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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. Samuel M. RubinsteinPeter C. YangAndrew J. Cowan, and Jeremy L. Warner. Standardizing Chemotherapy Regimen Nomenclature: A Proposal and Evaluation of the HemOnc and National Cancer Institute Thesaurus Regimen Content DOI: 10.1200/CCI.19.00122 JCO Clinical Cancer Informatics no. 4 (2020) 60-70. Published online January 28, 2020. PMID: 31990580


  1. Rashmie Abeysinghe, Michael A. Brooks, Jeffery Talbert, Cui Lico

    Quality Assurance of NCI Thesaurus by Mining Structural-Lexical Patterns

    AMIA Annu Symp Proc. 2017 Proc. 2017; 2017: 364–373. Published online 2018 Apr 16.

  2. 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]
  3. He Z, Chen Y, Geller J. Perceiving the Usefulness of the National Cancer Institute Metathesaurus for Enriching NCIt with Topological Patterns. Stud Health Technol Inform. 2017;245:863–867.

  4. 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 ]
  5. 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 ]
  6. 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 ]
  7. 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 ]
  8. 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]
  9. 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]
  10. 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]
  11. 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 ]
  12. 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]
  13. 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]
  14. 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]
  15. 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]
  16. 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 ]
  17. Hartel F, Fragoso G, Ong K, Dionne R.
    Enhancing Quality of Retrieval Through Concept Edit History.
    AMIA Annu Symp Proc. 2003:279-83. [PubMed]

  18. 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.

  19. 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]
  20. 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.
  21. 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 ]
  22. 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]

  23. 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. Po-Yen Lin F, Groza T, Kocbek S, Cancer

    Care Treatment Outcome Ontology: A Novel Computable Ontology for Profiling Treatment Outcomes in Patients With Solid Tumors

    September 2018, DOI: 10.1200/CCI.18.00026

  2. Zhang H, Guo Y, Li Q, et al.
    An ontology-guided semantic data integration framework to support integrative data analysis of cancer survival. 
    -- BMC Med Inform Decis Mak. 2018;18(Suppl 2):41. Published 2018 Jul 23. doi:10.1186/s12911-018-0636-4


  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]

  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 ]

  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 ]
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    Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis.
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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.
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    Summit on Translat Bioinforma. 2009 Mar 1;2009:44-8. PubMed PMID: 21347169; PubMed Central PMCID: PMC3041578. [PubMed] [Full Text]
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  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]

  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.
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    ICBO: International Conference on Biomedical Ontology. 2009 July 24-26. Buffalo, New York, USA.
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    LexRDF Model: An RDF-based Unified Model for Heterogeneous Biomedical Ontologies.
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    Adopting Graph Traversal Techniques for Context-Driven Value Sets Extraction from Biomedical Knowledge Sources.
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    LexValueSets: an approach for context-driven value sets extraction.
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  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
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  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.
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    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. Hickman H., Ver Hoef W., Hastak S., Neville J., Clunie D., Wagner U., Helton E. (2019). SDTM datasets of clinical data and measurements for selected cancer collections to TCIA [Dataset]. The Cancer Imaging Archive. doi: 10.7937/TCIA.2019.zfv154m9


  1. Karimi H, Kamandi A. Ontology alignment using inductive logic programming
    Conference: 2018 4th International Conference on Web Research (ICWR) DOI: 10.1109/ICWR.2018.8387247, April 2018
  2. He Z, Keloth VK, Chen Y, Geller J.
    -- Proceedings (IEEE Int Conf Bioinformatics Biomed). 2018;2018:1641–1648. doi:10.1109/BIBM.2018.8621564
  3. Kolyvakis P, Kalousis A, Smith B, Kiritsis D.
    -- J Biomed Semantics. 2018;9(1):21. Published 2018 Aug 15. doi:10.1186/s13326-018-0187-8
  4. Keloth VK, He Z, Chen Y, Geller J.
    -- AMIA Annu Symp Proc. 2018;2018:644–653. Published 2018 Dec 5.
  5. Zheng L, Chen Y, Elhanan G, Perl Y, Geller J, Ochs C. Complex overlapping concepts: An effective auditing methodology for families of similarly structured BioPortal ontologies. J Biomed Inform. 2018;83:135–149. doi:10.1016/j.jbi.2018.05.015


  1. Nikiema JN, Jouhet, Mougin F.
    Integrating cancer diagnosis terminologies based on logical definitions of SNOMED CT concepts.
    J Biomed Inform. 2017 Oct;74:46-58. doi: 10.1016/j.jbi.2017.08.013. Epub 2017 Aug 24. [PubMed]
  2. Min H, Zheng L, Perl Y, Halper M, De Coronado S, Ochs C.
    Relating Complexity and Error Rates of Ontology Concepts. More Complex NCIt Concepts Have More Errors.
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