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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 related scientific efforts. It does not include materials where EVS resources 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 standards maintained jointly with other partners such as CTCAE, FDA SPL and ICSR, and CDISC SDTM.

About EVS

  1. He Z, Chen Y, de Coronado S, Piskorski K, Geller J.
    Topological-Pattern-Based Recommendation of UMLS Concepts for National Cancer Institute Thesaurus.
    AMIA Annu Symp Proc. 2017 Feb 10;2016:618-627. PubMed PMID: 28269858. [PubMed]

    2013
  2. Copeland M, Gonçalves RS, Parsia B, Sattler U, Stevens R.
    Finding fault: Detecting issues in a versioned ontology.
    Proc Second International Workshop on Debugging Ontologies and Ontology Mappings (WoDOOM 2013) May 27, 2013, part of the European Semantic Web Symposium (ESWS 2013), Montpellier, France. [PDF Exit Disclaimer logo ]
     
    2012
  3. 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 Exit Disclaimer logo ]
     
    2011
  4. Gonçalves RS, Parsia B, Sattler U.
    Analysing the evolution of the NCI thesaurus.
    Proc IEEE Symposium on Computer-Based Medical Systems (CBMS-11) Bristol, United Kingdom, June 27-30, 2011. [At IEEE Xplore Exit Disclaimer logo ]
  5. Gonçalves RS, Parsia B, Sattler U.
    Analysing Multiple Versions of an Ontology: A Study of the NCI Thesaurus.
    Proc 24th International Workshop on Description Logics (DL 2011), Barcelona, Spain, July 13-16, 2011. [PDF Exit Disclaimer logo ]
     
    2009
  6. 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. [PubMed]
     
    2008
  7. Noy NF, de Coronado S, Solbrig H, Fragoso G, Hartel FW, Musen MA.
    Representing the NCI Thesaurus in OWL DL: Modeling tools help modeling languages.
    Appl Ontol. 2008 Jan 1;3(3):173-190. [PubMed] [Free PMC Article]
     
    2007
  8. 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. [PubMed] [Available online]
  9. 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. [PDF Exit Disclaimer logo ]
  10. 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
  11. 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
  12. De Coronado S, Haber MW, Sioutos N, Tuttle MS, Wright LW.
    NCI Thesaurus: Using Science-Based Terminology to Integrate Cancer Research Results.
    Proc 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]
  13. 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. [PubMed] [Free PMC Article]
     
    2003
  14. 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. [JWS Web Site Exit Disclaimer logo ]
  15. Hartel F, Fragoso G, Ong K, Dionne R.
    Enhancing Quality of Retrieval Through Concept Edit History.
    AMIA Annu Symp Proc. 2003:279-83. [PubMed]

    2002
  16. 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
  17. 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]
  18. 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.
  19. 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 Exit Disclaimer logo ]
  20. Silva JS, Ball MJ, Douglas JV.
    The Cancer Informatics Infrastructure (CII): An Architecture for Translating Clinical Research into Patient Care.
    Proc 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
  21. 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

  1. Gipson DS, Kirkendall ES, Gumbs-Petty B, Quinn T, Steen A, Hicks A, McMahon A, Nicholas S, Zhao-Wong A, Taylor-Zapata P, Turner M, Herreshoff E, Jones C, Davis JM, Haber M, Hirschfeld S.
    Development of a Pediatric Adverse Events Terminology.
    Pediatrics. 2017 Jan;139(1). Available online Dec 27, 2016. pii: e20160985. doi: 10.1542/peds.2016-0985. [Epub ahead of print] PubMed PMID: 28028203. [PubMed]
  2. Jouhet V, Mougin F, Bréchat B, Thiessard F.
    Building a model for disease classification integration in oncology, an approach based on the national cancer institute thesaurus.
    J Biomed Semantics. 2017 Feb 7;8(1):6. doi: 10.1186/s13326-017-0114-4. PubMed PMID: 28173841; PubMed Central PMCID: PMC5294908. [PubMed]
  3. Noor A, Assiri A, Ayvaz S, Clark C, Dumontier M.
    Drug-drug interaction discovery and demystification using Semantic Web technologies.
    J Am Med Inform Assoc. 2017. Available online 2016 Dec 28. pii: ocw128. doi: 10.1093/jamia/ocw128. [Epub ahead of print] [PubMed]
  4. Schilsky RL.
    Finding the Evidence in Real-World Evidence: Moving from Data to Information to Knowledge.
    J Am Coll Surg. 2017 Jan;224(1):1-7. doi: 10.1016/j.jamcollsurg.2016.10.025. PubMed PMID: 27989954. [PubMed]
  5. Sharma DK, Solbrig HR, Prud'hommeaux E, Pathak J, Jiang G.
    Standardized Representation of Clinical Study Data Dictionaries with CIMI Archetypes.
    AMIA Annu Symp Proc. 2017 Feb 10;2016:1119-1128. PubMed PMID: 28269909. [PubMed]
  6. Visvanathan K, Levit LA, Raghavan D, Hudis CA, Wong S, Dueck A, Lyman GH.
    Untapped Potential of Observational Research to Inform Clinical Decision Making: American Society of Clinical Oncology Research Statement.
    J Clin Oncol. 2017 Mar 30:JCO2017726414. doi: 10.1200/JCO.2017.72.6414. [Epub ahead of print] PubMed PMID: 28358653. [PubMed]
  7. Yan Z, Lacson R, Ip I, Valtchinov V, Raja A, Osterbur D, Khorasani R.
    Evaluating Terminologies to Enable Imaging-Related Decision Rule Sharing.
    AMIA Annu Symp Proc. 2017 Feb 10;2016:2082-2089. PubMed PMID: 28269968. [PubMed]

    2016
  8. Bonhoeffer J, Kochhar S, Hirschfeld S, Heath PT, Jones CE, Bauwens J, Honrado Á, Heininger U, Muñoz FM, Eckert L, Steinhoff M, Black S, Padula M, Sturkenboom M, Buttery J, Pless R, Zuber P; GAIA project participants.
    Global alignment of immunization safety assessment in pregnancy - The GAIA project.
    Vaccine. 2016 Dec 1;34(49):5993-5997. doi: 10.1016/j.vaccine.2016.07.006. PubMed PMID: 27751641. [PubMed]
  9. Fathiamini S, Johnson AM, Zeng J, Araya A, Holla V, Bailey AM, Litzenburger BC, Sanchez NS, Khotskaya Y, Xu H, Meric-Bernstam F, Bernstam EV, Cohen T.
    Automated identification of molecular effects of drugs (AIMED).
    J Am Med Inform Assoc. 2016 Jul;23(4):758-65. doi: 10.1093/jamia/ocw030. PubMed PMID: 27107438; PubMed Central PMCID: PMC4926748. [PubMed]
  10. Fernández JM, de la Torre V, Richardson D, Royo R, Puiggròs M, Moncunill V, Fragkogianni S, Clarke L; BLUEPRINT Consortium., Flicek P, Rico D, Torrents D, Carrillo de Santa Pau E, Valencia A.
    The BLUEPRINT Data Analysis Portal.
    Cell Syst. 2016 Nov 23;3(5):491-495.e5. doi: 10.1016/j.cels.2016.10.021. PubMed PMID: 27863955. [PubMed]
  11. Forbes SA, Beare D, Boutselakis H, Bamford S, Bindal N, Tate J, Cole CG, Ward S, Dawson E, Ponting L, Stefancsik R, Harsha B, Kok CY, Jia M, Jubb H, Sondka Z, Thompson S, De T, Campbell PJ.
    COSMIC: somatic cancer genetics at high-resolution.
    Nucleic Acids Res. 2016 Nov 28. pii: gkw1121. [Epub ahead of print] PubMed PMID: 27899578. [PubMed]
  12. Hochheiser H, Castine M, Harris D, Savova G, Jacobson RS.
    An information model for computable cancer phenotypes.
    BMC Med Inform Decis Mak. 2016 Sep 15;16(1):121. doi: 10.1186/s12911-016-0358-4. PubMed PMID: 27629872. [PubMed]
  13. Huang J, Eilbeck K, Smith B, Blake JA, Dou D, Huang W, Natale DA, Ruttenberg A, Huan J, Zimmermann MT, Jiang G, Lin Y, Wu B, Strachan HJ, He Y, Zhang S, Wang X, Liu Z, Borchert GM, Tan M.
    The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology.
    J Biomed Semantics. 2016 May 4;7:24. doi: 10.1186/s13326-016-0066-0. PubMed PMID: 27152146; PubMed Central PMCID: PMC4857245. [PubMed]
  14. Kaufman L, Gore K, Zandee JC.
    Data Standardization, Pharmaceutical Drug Development, and the 3Rs.
    ILAR J. 2016 Dec;57(2):109-119. doi: 10.1093/ilar/ilw030. PubMed PMID: 28053065. [PubMed]
  15. Kim E, Corte-Real M, Baloch Z.
    A Deep Semantic Mobile Application for Thyroid Cytopathology.
    SPIE Medical Imaging 2016: Advanced PACS-based Imaging Informatics and Therapeutic Applications, 2016. San Diego, California, USA, 27 Feb - 3 Mar 2016. [PubMed]
  16. Mottin L, Gobeill J, Pasche E, Michel PA, Cusin I, Gaudet P, Ruch P.
    neXtA5: accelerating annotation of articles via automated approaches in neXtProt.
    Database (Oxford). 2016 Jul 3;2016. pii: baw098. doi: 10.1093/database/baw098. PubMed PMID: 27374119; PubMed Central PMCID: PMC4930835. [PubMed]
  17. Piñero J, Bravo À, Queralt-Rosinach N, Gutiérrez-Sacristán A, Deu-Pons J, Centeno E, García-García J, Sanz F, Furlong LI.
    DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants.
    Nucleic Acids Res. 2016 Oct 19. pii: gkw943. [Epub ahead of print] PubMed PMID: 27924018. [PubMed]
  18. Ritter DI, Roychowdhury S, Roy A, Rao S, Landrum MJ, Sonkin D, Shekar M, Davis CF, Hart RK, Micheel C, Weaver M, Van Allen EM, Parsons DW, McLeod HL, Watson MS, Plon SE, Kulkarni S, Madhavan S; ClinGen Somatic Cancer Working Group.
    Somatic cancer variant curation and harmonization through consensus minimum variant level data.
    Genome Med. 2016 Nov 4;8(1):117. PubMed PMID: 27814769; PubMed Central PMCID: PMC5095986. [PubMed]
  19. Schilsky RL, Miller RS.
    Creating a Learning Health Care System in Oncology.
    Oncology Informatics: Using Health Information Technology to Improve Processes and Outcomes in Cancer. Hesse BW, Ahern DK, Beckjord E, eds. Elsevier Academic Press (2016), pp. 3–21.
  20. Souza AD, Almeida MB.
    Natural Language Definitions for the Leukemia Knowledge Domain.
    Proc International Conference on Biomedical Ontology 2016 (ICBO 2016). Corvallis, Oregon, USA, 1-4 Aug 2016. [PDF Exit Disclaimer logo ]
  21. Sward KA, Rubin S, Jenkins TL, Newth CJ, Dean JM; Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) Collaborative Pediatric Critical Care Research Network (CPCCRN).
    Case Study: Semantic Annotation of a Pediatric Critical Care Research Study.
    Comput Inform Nurs. 2016 Mar;34(3):101-4. doi: 10.1097/CIN.0000000000000236. PubMed PMID: 26958992; PubMed Central PMCID: PMC4788017. [PubMed]
  22. Warner JL, Rioth MJ, Mandl KD, Mandel JC, Kreda DA, Kohane IS, Carbone D, Oreto R, Wang L, Zhu S, Yao H, Alterovitz G.
    SMART precision cancer medicine: a FHIR-based app to provide genomic information at the point of care.
    J Am Med Inform Assoc. 2016 Mar 27. pii: ocw015. doi: 10.1093/jamia/ocw015. [Epub ahead of print] PubMed PMID: 27018265. [PubMed]
  23. Wood F.
    The Standard for the Exchange of Nonclinical Data (SEND): History, Basics, and Comparisons with Clinical Data.
    PharmaSUG 2016 Conference Proceedings. Denver, Colorado, May 8-11, 2016. [PDF Exit Disclaimer logo ]

    2015
  24. Anzai T, Kaminishi M, Sato K, Kaufman L, Iwata H, Nakae D.
    Responses to the Standard for Exchange of Nonclinical Data (SEND) in non-US countries.
    J Toxicol Pathol. 2015 Apr;28(2):57-64. doi: 10.1293/tox.2015-0007. Epub 2015 Apr 1. Review. PubMed PMID: 26028814; PubMed Central PMCID: PMC4444503. [PubMed][PDF Exit Disclaimer logo ]
  25. Duellman SJ, Zhou W, Meisenheimer P, Vidugiris G, Cali JJ, Gautam P, Wennerberg K, Vidugiriene J.
    Bioluminescent, Nonlytic, Real-Time Cell Viability Assay and Use in Inhibitor Screening.
    Assay Drug Dev Technol. 2015 Sep 18. [Epub ahead of print] PubMed PMID: 26383544. [PubMed]
  26. Dyke SO, Cheung WA, Joly Y, Ammerpohl O, Lutsik P, Rothstein MA, Caron M, Busche S, Bourque G, Rönnblom L, Flicek P, Beck S, Hirst M, Stunnenberg H, Siebert R, Walter J, Pastinen T.
    Epigenome data release: a participant-centered approach to privacy protection.
    Genome Biol. 2015 Jul 17;16(1):142. PubMed PMID: 26185018; PubMed Central PMCID: PMC4504083. [PubMed]
  27. Fransson MN, Rial-Sebbag E, Brochhausen M, Litton JE.
    Toward a common language for biobanking.
    Eur J Hum Genet. 2015 Jan;23(1):22-8. doi: 10.1038/ejhg.2014.45. Epub 2014 Apr 9. PubMed PMID: 24713663; PubMed Central PMCID: PMC4266732. [PubMed]
  28. Fu X, Batista-Navarro R, Rak R, Ananiadou S.
    Supporting the annotation of chronic obstructive pulmonary disease (COPD) phenotypes with text mining workflows.
    J Biomed Semantics. 2015 Mar 14;6:8. doi: 10.1186/s13326-015-0004-6. eCollection 2015. PubMed PMID: 25789153; PubMed Central PMCID: PMC4364458. [PubMed]
  29. Gaudet P, Michel PA, Zahn-Zabal M, Cusin I, Duek PD, Evalet O, Gateau A, Gleizes A, Pereira M, Teixeira D, Zhang Y, Lane L, Bairoch A.
    The neXtProt knowledgebase on human proteins: current status.
    Nucleic Acids Res. 2015 Jan 28;43(Database issue):D764-70. doi: 10.1093/nar/gku1178. PubMed PMID: 25593349. [PubMed]
  30. Hicks KA, Tcheng JE, Bozkurt B, Chaitman BR, Cutlip DE, Farb A, Fonarow GC, Jacobs JP, Jaff MR, Lichtman JH, Limacher MC, Mahaffey KW, Mehran R, Nissen SE, Smith EE, Targum SL.
    2014 ACC/AHA Key Data Elements and Definitions for Cardiovascular Endpoint Events in Clinical Trials: A Report of the American College of Cardiology/American Heart Association Task Force on Clinical Data Standards (Writing Committee to Develop Cardiovascular Endpoints Data Standards).
    J Am Coll Cardiol. 2015 Jul 28;66(4):403-69. doi: 10.1016/j.jacc.2014.12.018. Epub 2014 Dec 29. PubMed PMID: 25553722. [PubMed]
    J Nucl Cardiol. 2015 Jul 24. [Epub ahead of print] PubMed PMID: 26204990. [PubMed]
  31. Hostenkamp G, Lichtenberg FR.
    The impact of recent chemotherapy innovation on the longevity of myeloma patients: US and international evidence.
    Soc Sci Med. 2015 Apr;130:162-71. doi: 10.1016/j.socscimed.2015.02.003. Epub 2015 Feb 7. PubMed PMID: 25703669. [PubMed]
  32. Hsu W, Gonzalez NR, Chien A, Pablo Villablanca J, Pajukanta P, Viñuela F, Bui AA.
    An integrated, ontology-driven approach to constructing observational databases for research.
    J Biomed Inform. 2015 Jun;55:132-42. doi: 10.1016/j.jbi.2015.03.008. Epub 2015 Mar 26. PubMed PMID: 25817919; PubMed Central PMCID: PMC4464942. [PubMed]
  33. Huser V, Sastry C, Breymaier M, Idriss A, Cimino JJ.
    Standardizing Data Exchange for Clinical Research Protocols and Case Report Forms: An Assessment of the Suitability of the Clinical Data Interchange Standards Consortium (CDISC) Operational Data Model (ODM).
    J Biomed Inform. 2015 Jul 15. pii: S1532-0464(15)00133-1. doi: 10.1016/j.jbi.2015.06.023. [Epub ahead of print] PubMed PMID: 26188274. [PubMed]
  34. Jacobson RS, Becich MJ, Bollag RJ, Chavan G, Corrigan J, Dhir R, Feldman MD, Gaudioso C, Legowski E, Maihle NJ, Mitchell K, Murphy M, Sakthivel M, Tseytlin E, Weaver J.
    A Federated Network for Translational Cancer Research Using Clinical Data and Biospecimens.
    Cancer Res. 2015 Dec 15;75(24):5194-201. doi:10.1158/0008-5472.CAN-15-1973. Review. PubMed PMID: 26670560; PubMed Central PMCID: PMC4683415.[PubMed]
  35. Jiang G, Evans J, Oniki TA, Coyle JF, Bain L, Huff SM, Kush RD, Chute CG.
    Harmonization of detailed clinical models with clinical study data standards.
    Methods Inf Med. 2015;54(1):65-74. doi: 10.3414/ME13-02-0019. Epub 2014 Nov 26. PubMed PMID: 25426730. [PubMed]
  36. Jiang G, Sohn S, Zimmermann MT, Wang C, Liu H, Chute CG.
    Drug Normalization for Cancer Therapeutic and Druggable Genome Target Discovery.
    AMIA Jt Summits Transl Sci Proc. 2015 Mar 25;2015:72-6. eCollection 2015. PubMed PMID: 26306243; PubMed Central PMCID: PMC4525232. [PubMed]
  37. Keenan CM, Baker JF, Bradley AE, Goodman DG, Harada T, Herbert R, Kaufmann W, Kellner R, Mahler B, Meseck E, Nolte T, Rittinghausen S, Vahle J, Yoshizawa K.
    International Harmonization of Nomenclature and Diagnostic Criteria (INHAND): progress to date and future plans.
    J Toxicol Pathol. 2015 Jan;28(1):51-3. doi:10.1293/tox.2014-0049. Epub 2014 Nov 10. PubMed PMID: 26023262; PubMed Central PMCID: PMC4337500. [PubMed] [PubMed (orig)]
  38. Kim HH, Lee SY, Baik SY, Kim JH.
    MELLO: Medical Lifelog Ontology for Data Terms from Self-Tracking and Lifelog Devices.
    Int J Med Inform. 2015 Dec;84(12):1099-110. doi: 10.1016/j.ijmedinf.2015.08.005. Epub 2015 Aug 17. PubMed PMID: 26383495. [PubMed]
  39. Kim S, Thiessen PA, Bolton EE, Chen J, Fu G, Gindulyte A, Han L, He J, He S, Shoemaker BA, Wang J, Yu B, Zhang J, Bryant SH.
    PubChem Substance and Compound databases.
    Nucleic Acids Res. 2015 Sep 22. pii: gkv951. [Epub ahead of print] PubMed PMID: 26400175.[PubMed]
  40. Kogan A, Alpert K, Ambite JL, Marcus D, Wang L.
    Northwestern University schizophrenia data sharing for SchizConnect: A longitudinal dataset for large-scale integration.
    Neuroimage. 2015 Jun 16. pii: S1053-8119(15)00533-9. doi: 10.1016/j.neuroimage.2015.06.030. [Epub ahead of print] PubMed PMID: 26087378. [PubMed]
  41. Lacson R, Harris K, Brawarsky P, Tosteson TD, Onega T, Tosteson AN, Kaye A, Gonzalez I, Birdwell R, Haas JS.
    Evaluation of an Automated Information Extraction Tool for Imaging Data Elements to Populate a Breast Cancer Screening Registry.
    J Digit Imaging. 2015 Jan 6. [Epub ahead of print] PubMed PMID: 25561069. [PubMed]
  42. Leroux H, Lefort L.
    Semantic enrichment of longitudinal clinical study data using the CDISC standards and the semantic statistics vocabularies.
    J Biomed Semantics. 2015 Apr 9;6:16. doi: 10.1186/s13326-015-0012-6. eCollection 2015. PubMed PMID: 25973166; PubMed Central PMCID: PMC4429421. [PubMed]
  43. Liu L, Tao J, Yang Z, Towfic F.
    Shared Genetic Architecture In Autoimmune Disease - Preliminary Analysis.
    Procs 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2015, Bethesda, MD, US, Nov 9-12, 2015.
  44. Massicano F, Sasso1 A, Amaral-Silva1 H, Oleynik M, Nobrega1 C, Patrão DFC.
    An Ontology for TNM Clinical Stage Inference.
    Proc Brazilian Seminar on Ontologies (ONTOBRAS 2015). São Paulo, Brazil, Sept 8-11, 2015. [PDF Exit Disclaimer logo ]
  45. McIntosh LD, Sharma MK, Mulvihill D, Gupta S, Juehne A, George B, Khot SB, Kaushal A, Watson MA, Nagarajan R.
    caTissue suite to OpenSpecimen: Developing an extensible, open source, web-based biobanking management system.
    J Biomed Inform. 2015 Aug 29. pii: S1532-0464(15)00188-4. doi: 10.1016/j.jbi.2015.08.020. [Epub ahead of print] PubMed PMID: 26325296. [PubMed]
  46. Perrone RD, Neville J, Chapman AB, Gitomer BY, Miskulin DC, Torres VE, Czerwiec FS, Dennis E, Kisler B, Kopko S, Krasa HB, LeRoy E, Castedo J, Schrier RW, Broadbent S.
    Therapeutic Area Data Standards for Autosomal Dominant Polycystic Kidney Disease: A Report From the Polycystic Kidney Disease Outcomes Consortium (PKDOC).
    Am J Kidney Dis. 2015 Jun 15. pii: S0272-6386(15)00758-1. doi: 10.1053/j.ajkd.2015.04.044. [Epub ahead of print] PubMed PMID: 26088508. [PubMed]
  47. Quanico J, Franck J, Gimeno JP, Sabbagh R, Salzet M, Day R, Fournier I.
    Parafilm-assisted microdissection: a sampling method for mass spectrometry-based identification of differentially expressed prostate cancer protein biomarkers.
    Chem Commun (Camb). 2015 Mar 18;51(22):4564-7. doi: 10.1039/c4cc08331h. PubMed PMID: 25490716. [PubMed]
  48. Scholtalbers J, Boegel S, Bukur T, Byl M, Goerges S, Sorn P, Loewer M, Sahin U, Castle JC.
    TCLP: an online cancer cell line catalogue integrating HLA type, predicted neo-epitopes, virus and gene expression.
    Genome Med. 2015 Nov 20;7(1):118. PubMed PMID: 26589293.[PubMed]
  49. Subramanian SL, Kitchen RR, Alexander R, Carter BS, Cheung KH, Laurent LC, Pico A, Roberts LR, Roth ME, Rozowsky JS, Su AI, Gerstein MB, Milosavljevic A.
    Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies.
    J Extracell Vesicles. 2015 Aug 28;4:27497. doi: 10.3402/jev.v4.27497. eCollection 2015. PubMed PMID: 26320941. [PubMed]
  50. van Soest JPA, Dekker ALAJ, Georgi Nalbantov G.
    Application of Machine Learning for Multicenter Learning.
    Machine Learning in Radiation Oncology. El Naqa I, Li R, Murphy MJ, eds. Springer International Publishing; 2015, pp. 71-97. [Springer Exit Disclaimer logo ]
  51. Wu TJ, Schriml LM, Chen QR, Colbert M, Crichton DJ, Finney R, Hu Y, Kibbe WA, Kincaid H, Meerzaman D, Mitraka E, Pan Y, Smith KM, Srivastava S, Ward S, Yan C, Mazumder R.
    Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis.
    Database (Oxford). 2015 Apr 4;2015:bav032. doi: 10.1093/database/bav032. Print 2015. PubMed PMID: 25841438; PubMed Central PMCID: PMC4385274. [PubMed]

    2014
  52. Acosta-Martin AE, Lane L.
    Combining bioinformatics and MS-based proteomics: clinical implications.
    Expert Rev Proteomics. 2014 Jun;11(3):269-84. doi: 10.1586/14789450.2014.900446. Epub 2014 Apr 10. PubMed PMID: 24720436. [PubMed]
  53. Brechat B, Thiessard FMF, Jouhet V.
    Mapping de terminologies diagnostiques en cancérologie par l'intermédiaire du NCI Metathesaurus / Mapping of diagnostic terminologies in oncology using the NCI Metathesaurus.
    Proc / Actes 15es Journées francophones d'informatique médicale (JFIM 2014) co-located with 2e Congrès National d'Informatique Médicale (CNIM 2014). Fes, Morocco, June 12-13, 2014. (in CEUR Workshop Proceedings, Vol-1379, CEUR-WS.org, June 2014). [PDF Exit Disclaimer logo ]
  54. Cai MC, Xu Q, Pan YJ, Pan W, Ji N, Li YB, Jin HJ, Liu K, Ji ZL.
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    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 Exit Disclaimer logo ]
     
    2009
  147. 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]
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    Protein Eng Des Sel. 2009 Mar;22(3):221-4. PubMed PMID: 19224941. [PubMed] [Oxford full text Exit Disclaimer logo ]
     
    2008
  150. 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]
  151. 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]
  152. 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
  153. 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.
  154. 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]
  155. 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]
  156. 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]
  157. Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Varambally R, Yu J, Briggs BB, Barrette TR, Anstet MJ, Kincead-Beal C, Kulkarni P, Varambally S, Ghosh D, Chinnaiyan AM.
    Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles.
    Neoplasia. 2007 Feb;9(2):166-80. PubMed PMID: 17356713; PubMed Central PMCID: PMC1813932. [PubMed]
  158. 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.
  159. 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]
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    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
  161. 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]
  162. 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]
  163. 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. [PubMed] [Free PMC Article]
     
    2005
  164. 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]
  165. 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
  166. 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
  167. 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

  1. 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
  2. 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]
  3. 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
  4. 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]
  5. 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]
  6. 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
  7. 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]
  8. 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]
  9. 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
  10. 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

  1. Zhao L, Lim Choi Keung SN, Arvanitis TN.
    A BioPortal-Based Terminology Service for Health Data Interoperability.
    Stud Health Technol Inform. 2016;226:143-6. PubMed PMID: 27350488. [PubMed]

    2015
  2. Delaney BC, Curcin V, Andreasson A, Arvanitis TN, Bastiaens H, Corrigan D, Ethier JF, Kostopoulou O, Kuchinke W, McGilchrist M, van Royen P, Wagner P.
    Translational Medicine and Patient Safety in Europe: TRANSFoRm--Architecture for the Learning Health System in Europe.
    Biomed Res Int. 2015;2015:961526. doi: 10.1155/2015/961526. Epub 2015 Oct 11. PubMed PMID: 26539547; PubMed Central PMCID: PMC4619923. [PubMed]
  3. Ethier JF, Curcin V, Barton A, McGilchrist MM, Bastiaens H, Andreasson A, Rossiter J, Zhao L, Arvanitis TN, Taweel A, Delaney BC, Burgun A.
    Clinical data integration model. Core interoperability ontology for research using primary care data.
    Methods Inf Med. 2015;54(1):16-23. doi: 10.3414/ME13-02-0024. Epub 2014 Jun 18. PubMed PMID: 24954896. [PubMed]

    2014
  4. Arvanitis TN.
    Semantic interoperability in healthcare.
    Stud Health Technol Inform. 2014;202:5-8. PubMed PMID: 25000001. [PubMed]

    2013
  5. Ethier JF, Dameron O, Curcin V, McGilchrist MM, Verheij RA, Arvanitis TN, Taweel A, Delaney BC, Burgun A.
    A unified structural/terminological interoperability framework based on LexEVS: application to TRANSFoRm.
    J Am Med Inform Assoc. 2013 Sep 1;20(5):986-94. doi: 10.1136/amiajnl-2012-001312. Epub 2013 Apr 9. PubMed PMID: 23571850. [PubMed]
     
    2012
  6. 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 Exit Disclaimer logo ]
  7. Ouagne D, Hussain S, Sadou E, Jaulent MC, Daniel C.
    The Electronic Healthcare Record for Clinical Research (EHR4CR) information model and terminology.
    Stud Health Technol Inform. 2012;180:534-8. PubMed PMID: 22874248. [PDF Exit Disclaimer logo ]
  8. 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
  9. 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 Exit Disclaimer logo ]
  10. 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 Exit Disclaimer logo ]
     
    2010
  11. 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
  12. 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]
  13. 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.
  14. Tao C, Pathak J, Solbrig HR, Wei WQ, Chute CG.
    LexRDF Model: An RDF-based Unified Model for Heterogeneous Biomedical Ontologies.
    Proc 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 Exit Disclaimer logo ]
     
    2008
  15. 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]
  16. 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]
  17. 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

  1. de la Iglesia D, García-Remesal M, Anguita A, Muñoz-Mármol M, Kulikowski C, Maojo V.
    A Machine Learning Approach to Identify Clinical Trials Involving Nanodrugs and Nanodevices from ClinicalTrials.gov.
    PLoS One. 2014 Oct 27;9(10):e110331. doi: 10.1371/journal.pone.0110331. eCollection 2014. PubMed PMID: 25347075; PubMed Central PMCID: PMC4210133. [PubMed Exit Disclaimer logo ]
  2. Klaessig FG.
    Developing official practices for nanoEHS data compilation, curation and compliance.
    Innovation and responsibility: engaging with new and emerging technologies, S.NET 005. Coenen C, Dijkstra A, Fautz C, Guivant J, Konrad K, Milburn C, van Lente H, eds. Heidelberg: IOS Press and AKA; 2014. pp. 121–133. [PDF Exit Disclaimer logo ]
  3. Zhu Z.
    Flash Nanoprecipitation: Prediction and Enhancement of Particle Stability via Drug Structure.
    Mol Pharm. 2014 Feb 3. [Epub ahead of print] PubMed PMID: 24484077. [PubMed]
  4. de la Iglesia D, Cachau RE, García-Remesal M, Maojo V.
    Nanoinformatics knowledge infrastructures: bringing efficient information management to nanomedical research.
    Comput Sci Discov. 2013 Nov 27;6(1):014011. PubMed PMID: 24932210; PubMed Central PMCID: PMC4053539. [PubMed]
  5. Thomas DG, Gaheen S, Harper SL, Fritts M, Klaessig F, Hahn-Dantona E, Paik D, Pan S, Stafford GA, Freund ET, Klemm JD, Baker NA.
    ISA-TAB-Nano: a specification for sharing nanomaterial research data in spreadsheet-based format.
    BMC Biotechnol. 2013 Jan 14;13:2. doi: 10.1186/1472-6750-13-2. PubMed PMID: 23311978;
    PubMed Central PMCID: PMC3598649. [PubMed]
  6. 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 Sept/Oct 3(5):511–532. PubMed PMID: 21721140; PubMed Central PMCID: PMC3189420. [PubMed]
  7. 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]
  8. 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]

NLP, Ontology, Semantics, Tools

  1. Bamparopoulos G, Konstantinidis E, Bratsas C, Bamidis PD.
    Towards exergaming commons: composing the exergame ontology for publishing open game data.
    J Biomed Semantics. 2016 Feb 9;7:4. doi: 10.1186/s13326-016-0046-4. eCollection 2016. PubMed PMID: 26865947; PubMed Central PMCID: PMC4748514. [PubMed]
  2. Chang M, Chang M, Reed JZ, Milward D, Xu JJ, Cornell WD.
    Developing timely insights into comparative effectiveness research with a text-mining pipeline.
    Drug Discov Today. 2016 Feb 6. pii: S1359-6446(16)00032-5. doi: 10.1016/j.drudis.2016.01.012. [Epub ahead of print] Review. PubMed PMID: 26854423. [PubMed]
  3. Daniel C, Ouagne D, Sadou E, Forsberg K, Gilchrist MM, Zapletal E, Paris N, Hussain S, Jaulent MC, Md DK.
    Cross border semantic interoperability for clinical research: the EHR4CR semantic resources and services.
    AMIA Jt Summits Transl Sci Proc. 2016 Jul 20;2016:51-9. PubMed PMID: 27570649; PubMed Central PMCID: PMC5001763. [PubMed]
  4. Groß A, Pruski C, Rahm E.
    Evolution of biomedical ontologies and mappings: Overview of recent approaches.
    Comput Struct Biotechnol J. 2016 Aug 26;14:333-40. doi: 10.1016/j.csbj.2016.08.002. Review. PubMed PMID: 27642503; PubMed Central PMCID: PMC5018063. [PubMed]
  5. He Z, Geller J.
    Preliminary Analysis of Difficulty of Importing Pattern-Based Concepts into the National Cancer Institute Thesaurus.
    Stud Health Technol Inform. 2016;228:389-93. PubMed PMID: 27577410. [PubMed]
  6. McEntire R, Szalkowski D, Butler J, Kuo MS, Chang M, Chang M, Freeman D, McQuay S, Patel J, McGlashen M, Cornell WD, Xu JJ.
    Application of an automated natural language processing (NLP) workflow to enable federated search of external biomedical content in drug discovery and development.
    Drug Discov Today. 2016 May;21(5):826-35. doi: 10.1016/j.drudis.2016.03.006. Review. PubMed PMID: 26979546. [PubMed]
  7. Min H, Turner S, de Coronado S, Davis B, Whetzel T, Freimuth RR, Solbrig HR, Kiefer R, Riben M, Stafford GA, Wright LW, Ohira R.
    Towards a Standard Ontology Metadata Model.
    Proc International Conference on Biomedical Ontology 2016 (ICBO 2016). Corvallis, Oregon, USA, 1-4 Aug 2016. [PDF Exit Disclaimer logo ]
  8. Ochs C, Geller J, Perl Y, Musen MA.
    A unified software framework for deriving, visualizing, and exploring abstraction networks for ontologies.
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    DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases.
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    Using AberOWL for fast and scalable reasoning over BioPortal ontologies.
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    21st Internat Conf on Applications of Natural Language to Information Systems (NLDB 2016). Salford, UK, 22-24 June 2016.

    2015
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    Performance-based Ontology Matching, A Data-parallel approach for an Effectiveness-independent Performance-gain in Ontology Matching.
    Applied Intelligence. 2015 Sept, 43(2):356-385. [PDF Exit Disclaimer logo ]
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    A Parallel Approach for Matching Large-scale Ontologies.
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  14. Bekhuis T, Tseytlin E, Mitchell KJ.
    A Prototype for a Hybrid System to Support Systematic Review Teams: A Case Study of Organ Transplantation.
    2015 Intl Workshop on Biomedical and Health Informatics at the IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2015, Bethesda, MD, US, Nov 9-12, 2015.[PDF Exit Disclaimer logo ]
  15. Chen ES, Sarkar IN.
    *informatics: Identifying and Tracking Informatics Sub-Discipline Terms in the Literature.
    Methods Inf Med. 2015 Nov 27;54(6):530-9. doi: 10.3414/ME14-01-0088. Epub 2015 May 22. PubMed PMID: 25998007.[PubMed]
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    Towards Extracting Ontology Excerpts.
    Procs 8th Intl Conf Knowledge Science, Engineering and Management (KSEM 2015). Chongqing, China, Oct 28-30, 2015, pp.78-89.
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    Region Evolution eXplorer - A tool for discovering evolution trends in ontology regions.
    J Biomed Semantics. 2015 Jun 1;6:26. doi: 10.1186/s13326-015-0020-6. eCollection 2015. PubMed PMID: 26034559; PubMed Central PMCID: PMC4450457. [PubMed]
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    Agile Text Mining for the 2014 i2b2/UTHealth Cardiac Risk Factors Challenge.
    J Biomed Inform. 2015 Jul 21. pii: S1532-0464(15)00141-0. doi: 10.1016/j.jbi.2015.06.030. [Epub ahead of print] PubMed PMID: 26209007. [PubMed]
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    DyKOSMap: A framework for mapping adaptation between biomedical knowledge organization systems.
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    Abstraction networks for terminologies: Supporting management of "big knowledge".
    Artif Intell Med. 2015 May;64(1):1-16. doi: 10.1016/j.artmed.2015.03.005. Epub 2015 Apr 2. Review. PubMed PMID: 25890687. [PubMed]
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    CoMAGD: Annotation of Gene-Depression Relations.
    Proc 2015 Workshop on Biomedical Natural Language Processing (BioNLP 2015). Beijing, China, July 30, 2015, pp.104–113, Association for Computational Linguistics. [PDF Exit Disclaimer logo ]
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    Bayesian networks from ontological formalisms in radiation oncology.
    Thesis (Ph.D.) University of Washington, 2015. [PDF Exit Disclaimer logo ]
  23. Lambrix P, Wei-Kleiner F, Dragisic Z.
    Completing the is-a structure in light-weight ontologies.
    J Biomed Semantics. 2015 Mar 28;6:12. doi:10.1186/s13326-015-0002-8. eCollection 2015. PubMed PMID: 25883780; PubMed Central PMCID: PMC4399482. [PubMed]
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    Towards visualizing the mapping incoherences in Bioportal.
    Proc International Conference on Biomedical Ontology 2015 (ICBO 2015). Lisbon, Portugal, 27-30 July 2015. [PDF Exit Disclaimer logo ]
  25. Matos S, Campos D, Pinho R, Silva R, Mort M, Cooper DN, Oliveira JL.
    Assisted Mining and Curation of Genomic Variants using Egas.
    Proc Fifth BioCreative Challenge Evaluation Workshop. Sept 9, 2015, Sevilla, Spain, pp.396-402. [PDF Exit Disclaimer logo ]
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    Connecting GOMMA with STROMA: An Approach for Semantic Ontology Mapping in the Biomedical Domain.
    Thesis (B.Sc.) Leipzig University, 2015. [PDF Exit Disclaimer logo ]
  27. Otero-Cerdeira L, Rodríguez-Martínez FJ, Gómez-Rodríguez A.
    Ontology matching: A literature review.
    Expert Systems with Applications. 42(2):949–971, 1 Feb 2015, Epub 30 Aug 2014, ISSN 0957-4174, http://dx.doi.org/10.1016/j.eswa.2014.08.032. [ScienceDirect Exit Disclaimer logo ]
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    Determining similarity of scientific entities in annotation datasets.
    Database (Oxford). 2015 Feb 27;2015. pii: bau123. doi: 10.1093/database/bau123. Print 2015. PubMed PMID: 25725057; PubMed Central PMCID: PMC4343076. [PubMed]
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    Generic Ontology of Datatypes.
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    DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes.
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    Pay-As-You-Go Description Logic Reasoning by Coupling Tableau and Saturation Procedures
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  32. Trivela D, Stoilos G, Chortaras A, Stamou G.
    Optimising resolution-based rewriting algorithms for OWL ontologies.
    Web Semantics: Science, Services and Agents on the World Wide Web. Online 26 Feb 2015. [Online Exit Disclaimer logo ]
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    DL-Lite Ontology Revision Based on An Alternative Semantic Characterisation.
    ACM Transactions on Computational Logic (TOCL). 2015 (Accepted). [PDF Exit Disclaimer logo ]

    2014
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    University of California, Irvine-Pathology Extraction Pipeline: The pathology extraction pipeline for information extraction from pathology reports.
    Health Informatics J. 2014 Dec;20(4):288-305. doi: 10.1177/1460458213494032. Epub 2014 Aug 25. PubMed PMID: 25155030. [PubMed Exit Disclaimer logo ]
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    Quantifying the impact and extent of undocumented biomedical synonymy.
    PLoS Comput Biol. 2014 Sep 25;10(9):e1003799. doi: 10.1371/journal.pcbi.1003799. eCollection 2014 Sep. PubMed PMID: 25255227; PubMed Central PMCID: PMC4177665. [PubMed Exit Disclaimer logo ]
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    Towards a foundational representation of potential drug-drug interaction knowledge.
    First International Workshop on Drug Interaction Knowledge Representation (DIKR-2014) at the International Conference on Biomedical Ontologies (ICBO 2014). Houston, Texas, USA, Oct 6, 2014. [PDF Exit Disclaimer logo ]
  37. Djeddi WE, Khadir MT.
    XMap++ : Results for OAEI 2014.
    Ninth International Workshop on Ontology Matching (OM-2014) collocated with the 13th International Semantic Web Conference (ISWC-2014). Oct 20, 2014, Trentino, Italy. [PDF Exit Disclaimer logo ]
  38. Dos Reis JC.
    Mapping Adaptation between Biomedical Knowledge Organization Systems.
    Thesis (Ph.D.) Université de Paris-Sud, France, Oct 24, 2014. [PDF Exit Disclaimer logo ]
  39. Dragisic Z, Eckert K, Euzenat J, Faria D, Ferrara A, Granada R, Ivanova V, Jiménez-Ruiz E, Kempf AO, Lambrix P, Montanelli S, Paulheim H, Ritze D, Shvaiko P, Solimando A, Trojahn C, Zamazal O, Cuenca Grau B.
    Results of the Ontology Alignment Evaluation Initiative 2014.
    Proc 10th International Workshop on Ontology Matching(OM-2014), co-located with the 12th International Semantic Web Conference (ISWC 2014), Riva del Garda, Italy, 2014. [PDF Exit Disclaimer logo ]
  40. Faria D, Jiménez-Ruiz E, Pesquita C, Santos E, Couto FM.
    Towards annotating potential incoherences in BioPortal mappings.
    Proc 13th International Semantic Web Conference (ISWC-2014). Oct 19-23, 2014, Trentino, Italy, pp.17-32. [PDF Exit Disclaimer logo ]
  41. Faria D, Pesquita C, Santos E, Cruz IF, Couto FM.
    Automatic background knowledge selection for matching biomedical ontologies.
    PLoS One. 2014 Nov 7;9(11):e111226. doi: 10.1371/journal.pone.0111226. eCollection 2014. PubMed PMID: 25379899. [PubMed]
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    A Strategy for Annotating Clinical Records with Phenotypic Information relating to the Chronic Obstructive Pulmonary Disease.
    Proc Phenotype Day at ISMB 2014. Boston, MA, USA, July 12, 2014. [PDF Exit Disclaimer logo ]
  43. Gatens W, Konev B, Wolter F.
    Lower and Upper Approximations for Depleting Modules of Description Logic Ontologies.
    Proc 21st European Conference on Artificial Intelligence (ECAI 2014). Aug 18-22, 2014, Prague, Czech Republic. [PDF Exit Disclaimer logo ]
  44. Gonçalves JRLS.
    Impact Analysis in Description Logic Ontologies.
    Thesis (Ph.D.) Faculty of Engineering and Physical Sciences, University of Manchester, 2014. [PDF Exit Disclaimer logo ]
  45. Gupta S, MacLean DL, Heer J, Manning CD.
    Induced lexico-syntactic patterns improve information extraction from online medical forums.
    J Am Med Inform Assoc. 2014 Sep-Oct;21(5):902-9. doi: 10.1136/amiajnl-2014-002669. Epub 2014 Jun 26. PubMed PMID: 24970840; PubMed Central PMCID: PMC4147618. [PubMed Exit Disclaimer logo ]
  46. He Z, Geller J, Elhanan G.
    Categorizing the Relationships between Structurally Congruent Concepts from Pairs of Terminologies for Semantic Harmonization.
    Proc 2014 Summit on Translational Bioinformatics (TBI 2014). April 7-9, 2014, San Francisco, CA, pp.48-53.
  47. Hudson CL, Topaloglu U, Bian J, Hogan W, Kieber-Emmons T.
    Automated Tools for Clinical Research Data Quality Control using NCI Common Data Elements.
    Proc 2014 Summit on Translational Bioinformatics (TBI 2014). April 7-9, 2014, San Francisco, CA, pp.60-69.
  48. Ivanova V.
    Integration of Ontology Alignment and Ontology Debugging for Taxonomy Networks.
    Thesis (Licentiate) Linköping University, Department of Computer and Information Science, National Graduate School of Computer Science, Linköping, Sweden, 2014. [PDF Exit Disclaimer logo ]
  49. Ivanović M, Budimac Z.
    An overview of ontologies and data resources in medical domains.
    Expert Systems with Applications 2014 Sept 1; 41(11):5158-5166, ISSN 0957-4174. [DOI Exit Disclaimer logo ]
  50. Jiang G, Sharma DK, Solbrig HR, Tao C, Weng C, Chute CG.
    Building a Semantic Web-based Metadata Repository for Facilitating Detailed Clinical Modeling in Cancer Genome Studies.
    Proc 7th International Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2014). Berlin, Germany, Dec 9-11, 2014. [PDF Exit Disclaimer logo ]
  51. Loebe F, Chaudhri VK.
    Entities with Genetic Information – An Initial Perspective from the Core Theme of Continuity and Change in Biology.
    Ontologies and Data in Life Sciences (ODLS 2014). Freiburg im Breisgau, October 7-8, 2014. [PDF Exit Disclaimer logo ]
  52. Ludwig M.
    Just: a Tool for Computing Justifications w.r.t. ELH Ontologies.
    Proc 3rd International Workshop on OWL Reasoner Evaluation (ORE 2014). Vienna, Austria, July 13, 2014, pp.1-7. [PDF Exit Disclaimer logo ]
  53. Ludwig M, Konev B.
    Practical Uniform Interpolation and Forgetting for ALC TBoxes with Applications to Logical Difference.
    Proc 14th International Conference on Principles of Knowledge Representation and Reasoning (KR 2014). Vienna, Austria, July 20-24, 2014. [PDF Exit Disclaimer logo ]
  54. Ludwig M, Peñaloza R.
    Brave and Cautious Reasoning in EL.
    Proc 27th International Workshop on Description Logics (DL 2014). Vienna, Austria, July 17-20, 2014, pp.274-286. [PDF Exit Disclaimer logo ]
  55. Ludwig M, Peñaloza R.
    Error-Tolerant Reasoning in the Description Logic EL.
    Proceedings of the 14th European Conference on Logics in Artificial Intelligence (JELIA 2014). Sept 24-26, 2014,Madeira, Portugal. [PDF Exit Disclaimer logo ]
  56. Martínez-Romero M, Vázquez-Naya JM, Pereira J, Pazos A.
    BiOSS: A system for biomedical ontology selection.
    Computer Methods and Programs in Biomedicine, 2014 Apr;114(1):125-40. doi: 10.1016/j.cmpb.2014.01.020. Epub 2014 Feb 6. PubMed PMID: 24573129. [PubMed]
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    Semantic Web repositories for genomics data using the eXframe platform.
    J Biomed Semantics. 2014 Jun 3;5(Suppl 1 Proceedings of the Bio-Ontologies Spec Interest G):S3. doi: 10.1186/2041-1480-5-S1-S3. eCollection 2014. PubMed PMID: 25093072; PubMed Central PMCID: PMC4108874. [PubMed]
  58. Mortensen JM, Minty EP, Januszyk M, Sweeney TE, Rector AL, Noy NF, Musen MA.
    Using the wisdom of the crowds to find critical errors in biomedical ontologies: a study of SNOMED CT.
    J Am Med Inform Assoc. 2014 Oct 23. pii: amiajnl-2014-002901. doi: 10.1136/amiajnl-2014-002901. [Epub ahead of print] PubMed PMID: 25342179. [PubMed Exit Disclaimer logo ]
  59. Névéol A, Grosjean J, Darmoni S, Zweigenbaum P.
    Language Resources for French in the Biomedical Domain.
    Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC 2014). Reykjavik, Iceland, May 26-31, 2014. [PDF Exit Disclaimer logo ]
  60. Pesquita C, Ferreira JD, Couto FM, Silva MJ.
    The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources.
    J Biomed Semantics. 2014 Jan 17;5(1):4. doi: 10.1186/2041-1480-5-4. PubMed PMID: 24438387; PubMed Central PMCID: PMC3926306. [PubMed]
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    Publishing DisGeNET as Nanopublications.
    Semantic Web – Interoperability, Usability, Applicability (Semantic Web journal). 2014 Oct 15. [PDF Exit Disclaimer logo ]
  62. Raunich S, Rahm E.
    Target-driven merging of taxonomies with ATOM.
    Information Systems. 2014 June; 42(June):1-14. ISSN 0306-4379. [DOI] [URL Exit Disclaimer logo ]
  63. Reyes L, Molina D, Hidalgo Y, Roldán MM, Aldana JF.
    Exploring Incremental Reasoning Approaches based on Module Extraction.
    Proceedings of the 1st Cuban Workshop on Semantic Web 2014 (TCWS 2014) co-located with 13th International Congress on Information (INFO 2014). Havana, Cuba, Apr 16, 2014, pp.1-12. [PDF Exit Disclaimer logo ]
  64. Shen G, Liu Y, Wang F, Si J, Wang Z, Huang Z, Kang D.
    OMReasoner: combination of multi-matchers for ontology matching: results for OAEI 2014.
    Ninth International Workshop on Ontology Matching (OM-2014) collocated with the 13th International Semantic Web Conference (ISWC-2014). Oct 20, 2014, Trentino, Italy. [PDF Exit Disclaimer logo ]
  65. Shivade C, Cormack J, Milward D.
    Precise Medication Extraction using Agile Text Mining.
    Proceedings of the 5th International Workshop on Health Text Mining and Information Analysis (Louhi). 2014 April, Gothenburg, Sweden, Association for Computational Linguistics pp.75-79. [PDF Exit Disclaimer logo ]
  66. Silva MAA, Cavalcanti MC.
    Combining Ontology Modules for Scientific Text Annotation.
    Journal of Information and Data Management. 5(3):238-251, 2014. [PDF Exit Disclaimer logo ]
  67. Spasić I, Livsey J, Keane JA, Nenadić G.
    Text mining of cancer-related information: Review of current status and future directions.
    Int J Med Inform. 2014 Sep;83(9):605-623. doi: 10.1016/j.ijmedinf.2014.06.009. Epub 2014 Jun 24. Review. PubMed PMID: 25008281. [PubMed]
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    An Ontology-Driven Interface for Computable Modeling of Clinical Trial Eligibility Criteria.
    Thesis (M.S.), Case Western Reserve University, EECS - Computer and Information Sciences, 17 Mar 2014.
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  69. Walk S, Singer P, Strohmaier M.
    Sequential Action Patterns in Collaborative Ontology-Engineering Projects: A Case-Study in the Biomedical Domain.
    Proceedings of the 23rd ACM International Conference on Information and Knowledge Management (CIKM 2014). Nov 3-7, 2014 Shanghai, China. [PDF Exit Disclaimer logo ]
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    Discovering Beaten Paths in Collaborative Ontology-Engineering Projects using Markov Chains.
    J Biomed Inform. 2014 Oct;51:254-71. doi: 10.1016/j.jbi.2014.06.004. Epub 2014 Jun 17. PubMed PMID: 24953242; PubMed Central PMCID: PMC4194274.  [PubMed Exit Disclaimer logo ]
  71. Wu Q, Zhang H, Hong Q, Zheng Y, Wu M.
    Bursty topic detection based on K-states automaton model: An emerging trend in cancer field.
    Proceedings of the 6th International Conference on Bioinformatics and Computational Biology (BICoB 2014). 24-26 March 2014, Las Vegas, Nevada, USA, pp. 125-130.
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    K-State automaton burst detection model based on KOS: Emerging trends in cancer field.
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    Semantics and Inference for Probabilistic Description Logics.
    10th International Workshop on Uncertainty Reasoning for the Semantic Web (URSW 2014), collocated with the 13th International Semantic Web Conference (ISWC-2014). Oct 20, 2014, Trentino, Italy. [PDF Exit Disclaimer logo ]

    2013
  74. Amin MB, Batool R, Khan WA, Lee S, Huh EN.
    SPHeRe: A Performance Initiative Towards Ontology Matching by Implementing Parallelism over Cloud Platform.
    Journal of Supercomputing. October 2013. [PDF Exit Disclaimer logo ] [Springer Exit Disclaimer logo ]
  75. Armas Romero A, Grau BC, Horrocks I, Jiménez-Ruiz E.
    MORe: a Modular OWL Reasoner for Ontology Classification.
    Proceedings of the 2nd OWL Reasoner Evaluation Workshop (ORE 2013), Ulm, Germany, July 22, 2013. [PDF Exit Disclaimer logo ]
  76. Ba M, Diallo G.
    Large-scale biomedical ontology matching with ServOMap.
    IRBM, 2013. 34(1):56-59. Available online 13 February 2013. [DOI Exit Disclaimer logo ]
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    Developing Ontological Background Knowledge for Biomedicine.
    Thesis (Doktors der Naturwissenschaften), University of Mannheim, Mannheim, 2013. [PDF Exit Disclaimer logo ]
  78. Cross V, Yu X, Hu X.
    Unifying ontological similarity measures: A theoretical and empirical investigation.
    International Journal of Approximate Reasoning. 54(7):861 - 875 Sept 2013. [Full Text Exit Disclaimer logo ]
  79. Cuenca Grau B, Dragisic Z, Eckert K, Euzenat J, Ferrara A, Granada R, Ivanova V, Jiménez-Ruiz E, Kempf AO, Lambrix P, Nikolov A, Paulheim H, Ritze D, Scharffe F, Shvaiko P, Trojahn C, Zamazal O.
    Results of the Ontology Alignment Evaluation Initiative 2013.
    Proceedings of the 8th International Workshop on Ontology Matching (OM-2013), co-located with the 12th International Semantic Web Conference (ISWC 2013), Sydney, Australia, pp.61-100, October 21, 2013. [PDF Exit Disclaimer logo ]
  80. Dos Reis JC, Dinh D, Pruski C, Da Silveira M, Reynaud-Delaître C.
    Mapping Adaptation Actions for the Automatic Reconciliation of Dynamic Ontologies.
    Proceedings of the 22nd ACM International Conference on Information and Knowledge Management (CIKM '13) Oct 27 - Nov 1, 2013, San Francisco, California, USA. ACM, New York, NY, USA, 599-608. DOI=10.1145/2505515.2505564 [ACM Exit Disclaimer logo ]
  81. Freckleton RE.
    Scaling Ontology Alignment.
    Thesis (M.S.), University of Colorado Colorado Springs, Department of Computer Science, 2013. [PDF Exit Disclaimer logo ]
  82. Garcia Castro LJ, McLaughlin C, Garcia A.
    Biotea: RDFizing PubMed Central in support for the paper as an interface to the Web of Data.
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    OWL Reasoner Evaluation (ORE) Workshop 2013 Results: Short Report.
    Proceedings of the 2nd OWL Reasoner Evaluation Workshop (ORE 2013), Ulm, Germany, July 22, 2013 pp.1-18. [PDF Exit Disclaimer logo ]
  84. Gonçalves RS, Matentzoglu N, Parsia B, Sattler U.
    The Empirical Robustness of Description Logic Classification.
    Proceedings of the 26th International Workshop on Description Logics (DL 2013), Ulm, Germany, July 23-26, 2013 (in CEUR Workshop Proceedings. CEUR-WS.org, July 2013. [PDF Exit Disclaimer logo ]
  85. Gross A, Dos Reis JC, Hartung M, Pruski C, Rahm E.
    Semi-Automatic Adaptation of Mappings between Life Science Ontologies.
    Proc. 9th Intl. Conference on Data Integration in the Life Sciences (DILS), 2013 (to appear) July 11-12, 2013, Montreal, Quebec, Canada. [PDF Exit Disclaimer logo ]
  86. Hartung M, Gross A, Rahm E.
    Composition Methods for Link Discovery.
    Proc. of 15. GI-Fachtagung Datenbanksysteme für Business, Technologie und Web (BTW 2013). March 11-15, 2013, Magdeburg, Germany. [Leipzig Exit Disclaimer logo ] [PDF Exit Disclaimer logo ]
  87. 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]
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    Optimizing Similarity Computations for Ontology Matching - Experiences from GOMMA.
    Proc. 9th Intl. Conference on Data Integration in the Life Sciences (DILS), 2013 (to appear) July 11-12, 2013, Montreal, Quebec, Canada. [PDF Exit Disclaimer logo ]
  89. Hedeler C, Parsia B, Brandt S.
    Estimating Coordination in Medical Terminologies.
    Proceedings of the 6th International Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2013). Edinburgh, UK, December 10, 2013. [PDF Exit Disclaimer logo ]
  90. Karaiskos C.
    Enhanced Ontological Searching of Medical Scientific Information.
    Thesis (M.Sc.), University of Manchester, School of Computer Science, 2013. [PDF Exit Disclaimer logo ]
  91. Kocbek S, Kim JD, Perret JL, Whetzel PL.
    Visualizing ontology mappings to help ontology engineers identify relevant ontologies for their reuse.
    Proc of the 4th International Conference on Biomedical Ontology (ICBO 2013), Montreal, Quebec, Canada, July 8-9, 2013. [PDF Exit Disclaimer logo ]
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    Linked Open Data for Healthcare Professionals.
    Proceedings of International Conference on Information Integration and Web-based Applications and Services (IIWAS '13), 2013. ACM, New York, NY, USA. DOI=10.1145/2539150.2539195 [Online Exit Disclaimer logo ]
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    Using Linked Data for Better Navigation in Summaries of Product Characteristics.
    Proceedings of the 6th International Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2013). Edinburgh, UK, December 10, 2013. [PDF Exit Disclaimer logo ]
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    Debugging the missing is-a structure within taxonomies networked by partial reference alignments.
    Data & Knowledge Engineering, in press, available online 29 March 2013, ISSN 0169-023X, 10.1016/j.datak.2013.03.003. [Online Exit Disclaimer logo ]
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    Semantic Queries by Example.
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    Towards Practical Uniform Interpolation and Forgetting for ALC TBoxes.
    Proceedings of the 26th International Workshop on Description Logics (DL 2013), Ulm, Germany, July 23-26, 2013 (in CEUR Workshop Proceedings. CEUR-WS.org, July 2013. [PDF Exit Disclaimer logo ]
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    A Corpus of OWL DL Ontologies.
    Proceedings of the 26th International Workshop on Description Logics (DL 2013), Ulm, Germany, July 23-26, 2013 (in CEUR Workshop Proceedings. CEUR-WS.org, July 2013. [PDF Exit Disclaimer logo ]
  98. Milian K, Bucur A, van Harmelen F, ten Teije A.
    Identifying Most Relevant Concepts to Describe Clinical Trial Eligibility Criteria.
    Proc 6th International Conference on Health Informatics (HEALTHINF 2013), 13 Feb 2013, Barcelona Spain. [PDF Exit Disclaimer logo ]
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    Proceedings of the 12th International Semantic Web Conference (ISWC 2013), Sydney, Australia, Oct 21-25, 2013. [ISWC Exit Disclaimer logo ] [PDF Exit Disclaimer logo ]
  101. Noy NF, Alexander PR, Harpaz R, Whetzel PL, Fergerson RW, Musen MA.
    Getting Lucky in Ontology Search: A Data-Driven Evaluation Framework for Ontology Ranking.
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  102. Palma G, Vidal ME, Haag E, Raschid L, Thor A.
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    ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (ACM BCB 2013) Bethesda, MD, 2013 Sept 22-25. [PDF Exit Disclaimer logo ]
  103. Palma G, Vidal ME, Raschid L, Thor A.
    Exploiting Semantics from Ontologies and Shared Annotations to Find Patterns in Annotated Linked Open Data.
    3rd International Workshop on Linked Science 2013 (LISC 2013), in conjunction with International Semantic Web Conference (ISWC 2013), Oct 21-22 2013, Sydney, Australia. [PDF Exit Disclaimer logo ]
  104. Pesquita C, Faria F, Santos E, Couto FM.
    To Repair or Not To Repair: Reconciling Correctness and Coherence in Ontology Reference Alignments.
    Proceedings of the 8th International Workshop on Ontology Matching (OM-2013), co-located with the 12th International Semantic Web Conference (ISWC 2013), Sydney, Australia, pp.13-24, October 21, 2013. [PDF Exit Disclaimer logo ]
  105. Salvadores M, Alexander PR, Musen MA, Noy NF.
    BioPortal as a Dataset of Linked Biomedical Ontologies and Terminologies in RDF.
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  106. Shvaiko P, Euzenat J, Srinivas K, Mao M, Jiménez-Ruiz E, eds.
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  107. Sojic A.
    Biomedical Ontologies: Examining Aspects of Integration Across Breast Cancer Knowledge Domains.
    Thesis (Ph.D.) European School of Molecular Medicine (SEMM) and University of Milan Faculty of Medicine, 2013. [PDF Exit Disclaimer logo ]
  108. Strohmaier M, Walk S, Pöschko J, Lamprecht D, Tudorache T, Nyulas C, Musen MA, Noy NF.
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  109. Tao C, Pathak J, Solbrig HR, Wei WQ, Chute CG.
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    Proceedings of the 26th International Workshop on Description Logics (DL 2013), Ulm, Germany, July 23-26, 2013 (in CEUR Workshop Proceedings. CEUR-WS.org, July 2013. [PDF Exit Disclaimer logo ]
  112. Vergara-Niedermayr C, Wang F, Pan T, Kurc T, Saltz J.
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    Int. J. Semantic Computing. 2013 Sept;7(3). DOI: 10.1142/S1793351X13500037 [Online Exit Disclaimer logo ]
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    2012
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    Results of the Ontology Alignment Evaluation Initiative 2012.
    Proceedings of the Seventh International Workshop on Ontology Matching (OM-2012), collocated with the 11th International Semantic Web Conference (ISWC-2012), Nov 11, 2012, Boston, MA USA. [PDF Exit Disclaimer logo ]
  115. 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 Exit Disclaimer logo ]
  116. 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.
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  117. 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 Exit Disclaimer logo ]
  118. Bougie G.
    A Case Study of a New Era in Disease Classification: An Investigation of the Socio-technical Requirements for Inclusive Standardization Development.
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    Characterizing the use and contents of free-text family history comments in the Electronic Health Record.
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    Semantic Interoperability in Medical Informatics (SIMI 2012). Heraklion (Crete), Greece, May 27, 2012. [PDF Exit Disclaimer logo ]
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    Proc of the 3rd International Conference on Biomedical Ontology (ICBO 2012). 2012 July 21-25. Graz, Austria. [PDF Exit Disclaimer logo ]
  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.
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    9th Extended Semantic Web Conference (ESWC 2012), Heraklion, Crete, Greece, May 27-31, 2012. To appear in ESWC 2012 Workshops, Revised Selected Papers (LNCS) 2012-09. [Leipzig Exit Disclaimer logo ] [PDF Exit Disclaimer logo ]
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    J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. doi: 10.1136/amiajnl-2011-000523. Epub 2011 Nov 10. PubMed PMID: 22081220; PubMed Central PMCID: PMC3277625. [PubMed]
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    Thesis (Ph.D.) Universidade de Lisboa, Faculdade de Ciências, Departamento de Informática 2012. [U.Lisbon Exit Disclaimer logo ] [PDF Exit Disclaimer logo ]
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    DisGeNET: from MySQL to Nanopublication, Modelling Gene-Disease Associations for the Semantic Web.
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    Ontology Alignment Using Semantic Similarity with Refernce Ontologies.
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    Distributed Computing and Artificial Intelligence, Omatu S, et al., eds. Springer-Verlag; 2012. pp. 519-526. [Springer Exit Disclaimer logo ]
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    Semantic Interoperability in Medical Informatics (SIMI 2012). Heraklion (Crete), Greece, May 27, 2012. [Abstract Exit Disclaimer logo ]
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    Emory University Center for Comprehensive Informatics Technical Report CCI-TR-2012-1, January 12, 2012. [Emory Exit Disclaimer logo ]
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    Thesis (M.Sc.) Graz University of Technology, Knowledge Management Institute, Austria, April 19, 2012. [PDF Exit Disclaimer logo ]
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    Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis.
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    Emory University Center for Comprehensive Informatics Technical Report CCI-TR-2012-3, March 20, 2012. [Emory Exit Disclaimer logo ]
     
    2011
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    The justificatory structure of the NCBO bioportal ontologies.
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    Extracting finite sets of entailments from OWL ontologies.
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    The ACGT Master Ontology and its applications--towards an ontology-driven cancer research and management system.
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    An Analysis of Collaborative Patterns in Large-Scale Ontology Development Projects.
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    KCAP 2011 - Proceedings of the 2011 Knowledge Capture Conference, 2011, pp. 33-40. [Scopus Exit Disclaimer logo ]
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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 Exit Disclaimer logo ]
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    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 Exit Disclaimer logo ]
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    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.
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    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.
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    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 Exit Disclaimer logo ]
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    Ontology-based Queries over Cancer Data.
    Proceedings of the 3rd International Workshop on Semantic Web Applications and Tools for the Life Sciences, eds. Paschke A, Burger A, Splendiani A, Marshall MS, Romano P. Berlin, Germany, Dec 8-10, 2010. [PDF Exit Disclaimer logo ]
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    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 Exit Disclaimer logo ]
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    Building a biomedical ontology recommender web service.
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    Predicting Reasoning Performance Using Ontology Metrics.
    The Journal of Systems and Software, 83 (2010):803–814. [PDF Exit Disclaimer logo ]
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    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.
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    The Lexicon Builder Web service: Building Custom Lexicons from two hundred Biomedical Ontologies.
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    The TRITON Project: Design and Implementation of an Integrative Translational Research Information Management Platform.
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    Automated comparative auditing of NCIT genomic roles using NCBI.
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    Developing an application focused experimental factor ontology: embracing the OBO Community.
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    Detecting role errors in the gene hierarchy of the NCI Thesaurus.
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    Representing lexical components of medical terminologies in OWL.
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