture Model.
    Bioinformatics. 2011 May 15;27(10):1429-35. Epub 2011 Mar 29. PubMed PMID: 21450709; PubMed Central PMCID: PMC3087952. [PubMed] [Free PMC]
     
    2009
  81. 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]
  82. 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] [Full Text]
     
    2008
  83. 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]
  84. Oster S, Langella S, Hastings S, Ervin D, Madduri R, Phillips J, Kurc T, Siebenlist F, Covitz P, Shanbhag K, Foster I, Saltz J.
    caGrid 1.0: an enterprise Grid infrastructure for biomedical research.
    J Am Med Inform Assoc. 2008 Mar-Apr;15(2):138-49. Epub 2007 Dec 20. PubMed PMID: 18096909; PubMed Central PMCID: PMC2274794. [PubMed]
  85. 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]
     
    2006
  86. 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]
  87. Phillips J, Chilukuri R, Fragoso G, Warzel D, Covitz PA.
    The caCORE Software Development Kit: streamlining construction of interoperable biomedical information services.
    BMC Med Inform Decis Mak. 2006 Jan 6;6:2. PubMed PMID: 16398930; PubMed Central PMCID: PMC1379637. [PubMed]
  88. Saltz J, Oster S, Hastings S, Langella S, Kurc T, Sanchez W, Kher M, Manisundaram A, Shanbhag K, Covitz P.
    caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid.
    Bioinformatics. 2006 Aug 1;22(15):1910-6. Epub 2006 Jun 9. PubMed PMID: 16766552. [PubMed]
     
    2003
  89. Covitz PA, Hartel F, Schaefer C, De Coronado S, Fragoso G, Sahni H, Gustafson S, Buetow KH.
    caCORE: a common infrastructure for cancer informatics.
    Bioinformatics. 2003 Dec 12;19(18):2404-12. PubMed PMID: 14668224. [PubMed]
     

    LexEVS

     
  90. Lim Choi Keung SN, Zhao L, Tyler E, Hobbs FD, Arvanitis TN.
    Integrated Vocabulary Service for Health Data Interoperability.
    eTELEMED 2012, The Fourth International Conference on eHealth, Telemedicine, and Social Medicine. 2012 Jan 30:124-127. [PDF]
     
    2011
  91. Hazen R, Van Esbroeck AP, Mongkolwat P, Channin DS.
    Automatic Extraction of Concepts to Extend RadLex.
    Journal of Digital Imaging 2011 Feb;24(1):165-169. [PDF]
  92. Salvadores M, Alexander PR, Musen MA, Noy NF.
    The Quad Economy of a Semantic Web Ontology Repository.
    The 7th International Workshop on Scalable Semantic Web Knowledge Base Systems (SSWS 2011). pp.14-29. [PDF]
     
    2010
  93. 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]
     
    2009
  94. 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]
  95. Tao C, Pathak J, Solbrig HR, Chute CG.
    LexOWL: A Bridge from LexGrid to OWL.
    ICBO: International Conference on Biomedical Ontology. 2009 July 24-26. Buffalo, New York, USA.
  96. Tao C, Pathak J, Solbrig HR, Wei WQ, Chute CG.
    LexRDF Model: An RDF-based Unified Model for Heterogeneous Biomedical Ontologies.
    Proceedings of the Semantics for the Rest of Us - Variants of Semantic Web Languages in the Real World Workshop (SemRUs09). Washington DC, USA, 2009 Oct 26. PubMed PMID: 21804785; PubMed Central PMCID: PMC3146261. [PubMed] [PDF (CEUR Workshop Procs. v.521)]
     
    2008
  97. 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]
  98. 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]
  99. 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]
     

    Nanotechnology

     
  100. 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]
  101. 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]
  102. 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]
     

    Ontology, Semantics and NLP

     
  103. Beisswanger E, Hahn U.
    Towards valid and reusable reference alignments – ten basic quality checks for ontology alignments and their application to three different reference data sets.
    Journal of Biomedical Semantics 2012, 3(Suppl 1):S4. [PDF]
  104. Bougie G.
    A Case Study of a New Era in Disease Classification: An Investigation of the Socio-technical Requirements for Inclusive Standardization Development.
    Thesis (M.Sc.) University of Victoria, Department of Computer Science, 2012. [UVic]
  105. Chen Y, Gu H, Perl Y, Geller J.
    Overcoming an obstacle in expanding a UMLS semantic type extent.
    J Biomed Inform. 2012 Feb;45(1):61-70. Epub 2011 Sep 9. PubMed PMID: 21925287. [PubMed]
  106. Fung KW, Bodenreider O.
    Knowledge Representation and Ontologies.
    In: Richesson RL, Andrews JE, editors. Clinical research informatics. New York: Springer; 2012. Chapter 14, pp.255-275. [Springer] [PDF]
  107. Gonçalves RS, Parsia B, Sattler U.
    Concept-Based Semantic Difference in Expressive Description Logics.
    Proceedings of the 25th International Workshop on Description Logics (DL 2012), Rome, Italy, June 7-10, 2012. [PDF (CEUR Workshop Procs. v.846)]
  108. González-Beltrán A, Tagger B, Finkelstein A.
    Federated ontology-based queries over cancer data.
    BMC Bioinformatics 2012, 13(Suppl 1):S9. [BMC]
  109. Gross A, Hartung M, Thor A, Rahm E.
    How do Ontology Mappings Change in the Life Sciences?
    CoRR abs/1204.2731 April 2012. [PDF]
  110. Hartung M, Gross A, Kirsten T, Rahm E.
    Effective Mapping Composition for Biomedical Ontologies.
    Semantic Interoperability in Medical Informatics (SIMI 2012). [PDF]
  111. Hartung M, Gross A, Rahm E.
    COnto-Diff: Generation of Complex Evolution Mappings for Life Science Ontologies.
    J Biomed Inform. 2012 May 8. [Epub ahead of print] PubMed PMID: 22580476. [PubMed]
  112. Jiang G, Solbrig HR, Chute CG.
    Quality evaluation of value sets from cancer study common data elements using the UMLS semantic groups.
    J Am Med Inform Assoc. 2012 Apr 17. [Epub ahead of print] PubMed PMID: 22511016. [PubMed]
  113. Konev B, Ludwig M, Walther D, Wolter F.
    The Logical Diff for the Lightweight Description Logic EL.
    Journal of Artificial Intelligence Research, 2012 (Submitted). [PDF]
  114. Konev B, Ludwig M, Wolter F.
    Logical Difference Computation with CEX2.5.
    Proceedings of the 6th International Joint Conference on Automated Reasoning (IJCAR 2012). Springer-Verlag, 2012. [PDF]
  115. Lacson R, Andriole KP, Prevedello LM, Khorasani R.
    Information from Searching Content with an Ontology-Utilizing Toolkit (iSCOUT).
    Journal of Digital Imaging 2012 Feb 14:1-8 [Epub ahead of print] PubMed PMID: 22349993. [PubMed] [Online]
  116. Massot M, Cuggia M, Duvauferrier R, Bertaud-Gounot V.
    Représentation formelle des critères d’éligibilité aux essais cliniques: Exigences sémantiques de représentation des relations.
    In: Staccini P, Harmel A, Darmoni SJ, Gouider R, eds. Systèmes d’information pour l’amélioration de la qualité en santé. 2012:37-46. [Springer]
  117. Pathak J, Kiefer RC, Chute CG.
    Using Semantic Web Technologies for Cohort Identification from Electronic Health Records for Clinical Research.
    AMIA Clinical Research Informatics Summit 2012 Mar. [PDF]
  118. Szwabe A, Misiorek P, Walkowiak P.
    Reflective Relational Learning for Ontology Alignment.
    Distributed Computing and Artificial Intelligence, Omatu S, et al., eds. Springer-Verlag; 2012. pp. 519-526. [Springer]
  119. Vergara-Niedermayr C, Wang F, Pan T, Kurc T, Saltz J.
    Semantically Interoperable XML Data.
    Emory University Center for Comprehensive Informatics Technical Report CCI-TR-2012-1, January 12, 2012. [Emory]
  120. Wu ST, Liu H, Li D, Tao C, Musen MA, Chute CG, Shah NH.
    Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis.
    J Am Med Inform Assoc. 2012 Apr 4. [Epub ahead of print] PubMed PMID: 22493050. [PubMed]
  121. Zheng S, Wang F, Lu J, Saltz J.
    Enabling Ontology Based Semantic Queries in Biomedical Database Systems.
    Emory University Center for Comprehensive Informatics Technical Report CCI-TR-2012-3, March 20, 2012. [Emory]
     
    2011
  122. Bail S, Horridge M, Parsia B, Sattler U.
    The justificatory structure of the NCBO bioportal ontologies.
    The Semantic Web–ISWC 2011. Springer 2011 pp.67-82. [PDF]
  123. Bail S, Parsia B, Sattler U.
    Extracting finite sets of entailments from OWL ontologies.
    Proc. of DL-11. 2011. [PDF]
  124. Brochhausen M, Spear AD, Cocos C, Weiler G, Martín L, Anguita A, Stenzhorn H, Daskalaki E, Schera F, Schwarz U, Sfakianakis S, Kiefer S, Dörr M, Graf N, Tsiknakis M.
    The ACGT Master Ontology and its applications--towards an ontology-driven cancer research and management system.
    J Biomed Inform. 2011 Feb;44(1):8-25. Epub 2010 May 11. Review. PubMed PMID: 20438862. [PubMed]
  125. Chua WW, Kim JJ.
    BOAT: Automatic alignment of biomedical ontologies using term informativeness and candidate selection.
    J Biomed Inform. 2011 Dec 2. [Epub ahead of print] PubMed PMID: 22155335. [PubMed]
  126. Falconer SM, Tudorache T, Noy NF.
    An Analysis of Collaborative Patterns in Large-Scale Ontology Development Projects.
    Proceedings of the sixth international conference on Knowledge capture (K-CAP '11). 2011 ACM, New York, NY, USA. [ACM] [BMIR]
  127. Gennari JH, Neal ML, Galdzicki M, Cook DL.
    Multiple ontologies in action: composite annotations for biosimulation models.
    J Biomed Inform. 2011 Feb;44(1):146-54. Epub 2010 Jun 30. PubMed PMID: 20601121; PubMed Central PMCID: PMC2989341. [PubMed]
  128. Ghazvinian A, Noy NF, Musen MA.
    From mappings to modules: Using mappings to identify domain-specific modules in large ontologies.
    KCAP 2011 - Proceedings of the 2011 Knowledge Capture Conference, 2011, pp. 33-40. [Scopus]
  129. Gonçalves RS, Parsia B, Sattler U.
    Categorising logical differences between OWL ontologies.
    20th ACM Conference on Information and Knowledge Management (CIKM'11) (2011) Glasgow, 2011 Oct. 24-28, pp.1541-1546. [At IEEE Xplore]
  130. Gradie PR, Litster M, Thomas R, Vyas J, Schiller MR.
    SciReader enables reading of medical content with instantaneous definitions.
    BMC Med Inform Decis Mak. 2011 Jan 25;11:4. PubMed PMID: 21266060; PubMed Central PMCID: PMC3038137. [PubMed]
  131. Gross A, Hartung M, Kirsten T, Rahm E.
    Mapping Composition for Matching Large Life Science Ontologies.
    Proc of the 2nd International Conference on Biomedical Ontology (ICBO) 2011. [PDF]
  132. Jiang G, Solbrig HR, Chute CG.
    Quality evaluation of cancer study Common Data Elements using the UMLS Semantic Network.
    J Biomed Inform. 2011 Dec;44 Suppl 1:S78-85. Epub 2011 Aug 5. PubMed PMID: 21840422. [PubMed]
  133. Jiménez-Ruiz E, Grau BC, Horrocks I, Berlanga R.
    Logic-based assessment of the compatibility of UMLS ontology sources.
    J Biomed Semantics. 2011 Mar 7;2 Suppl 1:S2. PubMed PMID: 21388571; PubMed Central PMCID: PMC3105494. [PubMed]
  134. 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]
  135. Khoo CSG, Na JC, Wang VW, Chan S.
    Developing an Ontology for Encoding Disease Treatment Information in Medical Abstracts.
    DESIDOC Journal of Library and Information Technology, 2011 Mar;31(2):103-115. [PDF]
  136. Kirsten T, Gross A, Hartung M, Rahm E.
    GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution.
    J Biomed Semantics. 2011 Sep 13;2:6. PubMed PMID: 21914205; PubMed Central PMCID: PMC3198872. [PubMed] [Free PMC]
  137. Lee S, Choi J, Park K, Song M, Lee D.
    Inferring hidden relationships from biological literature with multi-level context terms.
    Proceedings of the ACM fifth international workshop on Data and text mining in biomedical informatics (DTMBIO '11). 2011: ACM New York, NY, USA. [ACM]
  138. 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. 2011;50(5):397-407. Epub 2010 Nov 8. [PubMed]
  139. Luciano JS, Andersson B, Batchelor C, Bodenreider O, Clark T, Denney CK, Domarew C, Gambet T, Harland L, Jentzsch A, Kashyap V, Kos P, Kozlovsky J, Lebo T, Marshall SM, McCusker JP, McGuinness DL, Ogbuji C, Pichler E, Powers RL, Prud'hommeaux E, Samwald M, Schriml L, Tonellato PJ, Whetzel PL, Zhao J, Stephens S, Dumontier M.
    The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside.
    J Biomed Semantics. 2011 May 17;2 Suppl 2:S1. PubMed PMID: 21624155; PubMed Central PMCID: PMC3102889. [PubMed] [Free PMC Article]
  140. Maier D, Kalus W, Wolff M, Kalko SG, Roca J, Marin de Mas I, Turan N, Cascante M, Falciani F, Hernandez M, Villà-Freixa J, Losko S.
    Knowledge management for systems biology a general and visually driven framework applied to translational medicine.
    BMC Syst Biol. 2011 Mar 5;5:38. PubMed PMID: 21375767; PubMed Central PMCID: PMC3060864. [PubMed]
  141. Martin M.
    Semantic Web may be cancer information's next step forward.
    J Natl Cancer Inst. 2011 Aug 17;103(16):1215-8. Epub 2011 Aug 3. PubMed PMID: 21813408. [PubMed] [Full Text]
  142. McCusker JP, Luciano JS, McGuinness DL.
    Towards an Ontology for Conceptual Modeling.
    Proc. of the International Conference on Biomedical Ontology, 2011. [Online]
  143. 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]
  144. Shamdasani J, Bloodsworth P, Hauer T, Branson A, Rogulin D, Odeh M, McClatchey R.
    MedMatch: Applying Semantic Matching in the Medical Domain.
    Journal of Web Semantics 2011 (Submitted). [PDF]
  145. Shaw M, Detwiler LT, Noy N, Brinkley J, Suciu D.
    vSPARQL: a view definition language for the semantic web.
    J Biomed Inform. 2011 Feb;44(1):102-17. Epub 2010 Aug 25. PubMed PMID: 20800106; PubMed Central PMCID: PMC3042057. [PubMed]
  146. Tudorache T, Musen MA.
    Collaborative Development of Large-Scale Biomedical Ontologies.
    Collaborative Computational Technologies for Biomedical Research (eds S. Ekins, M. A. Z. Hupcey and A. J. Williams), John Wiley & Sons, Inc., Hoboken, NJ, USA; 2011. pp. 179-200. doi: 10.1002/9781118026038.ch12
     
    2010
  147. 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.
  148. Chua WWK, Goh AES.
    An asymmetric similarity measure for ontologies based on the feature contrast model.
    Proceedings of the 2010 International Conference on Complex, Intelligent and Software Intensive Systems (CISIS '10), Krakow, Poland, 16 February 2010. IEEE Computer Society Washington, DC, USA ©2010. pp.1002–1007.
  149. Duan W, Yates A.
    Extracting glosses to disambiguate word senses.
    Human Language Technologies: The 2010 Annual Conference of the North American Chapter of the Association for Computational Linguistics. Association for Computational Linguistics, Stroudsburg, PA, 2010 pp.627-635. [PDF]
  150. Hartung M, Gross A, Kirsten T, Rahm E.
    Discovering evolving regions in life science ontologies.
    Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 6254 LNBI, 2010, pp. 19-34. [Scopus]
  151. 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] [PDF]
  152. 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.
  153. Obeid J, Gabriel D, Sanderson I.
    A biomedical research permissions ontology: cognitive and knowledge representation considerations.
    Proceedings of the 2010 Workshop on Governance of Technology, Information and Policies (GTIP '10). ACM, New York, NY, USA, 9-13. DOI=10.1145/1920320.1920322 http://doi.acm.org/10.1145/1920320.1920322
  154. 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] [PDF]
  155. 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] [Full Text]
  156. 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]
  157. 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] [Full Text]
     
    2009
  158. 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]
  159. Jonquet C, Shah NH, Musen MA.
    Prototyping a Biomedical Ontology Recommender Service.
    Bio-Ontologies: Knowledge in Biology, Stockholm, Sweden (2009).
  160. 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] [Full Text]
  161. 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]
  162. 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]
  163. Motik B, Shearer R, Horrocks I.
    Hypertableau Reasoning for Description Logics.
    Journal of Artificial Intelligence Research, 2009 Oct;36:165-228. [PDF]
  164. 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] [Full Text]
     
    2008
  165. Allemang D, Hendler J.
    Semantic Web for the Working Ontologist: Effective Modeling in RDFS and OWL.
    Elsevier, 2008.
  166. Bodenreider O.
    Biomedical ontologies in action: role in knowledge management, data integration and decision support.
    Yearbook of Medical Informatics (2008) pp.67-79.
  167. 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 (CEUR Workshop Procs. v.410)]
  168. 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]
  169. 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]
  170. 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]
  171. 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]
  172. 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]
  173. Noy N, Tudorache T, de Coronado S, Musen M.
    Developing biomedical ontologies collaboratively.
    AMIA Annu Symp Proc. 2008:520-4. [Available online]
  174. 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]
  175. 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]
  176. Sebastian A, Noy NF, Tudorache T, Musen MA.
    A generic ontology for collaborative ontology-development workflows.
    Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 5268 LNAI, 2008, pp. 318-328. [Scopus]
  177. Shah NH, Musen 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] [Full Text]
     
    2007
  178. 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). [PDF]
  179. 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]
     
    2006
  180. Bernhard D.
    Automatic acquisition of semantic relationships from morphological relatedness.
    Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 4139 LNAI, 2006, pp. 121-132. [Scopus]
  181. Cimino JJ, Zhu X.
    The practical impact of ontologies on biomedical informatics.
    Yearb Med Inform. 2006:124-35. Review. PubMed PMID: 17051306. [PubMed]
  182. Cuenca Grau B, Parsia B, Sirin E, Kalyanpur A.
    Modularity and web ontologies.
    Proc. of KR-06, 2006. [PDF]
  183. 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]
  184. 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]
  185. 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] [PDF]
  186. Plikus MV, Zhang Z, Chuong CM.
    PubFocus: semantic MEDLINE/PubMed citations analytics through integration of controlled biomedical dictionaries and ranking algorithm.
    BMC Bioinformatics. 2006 Oct 2;7:424. PubMed PMID: 17014720; PubMed Central PMCID: PMC1618408. [PubMed] [Full Text]
     
    2005
  187. 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]
  188. 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]
  189. Kumar A, Smith B.
    Oncology ontology in the NCI thesaurus.
    Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 3581 LNAI, 2005, pp. 213-220. [Scopus]
  190. Lintern R, Storey M.
    Jambalaya Express: Ontology Visualization-On-Demand. In
    8th Protege Conference, Madrid, Spain, July 18-21, 2005. [PDF]
  191. Supekar K, Chute CG, Solbrig H.
    Representing lexical components of medical terminologies in OWL.
    AMIA Annu Symp Proc. 2005:719-23. PubMed PMID: 16779134; PubMed Central PMCID: PMC1560674. [PubMed]
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