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MultiExcerptName	AppendBibliography

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.

Table of Contents

minLevel	2

About EVS

2020

Samuel M. Rubinstein, MD; Peter C. Yang, MD; Andrew J. Cowan, MD; and Jeremy L. Warner, MD, MS. 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

2017

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.
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]
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.

2013
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
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2012
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
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2011
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
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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
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2009
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
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
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]
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
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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
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
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]
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
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
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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
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
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]
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.
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
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Silva JS, Ball MJ, Douglas JV.
The Cancer Informatics Infrastructure (CII): An Architecture for Translating Clinical Research into Patient Care.
Proc 10th World Congress on Medical Informatics (Medinfo 2001) Amsterdam: IOS Press 2001, pp. 114-117. Also cited as: Stud Health Technol Inform. 2001;84(Pt 1):114-7. PubMed PMID: 11604717. [PubMed]

1999
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

2018

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
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

2017

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]
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]
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]
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]
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]
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]
Yan Z, Lacson R, Ip I, Valtchinov V, Raja A, Osterbur D, Khorasani R.
Evaluating Terminologies to Enable Imaging-Related Decision Rule Sharing.
AMIA Annu Symp Proc. 2017 Feb 10;2016:2082-2089. PubMed PMID: 28269968. [PubMed]

2016
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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.
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
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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]
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]
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
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2015
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
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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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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)]
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]
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]
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]
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]
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]
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.
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
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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]
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]
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]
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]
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]
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
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Wu TJ, Schriml LM, Chen QR, Colbert M, Crichton DJ, Finney R, Hu Y, Kibbe WA, Kincaid H, Meerzaman D, Mitraka E, Pan Y, Smith KM, Srivastava S, Ward S, Yan C, Mazumder R.
Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis.
Database (Oxford). 2015 Apr 4;2015:bav032. doi: 10.1093/database/bav032. Print 2015. PubMed PMID: 25841438; PubMed Central PMCID: PMC4385274. [PubMed]

2014
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]
Brechat B, Thiessard FMF, Jouhet V.
Mapping de terminologies diagnostiques en cancérologie par l'intermédiaire du NCI Metathesaurus / Mapping of diagnostic terminologies in oncology using the NCI Metathesaurus.
Proc / Actes 15es Journées francophones d'informatique médicale (JFIM 2014) co-located with 2e Congrès National d'Informatique Médicale (CNIM 2014). Fes, Morocco, June 12-13, 2014. (in CEUR Workshop Proceedings, Vol-1379, CEUR-WS.org, June 2014). [PDF
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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]
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]
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
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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
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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]
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
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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]
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
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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
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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]
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
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Meier A.
Challenges in Processing Clinical Lab Data.
PharmaSUG 2014 Conference Proceedings. San Diego, CA, USA, June 1-4, 2014. [PDF
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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
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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]
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
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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
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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]
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
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Santos RS, de Oliveira JM, Malheiros SM, Neto MAP.
Using reference ontology to elicit attributes of brain tumors database.
Information Society (i-Society), 2014 International Conference on.London, UK, 10-12 Nov. 2014, pp.181-186, doi: 10.1109/i-Society.2014.7009038 . [IEEE
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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
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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 .
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]
Winnenburg R, Bodenreider O.
Coverage of Phenotypes in Standard Terminologies.
Proc Phenotype Day at ISMB 2014. Boston, MA, USA, July 12, 2014. [PDF
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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
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.]
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
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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]
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]
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]
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]
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]
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]
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]
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]
Grove MJ.
Development of an Ontology for Rehabilitation: Traumatic Brain Injury.
Thesis (Ph.D.) University of Minnesota, 2013. [U.MN
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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]
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]
Phan JH, Young AN, Wang MD.
omniBiomarker: a Web-Based Application for Knowledge-Driven Biomarker Identification.
IEEE Trans Biomed Eng. Dec 2013, 60(12):3364-3367. PubMed PMID: 22893372. [PubMed] [IEEE
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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]
Santos RS, Malheiros SM, Cavalheiro S, de Oliveira JM.
A data mining system for providing analytical information on brain tumors to public health decision makers.
Comput Methods Programs Biomed. 2013 Mar;109(3):269-82. doi: 10.1016/j.cmpb.2012.10.010. Epub 2012 Oct 31. PubMed PMID: 23122302. [PubMed]
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
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]
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
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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]
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]
Elkin PL.
Springer Terminology Related Standards Development.
In Elkin PL, ed. Terminology and Terminological Systems, Ch.7 pp.107-123, Springer London, 2012. [Springer
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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
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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]
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
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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]
Hsu W, Taira RK, El-Saden S, Kangarloo H, Bui AA.
Context-based electronic health record: toward patient specific healthcare.
IEEE Trans Inf Technol Biomed. 2012 Mar;16(2):228-34. doi: 10.1109/TITB.2012.2186149. PubMed PMID: 22395637; PubMed Central PMCID: PMC4414061. [PubMed]
Machado CM, Couto FM, Fernandes AR, Santos S, Freitas AT.
Toward a Translational Medicine Approach for Hypertrophic Cardiomyopathy.
Proc 3rd International Conference on Information Technology in Bio- and Medical Informatics (ITBAM 2012), Vienna, Austria, September 4-5, 2012 (LNCS 7451:151-165). [PDF
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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
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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
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Parikh PP, Minning TA, Nguyen V, Lalithsena S, Asiaee AH, Sahoo SS, Doshi P, Tarleton R, Sheth AP.
A Semantic Problem Solving Environment for Integrative Parasite Research: Identification of Intervention Targets for Trypanosoma cruzi.
PLoS Negl Trop Dis. 2012 Jan;6(1):e1458. Epub 2012 Jan 17. PubMed PMID: 22272365; PubMed Central PMCID: PMC3260319. [PubMed]
Parker JL, Lushina N, Bal PS, Petrella T, Dent R, Lopes G.
Impact of biomarkers on clinical trial risk in breast cancer.
Breast Cancer Res Treat. 2012 Nov;136(1):179-85. doi: 10.1007/s10549-012-2247-6. Epub 2012 Sep 25. PubMed PMID: 23007573. [PubMed] [PDF
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Schriml LM, Arze C, Nadendla S, Chang YW, Mazaitis M, Felix V, Feng G, Kibbe WA.
Disease Ontology: a backbone for disease semantic integration.
Nucleic Acids Res. 2012 Jan;40(Database issue):D940-6. Epub 2011 Nov 12. PubMed PMID: 22080554; PubMed Central PMCID: PMC3245088. [PubMed]
Wang H, Yatawara M, Huang S, Dudley K, Szekely C, Holden S, Piantadosi S.
The Integrated Proactive Surveillance System for Prostate Cancer.
Open Med Inform J. 2012;6:1-8. Epub 2012 Mar 2. PubMed PMID: 22505956. [PubMed] [PDF
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2011
Adams N, Hoehndorf R, Gkoutos GV, Hansen G, Hennig C.
PIDO: The Primary Immunodeficiency Disease Ontology.
Bioinformatics. 2011 Nov 15;27(22):3193-9. doi: 10.1093/bioinformatics/btr531. Epub 2011 Sep 22. PubMed PMID: 21949270. [PubMed]
Bertaud-Gounot V, Donfack V, Lasbleiz J, Bourde A, Duvauferrier R.
Creating an ontology driven rules base for an expert system for medical diagnosis.
Stud Health Technol Inform. 2011;169:714-8. PubMed PMID: 21893840. [PubMed]
Chen S, Hsu C.
The TCR Cancer Registry Repository for Annotating Cancer Data.
Emergency Management and Management Sciences (ICEMMS), 2011 2nd IEEE International Conference on, 2011 Aug 8-10:297-300. [IEEE
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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]
Cuggia M, Bourde A, Turlin B, Vincendeau S, Bertaud V, Bohec C, Duvauferrier R.
Automatic Definition of the Oncologic EHR Data Elements from NCIT in OWL.
Stud Health Technol Inform. 2011;169:517-21. PubMed PMID: 21893803. [PubMed]
Foran DJ, Yang L, Chen W, Hu J, Goodell LA, Reiss M, Wang F, Kurc T, Pan T, Sharma A, Saltz JH.
ImageMiner: a software system for comparative analysis of tissue microarrays using content-based image retrieval, high-performance computing, and grid technology.
J Am Med Inform Assoc. 2011 Jul-Aug;18(4):403-15. doi: 10.1136/amiajnl-2011-000170. Epub 2011 May 23. PubMed PMID: 21606133; PubMed Central PMCID: PMC3128405. [PubMed]
Grenon P, Wimalaratne S, de Bono B.
Ontology-Strength Industry Standards: The Case of the Clinical Trial Domain.
Frontiers in Artificial Intelligence and Applications, Volume 229: Formal Ontologies Meet Industry, Proc 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
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Hu H, Correll M, Kvecher L, Osmond M, Clark J, Bekhash A, Schwab G, Gao D, Gao J, Kubatin V, Shriver CD, Hooke JA, Maxwell LG, Kovatich AJ, Sheldon JG, Liebman MN, Mural RJ.
DW4TR: A Data Warehouse for Translational Research.
J Biomed Inform. 2011 Dec;44(6):1004-19. PubMed PMID: 21872681. [PubMed]
Kush RD.
Interoperability for the Learning Health System.
Digital Infrastructure for the Learning Health System: The Foundation for Continuous Improvement in Health and Health Care: Workshop Series Summary. Grossmann C, Powers B, McGinnis JM eds. Institute of Medicine (2011) pp.108-114. [Online
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Lasbleiz J, Brillet E, Decaux O, Duvauferrier R, Bertaud-Gounot V.
Staging disease with Protégé 4: Example of multiple myeloma.
IRBM, 2011 32(6):329-331. Available online 21 November 2011, doi:10.1016/j.irbm.2011.10.003
Li X, Wang Q, Zheng Y, Lv S, Ning S, Sun J, Huang T, Zheng Q, Ren H, Xu J, Wang X, Li Y.
Prioritizing human cancer microRNAs based on genes' functional consistency between microRNA and cancer.
Nucleic Acids Res. 2011 Dec;39(22):e153. Epub 2011 Oct 5. PubMed PMID: 21976726; PubMed Central PMCID: PMC3239203. [PubMed
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Liu H, Burkhart Q, Bell DS.
Evaluation of the NCPDP Structured and Codified Sig Format for e-prescriptions.
J Am Med Inform Assoc. 2011 Sep 1;18(5):645-51. Epub 2011 May 25. PubMed PMID: 21613642; PubMed Central PMCID: PMC3168301. [PubMed]
Moser RP, Hesse BW, Shaikh AR, Courtney P, Morgan G, Augustson E, Kobrin S, Levin KY, Helba C, Garner D, Dunn M, Coa K.
Grid-enabled measures: using Science 2.0 to standardize measures and share data.
Am J Prev Med. 2011 May;40(5 Suppl 2):S134-43. PubMed PMID: 21521586; PubMed Central PMCID: PMC3088871. [PubMed]
Overton JA, Romagnoli C, Chhem R.
Open biomedical ontologies applied to prostate cancer.
Applied Ontology 2011;6(1):35-51. [ACM DL
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Pathak J, Wang J, Kashyap S, Basford M, Li R, Masys DR, Chute CG.
Mapping clinical phenotype data elements to standardized metadata repositories and controlled terminologies: the eMERGE Network experience.
J Am Med Inform Assoc. 2011 Jul-Aug;18(4):376-86. Epub 2011 May 19. PubMed PMID: 21597104; PubMed Central PMCID: PMC3128396. [PubMed]
Schad PA, Mobley LR, Hamilton CM.
Building a biomedical cyberinfrastructure for collaborative research.
Am J Prev Med. 2011 May;40(5 Suppl 2):S144-50. PubMed PMID: 21521587. [PubMed]
Sherman S, Shats O, Fleissner E, Bascom G, Yiee K, Copur M, Crow K, Rooney J, Mateen Z, Ketcham MA, Feng J, Sherman A, Gleason M, Kinarsky L, Silva-Lopez E, Edney J, Reed E, Berger A, Cowan K.
Multicenter breast cancer collaborative registry.
Cancer Inform. 2011;10:217-26. Epub 2011 Aug 31. PubMed PMID: 21918596; PubMed Central PMCID: PMC3169352. [PubMed]
Sherman S, Shats O, Ketcham MA, Anderson MA, Whitcomb DC, Lynch HT, Ghiorzo P, Rubinstein WS, Sasson AR, Grizzle WE, Haynatzki G, Feng J, Sherman A, Kinarsky L, Brand RE.
PCCR: Pancreatic Cancer Collaborative Registry.
Cancer Inform. 2011 Mar 23;10:83-91. PubMed PMID: 21552494; PubMed Central PMCID: PMC3085425. [PubMed]
Warden GI, Lacson R, Khorasani R.
Leveraging Terminologies for Retrieval of Radiology Reports with Critical Imaging Findings.
AMIA Annu Symp Proc. 2011 Oct;2011:1481-8. Epub 2011 Oct 22. PubMed PMID: 22195212; PubMed Central PMCID: PMC3243125. [PubMed]
Yong MY, Gonzalez-Beltran A, Begent R.
Establishing a knowledge trail from molecular experiments to clinical trials.
N Biotechnol. 2011 Sep;28(5):464-80. Epub 2011 Apr 5. PubMed PMID: 21473938. [PubMed]

2010
Besana P, Cuggia M, Zekri O, Bourde A, Burgun A.
Using Semantic Web Technologies for Clinical Trial Recruitment.
Proc. 9th Intl. Semantic Web Conference (ISWC 2010), Vol II, pp. 34-49, Shanghai, China, Nov. 7-11, 2010. [ACM
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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
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Deus HF, Veiga DF, Freire PR, Weinstein JN, Mills GB, Almeida JS.
Exposing the cancer genome atlas as a SPARQL endpoint.
J Biomed Inform. 2010 Dec;43(6):998-1008. PubMed PMID: 20851208; PubMed Central PMCID: PMC3071752. [PubMed]
Haroske G, Kramm T, Mörz M, Oberholzer M.
Onkologische Datenelemente in der Histopathologie [Oncological data elements in histopathology].
Pathologe. 2010 Sep;31(5):385-92. doi:10.1007/s00292-010-1289-y. Review. German. PubMed PMID: 20544201. [PubMed]
Hirschfeld S, Songco D, Kramer BS, Guttmacher AE.
National Children's Study: update in 2010.
Mt Sinai J Med. 2011 Jan-Feb;78(1):119-25. doi: 10.1002/msj.20227. PubMed PMID: 21259268. [PubMed]
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]
Kang HP, Borromeo CD, Berman JJ, Becich MJ.
The tissue microarray OWL schema: An open-source tool for sharing tissue microarray data.
J Pathol Inform. 2010 Jul 13;1. pii: 9. PubMed PMID: 20805954; PubMed Central PMCID: PMC2929536. [PubMed]
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
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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
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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]
Reed TL, Kaufman-Rivi D.
FDA adverse Event Problem Codes: standardizing the classification of device and patient problems associated with medical device use.
Biomed Instrum Technol. 2010 May-Jun;44(3):248-56. PubMed PMID: 20715359. [PubMed]
Sim I, Carini S, Tu S, Wynden R, Pollock BH, Mollah SA, Gabriel D, Hagler HK, Scheuermann RH, Lehmann HP, Wittkowski KM, Nahm M, Bakken S.
The Human Studies Database Project: Federating Human Studies Design Data Using the Ontology of Clinical Research.
AMIA Summits Transl Sci Proc. 2010: 51–55. [Online]
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]
Yip V, Mete M, Topaloglu U, Kockara S.
Concept Discovery for Pathology Reports using an N-gram Model.
AMIA Summits Transl Sci Proc. 2010 Mar 1;2010:43-7. PubMed PMID: 21347147; PubMed Central PMCID: PMC3041542. [PubMed]
Yong M, Begent R.
Best use of experimental data in cancer informatics.
Future Oncol. 2010 Oct;6(10):1551-62. Review. Erratum in: Future Oncol. 2011 Jan;7(1):154. PubMed PMID: 21062155. [PubMed] [PDF
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2009
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]
Shah NH, Jonquet C, Chiang AP, Butte AJ, Chen R, Musen MA.
Ontology-driven indexing of public datasets for translational bioinformatics.
BMC Bioinformatics. 2009 Feb 5;10 Suppl 2:S1. PubMed PMID: 19208184; PubMed Central PMCID: PMC2646250. [PubMed]
Yong M, Tolner B, Nagl S, Pedley RB, Chester K, Green AJ, Mayer A, Sharma S, Begent R.
Data standards for minimum information collection for antibody therapy experiments.
Protein Eng Des Sel. 2009 Mar;22(3):221-4. PubMed PMID: 19224941. [PubMed] [Oxford full text
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2008
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]
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]
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
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.
Burgun A, Bodenreider O.
Issues in integrating epidemiology and research information in oncology: experience with ICD-O3 and the NCI Thesaurus.
AMIA Annu Symp Proc. 2007 Oct 11:85-9. PubMed PMID: 18693803. [PubMed]
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]
Marquet G, Dameron O, Saikali S, Mosser J, Burgun A.
Grading glioma tumors using OWL-DL and NCI Thesaurus.
AMIA Annu Symp Proc. 2007 Oct 11:508-12. PubMed PMID: 18693888; PubMed Central PMCID: PMC2655830. [PubMed]
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]
Richesson RL, Krischer J.
Data standards in clinical research: gaps, overlaps, challenges and future directions.
J Am Med Inform Assoc. 2007 Nov-Dec;14(6):687-96. Epub 2007 Aug 21. Erratum in: J Am Med Inform Assoc. 2008. [PubMed]
Mar-Apr;15(2):265. PubMed PMID: 17712081; PubMed Central PMCID: PMC2213488.
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]
Shifman MA, Li Y, Colangelo CM, Stone KL, Wu TL, Cheung KH, Miller PL, Williams KR.
YPED: a web-accessible database system for protein expression analysis.
J Proteome Res. 2007 Oct;6(10):4019-24. Epub 2007 Sep 15. PubMed PMID: 17867667. [PubMed]

2006
Deitzer JR, Payne PR, Starren JB.
Coverage of clinical trials tasks in existing ontologies.
AMIA Annu Symp Proc. 2006:903. PubMed PMID: 17238522; PubMed Central PMCID: PMC1839431. [PubMed]
Shah NH, Rubin DL, Supekar KS, Musen MA.
Ontology-based annotation and query of tissue microarray data.
AMIA Annu Symp Proc. 2006:709-13. PubMed PMID: 17238433; PubMed Central PMCID: PMC1839511. [PubMed]
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
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]
Zhang S, Bodenreider O.
Alignment of multiple ontologies of anatomy: deriving indirect mappings from direct mappings to a reference.
AMIA Annu Symp Proc. 2005:864-8. PubMed PMID: 16779163; PubMed Central PMCID: PMC1560629. [PubMed]

2003
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
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

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
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]
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
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]
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]
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
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]
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]
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
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

2016

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

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

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

2013
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
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
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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
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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
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
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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
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2010
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
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]
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.
Tao C, Pathak J, Solbrig HR, Wei WQ, Chute CG.
LexRDF Model: An RDF-based Unified Model for Heterogeneous Biomedical Ontologies.
Proc Semantics for the Rest of Us - Variants of Semantic Web Languages in the Real World Workshop (SemRUs09). Washington DC, USA, 2009 Oct 26. PubMed PMID: 21804785; PubMed Central PMCID: PMC3146261. [PubMed] [PDF
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2008
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]
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]
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

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
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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
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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]
de la Iglesia D, Cachau RE, García-Remesal M, Maojo V.
Nanoinformatics knowledge infrastructures: bringing efficient information management to nanomedical research.
Comput Sci Discov. 2013 Nov 27;6(1):014011. PubMed PMID: 24932210; PubMed Central PMCID: PMC4053539. [PubMed]
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]
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]
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]
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

2019

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

2018

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
He Z, Keloth VK, Chen Y, Geller J.
Extended Analysis of Topological-Pattern-Based Ontology Enrichment.
-- Proceedings (IEEE Int Conf Bioinformatics Biomed). 2018;2018:1641–1648. doi:10.1109/BIBM.2018.8621564
Kolyvakis P, Kalousis A, Smith B, Kiritsis D.
Biomedical ontology alignment: an approach based on representation learning.
-- J Biomed Semantics. 2018;9(1):21. Published 2018 Aug 15. doi:10.1186/s13326-018-0187-8
Keloth VK, He Z, Chen Y, Geller J.
Leveraging Horizontal Density Differences between Ontologies to Identify Missing Child Concepts: A Proof of Concept.
-- AMIA Annu Symp Proc. 2018;2018:644–653. Published 2018 Dec 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

2017

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]
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.
— Methods Inf Med. 2017 May 18;56(3):200-208. doi: 10.3414/ME16-01-0085. Epub 2017 Feb 28. [PubMed]

2016

Bamparopoulos G, Konstantinidis E, Bratsas C, Bamidis PD.
Towards exergaming commons: composing the exergame ontology for publishing open game data.
J Biomed Semantics. 2016 Feb 9;7:4. doi: 10.1186/s13326-016-0046-4. eCollection 2016. PubMed PMID: 26865947; PubMed Central PMCID: PMC4748514. [PubMed]
Chang M, Chang M, Reed JZ, Milward D, Xu JJ, Cornell WD.
Developing timely insights into comparative effectiveness research with a text-mining pipeline.
Drug Discov Today. 2016 Feb 6. pii: S1359-6446(16)00032-5. doi: 10.1016/j.drudis.2016.01.012. [Epub ahead of print] Review. PubMed PMID: 26854423. [PubMed]
Daniel C, Ouagne D, Sadou E, Forsberg K, Gilchrist MM, Zapletal E, Paris N, Hussain S, Jaulent MC, Md DK.
Cross border semantic interoperability for clinical research: the EHR4CR semantic resources and services.
AMIA Jt Summits Transl Sci Proc. 2016 Jul 20;2016:51-9. PubMed PMID: 27570649; PubMed Central PMCID: PMC5001763. [PubMed]
Groß A, Pruski C, Rahm E.
Evolution of biomedical ontologies and mappings: Overview of recent approaches.
Comput Struct Biotechnol J. 2016 Aug 26;14:333-40. doi: 10.1016/j.csbj.2016.08.002. Review. PubMed PMID: 27642503; PubMed Central PMCID: PMC5018063. [PubMed]
He Z, Geller J.
Preliminary Analysis of Difficulty of Importing Pattern-Based Concepts into the National Cancer Institute Thesaurus.
Stud Health Technol Inform. 2016;228:389-93. PubMed PMID: 27577410. [PubMed]
McEntire R, Szalkowski D, Butler J, Kuo MS, Chang M, Chang M, Freeman D, McQuay S, Patel J, McGlashen M, Cornell WD, Xu JJ.
Application of an automated natural language processing (NLP) workflow to enable federated search of external biomedical content in drug discovery and development.
Drug Discov Today. 2016 May;21(5):826-35. doi: 10.1016/j.drudis.2016.03.006. Review. PubMed PMID: 26979546. [PubMed]
Min H, Turner S, de Coronado S, Davis B, Whetzel T, Freimuth RR, Solbrig HR, Kiefer R, Riben M, Stafford GA, Wright LW, Ohira R.
Towards a Standard Ontology Metadata Model.
Proc International Conference on Biomedical Ontology 2016 (ICBO 2016). Corvallis, Oregon, USA, 1-4 Aug 2016. [PDF
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Ochs C, Geller J, Perl Y, Musen MA.
A unified software framework for deriving, visualizing, and exploring abstraction networks for ontologies.
J Biomed Inform. 2016 Aug;62:90-105. doi: 10.1016/j.jbi.2016.06.008. PubMed PMID: 27345947; PubMed Central PMCID: PMC4987206. [PubMed]
Queralt-Rosinach N, Piñero J, Bravo À, Sanz F, Furlong LI.
DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases.
Bioinformatics. 2016 Jul 15;32(14):2236-8. doi:10.1093/bioinformatics/btw214. Epub 2016 Apr 22. PubMed PMID: 27153650; PubMed Central PMCID: PMC4937199. [PubMed]
Slater L, Gkoutos GV, Schofield PN, Hoehndorf R.
Using AberOWL for fast and scalable reasoning over BioPortal ontologies.
J Biomed Semantics. 2016 Aug 8;7(1):49. doi: 10.1186/s13326-016-0090-0. PubMed PMID: 27502585; PubMed Central PMCID: PMC4976511. [PubMed]
Zulkarnain NZ, Meziane F, Crofts G.
A methodology for biomedical ontology reuse.
21st Internat Conf on Applications of Natural Language to Information Systems (NLDB 2016). Salford, UK, 22-24 June 2016.

2015
Amin MB, Khan WA, Kang BH, Lee S.
Performance-based Ontology Matching, A Data-parallel approach for an Effectiveness-independent Performance-gain in Ontology Matching.
Applied Intelligence. 2015 Sept, 43(2):356-385. [PDF
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Araújo TB, Pires CE, Nobrega TP, Nascimento DC.
A Parallel Approach for Matching Large-scale Ontologies.
J of Information and Data Management. 6(1):18-31 Feb 2015.[PDF
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Bekhuis T, Tseytlin E, Mitchell KJ.
A Prototype for a Hybrid System to Support Systematic Review Teams: A Case Study of Organ Transplantation.
2015 Intl Workshop on Biomedical and Health Informatics at the IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2015, Bethesda, MD, US, Nov 9-12, 2015.[PDF
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Chen ES, Sarkar IN.
*informatics: Identifying and Tracking Informatics Sub-Discipline Terms in the Literature.
Methods Inf Med. 2015 Nov 27;54(6):530-9. doi: 10.3414/ME14-01-0088. Epub 2015 May 22. PubMed PMID: 25998007.[PubMed]
Chen J, Ludwig M, Ma Y, Walther D.
Towards Extracting Ontology Excerpts.
Procs 8th Intl Conf Knowledge Science, Engineering and Management (KSEM 2015). Chongqing, China, Oct 28-30, 2015, pp.78-89.
Christen V, Hartung M, Groß A.
Region Evolution eXplorer - A tool for discovering evolution trends in ontology regions.
J Biomed Semantics. 2015 Jun 1;6:26. doi: 10.1186/s13326-015-0020-6. eCollection 2015. PubMed PMID: 26034559; PubMed Central PMCID: PMC4450457. [PubMed]
Cormack J, Nath C, Milward D, Raja K, Jonnalagadda SR.
Agile Text Mining for the 2014 i2b2/UTHealth Cardiac Risk Factors Challenge.
J Biomed Inform. 2015 Jul 21. pii: S1532-0464(15)00141-0. doi: 10.1016/j.jbi.2015.06.030. [Epub ahead of print] PubMed PMID: 26209007. [PubMed]
Dos Reis JC, Pruski C, Da Silveira M, Reynaud-Delaître C.
DyKOSMap: A framework for mapping adaptation between biomedical knowledge organization systems.
J Biomed Inform. 2015 Apr 15. pii: S1532-0464(15)00068-4. doi:10.1016/j.jbi.2015.04.001. [Epub ahead of print] PubMed PMID: 25889690. [PubMed]
Halper M, Gu H, Perl Y, Ochs C.
Abstraction networks for terminologies: Supporting management of "big knowledge".
Artif Intell Med. 2015 May;64(1):1-16. doi: 10.1016/j.artmed.2015.03.005. Epub 2015 Apr 2. Review. PubMed PMID: 25890687. [PubMed]
Jin R, You J, Chung JW, Lee HJ, Wolters M, Park JC.
CoMAGD: Annotation of Gene-Depression Relations.
Proc 2015 Workshop on Biomedical Natural Language Processing (BioNLP 2015). Beijing, China, July 30, 2015, pp.104–113, Association for Computational Linguistics. [PDF
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Kalet AM.
Bayesian networks from ontological formalisms in radiation oncology.
Thesis (Ph.D.) University of Washington, 2015. [PDF
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Lambrix P, Wei-Kleiner F, Dragisic Z.
Completing the is-a structure in light-weight ontologies.
J Biomed Semantics. 2015 Mar 28;6:12. doi:10.1186/s13326-015-0002-8. eCollection 2015. PubMed PMID: 25883780; PubMed Central PMCID: PMC4399482. [PubMed]
Martins C, Jimenez-Ruiz E, Santos E, Pesquita C.
Towards visualizing the mapping incoherences in Bioportal.
Proc International Conference on Biomedical Ontology 2015 (ICBO 2015). Lisbon, Portugal, 27-30 July 2015. [PDF
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Matos S, Campos D, Pinho R, Silva R, Mort M, Cooper DN, Oliveira JL.
Assisted Mining and Curation of Genomic Variants using Egas.
Proc Fifth BioCreative Challenge Evaluation Workshop. Sept 9, 2015, Sevilla, Spain, pp.396-402. [PDF
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Möller MB.
Connecting GOMMA with STROMA: An Approach for Semantic Ontology Mapping in the Biomedical Domain.
Thesis (B.Sc.) Leipzig University, 2015. [PDF
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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
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Palma G, Vidal ME, Haag E, Raschid L, Thor A.
Determining similarity of scientific entities in annotation datasets.
Database (Oxford). 2015 Feb 27;2015. pii: bau123. doi: 10.1093/database/bau123. Print 2015. PubMed PMID: 25725057; PubMed Central PMCID: PMC4343076. [PubMed]
Panov P, Soldatova LN, Džeroski S.
Generic Ontology of Datatypes.
Information Sciences. 2015 Aug 9 (online, in press). doi: 10.1016/j.ins.2015.08.006.
Piñero J, Queralt-Rosinach N, Bravo À, Deu-Pons J, Bauer-Mehren A, Baron M, Sanz F, Furlong LI.
DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes.
Database (Oxford). 2015 Apr 15;2015:bav028. doi: 10.1093/database/bav028. Print 2015. PubMed PMID: 25877637; PubMed Central PMCID: PMC4397996. [PubMed]
Steigmiller A Glimm B.
Pay-As-You-Go Description Logic Reasoning by Coupling Tableau and Saturation Procedures
J of Artificial Intelligence Research. 2015 Dec 15; 54:535-592.[PDF
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Trivela D, Stoilos G, Chortaras A, Stamou G.
Optimising resolution-based rewriting algorithms for OWL ontologies.
Web Semantics: Science, Services and Agents on the World Wide Web. Online 26 Feb 2015. [Online
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Wang Z, Wang K, Topor R.
DL-Lite Ontology Revision Based on An Alternative Semantic Characterisation.
ACM Transactions on Computational Logic (TOCL). 2015 (Accepted). [PDF
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2014
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
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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
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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
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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
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Dos Reis JC.
Mapping Adaptation between Biomedical Knowledge Organization Systems.
Thesis (Ph.D.) Université de Paris-Sud, France, Oct 24, 2014. [PDF
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Dragisic Z, Eckert K, Euzenat J, Faria D, Ferrara A, Granada R, Ivanova V, Jiménez-Ruiz E, Kempf AO, Lambrix P, Montanelli S, Paulheim H, Ritze D, Shvaiko P, Solimando A, Trojahn C, Zamazal O, Cuenca Grau B.
Results of the Ontology Alignment Evaluation Initiative 2014.
Proc 10th International Workshop on Ontology Matching(OM-2014), co-located with the 12th International Semantic Web Conference (ISWC 2014), Riva del Garda, Italy, 2014. [PDF
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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
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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]
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.
Proc Phenotype Day at ISMB 2014. Boston, MA, USA, July 12, 2014. [PDF
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Gatens W, Konev B, Wolter F.
Lower and Upper Approximations for Depleting Modules of Description Logic Ontologies.
Proc 21st European Conference on Artificial Intelligence (ECAI 2014). Aug 18-22, 2014, Prague, Czech Republic. [PDF
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Gonçalves JRLS.
Impact Analysis in Description Logic Ontologies.
Thesis (Ph.D.) Faculty of Engineering and Physical Sciences, University of Manchester, 2014. [PDF
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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
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He Z, Geller J, Elhanan G.
Categorizing the Relationships between Structurally Congruent Concepts from Pairs of Terminologies for Semantic Harmonization.
Proc 2014 Summit on Translational Bioinformatics (TBI 2014). April 7-9, 2014, San Francisco, CA, pp.48-53.
Hudson CL, Topaloglu U, Bian J, Hogan W, Kieber-Emmons T.
Automated Tools for Clinical Research Data Quality Control using NCI Common Data Elements.
Proc 2014 Summit on Translational Bioinformatics (TBI 2014). April 7-9, 2014, San Francisco, CA, pp.60-69.
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
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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
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Jiang G, Sharma DK, Solbrig HR, Tao C, Weng C, Chute CG.
Building a Semantic Web-based Metadata Repository for Facilitating Detailed Clinical Modeling in Cancer Genome Studies.
Proc 7th International Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2014). Berlin, Germany, Dec 9-11, 2014. [PDF
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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
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Ludwig M.
Just: a Tool for Computing Justifications w.r.t. ELH Ontologies.
Proc 3rd International Workshop on OWL Reasoner Evaluation (ORE 2014). Vienna, Austria, July 13, 2014, pp.1-7. [PDF
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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
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Ludwig M, Peñaloza R.
Brave and Cautious Reasoning in EL.
Proc 27th International Workshop on Description Logics (DL 2014). Vienna, Austria, July 17-20, 2014, pp.274-286. [PDF
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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
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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]
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]
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
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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
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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]
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
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Raunich S, Rahm E.
Target-driven merging of taxonomies with ATOM.
Information Systems. 2014 June; 42(June):1-14. ISSN 0306-4379. [DOI] [URL
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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
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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
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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
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Silva MAA, Cavalcanti MC.
Combining Ontology Modules for Scientific Text Annotation.
Journal of Information and Data Management. 5(3):238-251, 2014. [PDF
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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]
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
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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
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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
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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.
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
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Zese R, Bellodi E, Lamma E, Riguzzi F, Aguiari F.
Semantics and Inference for Probabilistic Description Logics.
10th International Workshop on Uncertainty Reasoning for the Semantic Web (URSW 2014), collocated with the 13th International Semantic Web Conference (ISWC-2014). Oct 20, 2014, Trentino, Italy. [PDF
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2013
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
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] [Springer
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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
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Ba M, Diallo G.
Large-scale biomedical ontology matching with ServOMap.
IRBM, 2013. 34(1):56-59. Available online 13 February 2013. [DOI
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Beißwanger AE.
Developing Ontological Background Knowledge for Biomedicine.
Thesis (Doktors der Naturwissenschaften), University of Mannheim, Mannheim, 2013. [PDF
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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
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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
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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
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Freckleton RE.
Scaling Ontology Alignment.
Thesis (M.S.), University of Colorado Colorado Springs, Department of Computer Science, 2013. [PDF
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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]
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
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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
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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
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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
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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]
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
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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
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Karaiskos C.
Enhanced Ontological Searching of Medical Scientific Information.
Thesis (M.Sc.), University of Manchester, School of Computer Science, 2013. [PDF
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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
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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
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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
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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
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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
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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
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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
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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
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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]
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
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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
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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
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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
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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
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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
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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
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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
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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
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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]
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]
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
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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
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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
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
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Aguirre JL, Eckert K, Euzenat J, Ferrara A, van Hage WR, Hollink L, Meilicke C, Nikolov A, Ritze D, Scharffe F, Shvaiko P, Šváb-Zamazal O, Trojahn C, Jiménez-Ruiz E, Cuenca Grau B, Zapilko B.
Preliminary results of the Ontology Alignment Evaluation Initiative 2012.
Seventh International Workshop on Ontology Matching (ISWC 2012), 2012, Boston, Massachusetts, U.S.A. Nov 11, 2012. [PDF
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Beisswanger E, Hahn U.
Towards valid and reusable reference alignments – ten basic quality checks for ontology alignments and their application to three different reference data sets.
Journal of Biomedical Semantics 2012, 3(Suppl 1):S4. [PDF
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Benik J, Palma G, Raschid L, Thor A, Vidal ME.
Mining Patterns from Clinical Trial Annotated Datasets by Exploiting the NCI Thesaurus.
Proc. 11th Intl. Semantic Web Conference (ISWC 2012) 2012, Boston, Massachusetts, U.S.A. Nov 11-15, 2012. [PDF
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Bougie G.
A Case Study of a New Era in Disease Classification: An Investigation of the Socio-technical Requirements for Inclusive Standardization Development.
Thesis (M.Sc.) University of Victoria, Department of Computer Science, 2012. [UVic
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Chen ES, Melton GB, Burdick TE, Rosenau PT, Sarkar IN.
Characterizing the use and contents of free-text family history comments in the Electronic Health Record.
AMIA Annu Symp Proc. 2012;2012:85-92. Epub 2012 Nov 3. PubMed PMID: 23304276; PubMed Central PMCID: PMC3540518. [PubMed]
Chen Y, Gu H, Perl Y, Geller J.
Overcoming an obstacle in expanding a UMLS semantic type extent.
J Biomed Inform. 2012 Feb;45(1):61-70. Epub 2011 Sep 9. PubMed PMID: 21925287. [PubMed]
Chua WW, Kim JJ.
BOAT: Automatic alignment of biomedical ontologies using term informativeness and candidate selection.
J Biomed Inform. 2012 Apr;45(2):337-49. doi: 10.1016/j.jbi.2011.11.010. Epub 2011 Dec 2. PubMed PMID: 22155335. [PubMed]
Diallo G, Ba M.
Effective method for large scale ontology matching.
Proceedings of the 5th International Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2012), eds. Paschke A, Burger A, Romano P, Marshall MS, Splendiani A. Paris, France, November 28-30, 2012. [PDF
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Dos Reis JC, Pruski C, Da Silveira M, Reynaud-Delaître C.
Analyzing and Supporting the Mapping Maintenance Problem in Biomedical Knowledge Organization Systems.
Semantic Interoperability in Medical Informatics (SIMI 2012). Heraklion (Crete), Greece, May 27, 2012. [PDF
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Ferreira JD, Pesquita C, Couto FM, Silva MJ.
Bringing epidemiology into the Semantic Web.
Proc of the 3rd International Conference on Biomedical Ontology (ICBO 2012). 2012 July 21-25. Graz, Austria. [PDF
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Freimuth RR, Freund ET, Schick L, Sharma MK, Stafford GA, Suzek BE, Hernandez J, Hipp J, Kelley JM, Rokicki K, Pan S, Buckler A, Stokes TH, Fernandez A, Fore I, Buetow KH, Klemm JD.
Life sciences domain analysis model.
J Am Med Inform Assoc. 2012 Nov-Dec;19(6):1095-102. doi: 10.1136/amiajnl-2011-000763. Epub 2012 Jun 28. PubMed PMID: 22744959; PubMed Central PMCID: PMC3486731. [PubMed]
Fung KW, Bodenreider O.
Knowledge Representation and Ontologies.
In: Richesson RL, Andrews JE, editors. Clinical research informatics. New York: Springer; 2012. Chapter 14, pp.255-275. [Springer
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Giudicelli V, Lefranc MP.
IMGT-ONTOLOGY 2012.
Front Genet. 2012;3:79. Epub 2012 May 23. PubMed PMID: 22654892; PubMed Central PMCID: PMC3358611. [PubMed]
Gonçalves RS, Parsia B, Sattler U.
Concept-Based Semantic Difference in Expressive Description Logics.
Proceedings of the 25th International Workshop on Description Logics (DL 2012), Rome, Italy, June 7-10, 2012 (in CEUR Workshop Proceedings 846:191-201). [PDF
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Gonçalves RS, Parsia B, Sattler U.
Concept-Based Semantic Difference in Expressive Description Logics.
11th International Semantic Web Conference (ISWC 2012) Boston, Massachusetts, U.S.A. Nov 11-15, 2012 (LNCS 7649:99-115).
González-Beltrán A, Tagger B, Finkelstein A.
Federated ontology-based queries over cancer data.
BMC Bioinformatics 2012, 13(Suppl 1):S9. [BMC
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Grabar N, Hamon T, Bodenreider O.
Ontologies and terminologies: Continuum or dichotomy?
Applied Ontology. 2012; 7:375–386. IOS Press, DOI 10.3233/AO-2012-0119.[PDF]
Gross A, Hartung M, Kirsten T, Rahm E.
GOMMA Results for OAEI 2012.
Seventh International Workshop on Ontology Matching (ISWC 2012), 2012, Boston, Massachusetts, U.S.A. Nov 11, 2012. [PDF
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Gross A, Hartung M, Thor A, Rahm E.
How do computed ontology mappings evolve? - A case study for life science ontologies.
Proceedings of the 2nd Joint Workshop on Knowledge Evolution and Ontology Dynamics (EvoDyn 2012), in conjuction with 11th Intl. Semantic Web Conference (ISWC 2012) 2012, Boston, Massachusetts, U.S.A. Nov 12, 2012. [PDF
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Gross A, Hartung M, Thor A, Rahm E.
How do Ontology Mappings Change in the Life Sciences?
CoRR abs/1204.2731 April 2012. [PDF
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Hartung M, Gross A, Kirsten T, Rahm E.
Effective Composition of Mappings for Matching Biomedical Ontologies.
9th Extended Semantic Web Conference (ESWC 2012), Heraklion, Crete, Greece, May 27-31, 2012. To appear in ESWC 2012 Workshops, Revised Selected Papers (LNCS) 2012-09. [Leipzig
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Hartung M, Gross A, Kirsten T, Rahm E.
Effective Mapping Composition for Biomedical Ontologies.
Semantic Interoperability in Medical Informatics (SIMI 2012). Heraklion ,Crete, Greece, May 27, 2012. [PDF
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Ivanova V, Lambrix P.
A System for Debugging Taxonomies and their Alignments.
First International Workshop on Debugging Ontologies and Ontology Mappings, Galway, Ireland, Oct 8 2012. [PDF
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Jiang G, Solbrig HR, Chute CG.
Quality evaluation of value sets from cancer study common data elements using the UMLS semantic groups.
J Am Med Inform Assoc. 2012 Jun 1;19(e1):e129-e136. Epub 2012 Apr 17. PubMed PMID: 22511016; PubMed Central PMCID: PMC3392855. [PubMed]
Jimenez-Ruiz E, Cuenca Grau B, Horrocks I.
Exploiting the UMLS Metathesaurus in the Ontology Alignment Evaluation Initiative.
Proceedings of the 2nd International Workshop on Exploiting Large Knowledge Repositories (E-LKR'12) Castellón de la Plana, Spain, September 7, 2012. [PDF
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Konev B, Ludwig M, Walther D, Wolter F.
The Logical Diff for the Lightweight Description Logic EL.
Journal of Artificial Intelligence Research, 2012 (Submitted). [PDF
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Konev B, Ludwig M, Wolter F.
Logical Difference Computation with CEX2.5.
Proceedings of the 6th International Joint Conference on Automated Reasoning (IJCAR 2012). Springer-Verlag, 2012. [PDF
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Lacson R, Andriole KP, Prevedello LM, Khorasani R.
Information from Searching Content with an Ontology-Utilizing Toolkit (iSCOUT).
J Digit Imaging. 2012 Aug;25(4):512-9. PubMed PMID: 22349993; PubMed Central PMCID: PMC3389089. [PubMed] [Online
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Lambrix P, Ivanova V, Dragisic Z.
Contributions of LiU/ADIT to Debugging Ontologies and Ontology Mappings.
In Lambrix P, ed. Advances in Secure and Networked Information Systems – The ADIT Perspective, Dec. 2012, pp.109-120. [PDF
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Machado CM, Freitas AT, Couto FM.
Enrichment analysis applied to disease prognosis.
Proceedings of the 4th Workshop of the GI Workgroup Ontologies in Biomedicine and Life Sciences (OBML 2012) eds. Boeker M, Herre H, Hoehndorf R, Loebe F. Dresden, Germany, Sept 27-28, 2012. [PDF
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Massot M, Cuggia M, Duvauferrier R, Bertaud-Gounot V.
Représentation formelle des critères d’éligibilité aux essais cliniques: Exigences sémantiques de représentation des relations.
In: Staccini P, Harmel A, Darmoni SJ, Gouider R, eds. Systèmes d’information pour l’amélioration de la qualité en santé. 2012:37-46. [Springer
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Mathur S.
Ontology-Based Methods for Disease Similarity Estimation and Drug Repositioning.
Thesis (Ph.D.) University of Missouri Kansas City, Computer Science and Mathematics, 2012. [PDF
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McCusker J, Lee J, Thomas C, McGuinness DL.
Public Health Surveillance Using Global Health Explorer.
Joint Workshop on Semantic Technologies Applied to Biomedical Informatics and Individualized Medicine (SATBI+SWIM 2012) in conjunction with International Semantic Web Conference (ISWC 2012). Boston, Massachusetts, U.S.A. Nov 11-15, 2012. [PDF
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Meilicke C, Svab-Zamazal O, Trojahn C, Jimenez-Ruiz E, Aguirre JL, Stuckenschmidt H, Cuenca Grau B.
Evaluating Ontology Matching Systems on Large, Multilingual and Real-world Test Cases.
Technical Report of the OAEI 2011.5 Evaluation Campaign ArXiv e-prints, vol. 1208.3148, August, 2012. [PDF
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Min H, Wojtusiak J.
Clinical data analysis using ontology-guided rule learning.
Proceedings of the 2nd international workshop on Managing interoperability and compleXity in health systems (MIXHS '12) pp.17-22 (at 21st ACM International Conference on Information and Knowledge Management (CIKM'12) Maui, HI, USA Oct 29 - Nov 2, 2012. [ACM
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Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team.
The National Center for Biomedical Ontology.
J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. doi: 10.1136/amiajnl-2011-000523. Epub 2011 Nov 10. PubMed PMID: 22081220; PubMed Central PMCID: PMC3277625. [PubMed]
Pathak J, Kiefer RC, Bielinski SJ, Chute CG.
Applying semantic web technologies for phenome-wide scan using an electronic health record linked Biobank.
J Biomed Semantics. 2012 Dec 17;3(1):10. doi: 10.1186/2041-1480-3-10. PubMed PMID: 23244446; PubMed Central PMCID: PMC3554594. [PubMed]
Pathak J, Kiefer RC, Chute CG.
Using Semantic Web Technologies for Cohort Identification from Electronic Health Records for Clinical Research.
AMIA Clinical Research Informatics Summit 2012 Mar. [PDF
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Pesquita CLSC.
Automated Extension of Biomedical Ontologies.
Thesis (Ph.D.) Universidade de Lisboa, Faculdade de Ciências, Departamento de Informática 2012. [U.Lisbon
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Queralt-Rosinach N, Furlong LI.
DisGeNET: from MySQL to Nanopublication, Modelling Gene-Disease Associations for the Semantic Web.
Proceedings of the 5th International Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2012), eds. Paschke A, Burger A, Romano P, Marshall MS, Splendiani A. Paris, France, November 28-30, 2012. [PDF
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Saitwal H, Qing D, Jones S, Bernstam E, Chute CG, Johnson TR.
Cross-Terminology Mapping Challenges: A Demonstration Using Medication Terminological Systems.
J Biomed Inform. 2012 Aug;45(4):613-25. Epub 2012 Jun 28. PubMed PMID: 22750536. [PubMed]
Silwal P.
Ontology Alignment Using Semantic Similarity with Refernce Ontologies.
Thesis (M.Sc.) Miami University, Department of Computer Science and Software Engineering, Oxford, Ohio, 2012. [PDF
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Szwabe A, Misiorek P, Walkowiak P.
Reflective Relational Learning for Ontology Alignment.
Distributed Computing and Artificial Intelligence, Omatu S, et al., eds. Springer-Verlag; 2012. pp. 519-526. [Springer
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Tagaris A, Chondrogiannis E, Andronikou V, Tsatsaronis G, Mourtzoukos K, Roumier J, Matskanis N, Schroeder M, Massonet P, Koutsouris D, Varvarigou T.
Semantic Interoperability between Clinical Research and Healthcare: the PONTE approach.
Semantic Interoperability in Medical Informatics (SIMI 2012). Heraklion (Crete), Greece, May 27, 2012. [Abstract
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Vergara-Niedermayr C, Wang F, Pan T, Kurc T, Saltz J.
Semantically Interoperable XML Data.
Emory University Center for Comprehensive Informatics Technical Report CCI-TR-2012-1, January 12, 2012. [Emory
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Walk S.
Pragmatic analysis of collaborative ontology engineering processes.
Thesis (M.Sc.) Graz University of Technology, Knowledge Management Institute, Austria, April 19, 2012. [PDF
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Wu ST, Liu H, Li D, Tao C, Musen MA, Chute CG, Shah NH.
Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis.
J Am Med Inform Assoc. 2012 Jun;19(1e):e149-56. Epub 2012 Apr 4. PubMed PMID: 22493050; PubMed Central PMCID: PMC3392861. [PubMed]
Zheng S, Wang F, Lu J, Saltz J.
Enabling Ontology Based Semantic Queries in Biomedical Database Systems.
Emory University Center for Comprehensive Informatics Technical Report CCI-TR-2012-3, March 20, 2012. [Emory
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2011
Bail S, Horridge M, Parsia B, Sattler U.
The justificatory structure of the NCBO bioportal ontologies.
The Semantic Web–ISWC 2011. Springer 2011 pp.67-82. [PDF
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Bail S, Parsia B, Sattler U.
Extracting finite sets of entailments from OWL ontologies.
Proc. of DL-11. 2011. [PDF
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Brochhausen M, Spear AD, Cocos C, Weiler G, Martín L, Anguita A, Stenzhorn H, Daskalaki E, Schera F, Schwarz U, Sfakianakis S, Kiefer S, Dörr M, Graf N, Tsiknakis M.
The ACGT Master Ontology and its applications--towards an ontology-driven cancer research and management system.
J Biomed Inform. 2011 Feb;44(1):8-25. Epub 2010 May 11. Review. PubMed PMID: 20438862. [PubMed]
Dentler K, Cornet R, ten Teije A, de Keizer N.
Comparison of reasoners for large ontologies in the OWL 2 EL profile.
Semantic Web Journal, 2(2):71-87,2011. [Online
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Falconer SM, Tudorache T, Noy NF.
An Analysis of Collaborative Patterns in Large-Scale Ontology Development Projects.
Proceedings of the sixth international conference on Knowledge capture (K-CAP '11). 2011 ACM, New York, NY, USA. [ACM
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Gennari JH, Neal ML, Galdzicki M, Cook DL.
Multiple ontologies in action: composite annotations for biosimulation models.
J Biomed Inform. 2011 Feb;44(1):146-54. Epub 2010 Jun 30. PubMed PMID: 20601121; PubMed Central PMCID: PMC2989341. [PubMed]
Ghazvinian A, Noy NF, Musen MA.
From mappings to modules: Using mappings to identify domain-specific modules in large ontologies.
KCAP 2011 - Proceedings of the 2011 Knowledge Capture Conference, 2011, pp. 33-40. [Scopus
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Gonçalves RS, Parsia B, Sattler U.
Categorising logical differences between OWL ontologies.
20th ACM Conference on Information and Knowledge Management (CIKM'11) (2011) Glasgow, 2011 Oct. 24-28, pp.1541-1546. [At IEEE Xplore
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Gradie PR, Litster M, Thomas R, Vyas J, Schiller MR.
SciReader enables reading of medical content with instantaneous definitions.
BMC Med Inform Decis Mak. 2011 Jan 25;11:4. PubMed PMID: 21266060; PubMed Central PMCID: PMC3038137. [PubMed]
Gross A, Hartung M, Kirsten T, Rahm E.
Mapping Composition for Matching Large Life Science Ontologies.
Proc of the 2nd International Conference on Biomedical Ontology (ICBO) 2011. [PDF
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Groza T, Zankl A, Li YF, Hunter J.
Using Semantic Web Technologies to Build a Community-Driven Knowledge Curation Platform for the Skeletal Dysplasia Domain.
Proceedings of the 10th International Semantic Web Conference (ISWC 2011), Springer, Bonn, Germany, October 23-27, 2011. [PDF
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Jiang G, Solbrig HR, Chute CG.
Quality evaluation of cancer study Common Data Elements using the UMLS Semantic Network.
J Biomed Inform. 2011 Dec;44 Suppl 1:S78-85. Epub 2011 Aug 5. PubMed PMID: 21840422. [PubMed]
Jiménez-Ruiz E, Grau BC, Horrocks I, Berlanga R.
Logic-based assessment of the compatibility of UMLS ontology sources.
J Biomed Semantics. 2011 Mar 7;2 Suppl 1:S2. PubMed PMID: 21388571; PubMed Central PMCID: PMC3105494. [PubMed]
Jonquet C, LePendu P, Falconer S, Coulet A, Noy NF, Musen MA, Shah NH
NCBO Resource Index: Ontology-based search and mining of biomedical resources
Web Semantics: Science, Services and Agents on the World Wide Web, Volume 9, Issue 3, September 2011, Pages 316-324, ISSN 1570-8268, 10.1016/j.websem.2011.06.005. [PDF
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Khoo CSG, Na JC, Wang VW, Chan S.
Developing an Ontology for Encoding Disease Treatment Information in Medical Abstracts.
DESIDOC Journal of Library and Information Technology, 2011 Mar;31(2):103-115. [DESIDOC
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Kirsten T, Gross A, Hartung M, Rahm E.
GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution.
J Biomed Semantics. 2011 Sep 13;2:6. PubMed PMID: 21914205; PubMed Central PMCID: PMC3198872. [PubMed] [Free PMC]
Lee S, Choi J, Park K, Song M, Lee D.
Inferring hidden relationships from biological literature with multi-level context terms.
Proceedings of the ACM fifth international workshop on Data and text mining in biomedical informatics (DTMBIO '11). 2011: ACM New York, NY, USA. [ACM
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Lim Choi Keung SN, Zhao L, Ogunsina I, Arvanitis TN, Tyler E.
A Framework for Vocabulary Controlled Queries of Distributed Electronic Healthcare Records.
Proc 3rd International Workshop on Knowledge Representation for Health Care (KR4HC 2011) in conjunction with the 13th Conference on Artificial Intelligence in Medicine (AIME 2011), pp. 196-209, 2011. [PDF
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Liu K, Chapman WW, Savova G, Chute CG, Sioutos N, Crowley RS.
Effectiveness of Lexico-syntactic Pattern Matching for Ontology Enrichment with Clinical Documents.
Methods Inf Med. 2011;50(5):397-407. Epub 2010 Nov 8. [PubMed]
Luciano JS, Andersson B, Batchelor C, Bodenreider O, Clark T, Denney CK, Domarew C, Gambet T, Harland L, Jentzsch A, Kashyap V, Kos P, Kozlovsky J, Lebo T, Marshall SM, McCusker JP, McGuinness DL, Ogbuji C, Pichler E, Powers RL, Prud'hommeaux E, Samwald M, Schriml L, Tonellato PJ, Whetzel PL, Zhao J, Stephens S, Dumontier M.
The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside.
J Biomed Semantics. 2011 May 17;2 Suppl 2:S1. PubMed PMID: 21624155; PubMed Central PMCID: PMC3102889. [PubMed] [Free PMC Article]
Maier D, Kalus W, Wolff M, Kalko SG, Roca J, Marin de Mas I, Turan N, Cascante M, Falciani F, Hernandez M, Villà-Freixa J, Losko S.
Knowledge management for systems biology a general and visually driven framework applied to translational medicine.
BMC Syst Biol. 2011 Mar 5;5:38. PubMed PMID: 21375767; PubMed Central PMCID: PMC3060864. [PubMed]
Martin M.
Semantic Web may be cancer information's next step forward.
J Natl Cancer Inst. 2011 Aug 17;103(16):1215-8. Epub 2011 Aug 3. PubMed PMID: 21813408. [PubMed
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McCusker JP, Luciano JS, McGuinness DL.
Towards an Ontology for Conceptual Modeling.
Proc. of the International Conference on Biomedical Ontology, 2011. [Online
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Payne PR, Borlawsky TB, Lele O, James S, Greaves AW.
The TOKEn project: knowledge synthesis for in silico science.
J Am Med Inform Assoc. 2011 Dec;18 Suppl 1:i125-31. doi: 10.1136/amiajnl-2011-000434. Epub 2011 Oct 7. PubMed PMID: 21984589; PubMed Central PMCID: PMC3241179. [PubMed]
Shamdasani J, Bloodsworth P, Hauer T, Branson A, Rogulin D, Odeh M, McClatchey R.
MedMatch: Applying Semantic Matching in the Medical Domain.
Journal of Web Semantics 2011 (Submitted). [PDF
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Shaw M, Detwiler LT, Noy N, Brinkley J, Suciu D.
vSPARQL: a view definition language for the semantic web.
J Biomed Inform. 2011 Feb;44(1):102-17. Epub 2010 Aug 25. PubMed PMID: 20800106; PubMed Central PMCID: PMC3042057. [PubMed]
Tudorache T, Musen MA.
Collaborative Development of Large-Scale Biomedical Ontologies.
Collaborative Computational Technologies for Biomedical Research (eds S. Ekins, M. A. Z. Hupcey and A. J. Williams), John Wiley & Sons, Inc., Hoboken, NJ, USA; 2011. pp. 179-200. doi: 10.1002/9781118026038.ch12

2010
Amin W, Kang HP, Becich MJ.
Data Management, Databases, and Warehousing.
Biomedical Informatics for Cancer Research. (M.F. Ochs, J.T. Casagrande, R.V. Davuluri, eds). DOI 10.1007/978-1-4419-5714-6_3, © Springer Science+Business Media, LLC 2010. pp.39-71.
Chua WWK, Goh AES.
An asymmetric similarity measure for ontologies based on the feature contrast model.
Proceedings of the 2010 International Conference on Complex, Intelligent and Software Intensive Systems (CISIS '10), Krakow, Poland, 16 February 2010. IEEE Computer Society Washington, DC, USA ©2010. pp.1002–1007.
Duan W, Yates A.
Extracting glosses to disambiguate word senses.
Human Language Technologies: The 2010 Annual Conference of the North American Chapter of the Association for Computational Linguistics. Association for Computational Linguistics, Stroudsburg, PA, 2010 pp.627-635. [PDF
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González-Beltrán A, Tagger B, Finkelstein A.
Ontology-based Queries over Cancer Data.
Proceedings of the 3rd International Workshop on Semantic Web Applications and Tools for the Life Sciences, eds. Paschke A, Burger A, Splendiani A, Marshall MS, Romano P. Berlin, Germany, Dec 8-10, 2010. [PDF
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Hartung M, Gross A, Kirsten T, Rahm E.
Discovering evolving regions in life science ontologies.
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 6254 LNBI, 2010, pp. 19-34. [Scopus
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Jonquet C, Musen MA, Shah NH.
Building a biomedical ontology recommender web service.
J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S1. PubMed PMID: 20626921; PubMed Central PMCID: PMC2903720. [PubMed] [PDF
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Kang YB, Li YF, Krishnaswamy S.
Predicting Reasoning Performance Using Ontology Metrics.
The Journal of Systems and Software, 83 (2010):803–814. [PDF
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Martinez-Romero M, Vazquez-Naya J, Munteanu CR, Pereira J, Pazos A.
An approach for the automatic recommendation of ontologies using collaborative knowledge.
Proceedings of the 14th international conference on Knowledge-based and intelligent information and engineering systems: Part II (KES\'10), Rossitza Setchi, Ivan Jordanov, Robert J. Howlett, and Lakhmi C. Jain (Eds.). Springer-Verlag, Berlin, Heidelberg, 74-81.
Obeid J, Gabriel D, Sanderson I.
A biomedical research permissions ontology: cognitive and knowledge representation considerations.
Proceedings of the 2010 Workshop on Governance of Technology, Information and Policies (GTIP '10). ACM, New York, NY, USA, 9-13. DOI=10.1145/1920320.1920322 doi.acm,org
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Parai GK, Jonquet C, Xu R, Musen MA, Shah NH.
The Lexicon Builder Web service: Building Custom Lexicons from two hundred Biomedical Ontologies.
AMIA Annu Symp Proc. 2010 Nov 13;2010:587-91. PubMed PMID: 21347046; PubMed Central PMCID: PMC3041331. [PubMed] [PDF]
Payne PR, Borlawsky TB, Stephens W, Barrett MC, Nguyen-Pham T, Greaves AW.
The TRITON Project: Design and Implementation of an Integrative Translational Research Information Management Platform.
AMIA Annu Symp Proc. 2010 Nov 13;2010:617-21. PubMed PMID: 21347052; PubMed Central PMCID: PMC3041280. [PubMed] [Full Text]
Schulz S, Schober D, Tudose I, Stenzhorn H.
The Pitfalls of Thesaurus Ontologization - the Case of the NCI Thesaurus.
AMIA Annu Symp Proc. 2010 Nov 13;2010:727-31. PubMed PMID: 21347074; PubMed Central PMCID: PMC3041372. [PubMed]
Sun P, Zhang S.
Identifying Granularity Differences between Large Biomedical Ontologies through Rules.
AMIA Annu Symp Proc. 2010 Nov 13;2010:927-31. PubMed PMID: 21347114; PubMed Central PMCID: PMC3041335. [PubMed] [Full Text]
Zhang H, Li YF, Tan HBK.
Measuring Design Complexity of Semantic Web Ontologies.
Journal of Systems and Software, 83(5):803-814, 2010. [PDF
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2009
Borlawsky TB, Dhaval R, Hastings SL, Payne PR.
Development of an agile knowledge engineering framework in support of multi-disciplinary translational research.
Summit on Translat Bioinforma. 2009 Mar 1;2009:14-8. PubMed PMID: 21347164; PubMed Central PMCID: PMC3041563. [PubMed]
Ghazvinian A, Noy NF, Musen MA.
Creating mappings for ontologies in biomedicine: simple methods work.
AMIA Annu Symp Proc. 2009 Nov 14;2009:198-202. PubMed PMID: 20351849; PubMed Central PMCID: PMC2815474. [PubMed]
Jonquet C, Shah NH, Musen MA.
Prototyping a Biomedical Ontology Recommender Service.
Bio-Ontologies: Knowledge in Biology, Stockholm, Sweden (2009).
Jonquet C, Shah NH, Musen MA.
The open biomedical annotator.
Summit on Translat Bioinforma. 2009 Mar 1;2009:56-60. PubMed PMID: 21347171; PubMed Central PMCID: PMC3041576. [PubMed] [Full Text]
Kementsietsidis A, Lim L, Wang M.
Profile-based retrieval of records in medical databases.
AMIA Annu Symp Proc. 2009 Nov 14;2009:312-6. PubMed PMID: 20351871; PubMed Central PMCID: PMC2815445. [PubMed]
McCusker JP, Phillips JA, González Beltrán A, Finkelstein A, Krauthammer M.
Semantic web data warehousing for caGrid.
BMC Bioinformatics. 2009 Oct 1;10 Suppl 10:S2. PubMed PMID: 19796399; PubMed Central PMCID: PMC2755823. [PubMed]
Motik B, Shearer R, Horrocks I.
Hypertableau Reasoning for Description Logics.
Journal of Artificial Intelligence Research, 2009 Oct;36:165-228. [PDF
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Shah NH, Bhatia N, Jonquet C, Rubin D, Chiang AP, Musen MA.
Comparison of concept recognizers for building the Open Biomedical Annotator.
BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14. PubMed PMID: 19761568; PubMed Central PMCID: PMC2745685. [PubMed] [Full Text
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2008
Allemang D, Hendler J.
Semantic Web for the Working Ontologist: Effective Modeling in RDFS and OWL.
Elsevier, 2008.
Bodenreider O.
Biomedical ontologies in action: role in knowledge management, data integration and decision support.
Yearbook of Medical Informatics (2008) pp.67-79.
Bodenreider O.
Comparing SNOMED CT and the NCI Thesaurus through Semantic Web technologies.
Proceedings of the Third International Conference on Knowledge Representation in Medicine (KR-MED 2008), 2008: p. 37-43. [PDF
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Cohen B, Oren M, Min H, Perl Y, Halper M.
Automated comparative auditing of NCIT genomic roles using NCBI.
J Biomed Inform. 2008 Dec;41(6):904-13. Epub 2008 Mar 28. PubMed PMID: 18486558; PubMed Central PMCID: PMC2630966. [PubMed]
Detwiler LT, Suciu D, Brinkley JF.
Regular paths in SparQL: querying the NCI Thesaurus.
AMIA Annu Symp Proc. 2008 Nov 6:161-5. PubMed PMID: 18999137; PubMed Central PMCID: PMC2656016. [PubMed]
Jiménez-Ruiz E, Grau BC, Sattler U, Schneider T, Berlanga R.
Safe and Economic Re-Use of Ontologies: A Logic-Based Methodology and Tool Support.
Proceedings of the 5th European semantic web conference on the semantic web: research and applications. Berlin, Heidelberg; 2008. LNCS v.5021 p. 185–99. [Springer
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Kementsietsidis A, Lim L, Wang M.
Supporting ontology-based keyword search over medical databases.
AMIA Annu Symp Proc. 2008 Nov 6:409-13. PubMed PMID: 18998839; PubMed Central PMCID: PMC2656038. [PubMed]
Malone J, Rayner TF, Bradley XZ, Parkinson H.
Developing an application focused experimental factor ontology: embracing the OBO Community.
Bio-Ontologies SIG, ISMB 2008 Toronto Canada, 20 July 2008. [PDF
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Min H, Cohen B, Halper M, Oren M, Perl Y.
Detecting role errors in the gene hierarchy of the NCI Thesaurus.
Cancer Inform. 2008;6:293-313. PubMed PMID: 19221606; PubMed Central PMCID: PMC2623310. [PubMed]
Mougin F, Bodenreider O.
Auditing the NCI thesaurus with semantic web technologies.
AMIA Annu Symp Proc. 2008 Nov 6:500-4. PubMed PMID: 18999265; PubMed Central PMCID: PMC2655981. [PubMed]
Noy N, Tudorache T, de Coronado S, Musen M.
Developing biomedical ontologies collaboratively.
AMIA Annu Symp Proc. 2008:520-4. [PubMed] [Available online]
Payne PR, Borlawsky TB, Kwok A, Dhaval R, Greaves AW.
Ontology-anchored Approaches to Conceptual Knowledge Discovery in a Multi-dimensional Research Data Repository.
Summit on Translat Bioinforma. 2008 Mar 1;2008:85-9. PubMed PMID: 21347129; PubMed Central PMCID: PMC3041525. [PubMed]
Redmond T, Smith M, Drummond N, Tudorache T.
Managing Change: An Ontology Version Control System.
OWL: Experiences and Directions, Procs of Fifth OWLED Workshop (2008), Karlsruhe, Germany, Oct 26-27, 2008. CEUR-WS.org (2008) [PDF
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Rubin DL, Shah NH, Noy NF.
Biomedical ontologies: a functional perspective.
Brief Bioinform. 2008 Jan;9(1):75-90. Epub 2007 Dec 12. Review. PubMed PMID: 18077472. [PubMed]
Sebastian A, Noy NF, Tudorache T, Musen MA.
A generic ontology for collaborative ontology-development workflows.
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 5268 LNAI, 2008, pp. 318-328. [Scopus
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Shah NH, Musen MA.
UMLS-Query: a perl module for querying the UMLS.
AMIA Annu Symp Proc. 2008 Nov 6:652-6. PubMed PMID: 18998805; PubMed Central PMCID: PMC2656020. [PubMed] [Full Text]

2007
Dmitrieva J, Bei Y, Verbeek FJ.
Ontological context visualization.
OWLED 2007 Workshop on OWL. eds Golbreich C, Kalyanpur A, Parsia B. CEUR-WS.org (2007). [PDF
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Zhang S, Bodenreider O.
Experience in Aligning Anatomical Ontologies.
Int J Semant Web Inf Syst. 2007;3(2):1-26. PubMed PMID: 18974854; PubMed Central PMCID: PMC2575410. [PubMed]

2006
Bernhard D.
Automatic acquisition of semantic relationships from morphological relatedness.
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 4139 LNAI, 2006, pp. 121-132. [Scopus
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Cimino JJ, Zhu X.
The practical impact of ontologies on biomedical informatics.
Yearb Med Inform. 2006:124-35. Review. PubMed PMID: 17051306. [PubMed]
Cuenca Grau B, Parsia B, Sirin E, Kalyanpur A.
Modularity and web ontologies.
Proc. of KR-06, 2006. [PDF
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Min H, Perl Y, Chen Y, Halper M, Geller J, Wang Y.
Auditing as part of the terminology design life cycle.
J Am Med Inform Assoc. 2006 Nov-Dec;13(6):676-90. Epub 2006 Aug 23. PubMed PMID: 16929044; PubMed Central PMCID: PMC1656963. [PubMed]
Nadkarni PM, Brandt CA.
The Common Data Elements for cancer research: remarks on functions and structure.
Methods Inf Med. 2006;45(6):594-601. PubMed PMID: 17149500; PubMed Central PMCID: PMC2980785. [PubMed]
Noy NF, Chugh A, Liu W, Musen MA.
A Framework for Ontology Evolution in Collaborative Environments.
The Semantic Web - ISWC 2006. Lecture Notes in Computer Science 4273 pp.544-558, DOI: 10.1007/11926078_39 [Springer
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Plikus MV, Zhang Z, Chuong CM.
PubFocus: semantic MEDLINE/PubMed citations analytics through integration of controlled biomedical dictionaries and ranking algorithm.
BMC Bioinformatics. 2006 Oct 2;7:424. PubMed PMID: 17014720; PubMed Central PMCID: PMC1618408. [PubMed] [Full Text]

2005
Crowley RS, Tseytlin E, Jukic D.
ReportTutor - an intelligent tutoring system that uses a natural language interface.
AMIA Annu Symp Proc. 2005:171-5. PubMed PMID: 16779024; PubMed Central PMCID: PMC1560511. [PubMed]
Ceusters W, Smith B, Goldberg L.
A terminological and ontological analysis of the NCI Thesaurus.
Methods Inf Med. 2005;44(4):498-507. PubMed PMID: 16342916. [PubMed]
Kumar A, Smith B.
Oncology ontology in the NCI thesaurus.
10th Conference on Artificial Intelligence in Medicine, AIME Aberdeen July 23-27 2005. In: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) LNAI:3581:213-220. [Scopus
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Lintern R, Storey M.
Jambalaya Express: Ontology Visualization-On-Demand. In
8th Protege Conference, Madrid, Spain, July 18-21, 2005. [PDF
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Supekar K, Chute CG, Solbrig H.
Representing lexical components of medical terminologies in OWL.
AMIA Annu Symp Proc. 2005:719-23. PubMed PMID: 16779134; PubMed Central PMCID: PMC1560674. [PubMed]

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