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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 terminologies and standards (such as CTCAE, FDA SPL and ICSR, and CDISC SDTM) often maintained jointly with other NCI units, NIH institutes, federal agencies and other partners.

About EVS

  1. Copeland M, Gonçalves RS, Parsia B, Sattler U, Stevens R.
    Finding fault: Detecting issues in a versioned ontology.
    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
  2. 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
  3. Gonçalves RS, Parsia B, Sattler U.
    Analysing the evolution of the NCI thesaurus.
    Proceedings - IEEE Symposium on Computer-Based Medical Systems (CBMS-11) Bristol, United Kingdom, June 27-30, 2011. [At IEEE Xplore Exit Disclaimer logo ]
  4. 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 Exit Disclaimer logo ]
     
    2009
  5. 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
  6. 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
  7. 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]
  8. 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 ]
  9. 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
  10. 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
  11. 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]
  12. 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
  13. 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 ]
  14. 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
  15. 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
  16. 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]
  17. 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.
  18. 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 ]
  19. 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
  20. 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. 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]
  2. 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]
  3. 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, doi: 10.1016/j.jacc.2014.12.018. [Epub ahead of print] PubMed PMID: 25553722. [PubMed]
  4. 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]

    2014
  5. 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]
  6. Cai MC, Xu Q, Pan YJ, Pan W, Ji N, Li YB, Jin HJ, Liu K, Ji ZL.
    ADReCS: an ontology database for aiding standardization and hierarchical classification of adverse drug reaction terms.
    Nucleic Acids Res. 2014 Oct 31. pii: gku1066. [Epub ahead of print] PubMed PMID: 25361966. [PubMed]
  7. Carrell DS, Halgrim S, Tran DT, Buist DS, Chubak J, Chapman WW, Savova G.
    Using Natural Language Processing to Improve Efficiency of Manual Chart Abstraction in Research: The Case of Breast Cancer Recurrence.
    Am J Epidemiol. 2014 Mar 15;179(6):749-58. doi: 10.1093/aje/kwt441. Epub 2014 Jan 30. PubMed PMID: 24488511. [PubMed]
  8. Doods J, Botteri F, Dugas M, Fritz F; EHR4CR WP7.
    A European inventory of common electronic health record data elements for clinical trial feasibility.
    Trials. 2014 Jan 10;15(1):18. doi: 10.1186/1745-6215-15-18. PubMed PMID:24410735. [PubMed] [PDF Exit Disclaimer logo ]
  9. Johnson D, Connor AJ, McKeever S, Wang Z, Deisboeck TS, Quaiser T, Shochat E.
    Semantically linking in silico cancer models.
    Cancer Inform. 2014 Dec 8;13(Suppl 1):133-43. doi: 10.4137/CIN.S13895. eCollection 2014. PubMed PMID: 25520553; PubMed Central PMCID: PMC4260769. [PubMed Exit Disclaimer logo ]
  10. Jouhet V, Bréchat B, Mougin F, Thiessard F.
    Intégration de terminologies diagnostiques en cancérologie: le NCI thésaurus comme pivot?
    Rev Epidemiol Sante Publique. 2014 Sept;62(Suppl.5):S185.  [ScienceDirect]
  11. Kahn MG, Bailey LC, Forrest CB, Padula MA, Hirschfeld S.
    Building a Common Pediatric Research Terminology for Accelerating Child Health Research.
    Pediatrics, 2014. Available online Feb 17, 2014. DOI: 10.1542/peds.2013-1504. [Online Exit Disclaimer logo ]
  12. Keenan CM, Baker J, Bradley A, 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.
    Toxicol Pathol. 2014 Dec 21. pii: 0192623314560031. [Epub ahead of print] PubMed PMID: 25530274. [PubMed]
  13. Keenan CM, Goodman DG.
    Regulatory Forum Commentary: Through the Looking Glass--SENDing the Pathology Data We Have INHAND.
    Toxicol Pathol. 2014 July, 42(5):807-810. Epub 2013 Apr 18. PubMed PMID: 23599411. [PubMed]
  14. Kibbe WA, Arze C, Felix V, Mitraka E, Bolton E, Fu G, Mungall CJ, Binder JX, Malone J, Vasant D, Parkinson H, Schriml LM.
    Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.
    Nucleic Acids Res. 2014 Oct 27. pii: gku1011. [Epub ahead of print] PubMed PMID: 25348409. [PubMed Exit Disclaimer logo ]
  15. Köpcke F, Prokosch HU.
    Employing computers for the recruitment into clinical trials: a comprehensive systematic review.
    J Med Internet Res. 2014 Jul 1;16(7):e161. doi: 10.2196/jmir.3446. PubMed PMID: 24985568; PubMed Central PMCID: PMC4128959. [PubMed Exit Disclaimer logo ]
  16. Kurian AW, Mitani A, Desai M, Yu PP, Seto T, Weber SC, Olson C, Kenkare P, Gomez SL, de Bruin MA, Horst K, Belkora J, May SG, Frosch DL, Blayney DW, Luft HS, Das AK.
    Breast cancer treatment across health care systems: linking electronic medical records and state registry data to enable outcomes research.
    Cancer. 2014 Jan 1;120(1):103-11. doi: 10.1002/cncr.28395. Epub 2013 Sep 24. PubMed PMID: 24101577; PubMed Central PMCID: PMC3867595. [PubMed]
  17. Lee HJ, Dang TC, Lee H, Park JC.
    OncoSearch: cancer gene search engine with literature evidence.
    Nucleic Acids Res. 2014 Jul;42(Web Server issue):W416-21. doi: 10.1093/nar/gku368. Epub 2014 May 9. PubMed PMID: 24813447; PubMed Central PMCID: PMC4086113. [PubMed] [Full Text Exit Disclaimer logo ]
  18. Meier A.
    Challenges in Processing Clinical Lab Data.
    PharmaSUG 2014 Conference Proceedings. San Diego, CA, USA, June 1-4, 2014. [PDF Exit Disclaimer logo ]
  19. Meldolesi E, van Soest J, Alitto AR, Autorino R, Dinapoli N, Dekker A, Gambacorta MA, Gatta R, Tagliaferri L, Damiani A, Valentini V.
    VATE: VAlidation of high TEchnology based on large database analysis by learning machine.
    Colorectal Cancer. 3(5)435-450 , DOI 10.2217/crc.14.34 (doi:10.2217/crc.14.34). [Online Exit Disclaimer logo ]
  20. Meldolesi E, van Soest J, Dinapoli N, Dekker A, Damiani A, Gambacorta MA, Valentini V.
    An umbrella protocol for standardized data collection (SDC) in rectal cancer: a prospective uniform naming and procedure convention to support personalized medicine.
    Radiother Oncol. 2014 Jul;112(1):59-62. doi:10.1016/j.radonc.2014.04.008. Epub 2014 May 19. PubMed PMID: 24853366. [PubMed]
  21. Min H, Ohira R, Collins MA, Bondy J, Avis NE, Tchuvatkina O, Courtney PK, Moser RP, Shaikh AR, Hesse BW, Cooper M, Reeves D, Lanese B, Helba C, Miller SM, Ross EA.
    Sharing behavioral data through a grid infrastructure using data standards.
    J Am Med Inform Assoc. 2014 Jul-Aug;21(4):642-9. doi: 10.1136/amiajnl-2013-001763. Epub 2013 Sep 27. PubMed PMID: 24076749; PubMed Central PMCID: PMC4078270. [PubMed Exit Disclaimer logo ]
  22. Mongkolwat P, Kleper V, Talbot S, Rubin D.
    The National Cancer Informatics Program (NCIP) Annotation and Image Markup (AIM) Foundation Model.
    J Digit Imaging. 2014 Dec;27(6):692-701. doi: 10.1007/s10278-014-9710-3. PubMed PMID: 24934452. [PubMed Exit Disclaimer logo ]
  23. Pang C, Hendriksen D, Dijkstra M, van der Velde KJ, Kuiper J, Hillege H, Swertz M.
    BiobankConnect: software to rapidly connect data elements for pooled analysis across biobanks using ontological and lexical indexing.
    J Am Med Inform Assoc. 2014 Oct 31. pii: amiajnl-2013-002577. doi: 10.1136/amiajnl-2013-002577. [Epub ahead of print] PubMed PMID: 25361575. [PubMed]
  24. 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). 2014 Dec 9. [Epub ahead of print] PubMed PMID: 25490716. [PubMed Exit Disclaimer logo ]
  25. Sahoo SS, Tao S, Parchman A, Luo Z, Cui L, Mergler P, Lanese R, Barnholtz-Sloan JS, Meropol NJ, Zhang GQ.
    Trial prospector: matching patients with cancer research studies using an automated and scalable approach.
    Cancer Inform. 2014 Dec 4;13:157-66. doi: 10.4137/CIN.S19454. eCollection 2014. PubMed PMID: 25506198; PubMed Central PMCID: PMC4259509. [PubMed Exit Disclaimer logo ]
  26. Tamir A, Jag U, Sarojini S, Schindewolf C, Tanaka T, Gharbaran R, Patel H, Sood A, Hu W, Patwa R, Blake P, Chirina P, Oh Jeong J, Lim H, Goy A, Pecora A, Suh K.
    Kallikrein family proteases KLK6 and KLK7 are potential early detection and diagnostic biomarkers for serous and papillary serous ovarian cancer subtypes.
    J Ovarian Res. 2014 Dec 5;7(1):109. [Epub ahead of print] PubMed PMID: 25477184; PubMed Central PMCID: PMC4271347. [PubMed Exit Disclaimer logo ]
  27. Tradigo G, Veneziano C, Greco S, Veltri P.
    An Architecture for Integrating Genetic and Clinical Data.
    14th International Conference on Computational Science (ICCS 2014). Procedia Computer Science, Volume 29, 2014, Pages 1959-1969. doi: 10.1016/j.procs.2014.05.180 .
  28. Treepongkaruna S, Simakachorn N, Pienvichit P, Varavithya W, Tongpenyai Y, Garnier P, Mathiex-Fortunet H.
    A randomised, double-blind study of polyethylene glycol 4000 and lactulose in the treatment of constipation in children.
    BMC Pediatr. 2014 Jun 19;14:153. doi: 10.1186/1471-2431-14-153. PubMed PMID: 24943105; PubMed Central PMCID: PMC4075982. [PubMed]
  29. Winnenburg R, Bodenreider O.
    Coverage of Phenotypes in Standard Terminologies.
    Proceedings of the Phenotype Day at ISMB 2014. Boston, MA, USA, July 12, 2014. [PDF Exit Disclaimer logo ]
  30. Zunner C, Ganslandt T, Prokosch HU, Bürkle T.
    A reference architecture for semantic interoperability and its practical application.
    Stud Health Technol Inform. 2014;198:40-6. PubMed PMID: 24825683. [PubMed]
     
    2013
  31. Abate F, Acquaviva A, Ficarra E, Piva R, Macii E.
    Gelsius: A Literature-Based Workflow for Determining Quantitative Associations Between Genes and Biological Processes.
    IEEE/ACM Trans Comput Biol Bioinform. 2013 May-Jun;10(3):619-31. doi: 10.1109/TCBB.2013.11. PubMed PMID: 24091396 prev. 23439219. [PubMed] [prev.]
  32. Abate F, Acquaviva A, Ficarra E, Macii E.
    Integration of literature with heterogeneous information for genes correlation scoring.
    ACM Journal on Emerging Technologies in Computing Systems. 2013 Nov 9(4) Article number 28. [ACM Exit Disclaimer logo ]
  33. Anderson HV, Weintraub WS, Radford MJ, Kremers MS, Roe MT, Shaw RE, Pinchotti DM, Tcheng JE.
    Standardized Cardiovascular Data for Clinical Research, Registries, and Patient Care: A Report from the Data Standards Workgroup of the National Cardiovascular Research Infrastructure Project.
    J Am Coll Cardiol. 2013 May 7;61(18):1835-46. doi: 10.1016/j.jacc.2012.12.047. Epub 2013 Mar 6. PubMed PMID: 23500238. [PubMed]
  34. Buckler AJ, Liu TT, Savig E, Suzek BE, Rubin DL, Paik D.
    Quantitative Imaging Biomarker Ontology (QIBO) for Knowledge Representation of Biomedical Imaging Biomarkers.
    J Digit Imaging. 2013 Aug;26(4):630-41. PubMed PMID: 23589184; PubMed Central PMCID: PMC3705004. [PubMed]
  35. Buckler AJ, Paik D, Ouellette M, Danagoulian J, Wernsing G, Suzek BE.
    A Novel Knowledge Representation Framework for the Statistical Validation of Quantitative Imaging Biomarkers.
    J Digit Imaging. Aug;26(4):614-29. doi: 10.1007/s10278-013-9598-3. PubMed PMID: 23546775; PubMed Central PMCID: PMC3705009. [PubMed]
  36. Chang JF, Popescu M, Arthur GL.
    Automated extraction of precise protein expression patterns in lymphoma by text mining abstracts of immunohistochemical studies.
    J Pathol Inform. 2013 Jul 31;4:20. doi: 10.4103/2153-3539.115880. eCollection 2013. PubMed PMID: 23967385; PubMed Central PMCID: PMC3746413. [PubMed]
  37. Cimino JJ, Ayres EJ, Remennik L, Rath S, Freedman R, Beri A, Chen Y, Huser V.
    The National Institutes of Health's Biomedical Translational Research Information System (BTRIS): Design, contents, functionality and experience to date.
    J Biomed Inform. 2013 Nov 19. pii: S1532-0464(13)00181-0. doi: 10.1016/j.jbi.2013.11.004. [Epub ahead of print] PubMed PMID: 24262893. [PubMed]
  38. da Silva KR, Costa R, Crevelari ES, Lacerda MS, de Moraes Albertini CM, Filho MM, Santana JE, Vissoci JR, Pietrobon R, Barros JV.
    Glocal clinical registries: pacemaker registry design and implementation for global and local integration - methodology and case study.
    PLoS One. 2013 Jul 25;8(7):e71090. doi:10.1371/journal.pone.0071090. Print 2013. PubMed PMID: 23936257. [PubMed]
  39. Gómez-Pérez A, Martínez-Romero M, Rodríguez-González A, Vázquez G, Vázquez-Naya JM.
    Ontologies in medicinal chemistry: current status and future challenges.
    Curr Top Med Chem. 2013 Mar 1;13(5):576-90. PubMed PMID: 23548021. [PubMed]
  40. Goss FR, Zhou L, Plasek JM, Broverman C, Robinson G, Middleton B, Rocha RA.
    Evaluating standard terminologies for encoding allergy information.
    J Am Med Inform Assoc. 2013 Sep-Oct;20(5):969-79. doi: 10.1136/amiajnl-2012-000816. Epub 2013 Feb 9. PubMed PMID: 23396542. [PubMed]
  41. Grove MJ.
    Development of an Ontology for Rehabilitation: Traumatic Brain Injury.
    Thesis (Ph.D.) University of Minnesota, 2013. [U.MN Exit Disclaimer logo ]
  42. 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]
  43. Petkov VI, Penberthy LT, Dahman BA, Poklepovic A, Gillam CW, McDermott JH.
    Automated determination of metastases in unstructured radiology reports for eligibility screening in oncology clinical trials.
    Exp Biol Med (Maywood). 2013 Dec;238(12):1370-8. doi: 10.1177/1535370213508172. Epub 2013 Oct 9. PubMed PMID: 24108448. [PubMed]
  44. Ries M, Prokosch HU, Beckmann MW, Bürkle T.
    Single-Source Tumor Documentation – Reusing Oncology Data for Different Purposes.
    Onkologie 2013;36(3):136-41. doi: 10.1159/000348528. Epub 2013 Feb 21. PubMed PMID: 23486003. [PubMed]
  45. 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. 2013 Apr;46(2):286-93. doi: 10.1016/j.jbi.2012.11.004. Epub 2012 Nov 29. PubMed PMID: 23201637; PubMed Central PMCID: PMC3606279. [PubMed]
     
    2012
  46. Chen AP, Setser A, Anadkat MJ, Cotliar J, Olsen EA, Garden BC, Lacouture ME.
    Grading dermatologic adverse events of cancer treatments: the Common Terminology Criteria for Adverse Events Version 4.0.
    J Am Acad Dermatol. 2012 Nov;67(5):1025-39. doi: 10.1016/j.jaad.2012.02.010. Epub 2012 Apr 11. PubMed PMID: 22502948. [PubMed]
  47. 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 Exit Disclaimer logo ]
  48. 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]
  49. 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]
  50. Elkin PL.
    Springer Terminology Related Standards Development.
    In Elkin PL, ed. Terminology and Terminological Systems, Ch.7 pp.107-123, Springer London, 2012. [Springer Exit Disclaimer logo ]
  51. 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 Exit Disclaimer logo ]
  52. 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]
  53. 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 Exit Disclaimer logo ]
  54. 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]
  55. Machado CM, Couto FM, Fernandes AR, Santos S, 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 Exit Disclaimer logo ] [DOI Exit Disclaimer logo ]
  56. 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 Exit Disclaimer logo ]
  57. 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 Exit Disclaimer logo ]
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    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]
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    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 Exit Disclaimer logo ]
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    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 Exit Disclaimer logo ]
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    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]
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    2011
  63. Adams N, Hoehndorf R, Gkoutos GV, Hansen G, Hennig C.
    PIDO: The Primary Immunodeficiency Disease Ontology.
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    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 Exit Disclaimer logo ]
  66. 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]
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    Ontology-Strength Industry Standards: The Case of the Clinical Trial Domain.
    Frontiers in Artificial Intelligence and Applications, Volume 229: Formal Ontologies Meet Industry, Proceedings of the Fifth International Workshop, FOMI 2011, July 7-8, 2011, Delft, Netherlands. (eds. Vermaas PE, Dignum V) IOS Press 2011 pp.41-49. ISBN 978-1-60750-784-0 (print) 978-1-60750-785-7 (online), DOI 10.3233/978-1-60750-785-7-41 [IOS Press Exit Disclaimer logo ]
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    Interoperability for the Learning Health System.
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    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
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    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 Exit Disclaimer logo ]
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    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]
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    Grid-enabled measures: using Science 2.0 to standardize measures and share data.
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    Open biomedical ontologies applied to prostate cancer.
    Applied Ontology 2011;6(1):35-51. [ACM DL Exit Disclaimer logo ]
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    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]
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    Building a biomedical cyberinfrastructure for collaborative research.
    Am J Prev Med. 2011 May;40(5 Suppl 2):S144-50. PubMed PMID: 21521587. [PubMed]
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    Multicenter breast cancer collaborative registry.
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    PCCR: Pancreatic Cancer Collaborative Registry.
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    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]
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    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
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    Proc. 9th Intl. Semantic Web Conference (ISWC 2010), Vol II, pp. 34-49, Shanghai, China, Nov. 7-11, 2010. [ACM Exit Disclaimer logo ]
  83. 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 Exit Disclaimer logo ]
  84. Deus HF, Veiga DF, Freire PR, Weinstein JN, Mills GB, Almeida JS.
    Exposing the cancer genome atlas as a SPARQL endpoint.
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  86. 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]
  87. Kang HP, Borromeo CD, Berman JJ, Becich MJ.
    The tissue microarray OWL schema: An open-source tool for sharing tissue microarray data.
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  88. 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 Exit Disclaimer logo ]
  89. 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 Exit Disclaimer logo ]
  90. 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]
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    FDA adverse Event Problem Codes: standardizing the classification of device and patient problems associated with medical device use.
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    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]
  93. 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]
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    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]
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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
  96. 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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    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]
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    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 Exit Disclaimer logo ]
     
    2008
  99. 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]
  100. 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]
  101. 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
  102. 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.
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    Issues in integrating epidemiology and research information in oncology: experience with ICD-O3 and the NCI Thesaurus.
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  104. 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]
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    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]
  106. 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]
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    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.
  108. 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
  110. Deitzer JR, Payne PR, Starren JB.
    Coverage of clinical trials tasks in existing ontologies.
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    Ontology-based annotation and query of tissue microarray data.
    AMIA Annu Symp Proc. 2006:709-13. PubMed PMID: 17238433; PubMed Central PMCID: PMC1839511. [PubMed]
  112. 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
  113. 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]
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    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
  115. 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
  116. 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. 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
  2. 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 ]
  3. 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 ]
  4. 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
  5. 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 ]
  6. 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
  7. 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
  8. 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]
  9. 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.
  10. 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 Exit Disclaimer logo ]
     
    2008
  11. 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]
  12. 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]
  13. 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. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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. 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 ]

    2014
  2. Ashish N, Dahm L, Boicey C.
    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 ]
  3. Blair DR, Wang K, Nestorov S, Evans JA, Rzhetsky A.
    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 ]
  4. Brochhausen M, Schneider J, Malone D, Empey PE, Hogan WR, Boyce RD.
    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 ]
  5. 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 ]
  6. 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 ]
  7. 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.
    Proceedings of the 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 ]
  8. 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 ]
  9. 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]
  10. Fu X, Batista-Navarro R, Rak R, Ananiadou S.
    A Strategy for Annotating Clinical Records with Phenotypic Information relating to the Chronic Obstructive Pulmonary Disease.
    Proceedings of the Phenotype Day at ISMB 2014. Boston, MA, USA, July 12, 2014. [PDF Exit Disclaimer logo ]
  11. Gatens W, Konev B, Wolter F.
    Lower and Upper Approximations for Depleting Modules of Description Logic Ontologies.
    Proceedings of the 21st European Conference on Artificial Intelligence (ECAI 2014). Aug 18-22, 2014, Prague, Czech Republic. [PDF Exit Disclaimer logo ]
  12. 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 ]
  13. 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 ]
  14. He Z, Geller J, Elhanan G.
    Categorizing the Relationships between Structurally Congruent Concepts from Pairs of Terminologies for Semantic Harmonization.
    Proceedings, 2014 Summit on Translational Bioinformatics (TBI 2014). April 7-9, 2014, San Francisco, CA, pp.48-53.
  15. Hudson CL, Topaloglu U, Bian J, Hogan W, Kieber-Emmons T.
    Automated Tools for Clinical Research Data Quality Control using NCI Common Data Elements.
    Proceedings, 2014 Summit on Translational Bioinformatics (TBI 2014). April 7-9, 2014, San Francisco, CA, pp.60-69.
  16. 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 ]
  17. 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 ]
  18. 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.
    Proceedings of the 7th International Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2014). Berlin, Germany, Dec 9-11, 2014. [PDF Exit Disclaimer logo ]
  19. 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 ]
  20. Ludwig M.
    Just: a Tool for Computing Justifications w.r.t. ELH Ontologies.
    Proceedings of the 3rd International Workshop on OWL Reasoner Evaluation (ORE 2014). Vienna, Austria, July 13, 2014, pp.1-7. [PDF Exit Disclaimer logo ]
  21. 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 ]
  22. Ludwig M, Peñaloza R.
    Brave and Cautious Reasoning in EL.
    Proceedings of the 27th International Workshop on Description Logics (DL 2014). Vienna, Austria, July 17-20, 2014, pp.274-286. [PDF Exit Disclaimer logo ]
  23. 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 ]
  24. 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]
  25. Merrill E, Corlosquet S, Ciccarese P, Clark T, Das S.
    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]
  26. 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 ]
  27. 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 ]
  28. 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]
  29. Queral-Rosinach N, Kuhn T, Chichester C, Dumontier M, Sanz F, Furlong LI.
    Publishing DisGeNET as Nanopublications.
    Semantic Web – Interoperability, Usability, Applicability (Semantic Web journal). 2014 Oct 15. [PDF Exit Disclaimer logo ]
  30. 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 ]
  31. 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 ]
  32. 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 ]
  33. 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 ]
  34. 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 ]
  35. 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]
  36. Tao S.
    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.
    [OhioLINK Exit Disclaimer logo ]
  37. 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 ]
  38. Walk S, Singer P, Strohmaier M, Tudorache T, Musen MA, Noy NF.
    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 ]
  39. 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.
  40. Wu Q, Zhang H, Lan J.
    K-State automaton burst detection model based on KOS: Emerging trends in cancer field.
    Journal of Information Science. Oct 3, 2014. doi: 10.1177/0165551514551500. [Online Exit Disclaimer logo ]

    2013
  41. 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 ]
  42. 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 ]
  43. 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 ]
  44. Beißwanger AE.
    Developing Ontological Background Knowledge for Biomedicine.
    Thesis (Doktors der Naturwissenschaften), University of Mannheim, Mannheim, 2013. [PDF Exit Disclaimer logo ]
  45. 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 ]
  46. 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 ]
  47. 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 ]
  48. Freckleton RE.
    Scaling Ontology Alignment.
    Thesis (M.S.), University of Colorado Colorado Springs, Department of Computer Science, 2013. [PDF Exit Disclaimer logo ]
  49. Garcia Castro LJ, McLaughlin C, Garcia A.
    Biotea: RDFizing PubMed Central in support for the paper as an interface to the Web of Data.
    J Biomed Semantics. 2013 Apr 15;4 Suppl 1:S5. doi: 10.1186/2041-1480-4-S1-S5. Epub 2013 Apr 15. PubMed PMID: 23734622. [PubMed]
  50. Gonçalves RS, Bail S, Jimenez-Ruiz E, Matentzoglu N, Parsia B, Glimm B, Kazakov Y.
    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 ]
  51. 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 ]
  52. 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 ]
  53. 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 ]
  54. 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]
  55. Hartung M, Kolb L, Gross A, Rahm E.
    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 ]
  56. 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 ]
  57. Karaiskos C.
    Enhanced Ontological Searching of Medical Scientific Information.
    Thesis (M.Sc.), University of Manchester, School of Computer Science, 2013. [PDF Exit Disclaimer logo ]
  58. 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 ]
  59. Kozák J, Nečaský M, Dědek J, Klímek J, Pokorný J.
    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 ]
  60. Kozák J, Necaský M, Dedek J, Klímek J, Pokorný J.
    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 ]
  61. Lambrix P, Liu Q.
    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 ]
  62. Lim L, Wang H, Wang M.
    Semantic Queries by Example.
    Proceedings of the 16th International Conference on Extending Database Technology (EDBT 2013) Genoa, Italy, 2013 Mar 18-22:347-358. ACM New York, NY, USA, 2013. [PDF Exit Disclaimer logo ] [ACM DL Exit Disclaimer logo ]
  63. Ludwig M, Konev B.
    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 ]
  64. Matentzoglu N, Bail S, Parsia B.
    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 ]
  65. 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 ]
  66. Mudunuri US, Khouja M, Repetski S, Venkataraman G, Che A, Luke BT, Girard FP, Stephens RM.
    Knowledge and Theme Discovery across Very Large Biological Data Sets Using Distributed Queries: A Prototype Combining Unstructured and Structured Data.
    PLoS One. 2013 Dec 2;8(12):e80503. doi: 10.1371/journal.pone.0080503. eCollection 2013. PubMed PMID: 24312478; PubMed Central PMCID: PMC3846626. [PubMed]
  67. Nikitina N, Schewe S.
    Simplifying Description Logic Ontologies.
    Proceedings of the 12th International Semantic Web Conference (ISWC 2013), Sydney, Australia, Oct 21-25, 2013. [ISWC Exit Disclaimer logo ] [PDF Exit Disclaimer logo ]
  68. 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.
    Proceedings of the 12th International Semantic Web Conference (ISWC 2013), Sydney, Australia, 21-25 Oct 2013. [PDF Exit Disclaimer logo ]
  69. Palma G, Vidal ME, Haag E, Raschid L, Thor A.
    Measuring Relatedness Between Scientific Entities in Annotation Datasets.
    ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (ACM BCB 2013) Bethesda, MD, 2013 Sept 22-25. [PDF Exit Disclaimer logo ]
  70. 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 ]
  71. 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 ]
  72. Salvadores M, Alexander PR, Musen MA, Noy NF.
    BioPortal as a Dataset of Linked Biomedical Ontologies and Terminologies in RDF.
    Semantic Web Journal 2013; 4(3):277-284. Available online 31 Oct 2012. [PDF Exit Disclaimer logo ] [Online Exit Disclaimer logo ]
  73. Shvaiko P, Euzenat J, Srinivas K, Mao M, Jiménez-Ruiz E, eds.
    Ontology Matching (OM-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.101-108, October 21, 2013. [CEUR-WS Exit Disclaimer logo ] [PDF Exit Disclaimer logo ]
  74. 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 ]
  75. Strohmaier M, Walk S, Pöschko J, Lamprecht D, Tudorache T, Nyulas C, Musen MA, Noy NF.
    How Ontologies are Made: Studying the Hidden Social Dynamics Behind Collaborative Ontology Engineering Projects.
    Web Semantics: Science, Services and Agents on the World Wide Web, North America, April 2013. [PDF Exit Disclaimer logo ]
  76. 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]
  77. Thibault JC, Frey L.
    Biomedical Terminology Mapper for UML projects.
    AMIA Summits Transl Sci Proc. 2013 Mar 18;2013:257-61. eCollection 2013. PubMed PMID:
    24303278; PubMed Central PMCID: PMC3845744. [PubMed]
  78. Trivela D, Stoilos G, Chortaras A, Stamou G.
    Optimising Resolution-Based Rewriting Algorithms for 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 ]
  79. Vergara-Niedermayr C, Wang F, Pan T, Kurc T, Saltz J.
    Semantically Interoperable XML Data.
    Int. J. Semantic Computing. 2013 Sept;7(3). DOI: 10.1142/S1793351X13500037 [Online Exit Disclaimer logo ]
  80. 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
  81. 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.
    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 ]
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    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 Exit Disclaimer logo ]
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    Applying semantic web technologies for phenome-wide scan using an electronic health record linked Biobank.
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    Automated Extension of Biomedical Ontologies.
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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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    The ACGT Master Ontology and its applications--towards an ontology-driven cancer research and management system.
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    Categorising logical differences between OWL ontologies.
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    Using Semantic Web Technologies to Build a Community-Driven Knowledge Curation Platform for the Skeletal Dysplasia Domain.
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    GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution.
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    The TOKEn project: knowledge synthesis for in silico science.
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    MedMatch: Applying Semantic Matching in the Medical Domain.
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    Data Management, Databases, and Warehousing.
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    An asymmetric similarity measure for ontologies based on the feature contrast model.
    Proceedings of the 2010 International Conference on Complex, Intelligent and Software Intensive Systems (CISIS '10), Krakow, Poland, 16 February 2010. IEEE Computer Society Washington, DC, USA ©2010. pp.1002–1007.
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    Extracting glosses to disambiguate word senses.
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    Ontology-based Queries over Cancer Data.
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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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    Predicting Reasoning Performance Using Ontology Metrics.
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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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    A biomedical research permissions ontology: cognitive and knowledge representation considerations.
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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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    The Pitfalls of Thesaurus Ontologization - the Case of the NCI Thesaurus.
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    Measuring Design Complexity of Semantic Web Ontologies.
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    Development of an agile knowledge engineering framework in support of multi-disciplinary translational research.
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