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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]
     
    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. [PDF]
  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. Pan H, Ardini MA, Bakalov V, Delatte M, Eggers P, Ganapathi L, Hollingsworth CR, Levy J, Li S, Pratt J, Pugh N, Qin Y, Rasooly R, Ray H, Richardson JE, Flynn Riley A, Rogers SM, Tan S, Turner CF, White S, Cooley PC.
    'What's in the NIDDK CDR?'--public query tools for the NIDDK central data repository.
    Database (Oxford). 2013 Feb 8;2013:bas058. doi: 10.1093/database/bas058. Print 2013. PubMed PMID: 23396299. [PubMed]
     
    2012
  21. 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]
  22. de Bree E, Romanos J, Tsogkas J, Askoxylakis J, Metaxari M, Michalakis J, Volakakis E, Melissas J, Tsiftsis DD.
    Complications and Toxicity After Abdominal and Pelvic Hypoxic Stop-Flow Perfusion Chemotherapy: Incidence and Assessment of Risk Factors.
    Ann Surg Oncol. 2012 Oct;19(11):3591-7. doi:10.1245/s10434-012-2383-6. Epub 2012 May 11. PubMed PMID: 22576062. [PubMed]
  23. Donfack Guefack V, Bertaud Gounot V, Duvauferrier R, Bourde A, Morelli J, Lasbleiz J.
    Ontology driven decision support systems for medical diagnosis - an interactive form for consultation in patients with plasma cell disease.
    Stud Health Technol Inform. 2012;180:108-12. PubMed PMID: 22874162. [PubMed]
  24. Elkin PL.
    Springer Terminology Related Standards Development.
    In Elkin PL, ed. Terminology and Terminological Systems, Ch.7 pp.107-123, Springer London, 2012. [Springer]
  25. Gazder Y.
    Scoping the Processes and Feasibility of a Synoptic Breast Pathology Reporting Module.
    Dalhousie University Department of Diagnostic Radiology Internship Report 2012 Aug 10, Halifax, Nova Scotia, Canada. [PDF]
  26. 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;13:50. doi: 10.1186/1471-2105-13-50. PubMed PMID: 22449239; PubMed Central PMCID: PMC3338382. [PubMed]
  27. 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]
  28. 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]
  29. Machado CM, Couto F, Fernandes AR, Santos S, Cardim N, Freitas AT.
    Toward a Translational Medicine Approach for Hypertrophic Cardiomyopathy.
    Proceedings of the 3rd International Conference on Information Technology in Bio- and Medical Informatics (ITBAM 2012), Vienna, Austria, September 4-5, 2012 (LNCS 7451:151-165). [PDF]
  30. 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]
  31. Milacic M, Haw R, Rothfels K, Wu G, Croft D, Hermjakob H, D’Eustachio P, Stein L.
    Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome.
    Cancers. 2012 4(4), 1180-1211; doi:10.3390/cancers4041180. [PDF]
  32. 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]
  33. Parker JL, Lushina N, Bal PS, Petrella T, Dent R, Lopes G.
    Impact of biomarkers on clinical trial risk in breast cancer.
    Breast Cancer Res Treat. 2012 Nov;136(1):179-85. doi: 10.1007/s10549-012-2247-6. Epub 2012 Sep 25. PubMed PMID: 23007573. [PubMed] [PDF]
  34. Santos RS, Malheiros SMF, Cavalheiro S, Parente de Oliveira JM.
    A data mining system for providing analytical information on brain tumors to public health decision makers.
    Computer Methods and Programs in Biomedicine, Available online 30 October 2012. [ScienceDirect]
  35. 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]
  36. 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]
  37. Zhu Q, Freimuth RR, Lian Z, Bauer S, Pathak J, Tao C, Durski MJ, Chute CG.
    Harmonization and semantic annotation of data dictionaries from the Pharmacogenomics Research Network: A case study.
    J Biomed Inform. 2012 Nov 29. doi:pii: S1532-0464(12)00178-5. 10.1016/j.jbi.2012.11.004. [Epub ahead of print] PubMed PMID: 23201637. [PubMed]
     
    2011
  38. Adams N, Hoehndorf R, Gkoutos GV, Hansen G, Hennig C.
    PIDO: The Primary Immunodeficiency Disease Ontology.
    Bioinformatics. 2011 Nov 15;27(22):3193-9. doi: 10.1093/bioinformatics/btr531. Epub 2011 Sep 22. PubMed PMID: 21949270. [PubMed]
  39. 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]
  40. 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]
  41. 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]
  42. 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]
  43. 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]
  44. 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]
  45. 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
  46. 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]
  47. 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]
  48. 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]
  49. Overton JA, Romagnoli C, Chhem R.
    Open biomedical ontologies applied to prostate cancer.
    Applied Ontology 2011;6(1):35-51. [ACM DL]
  50. 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]
  51. 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]
  52. 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]
  53. 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]
  54. 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]
  55. 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
  56. 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]
  57. 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]
  58. 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]
  59. 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]
  60. 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]
  61. 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]
  62. 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]
  63. 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]
  64. 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]
  65. 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]
  66. 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]
  67. 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]
  68. 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
  69. 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]
  70. 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]
  71. 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
  72. 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]
  73. 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]
  74. 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
  75. 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.
  76. 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]
  77. 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]
  78. 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]
  79. 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.
  80. 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]
  81. 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
  82. 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]
  83. 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]
  84. 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
  85. 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]
  86. 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
  87. 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
  88. 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

     
  89. 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
  90. 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]
  91. 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
  92. 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]
  93. 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]
  94. 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
  95. 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]
  96. 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]
  97. 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
  98. 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

     
  99. 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]
  100. Zhao L, Lim Choi Keung SN, Taweel A, Tyler E, Ogunsina I, Rossiter J, Delaney BC, Peterson KA, Hobbs FD, Arvanitis TN.
    A Loosely Coupled Framework for Terminology Controlled Distributed EHR Search for Patient Cohort Identification in Clinical Research.
    Stud Health Technol Inform. 2012;180:519-23. PubMed PMID: 22874245. [PubMed]
     
    2011
  101. 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]
  102. 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
  103. 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
  104. 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]
  105. 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.
  106. 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]
     
    2008
  107. 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]
  108. 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]
  109. 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

     
  110. 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 Central PMCID: PMC3189420. [PubMed]
  111. 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]
  112. 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

     
  113. Ba M, Diallo G.
    Large-scale biomedical ontology matching with ServOMap.
    IRBM, 2013. In Press. Available online 13 February 2013. [http://dx.doi.org/10.1016/j.irbm.2012.12.011]
  114. Hartung M, Gross A, Rahm E.
    COnto-Diff: Generation of Complex Evolution Mappings for Life Science Ontologies.
    J Biomed Inform. 2013 Feb;46(1):15-32. doi:10.1016/j.jbi.2012.04.009. Epub 2012 May 8. PubMed PMID: 22580476. [PubMed]
  115. Tao C, Pathak J, Solbrig HR, Wei WQ, Chute CG.
    Terminology Representation Guidelines for Biomedical Ontologies in the Semantic Web Notations.
    J Biomed Inform. 2013 Feb;46(1):128-38. doi: 10.1016/j.jbi.2012.09.003. Epub 2012 Sep 28. PubMed PMID: 23026232; PubMed Central PMCID: PMC3563768. [PubMed]
  116. Wang Z, Sagotsky J, Taylor T, Shironoshita P, Deisboeck TS.
    Accelerating cancer systems biology research through Semantic Web technology.
    Wiley Interdiscip Rev Syst Biol Med. 2013 Mar;5(2):135-51. doi: 10.1002/wsbm.1200. Epub 2012 Nov 27. PubMed PMID: 23188758; PubMed Central PMCID: PMC3558557. [PubMed]
     
    2012
  117. Aguirre JL, Eckert K, Euzenat J, Ferrara A, van Hage WR, Hollink L, Meilicke C, Nikolov A, Ritze D, Scharffe F, Shvaiko P, Šváb-Zamazal O, Trojahn C, Jiménez-Ruiz E, Cuenca Grau B, Zapilko B.
    Preliminary results of the Ontology Alignment Evaluation Initiative 2012.
    Seventh International Workshop on Ontology Matching (ISWC 2012), 2012, Boston, Massachusetts, U.S.A. Nov 11, 2012. [PDF]
  118. 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]
  119. Benik J, Palma G, Raschid L, Thor A, Vidal ME.
    Mining Patterns from Clinical Trial Annotated Datasets by Exploiting the NCI Thesaurus.
    Proc. 11th Intl. Semantic Web Conference (ISWC 2012) 2012, Boston, Massachusetts, U.S.A. Nov 11-15, 2012. [PDF]
  120. 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]
  121. 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]
  122. Chua WW, Kim JJ.
    BOAT: Automatic alignment of biomedical ontologies using term informativeness and candidate selection.
    J Biomed Inform. 2012 Apr;45(2):337-49. doi: 10.1016/j.jbi.2011.11.010. Epub 2011 Dec 2. PubMed PMID: 22155335. [PubMed]
  123. Dos Reis JC, Pruski C, Da Silveira M, Reynaud-Delaître C.
    Analyzing and Supporting the Mapping Maintenance Problem in Biomedical Knowledge Organization Systems.
    Semantic Interoperability in Medical Informatics (SIMI 2012). Heraklion (Crete), Greece, May 27, 2012. [PDF]
  124. Ferreira JD, Pesquita C, Couto FM, Silva MJ.
    Bringing epidemiology into the Semantic Web.
    Proc of the 3rd International Conference on Biomedical Ontology (ICBO 2012). 2012 July 21-25. Graz, Austria. [PDF]
  125. Freimuth RR, Freund ET, Schick L, Sharma MK, Stafford GA, Suzek BE, Hernandez J, Hipp J, Kelley JM, Rokicki K, Pan S, Buckler A, Stokes TH, Fernandez A, Fore I, Buetow KH, Klemm JD.
    Life sciences domain analysis model.
    J Am Med Inform Assoc. 2012 Nov-Dec;19(6):1095-102. doi: 10.1136/amiajnl-2011-000763. Epub 2012 Jun 28. PubMed PMID: 22744959; PubMed Central PMCID: PMC3486731. [PubMed]
  126. 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]
  127. Giudicelli V, Lefranc MP.
    IMGT-ONTOLOGY 2012.
    Front Genet. 2012;3:79. Epub 2012 May 23. PubMed PMID: 22654892; PubMed Central PMCID: PMC3358611. [PubMed]
  128. 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 (in CEUR Workshop Proceedings 846:191-201). [PDF]
  129. Gonçalves RS, Parsia B, Sattler U.
    Concept-Based Semantic Difference in Expressive Description Logics.
    11th International Semantic Web Conference (ISWC 2012) Boston, Massachusetts, U.S.A. Nov 11-15, 2012 (LNCS 7649:99-115).
  130. González-Beltrán A, Tagger B, Finkelstein A.
    Federated ontology-based queries over cancer data.
    BMC Bioinformatics 2012, 13(Suppl 1):S9. [BMC]
  131. Gross A, Hartung M, Kirsten T, Rahm E.
    GOMMA Results for OAEI 2012.
    Seventh International Workshop on Ontology Matching (ISWC 2012), 2012, Boston, Massachusetts, U.S.A. Nov 11, 2012. [PDF]
  132. Gross A, Hartung M, Thor A, Rahm E.
    How do computed ontology mappings evolve? - A case study for life science ontologies.
    Proceedings of the 2nd Joint Workshop on Knowledge Evolution and Ontology Dynamics (EvoDyn 2012), in conjuction with 11th Intl. Semantic Web Conference (ISWC 2012) 2012, Boston, Massachusetts, U.S.A. Nov 12, 2012. [PDF]
  133. Gross A, Hartung M, Thor A, Rahm E.
    How do Ontology Mappings Change in the Life Sciences?
    CoRR abs/1204.2731 April 2012. [PDF]
  134. Hartung M, Gross A, Kirsten T, Rahm E.
    Effective Mapping Composition for Biomedical Ontologies.
    Semantic Interoperability in Medical Informatics (SIMI 2012). Heraklion (Crete), Greece, May 27, 2012. [PDF]
  135. Ivanova V, Lambrix P.
    A System for Debugging Taxonomies and their Alignments.
    First International Workshop on Debugging Ontologies and Ontology Mappings, Galway, Ireland, Oct 8 2012. [PDF]
  136. 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 Jun 1;19(e1):e129-e136. Epub 2012 Apr 17. PubMed PMID: 22511016; PubMed Central PMCID: PMC3392855. [PubMed]
  137. Jimenez-Ruiz E, Cuenca Grau B, Horrocks I.
    Exploiting the UMLS Metathesaurus in the Ontology Alignment Evaluation Initiative.
    Proceedings of the 2nd International Workshop on Exploiting Large Knowledge Repositories (E-LKR'12) Castellón de la Plana, Spain, September 7, 2012. [PDF]
  138. 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]
  139. 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]
  140. Lacson R, Andriole KP, Prevedello LM, Khorasani R.
    Information from Searching Content with an Ontology-Utilizing Toolkit (iSCOUT).
    J Digit Imaging. 2012 Aug;25(4):512-9. PubMed PMID: 22349993; PubMed Central PMCID: PMC3389089. [PubMed] [Online]
  141. Machado CM, Freitas AT, Couto FM.
    Enrichment analysis applied to disease prognosis.
    Proceedings of the 4th Workshop of the GI Workgroup Ontologies in Biomedicine and Life Sciences (OBML 2012) eds. Boeker M, Herre H, Hoehndorf R, Loebe F. Dresden, Germany, Sept 27-28, 2012. [PDF]
  142. Malone J, Rayner TF, Bradley XZ, Parkinson H.
    Developing an application focused experimental factor ontology: embracing the OBO Community.
    Bio-Ontologies SIG, ISMB 2008 Toronto Canada, 20 July 2008. [PDF]
  143. 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]
  144. Mathur S.
    Ontology-Based Methods for Disease Similarity Estimation and Drug Repositioning.
    Thesis (Ph.D.) University of Missouri Kansas City, Computer Science and Mathematics, 2012. [PDF]
  145. McCusker J, Lee J, Thomas C, McGuinness DL.
    Public Health Surveillance Using Global Health Explorer.
    Joint Workshop on Semantic Technologies Applied to Biomedical Informatics and Individualized Medicine (SATBI+SWIM 2012) in conjunction with International Semantic Web Conference (ISWC 2012). Boston, Massachusetts, U.S.A. Nov 11-15, 2012. [PDF]
  146. Meilicke C, Svab-Zamazal O, Trojahn C, Jimenez-Ruiz E, Aguirre JL, Stuckenschmidt H, Cuenca Grau B.
    Evaluating Ontology Matching Systems on Large, Multilingual and Real-world Test Cases.
    Technical Report of the OAEI 2011.5 Evaluation Campaign ArXiv e-prints, vol. 1208.3148, August, 2012. [PDF]
  147. Min H, Wojtusiak J.
    Clinical data analysis using ontology-guided rule learning.
    Proceedings of the 2nd international workshop on Managing interoperability and compleXity in health systems (MIXHS '12) pp.17-22 (at 21st ACM International Conference on Information and Knowledge Management (CIKM'12) Maui, HI, USA Oct 29 - Nov 2, 2012. [ACM]
  148. 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]
  149. Pesquita CLSC.
    Automated Extension of Biomedical Ontologies.
    Thesis (Ph.D.) Universidade de Lisboa, Faculdade de Ciências, Departamento de Informática 2012. [U.Lisbon] [PDF]
  150. Saitwal H, Qing D, Jones S, Bernstam E, Chute CG, Johnson TR.
    Cross-Terminology Mapping Challenges: A Demonstration Using Medication Terminological Systems.
    J Biomed Inform. 2012 Aug;45(4):613-25. Epub 2012 Jun 28. PubMed PMID: 22750536. [PubMed]
  151. Salvadores M, Alexander PR, Musen MA, Noy NF.
    BioPortal as a Dataset of Linked Biomedical Ontologies and Terminologies in RDF.
    Semantic Web Journal In Press. Available online 31 Oct 2012. [Online]
  152. 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]
  153. Tagaris A, Chondrogiannis E, Andronikou V, Tsatsaronis G, Mourtzoukos K, Roumier J, Matskanis N, Schroeder M, Massonet P, Koutsouris D, Varvarigou T.
    Semantic Interoperability between Clinical Research and Healthcare: the PONTE approach.
    Semantic Interoperability in Medical Informatics (SIMI 2012). Heraklion (Crete), Greece, May 27, 2012. [PDF]
  154. 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]
  155. 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 Jun;19(1e):e149-56. Epub 2012 Apr 4. PubMed PMID: 22493050; PubMed Central PMCID: PMC3392861. [PubMed]
  156. 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
  157. 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]
  158. Bail S, Parsia B, Sattler U.
    Extracting finite sets of entailments from OWL ontologies.
    Proc. of DL-11. 2011. [PDF]
  159. 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]
  160. Dentler K, Cornet R, ten Teije A, de Keizer N.
    Comparison of reasoners for large ontologies in the OWL 2 EL profile.
    Semantic Web Journal, 2(2):71-87,2011. [Online]
  161. 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]
  162. 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]
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    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]
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    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]
  165. 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]
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    Mapping Composition for Matching Large Life Science Ontologies.
    Proc of the 2nd International Conference on Biomedical Ontology (ICBO) 2011. [PDF]
  167. Groza T, Zankl A, Li YF, Hunter J.
    Using Semantic Web Technologies to Build a Community-Driven Knowledge Curation Platform for the Skeletal Dysplasia Domain.
    Proceedings of the 10th International Semantic Web Conference (ISWC 2011), Springer, Bonn, Germany, October 23-27, 2011. [PDF]
  168. 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]
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    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]
  170. 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]
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    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]
  172. 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]
  173. 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]
  174. Lim Choi Keung SN, Zhao L, Ogunsina I, Arvanitis TN, Tyler E.
    A Framework for Vocabulary Controlled Queries of Distributed Electronic Healthcare Records.
    Proc 3rd International Workshop on Knowledge Representation for Health Care (KR4HC 2011) in conjunction with the 13th Conference on Artificial Intelligence in Medicine (AIME 2011), pp. 196-209, 2011. [PDF] [IOS Press]
  175. Liu K, Chapman WW, Savova G, Chute CG, Sioutos N, Crowley RS.
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