| National Library of Medicine

Lu C, Payne A, Demner-Fushman D. Classification Types: A New Feature in the SPECIALIST Lexicon MIA 2019 Annual Symposium, Washington, DC, November 16-20, 2019.

Abstract

Lu C, Aronson AR, Shooshan SE, Demner-Fushman D. Spell checker for consumer language (CSpell) Journal of the American Medical Informatics Association, Volume 26, Issue 3, 1 March 2019, Pages 211-218, https://doi.org/10.1093/jamia/ocy171 21 January 2019 (Editor's Choice)

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Rosemblat G, Fiszman, M, Shin D, Kilicoglu H. Towards a characterization of apparent contradictions in the biomedical literature using context analysis. Journal of Biomedical Informatics. 2019. In Press. https://doi.org/10.1016/j.jbi.2019.103275.

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Divita G, Rosemblat G, Browne AC. Building a medical Spanish lexicon. AMIA Annu Symp Proc. 2007 Oct 11:941.

Abstract | PMID: 18694041

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Kilicoglu H, Peng Z, Tafreshi S, Tran T, Rosemblat G, Schneider J. Confirm or Refute?: A Comparative Study on Citation Sentiment Classification in Clinical Research Publications. J Biomed Inform. 2019 Feb 9:103123. doi: 10.1016/j.jbi.2019.103123.

Abstract | PMID: 30753947

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Rodriguez L, Demner-Fushman D. Finding Understudied Disorders Potentially Associated with Maternal Morbidity and Mortality. AJP Rep. 2019 Jan;9(1):e36-e43. doi: 10.1055/s-0039-1683363. Epub 2019 Mar 4.

Abstract | pub9896.pdf | PMID: 30838163

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Lu C, Aronson, AR, Shooshan SE, Demner-Fushman D. Spell checker for consumer language (CSpell). J Am Med Inform Assoc. 2019 Jan 21. doi: 10.1093/jamia/ocy171. [Epub ahead of print]

Abstract | PMID: 30668712

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Scarton LA, Wang L, Kilicoglu H, Jahries M, Del Fiol M. Expanding vocabularies for complementary and alternative medicine therapies. Int J Med Inform. 2019 Jan;121:64-74. doi: 10.1016/j.ijmedinf.2018.11.009. Epub 2018 Nov 22.

Abstract | PMID: 30545491

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Rindflesch TC, Blake CL, Cairelli MJ, Fiszman M, Zeiss CJ, Kilicoglu H. Investigating the role of interleukin-1 beta and glutamate in inflammatory bowel disease and epilepsy using discovery browsing. J Biomed Semantics. 2018 Dec 27;9(1):25. doi: 10.1186/s13326-018-0192-y.

Abstract | PMID: 30587224 | PMCID: PMC6307110

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Thoma, GR. Where we’ve been.. And where we’re going. Talk given by George Thoma at his retirement.

Abstract | pub9882.pdf

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Lu C, Demner-Fushman D. Improving Spelling Correction with Consumer Health Terminology Improving Spelling Correction with Consumer Health Terminology AMIA 2018 Annual Symposium, San Francisco, CA, November 3-7, 2018, p. 2053.

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Lu C, Demner-Fushman D. Improving Spelling Correction with Consumer Health Terminology . AMIA 2018 Annual Symposium, San Francisco, CA, November 3-7, 2018, p. 2053.

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Bodenreider O, Cornet R, Vreeman DJ. Recent Developments in Clinical Terminologies - SNOMED CT, LOINC, and RxNorm. Yearb Med Inform. 2018 Aug;27(1):129-139. doi: 10.1055/s-0038-1667077. Epub 2018 Aug 29.

Abstract | PMID: 30157516

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Kilicoglu H, Rosemblat G, Malicki M, Ter Riet G. Automatic recognition of self-acknowledged limitations in clinical research literature. J Am Med Inform Assoc. 2018 Jul 1;25(7):855-861. doi: 10.1093/jamia/ocy038.

Abstract | PMID: 29718377 | PMCID: PMC6016608

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Kayaalp M. Modes of De-identification. AMIA Annu Symp Proc. 2018 Apr 16;2017:1044-1050. eCollection 2017.

Abstract | pub9526.pdf | PMID: 29854172 | PMCID: PMC5977668

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Rodriguez L, Morrison SM, Greenberg K, Demner-Fushman D. Mining the literature for genes associated with placenta-mediated maternal diseases. AMIA Annu Symp Proc. 2018 Apr 16;2017:1498-1506. eCollection 2017.

Abstract | pub9572.pdf | PMID: 29854219 | PMCID: PMC5977710

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Janakiram C, Chalmers NI, Fontelo P, Huser V, Lopez Mitnik G, Iafolla TJ, Brow AR, Dye BA. Sex and race or ethnicity disparities in opioid prescriptions for dental diagnoses among patients receiving Medicaid. J Am Dent Assoc. 2018 Apr;149(4):246-255. doi: 10.1016/j.adaj.2018.02.010

Abstract | PMID: 29599018

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Cui L, Bodenreider O, Shi J, Zhang GQ. Auditing SNOMED CT hierarchical relations based on lexical features of concepts in non-lattice subgraphs. Biomed Inform. 2018 Feb;78:177-184. doi: 10.1016/j.jbi.2017.12.010. Epub 2017 Dec 20.

Abstract | PMID: 29274386 | PMCID: PMC5835197

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Kayaalp M. Patient Privacy in the Era of Big Data. Balkan Med J. 2018 Jan 20;35(1):8-17. doi: 10.4274/balkanmedj.2017.0966. Epub 2017 Sep 13.

Abstract | PMID: 28903886 | PMCID: PMC5820452

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Huser V, Kahn MG, Brown JS, Gouripeddi R. Methods for examining data quality in healthcare integrated data repositories. Pac Symp Biocomput. 2018;23:628-633.

Abstract | PMID: 29218922

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Harpaz R, DuMouchel W, Schuemie M, Bodenreider O, Friedman C, Horvitz E, Ripple A, Sorbello A, White RW, Winnenburg R, Shah NH. Toward multimodal signal detection of adverse drug reactions. J Biomed Inform. 2017 Dec;76:41-49. doi: 10.1016/j.jbi.2017.10.013. Epub 2017 Nov 1.

Abstract | PMID: 29081385

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Lu C, Tormey D, McCreedy L, Browne AC. Enhancing LexSynonym Features in the Lexical Tools AMIA 2017 Annual Symposium, Washington, DC, November 04-08, 2017, p. 2090

Abstract | pub9775.pdf

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Baik SH, Kury F, McDonald CJ. Risk of Alzheimer's Disease Among Senior Medicare Beneficiaries Treated With Androgen Deprivation Therapy for Prostate Cancer. J Clin Oncol. 2017 Oct 20;35(30):3401-3409. doi: 10.1200/JCO.2017.72.6109. Epub 2017 Aug 25.

Abstract | PMID: 28841388 | PMCID: PMC5648173

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Bhupatiraju R, Huser V, Fung K. Phenotype modelling tools utilizing standardized EHR data in a Common Data Model format [Poster]. NIH Research Festival 2017.

Abstract | pub9631.pdf

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Raje S, Bodenreider O. Interoperability of disease concepts in clinical and research ontologies – Contrasting coverage and structure in the Disease Ontology and SNOMED CT. Stud Health Technol Inform. 2017;245:925-929.

Abstract | PMID: 29295235 | PMCID: PMC5881393

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Bhupatiraju R, Fung K, Bodenreider O. MetaMapLite in Excel: Biomedical named-entity recognition for non-technical users. Stud Health Technol Inform (Proc Medinfo): 1252.

Abstract | PMID: 29295337 | PMCID: PMC5884681

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Blake C, Rindflesch TC. Leveraging syntax to better capture the semantics of elliptical coordinated compound noun phrases. J Biomed Inform. 2017 Aug;72:120-131. doi: 10.1016/j.jbi.2017.07.001. Epub 2017 Jul 4.

Abstract | PMID: 28687199

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Mrabet Y, Kilicoglu H, Demner-Fushman D. TextFlow: A Text Similarity Measure based on Continuous Sequences. Proceedings of the 55th Annual Meeting of the Association for Computational Linguistics, 2017, Vancouver, Canada, July 30 - August 4, Volume

Abstract | URL: https://doi.org/10.18653/v1/P17-1071

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Kilicoglu H, Rosemblat G, Rindflesch TC. Assigning factuality values to semantic relations extracted from biomedical research literature. PLoS One. 2017 Jul 5;12(7):e0179926. doi: 10.1371/journal.pone.0179926. eCollection 2017.

Abstract | PMID: 28678823 | PMCID: PMC5497973

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Cui L, Zhu W, Tao S, Case JT, Bodenreider O, Zhang GQ. Mining non-lattice subgraphs for detecting missing hierarchical relations and concepts in SNOMED CT. J Am Med Inform Assoc. 2017 Jul 1;24(4):788-798. doi: 10.1093/jamia/ocw175.

Abstract | PMID: 28339775 | PMCID: PMC6080685

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Fung K, Kapusnik-Uner J, Cunningham J, Higby-Baker S, Bodenreider O. Comparison of three commercial knowledge bases for detection of drug-drug interactions in clinical decision support. J Am Med Inform Assoc. 2017 Jul 1;24(4):806-812. doi: 10.1093/jamia/ocx010.

Abstract | PMID: 28339701 | PMCID: PMC6080681

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Rindflesch TC, Blake CL, Fiszman M, Kilicoglu H, Rosemblat G, Schneider J, Zeiss CJ. Informatics Support for Basic Research in Biomedicine. ILAR J. 2017 Jul 1;58(1):80-89. doi: 10.1093/ilar/ilx004.

Abstract | PMID: 28838071 | PMCID: PMC5886329

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Kilicoglu H. Biomedical text mining for research rigor and integrity: tasks, challenges, directions. Brief Bioinform. 2017 Jun 13. doi: 10.1093/bib/bbx057.

Abstract | PMID: 28633401

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Raje S, Bodenreider O. Investigating the coverage of diseases across biomedical research and clinical ontologies. Proceedings of the AMIA Joint Summits on Translational Science CRI: 384-385.

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Sorbello A, Ripple AM, Tonning J, Munoz M, Hasan R, Ly T, Francis H, Bodenreider O. Harnessing scientific literature reports for pharmacovigilance. Prototype software analytical tool development and usability testing. Appl Clin Inform. 2017 Mar 22;8(1):291-305. doi: 10.4338/ACI-2016-11-RA-0188.

Abstract | PMID: 28326432 | PMCID: PMC5373771

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Collins H, Calvo SC, Greenberg K, Forman NL, Morrison SM. Using Genetics Home Reference to Reinforce Patient Education [Poster]. American College of Medical Genetics Annual Meeting, Phoenix, AZ, March 21-25, 2017.

Abstract | pub9564.pdf

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Mork JG, Aronson A, Demner-Fushman D. 12 years on - Is the NLM medical text indexer still useful and relevant? J Biomed Semantics. 2017 Feb 23;8(1):8. doi: 10.1186/s13326-017-0113-5.

Abstract | PMID: 28231809 | PMCID: PMC5324252

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Lu C, Tormey D, McCreedy L, Browne AC. Generating A Distilled N-Gram Set: Effective Lexical Multiword Building in the SPECIALIST Lexicon. The 10th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2017), Vol(5): HEALTHINF, PORTO, Portugal, February 21-23, 2017, p. 77-87.

Abstract | pub9575.pdf

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Kilicoglu H. Dataset: Consumer Health Spelling Error Dataset

Abstract | URL: https://ceb.nlm.nih.gov/ridem/infobot_docs/CHQA_SpellCorrection_Dataset.zip

Abstract External link

Mrabet Y, Kilicoglu H, Roberts K, Demner-Fushman D. Combining Open-domain and Biomedical Knowledge for Topic Recognition in Consumer Health Questions. AMIA Annu Symp Proc. 2017 Feb 10;2016:914-923. eCollection 2016.

Abstract | pub9458.pdf | PMID: 28269888 | PMCID: PMC5333243

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Workman E, Weir, C, Rindflesch TC. Differentiating Sense through Semantic Interaction Data. AMIA Annu Symp Proc. 2017 Feb 10;2016:1238-1247. eCollection 2016.

Abstract | PMID: 28269921 | PMCID: PMC5333208

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Peters L, Nguyen T, Bodenreider O. Terminology Status APIs - Mapping Obsolete Codes to Current RxNorm, SNOMED CT, and LOINC Concepts. Stud Health Technol Inform. 2017;245:1333.

Abstract | PMID: 29295414 | PMCID: PMC5875440

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Demner-Fushman D, Rogers W, Aronson A. MetaMap Lite: an evaluation of a new Java implementation of MetaMap. J Am Med Inform Assoc. 2017 Jul 1;24(4):841-844. doi: 10.1093/jamia/ocw177.

Abstract | PMID: 28130331

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Bahr NJ, Nelson SD, Winnenburg R, Bodenreider O. Eliciting the Intension of Drug Value Sets - Principles and Quality Assurance Applications. Stud Health Technol Inform. 2017;245:843-847.

Abstract | PMID: 29295218 | PMCID: PMC5881398

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Deardorff A, Masterton K, Roberts K, Kilicoglu H, Demner-Fushman D. A protocol-driven approach to automatically finding authoritative answers to consumer health questions in online resources. JASIST, 68(7): 1724-1736. doi: 10.1002/asi.23806.

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Dhombres F, Bodenreider O. Trends in Fetal Medicine: A 10-Year Bibliometric Analysis of Prenatal Diagnosis. Stud Health Technol Inform. 2017;245:853-857.

Abstract | PMID: 29295220 | PMCID: PMC5884683

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Lu C, Tormey D, McCreedy L, Browne AC. Enhanced LexSynonym Acquisition for Effective UMLS Concept Mapping. Stud Health Technol Inform. 2017;245:501-505.

Abstract | pub9776.pdf | PMID: 29295145

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Yu Z, Nguyen T, Dhombres F, Johnson T, Bodenreider O. "Hybrid Topics" - Facilitating the Interpretation of Topics Through the Addition of MeSH Descriptors to Bags of Words. Stud Health Technol Inform. 2017;245:662-666.

Abstract | PMID: 29295179 | PMCID: PMC5875427

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Kilicoglu H. Inferring Implicit Causal Relationships in Biomedical Literature. Proc 15th Workshop on Biomedical Natural Language Processing. Pages 46-55. 2016.

Abstract | pub9441.pdf

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Huser V, DeFalco FJ, Schuemie M, Ryan PB, Shang N, Velez M, Park RW, Boyce RD, Duke J, Khare R, Utidjian L, Bailey L. Multisite Evaluation of a Data Quality Tool for Patient-Level Clinical Data Sets. EGEMS (Wash DC). 2016 Nov 30;4(1):1239. doi: 10.13063/2327-9214.1239. eCollection 2016.

Abstract | PMID: 28154833 | PMCID: PMC5226382

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Greenberg K, Calvo SC, Collins H, Foreman NL, Morrison SM. Genetics Home Reference: A point of care resource in the genomic medicine era [Poster]. American Society of Human Genetics Annual Meeting, Vancouver, British Columbia, Canada, November 18-22, 2016.

Abstract | pub9563.pdf

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Ben Abacha A, de Herrera A, Wang Ke, Long LR, Antani SK, Demner-Fushman D. Named entity recognition in functional neuroimaging literature. 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Kansas City, MO, 2017, pp. 2218-2220.

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Demner-Fushman D, Elhadad N. Aspiring to Unintended Consequences of Natural Language Processing: A Review of Recent Developments in Clinical and Consumer-Generated Text Processing. IMIA Yearbook of Medical Informatics 2016.

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Kastrin A, Rindflesch TC, Hristovski D. Link prediction on a network of co-occurring MeSH terms: Towards literature-based discovery. Methods of Information in Medicine 55(4):340-6.

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Mrabet Y, Vougiouklis P, Kilicoglu H, Gardent C, Demner-Fushman D, Hare J, Simperl E. Aligning Texts and Knowledge Bases with Semantic Sentence Simplification. WebNLG 2016.

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Oellrich A, Collier N, Groza T, Rebholz-Schuhmann D, Shah N, Bodenreider O, Borlan MR, Georgiev I, Liu H, Livingston K, Luna A, Mallon AM, Manda P, Robinson PM, Rustici G, Simonn M, Wang L, Winnenburg R, Dumontier M. The digital revolution in phenotyping. Brief Bioinform. 2016 Sep;17(5):819-30. doi: 10.1093/bib/bbv083. Epub 2015 Sep 29.

Abstract | PMID: 26420780 | PMCID: PMC5036847

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Mrabet Y, Kilicoglu H, Demner-Fushman D. Unsupervised Ranking of Knowledge Bases for Named Entity Recognition. ECAI 2016, The Hague, The Netherlands, 1248-1255.

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Boyce RD, Voss EA, Huser V, Evans L, Reich C, Duke JD, Tatonetti NP, Lorberbaum T, Dumontier M, Hauben M, Wallberg M. LAERTES: An open scalable architecture for linking pharmacovigilance evidence sources with clinical data. Proc International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016). http://icbo2016.cgrb.oregonstate.edu/node/354.

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Hristovski D, Kastrin A, Dinevski D, Burgun A, Ziberna L, Rindflesch TC. Using Literature-Based Discovery to Explain Adverse Drug Effects. J Med Syst. 2016 Aug;40(8):185. doi: 10.1007/s10916-016-0544-z. Epub 2016 Jun 18.

Abstract | PMID: 27318993

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Homer ML, Palmer NP, Bodenreider O, Cami A, Chadwick L, Mandl KD. The Drug Data to Knowledge Pipeline: Large-Scale Claims Data Classification for Pharmacologic Insight. AMIA Jt Summits Transl Sci Proc. 2016 Jul 20;2016:105-11. eCollection 2016.

Abstract | pub9334.pdf | PMID: 27570659 | PMCID: PMC5001754

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Huser V, Cimino JJ. Impending Challenges for the Use of Big Data. Int J Radiat Oncol Biol Phys. 2016 Jul 1;95(3):890-894. doi: 10.1016/j.ijrobp.2015.10.060. Epub 2015 Nov 5.

Abstract | PMID: 26797535 | PMCID: PMC4860172

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Kilicoglu H, Ben Abacha A, Mrabet Y, Roberts K, Rodriguez L, Shooshan SE, Demner-Fushman D. Annotating named entities in consumer health questions. LREC,23-28 May 2016, Portorož.

Abstract | pub9349.pdf

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Kilicoglu H. Software: Bio-SCoRes

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Kilicoglu H. Dataset: Sortal Anaphora Dataset

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Kilicoglu H. Dataset: Structured Drug Product Label (SPL) Coreference Dataset

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Lu C, Tormey D, McDreedy L, Browne AC. Multiword frequency analysis based on MEDLINE N - gram set [Poster]. AMIA 2016 Annual Symposium, Chicago, IL, November 12-16, 2016.

Abstract | pub9343.pdf

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Collins H, Calvo SC, Greenberg K, Forman, NL, Morrison SM. Information Needs in the Precision Medicine Era: How Genetics Home Reference Can Help. Interact J Med Res 2016;5(2):e13 DOI: 10.2196/ijmr.5199

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Kilicoglu H, Rosemblat G, Fiszman M, Rindflesch TC. Sortal anaphora resolution to enhance relation extraction from biomedical literature. BMC Bioinformatics. 2016 Apr 14;17:163. doi: 10.1186/s12859-016-1009-6.

Abstract | PMID: 27080229 | PMCID: PMC4832532

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Moyer E, Hagenauer M, Lesko M, Francis F, Rodriguez O, Nagarajan V, Huser V, Busby B. MetaNetVar: Pipeline for applying network analysis tools for genomic variants analysis. F1000Res. 2016 Apr 13;5:674. doi: 10.12688/f1000research.8288.1. eCollection 2016.

Abstract | PMID: 27158457 | PMCID: PMC4857755

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Morid MA, Fiszman M, Raja K, Jonnalagadda SR, Del Fiol G. Classification of clinically useful sentences in clinical evidence resources. J Biomed Inform. 2016 Apr;60:14-22. doi: 10.1016/j.jbi.2016.01.003. Epub 2016 Jan 13.

Abstract | PMID: 26774763 | PMCID: PMC4836984

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Workman TE, Fiszman M, Cairelli MJ, Nahl D, Rindflesch TC. Spark, an application based on Serendipitous Knowledge Discovery. J Biomed Inform. 2016 Apr;60:23-37. doi: 10.1016/j.jbi.2015.12.014. Epub 2015 Dec 28.

Abstract | PMID: 26732995

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Kilicoglu H, Demner-Fushman D. Bio-SCoRes: A Smorgasbord Architecture for Coreference Resolution in Biomedical Text. PLoS One. 2016 Mar 2;11(3):e0148538. doi: 10.1371/journal.pone.0148538. eCollection 2016.

Abstract | PMID: 26934708 | PMCID: PMC4774913

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Lu C, Tormey D, McDreedy L, Browne AC. Generating SD-Rules in the SPECISLIST Lexical Tools - Optimization for suffix derivation rule set [Poster]. BIOSTEC 2016), Vol(5): HEALTHINF, Rome, Italy, February 21-23, 2016, p. 353-358 (9th International Conference on Health Informatics, HEALTHINF/BIOSTEC, 2016 Best Poster Award

Abstract | pub9344.pdf

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Dhombres F, Bodenreider O. Interoperability between phenotypes in research and healthcare terminologies--Investigating partial mappings between HPO and SNOMED CT. J Biomed Semantics. 2016 Feb 9;7:3. doi: 10.1186/s13326-016-0047-3. eCollection 2016.

Abstract | PMID: 26865946 | PMCID: PMC4748471

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Bodenreider O. Identifying missing hierarchical relations in SNOMED CT from logical definitions based on the lexical features of concept names. Proceedings of the 6th International Conference on Biomedical Ontology (ICBO 2016), 2016: p. (electronic proceedings: http://ceur-ws.org/Vol-1747/IT601_ICBO2016.pdf).

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Kury F, Bodenreider O. Desiderata for drug classification systems for their use in analyzing large drug prescription datasets. Proceedings of the 3rd Workshop on Data Mining for Medical Informatics (DMMI 2016), 2016.

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Lu C, Tormey D, MCreedy L, Browne AC. Generating the MEDLINE N-Gram Set [Poster]. AMIA 2015 Annual Symposium, San Francisco, CA, November 14-18, 2015, p. 1569.

Abstract | pub9345.pdf

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Demner-Fushman D, Mork JG. Extracting Characteristics of the Study Subjects from Full-Text Articles. AMIA Annu Symp Proc. 2015 Nov 5;2015:484-91. eCollection 2015.

Abstract | PMID: 26958181 | PMCID: PMC4765643

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Kayaalp M, Browne AC, Sagan P, McGee T, McDonald CJ. Challenges and Insights in Using HIPAA Privacy Rule for Clinical Text Annotation. AMIA Annu Symp Proc. 2015 Nov 5;2015:707-16. eCollection 2015.

Abstract | PMID: 26958206 | PMCID: PMC4765667

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Kilicoglu H, Fiszman M, Roberts K, Demner-Fushman D. An Ensemble Method for Spelling Correction in Consumer Health Questions. AMIA Annu Symp Proc. 2015 Nov 5;2015:727-36. eCollection 2015.

Abstract | PMID: 26958208 | PMCID: PMC4765565

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Kury F, Huser V, Cimino JJ. Reproducing a Prospective Clinical Study as a Computational Retrospective Study in MIMIC-II. AMIA Annu Symp Proc. 2015 Nov 5;2015:804-13. eCollection 2015.

Abstract | PMID: 26958216 | PMCID: PMC4765583

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Morid MA, Jonnalagadda S, Fiszman M, Raja K, Del Fiol G. Classification of Clinically Useful Sentences in MEDLINE. AMIA Annu Symp Proc. 2015 Nov 5;2015:2015-24. eCollection 2015.

Abstract | PMID: 26958301 | PMCID: PMC4765649

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Peters LB, Bodenreider O. Approaches to Supporting the Analysis of Historical Medication Datasets with RxNorm. AMIA Annu Symp Proc. 2015 Nov 5;2015:1034-41. eCollection 2015.

Abstract | PMID: 26958241 | PMCID: PMC4765580

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Kayaalp M, Browne AC, Dodd ZA, Sagan P, McDonald CJ. An Easy-to-Use Clinical Text De-identification Tool for Clinical Scientists: NLM Scrubber [Poster]. Proceedings of the Annual American Medical Informatics Association Fall Symposium: 1522.

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Sorbello A, Ripple AM, Bodenreider O. A pilot study to support prospective detection of emerging adverse drug events [Poster]. AMIA Annu Symp Proc 2015:1699.

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Szolovits P, Aberdeen J, Meystre S, Kayaalp M. Panel on: State of the Art of Clinical Narrative Report De-Identification and Its Future [Poster]. Proceedings of the Annual American Medical Informatics Association Fall Symposium: 240–242.

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Winnenburg R, Sorbello A, Ripple AM, Harpaz R, Tonning J, Szarfman A, Francis H, Bodenreider O. Leveraging MEDLINE indexing for pharmacovigilance - Inherent limitations and mitigation strategies. J Biomed Inform. 2015 Oct;57:425-35. doi: 10.1016/j.jbi.2015.08.022. Epub 2015 Sep 2.

Abstract | PMID: 26342964 | PMCID: PMC4775467

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Dhombres F, Bodenreider O. Investigating the lexico-syntactic properties of phenotype terms – Application to interoperability between HPO and SNOMED CT. Proc Joint Bio-Ontologies and BioLINK ISMB'2015 SIG session "Phenotype Day" 2015:8-11.

Abstract | pub9335.pdf

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Kilicoglu H, Rosemblat G, Cairelli M, Rindflesch TC. A Compositional Interpretation of Biomedical Event Factuality. Proc of the Second Workshop on Extra-Propositional Aspects of Meaning in Computational Semantics (ExProM 2015).

Abstract | pub9223.pdf

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Cairelli MJ, Fiszman M, Zhang H, Rindflesch TC. Networks of neuroinjury semantic predications to identify biomarkers for mild traumatic brain injury. J Biomed Semantics. 2015 May 18;6:25. doi: 10.1186/s13326-015-0022-4. eCollection 2015.

Abstract | PMID: 25992264 | PMCID: PMC4436163

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Peters LB, Bahr N, Bodenreider O. Evaluating drug-drug interaction information in NDF-RT and DrugBank. J Biomed Semantics. 2015 May 11;6:19. doi: 10.1186/s13326-015-0018-0. eCollection 2015.

Abstract | PMID: 25964850 | PMCID: PMC4426554

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Cho D, Mork JG, Aronson A, Demner-Fushman D, Schmidt S, Ozga D, Pash J, Kilbourne J. MeSH on demand: an easy way to identify relevant MeSH terms and related articles from text [Poster]. National Cancer Institute (NCI) Symposium "RNA Biology 2015".

Abstract | pub9358.pdf

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Winnenburg R, Sorbello A, Bodenreider O. Exploring adverse drug events at the class level. J Biomed Semantics. 2015 May 1;6:18. doi: 10.1186/s13326-015-0017-1. eCollection 2015.

Abstract | PMID: 25937884 | PMCID: PMC4416343

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Jimeno Yepes AJ, Plaza L, Carrillo-de-Albornoz J, Mork JG, Aronson A. Feature engineering for MEDLINE citation categorization with MeSH. BMC Bioinformatics. 2015 Apr 8;16:113. doi: 10.1186/s12859-015-0539-7.

Abstract | PMID: 25887792 | PMCID: PMC4407321

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Cameron D, Kavuluru R, Rindflesch TC, Sheth AP, Thirunarayan K, Bodenreider O. Context-driven automatic subgraph creation for literature-based discovery. J Biomed Inform. 2015 Apr;54:141-57. doi: 10.1016/j.jbi.2015.01.014. Epub 2015 Feb 7.

Abstract | PMID: 25661592 | PMCID: PMC4888806

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Winnenburg R, Mortensen JM, Bodenreider O. Using description logics to evaluate the consistency of drug-class membership relations in NDF-RT. J Biomed Semantics. 2015 Mar 28;6:13. doi: 10.1186/s13326-015-0007-3. eCollection 2015.

Abstract | PMID: 25866612 | PMCID: PMC4392727

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Tao S, Cui L, Zhu W, Sun M, Bodenreider O, Zhang GQ. Mining Relation Reversals in the Evolution of SNOMED CT Using MapReduce. AMIA Jt Summits Transl Sci Proc. 2015 Mar 23;2015:46-50. eCollection 2015.

Abstract | PMID: 26306232 | PMCID: PMC4525241

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Wei W, Demner-Fushman D, Wang S, Jiang X, Ohno-Machado L. Ranking Medical Subject Headings using a factor graph model. AMIA Jt Summits Transl Sci Proc. 2015 Mar 23;2015:56-63. eCollection 2015.

Abstract | pub9268.pdf | PMID: 26306236 | PMCID: PMC4525219

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Zhang R, Adam TJ, Simon G, Cairelli MJ, Rindflesch T, Pakhomov S, Melton GB. Mining Biomedical Literature to Explore Interactions between Cancer Drugs and Dietary Supplements. AMIA Jt Summits Transl Sci Proc. 2015 Mar 23;2015:69-73. eCollection 2015.

Abstract | PMID: 26306241 | PMCID: PMC4525230

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Gopal AD, Desai NR, Tse T, Ross JS. Reporting of noninferiority trials in ClinicalTrials.gov and corresponding publications. JAMA. 2015 Mar 17;313(11):1163-5. doi: 10.1001/jama.2015.1697.

Abstract | PMID: 25781447

Abstract

Hristovski D, Dinevski D, Kastrin A, Rindflesch TC. Biomedical question answering using semantic relations. BMC Bioinformatics. 2015 Jan 16;16:6. doi: 10.1186/s12859-014-0365-3.

Abstract | PMID: 25592675 | PMCID: PMC4307891

Abstract

Amini S, Kilicoglu H, Hooft L, ter Riet G. Are we expressing uncertainty of our claims enough? Towards automatic detection of overstatement of claims [Poster]. 2015. World Conference on Research Integrity (WCRI).

Abstract

Fu GE, Bolton NQ, Rosinach LI, Furlong V, Nguyen AP, Sheth O, Bodenreider O, Dumontier M. Exposing provenance metadata using different RDF models. Proceedings of the International Conference on Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2015), 2015: p. (electronic proceedings: http://www.swat4ls.org/wp-content/uploads/2015/10/SWAT4LS_2015_paper_11.pdf).

Abstract

Dhombres F, Winnenburg R, Case JT, Bodenreider O. Extending the coverage of phenotypes in SNOMED CT through post-coordination. Stud Health Technol Inform. 2015;216:795-9.

Abstract | PMID: 26262161

Abstract

Hripcsak G, Duke JD, Shah NH, Reich CG, Huser V, Schuemie MJ, Suchard MA, Park RW, Wong IC, Rijnbeek PR, van der Lei J, Pratt N, Norén GN, Li YC, Stang PE, Madigan D, Ryan PB. Observational Health Data Sciences and Informatics (OHDSI): Opportunities for Observational Researchers. Stud Health Technol Inform. 2015;216:574-8.

Abstract | PMID: 26262116 | PMCID: PMC4815923

Abstract

Kilicoglu H, Rogers W. A Hybrid System for Extracting Chemical-Disease Relationships from Scientific Literature. 2015. BioCreative 5 Proceedings.

Abstract | pub9350.pdf

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Rance B, Le T, Bodenreider O. Fingerprinting Biomedical Terminologies--Automatic Classification and Visualization of Biomedical Vocabularies through UMLS Semantic Group Profiles. Stud Health Technol Inform. 2015;216:771-5.

Abstract | PMID: 26262156

Abstract

Kayaalp M, Dodd Z, Browne AC, Sagan, P, McDonald CJ. Software: NLM-Scrubber

Abstract | URL: https://scrubber.nlm.nih.gov/

Abstract External link

Mishra R, Bian J, Fiszman M, Weir CR, Mostafa J, Fiol GD. Text summarization in the biomedical domain: a systematic review of recent research. J Biomed Inform. 2014 Dec;52:457-67. doi: 10.1016/j.jbi.2014.06.009. Epub 2014 Jul 10.

Abstract | PMID: 25016293 | PMCID: PMC4261035

Abstract

Shang N, Xu H, Rindflesch TC, Cohen T. Identifying plausible adverse drug reactions using knowledge extracted from the literature. J Biomed Inform. 2014 Dec;52:293-310. doi: 10.1016/j.jbi.2014.07.011. Epub 2014 Jul 19.

Abstract | PMID: 25046831 | PMCID: PMC4261011

Abstract

Browne AC, Kayaalp M, Dodd Z, Sagan, P, McDonald CJ. The Challenges of Creating a Gold Standard for De-identification Research. AMIA Annu Symp Proc. 2014 Nov 14;2014:353-8. eCollection 2014.

Abstract | pub8927.pdf | PMID: 25954338 | PMCID: PMC4420002

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Culbertson A, Fiszman M, Shin D, Rindflesch TC. Semantic processing to identify adverse drug event information from black box warnings. AMIA Annu Symp Proc. 2014 Nov 14;2014:442-8. eCollection 2014.

Abstract | PMID: 25954348 | PMCID: PMC4419903

Abstract

Fung KW, Richesson R, Bodenreider O. Coverage of rare disease names in standard terminologies and implications for patients, providers, and research. AMIA Annu Symp Proc. 2014 Nov 14;2014:564-72. eCollection 2014.

Abstract | PMID: 25954361 | PMCID: PMC4419993

Abstract

Huser, V, Kayaalp M, Dodd Z, Cimino J. Piloting a deceased subject integrated data repository and protecting privacy of relatives. AMIA Annu Symp Proc. 2014 Nov 14;2014:719-28. eCollection 2014.

Abstract | pub8928.pdf | PMID: 25954378 | PMCID: PMC4420001

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Kayaalp M, Browne AC, Dodd Z, Sagan P, McDonald CJ. De-identification of Address, Date, and Alphanumeric Identifiers in Narrative Clinical Reports. AMIA Annu Symp Proc. 2014 Nov 14;2014:767-76. eCollection 2014.

Abstract | pub8926.pdf | PMID: 25954383 | PMCID: PMC4419982

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Lu C, Tormey D, McDreedy L, Browne AC. Using element words to generate (multi)words for the SPECIALIST Lexicon [Poster]. AMIA 2014 Annual Symposium, Washington, DC, November 15-19, 2014, p. 1499. Poster

Abstract | pub9346.pdf

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Ozturk S, Kayaalp M, McDonald CJ. Visualization of patient prescription history data in emergency care. AMIA Annu Symp Proc. 2014 Nov 14;2014:963-8. eCollection 2014.

Abstract | PMID: 25954404 | PMCID: PMC4419971

Abstract

Roberts K, Kilicoglu H, Fiszman M, Demner-Fushman D. Automatically classifying question types for consumer health questions. AMIA Annu Symp Proc. 2014 Nov 14;2014:1018-27. eCollection 2014.

Abstract | pub8972.pdf | PMID: 25954411 | PMCID: PMC4420005 | URL: http://knowledge.amia.org/56638-amia-1.1540970/t-004-1.1544972/f-004-1.1544973/a...

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Winnenburg R, Bodenreider O. Desiderata for an authoritative Representation of MeSH in RDF. AMIA Annu Symp Proc. 2014 Nov 14;2014:1218-27. eCollection 2014.

Abstract | PMID: 25954433 | PMCID: PMC4419968

Abstract

Harpaz R, Odgers D, Gaskin G, DuMouchel W, Winnenburg R, Bodenreider O, Ripple AM, Szarfman A, Sorbello A, Horvitz E, White RW, Shah NH. A time-indexed reference standard of adverse drug reactions. Sci Data. 2014 Nov 11;1:140043. doi: 10.1038/sdata.2014.43.

Abstract | PMID: 25632348 | PMCID: PMC4306188

Abstract

Khatipov E, Madden M, Chiang P, Chuang P, Nguyen D, D'Souza I, Winnenburg R, Bodenreider O, Skapik J, McClure R, Emrick S. Creating, maintaining and publishing value sets in the VSAC [Poster]. AMIA Annu Symp Proc, 2014: p. 1459.

Abstract

Nguyen T, Peters L, Bodenreider O. RxClass - Navigating between drug classes and RxNorm drugs [Poster]. AMIA Annu Symp Proc, 2014: p. 1529.

Abstract

Winnenburg R, Bodenreider O. Desiderata for an authoritative representation of MeSH in RDF. AMIA Annu Symp Proc 2014:1218-1227.

Abstract

Zhang R, Cairelli MJ, Fiszman M, Kilicoglu H, Rindflesch TC, Pakhomov SV, Melton GB. Exploiting Literature-derived Knowledge and Semantics to Identify Potential Prostate Cancer Drugs. Cancer Inform. 2014 Oct 14;13(Suppl 1):103-11. doi: 10.4137/CIN.S13889. eCollection 2014.

Abstract | PMID: 25392688 | PMCID: PMC4216049

Abstract

Bodenreider O, Peters L, Nguyen T. RxClass – Navigating between Drug Classes and RxNorm Drugs (Demo). Prc. ICBO 2014

Abstract | URL: http://ceur-ws.org/Vol-1327/icbo2014_paper_49.pdf

Abstract External link

Cohen T, Widdows D, Stephan C, Zinner R, Kim J, Rindflesch TC, Davies P. Predicting high-throughput screening results with scalable literature-based discovery methods. CPT Pharmacometrics Syst Pharmacol. 2014 Oct 8;3:e140. doi: 10.1038/psp.2014.37.

Abstract | PMID: 25295575 | PMCID: PMC4474167

Abstract

Richesson RL, Fung K, Bodenreider O. Coverage of rare disease names in cinical coding systems and ontologies and implications for electronic health records-based research [Poster]. Proc 5th Int'l Conf Conference on Biomedical Ontology.

Abstract

Zhang GQ, Zhu W, Sun M, Tao S, Bodenreider O, Cui L. MaPLE: A MapReduce Pipeline for Lattice-based Evaluation and Its Application to SNOMED CT. Proc IEEE Int Conf Big Data. 2014 Oct;2014:754-759.

Abstract | PMID: 25705725 | PMCID: PMC4334137

Abstract

Hanauer DA, Saeed M, Zheng K, Mei Q, Shedden K, Aronson AR, Ramakrishnan N. Applying MetaMap to Medline for identifying novel associations in a large clinical dataset: a feasibility analysis. J Am Med Inform Assoc. 2014 Sep-Oct;21(5):925-37. doi: 10.1136/amiajnl-2014-002767. Epub 2014 Jun 13.

Abstract | PMID: 24928177 | PMCID: PMC4147617

Abstract

Winnenburg R, Bodenreider O. A framework for assessing the consistency of drug classes across sources. J Biomed Semantics. 2014 Jul 9;5:30. doi: 10.1186/2041-1480-5-30. eCollection 2014.

Abstract | pub8935.pdf | PMID: 25101165 | PMCID: PMC4120719

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Kilicoglu H, Demner-Fushman D. Coreference Resolution for Structured Drug Product Labels Proceedings of BioNLP 2014. pp. 44-53.

Abstract | pub8919.pdf

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Chen G, Cairelli MJ, Kilicoglu H, Shin D, Rindflesch TC. Augmenting microarray data with literature-based knowledge to enhance gene regulatory network inference. PLoS Comput Biol. 2014 Jun 12;10(6):e1003666. doi: 10.1371/journal.pcbi.1003666. eCollection 2014 Jun.

Abstract | PMID: 24921649 | PMCID: PMC4055569

Abstract

Zhang R, Cairelli MJ, Fiszman M, Rosemblat G, Kilicoglu H, Rindflesch TC, Pakhomov SV, Melton GB. Using semantic predications to uncover drug-drug interactions in clinical data. J Biomed Inform. 2014 Jun;49:134-47. doi: 10.1016/j.jbi.2014.01.004. Epub 2014 Jan 19.

Abstract | PMID: 24448204 | PMCID: PMC4058371

Abstract

Roberts K, Masterton K, Kilicoglu H, Fiszman M, Demner-Fushman D. Annotating Question Decomposition on Complex Medical Questions. LREC 2014.

Abstract | pub7076.pdf

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Roberts K, Masterton K, Fiszman M, Kilicoglu H, Demner-Fushman D. Annotating Question Types for Consumer Health Questions. LREC 2014, BioTxtM workshop.

Abstract | pub7077.pdf

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Roberts K, Kilicoglu H, Fiszman M, Demner-Fushman D. Decomposing consumer health questions. BioNLP 2014.

Abstract | pub7078.pdf

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Del Fiol G, Workman TE, Gorman PN. Clinical questions raised by clinicians at the point of care: a systematic review. JAMA Intern Med. 2014 May;174(5):710-8. doi: 10.1001/jamainternmed.2014.368.

Abstract | PMID: 24663331

Abstract

Nguyen V, Bodenreider O, Sheth AP. Don't Like RDF Reification? Making Statements about Statements Using Singleton Property. Proc Int World Wide Web Conf. 2014 Apr 11;2014:759-770.

Abstract | pub8934.pdf | PMID: 25750938 | PMCID: PMC4350149

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Hartung DM, Zarin D, Guise JM, McDonagh M, Paynter R, Helfand M. Reporting discrepancies between the ClinicalTrials.gov results database and peer-reviewed publications. Ann Intern Med. 2014 Apr 1;160(7):477-83. doi: 10.7326/M13-0480.

Abstract | PMID: 24687070 | PMCID: PMC4617780

Abstract

Bodenreider O. Multi-lingual features of the Unified Medical Language System. Proc. CLEF-ER 2013 workshop 2013.

Abstract | 2013-clef_er-ob-abstract.pdf | URL: http://www.clef2013.org/index.php?page=Pages/proceedings.php

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Cohen T, Widdows D, Rindflesch TC. Expansion-by-analogy: A vector symbolic approach to semantic search. AAAI-Fall 2014 Symposium on Quantum Informatics for Cognitive, Social, and Semantic Processes.

Abstract

Kastrin A, Rindflesch TC, Hristovski D. Link prediction in a MeSH co-occurrence network: preliminary results. Stud Health Technol Inform. 2014;205:579-83.

Abstract | PMID: 25160252

Abstract

Kastrin A, Rindflesch TC, Hristovski D. Link prediction on the Semantic MEDLINE Network. Proceedings of the 17th International conference on Discovery Science.

Abstract

Mork JG, Demner-Fushman D, Schmidt SC, Aronson A. Recent Enhancements to the NLM Medical Text Indexer. BioASQ 2014.

Abstract

Mork JG, Demner-Fushman D, Schmidt SC, Aronson A. Vocabulary Density Method for Personalized Indexing of MEDLINE Journals [Poster]. 2014 AMIA Symposium.

Abstract

Osborne R, Aronson A, Cohen K. A repository of semantic types in the MIMIC II database clinical notes. BioNLP 2014. pp. 93-97.

Abstract

Ripple AM, Mork JG, Schmidt SC, Thomson H, Knecht LS. Performance Comparison of MEDLINE Structured Abstract to Unstructured Abstracts [Poster]. 2014 NIH Research Festival.

Abstract

Winnenburg R, Bodenreider O. Coverage of phenotypes in standard terminologies. Joint Bio-Ontologies and BioLINK ISMB'2014 SIG session "Phenotype Day" 2014:41-44.

Abstract | pub8937.pdf

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Winnenburg R, Bodenreider O. Evaluating the consistency of inferred drug-class membership relations in NDF-RT. Proc 17th ISMB'2014 SIG meeting "Bio-Ontologies" 2014

Abstract | pub8936.pdf | URL: https://drive.google.com/file/d/0B6AZUdKw1IVHeGVtTVZCRXJhbFk/

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Kilicoglu H, Fiszman M, Demner-Fushman D. Interpreting Consumer Health Questions: The Role of Anaphora and Ellipsis. Proceedings of BioNLP 2013. Pages 54-62.

Abstract | pub7057.pdf

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Bodenreider O. Disease Ontologies In: Dubitzky W, Wolkenhauer O, Cho K-H, Yokota H, editors. Encyclopedia of Systems Biology: Springer; 2013. p. 578-581.

Abstract | pub2011017.pdf

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Rosemblat G, Shin D, Kilicoglu H, Sneiderman C, Rindflesch TC. A methodology for extending domain coverage in SemRep. J Biomed Inform. 2013 Dec;46(6):1099-107. doi: 10.1016/j.jbi.2013.08.005. Epub 2013 Aug 21.

Abstract | PMID: 23973273 | PMCID: PMC3844019

Abstract

Schulz S, Balkanyi L, Cornet R, Bodenreider O. From concept representations to ontologies: a paradigm shift in health informatics? Healthc Inform Res. 2013 Dec;19(4):235-42. doi: 10.4258/hir.2013.19.4.235. Epub 2013 Dec 31.

Abstract | PMID: 24523987 | PMCID: PMC3920035

Abstract

Cairelli MJ, Miller CM, Fiszman M, Workman TE, Rindflesch TC. Semantic MEDLINE for discovery browsing: using semantic predications and the literature-based discovery paradigm to elucidate a mechanism for the obesity paradox. AMIA Annu Symp Proc. 2013 Nov 16;2013:164-73. eCollection 2013.

Abstract | PMID: 24551329 | PMCID: PMC3900170

Abstract

Demner-Fushman D, Mork JG, Aronson AR. Mining MEDLINE for problems associated with vitamin D. AMIA Annu Symp Proc. 2013 Nov 16;2013:300-8. eCollection 2013.

Abstract | PMID: 24551339 | PMCID: PMC3900180

Abstract

Lu C, Tormey D, McDreedy L, Browne AC. Implementing comprehensive derivational features in Llexical tools using a systematical approach [Poster]. AMIA 2013 Annual Symposium, Washington, DC, November 16-20, 2013, p. 904

Abstract | pub9347.pdf

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Mishra R, Del Fiol G, Kilicoglu H, Jonnalagadda S, Fiszman M. Automatically extracting clinically useful sentences from UpToDate to support clinicians' information needs. AMIA Annu Symp Proc. 2013 Nov 16;2013:987-92. eCollection 2013.

Abstract | pub8952.pdf | PMID: 24551389 | PMCID: PMC3900230

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Winnenburg R, Bodenreider O. Metrics for assessing the quality of value sets in clinical quality measures. AMIA Annu Symp Proc. 2013 Nov 16;2013:1497-505. eCollection 2013.

Abstract | PMID: 24551422 | PMCID: PMC3900160

Abstract

Workman TE, Rosemblat G, Fiszman M, Rindflesch TC. A literature-based assessment of concept pairs as a measure of semantic relatedness. AMIA Annu Symp Proc. 2013 Nov 16;2013:1512-21. eCollection 2013.

Abstract | PMID: 24551423 | PMCID: PMC3900161

Abstract

Yepes AJ, Mork JG, Demner-Fushman D, Aronson AR. Comparison and combination of several MeSH indexing approaches. AMIA Annu Symp Proc. 2013 Nov 16;2013:709-18. eCollection 2013.

Abstract | PMID: 24551371 | PMCID: PMC3900212

Abstract

Le T, Rance B, Bodenreider O. Network visualization of UMLS source vocabularies using semantic groups. AMIA Annu Symp Proc, 2013: p. 90

Abstract

Peters L, Nguyen T, Bodenreider O. Displaying drug classes in RxNav [Poster]. AMIA Annu Symp Proc, 2013: p. 1134.

Abstract

Friedman C, Rindflesch TC, Corn M. Natural language processing: state of the art and prospects for significant progress, a workshop sponsored by the National Library of Medicine. J Biomed Inform. 2013 Oct;46(5):765-73. doi: 10.1016/j.jbi.2013.06.004. Epub 2013 Jun 25.

Abstract | PMID: 23810857

Abstract

Rosemblat G, Resnick MP, Auston I, Shin D, Sneiderman C, Fizsman M, Rindflesch TC. Extending SemRep to the Public Health Domain. J Am Soc Inf Sci Technol. 2013 Oct;64(10):1963-1974.

Abstract | PMID: 24729747 | PMCID: PMC3981099

Abstract

Jonnalagadda SR, Del Fiol G, Medlin R, Weir C, Fiszman M, Mostafa J, Liu H. Automatically extracting sentences from Medline citations to support clinicians' information needs. J Am Med Inform Assoc. 2013 Sep-Oct;20(5):995-1000. doi: 10.1136/amiajnl-2012-001347. Epub 2012 Oct 25.

Abstract | pub7003.pdf | PMID: 23100128 | PMCID: PMC3756259

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Kang YS, Kayaalp M. Extracting laboratory test information from biomedical text. J Pathol Inform. 2013 Aug 31;4:23. doi: 10.4103/2153-3539.117450. eCollection 2013.

Abstract | PMID: 24083058 | PMCID: PMC3779392

Abstract

Zarin D. Participant-level data and the new frontier in trial transparency [Letter]. N Engl J Med. 2013 Aug 1;369(5):468-9. doi: 10.1056/NEJMe1307268.

Abstract | PMID: 23902488

Abstract

Winnenburg R, Rodriguez L, Callaghan F, Sorbello A, Szarfman A, Bodenreider O. Aligning Pharmacologic Classes Between MeSH and ATC. 4th International Conference on Biomedical Ontology · ICBO 2013

Abstract | pub9580.pdf

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Zarin D, Tse T. Trust but verify: trial registration and determining fidelity to the protocol [Letter]. Ann Intern Med. 2013 Jul 2;159(1):65-7. doi: 10.7326/0003-4819-159-1-201307020-00011.

Abstract | PMID: 23817705

Abstract

Jimeno-Yepes AJ, Plaza L, Mork JG, Aronson AR, Díaz A. MeSH indexing based on automatically generated summaries. BMC Bioinformatics. 2013 Jun 26;14:208. doi: 10.1186/1471-2105-14-208.

Abstract | PMID: 23802936 | PMCID: PMC3706357

Abstract

Jimeno-Yepes AJ, Sticco JC, Mork JG, Aronson AR. GeneRIF indexing: sentence selection based on machine learning. BMC Bioinformatics. 2013 May 31;14:171. doi: 10.1186/1471-2105-14-171.

Abstract | PMID: 23725347 | PMCID: PMC3687823

Abstract

Workman TE, Fiszman M, Rindflesch TC, Nahl D. Framing Serendipitous Information Seeking Behavior for Facilitating Literature-Based Discovery: A Proposed Model. Journal of the American Society for Information Science and Technology 2013, in press.

Abstract

Ross JS, Mocanu M, Lampropulos JF, Tse T, Krumholz HM. Time to publication among completed clinical trials. JAMA Intern Med. 2013 May 13;173(9):825-8. doi: 10.1001/jamainternmed.2013.136.

Abstract | PMID: 23460252 | PMCID: PMC3691813

Abstract

Zarin D, Tse T. Clarification about ClinicalTrials.gov [Letter]. IRB. 2013 May-Jun;35(3):19.

Abstract | PMID: 23822048

Abstract

Yepes AJ, Prieur-Gaston E, Névéol A. Combining MEDLINE and publisher data to create parallel corpora for the automatic translation of biomedical text. BMC Bioinformatics. 2013 Apr 30;14:146. doi: 10.1186/1471-2105-14-146.

Abstract | PMID: 23631733 | PMCID: PMC3651320

Abstract

Cameron D, Bodenreider O, Yalamanchili H, Danh T, Vallabhaneni S, Thirunarayan K, Sheth AP, Rindflesch TC. A graph-based recovery and decomposition of Swanson's hypothesis using semantic predications. J Biomed Inform. 2013 Apr;46(2):238-51. doi: 10.1016/j.jbi.2012.09.004. Epub 2012 Sep 28.

Abstract | PMID: 23026233 | PMCID: PMC4031661

Abstract

Hristovski D, Rindflesch TC, Peterlin B. Using literature-based discovery to identify novel therapeutic approaches. Cardiovasc Hematol Agents Med Chem. 2013 Mar;11(1):14-24.

Abstract | PMID: 22845900

Abstract

Zarin DA, Tse T. Unambiguous identification of obesity trials [Letter]. N Engl J Med. 2013 Feb 7;368(6):580-1. doi: 10.1056/NEJMc1215018.

Abstract | nejmc1215018.pdf | PMID: 23388022 | URL: http://www.nejm.org/doi/full/10.1056/NEJMc1215018

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Williams RJ. Tutorial: ClinicalTrials.gov: Registration and Results Submission Requirements

Abstract

Balkanyi L, Schulz S, Cornet R, Bodenreider O. Medical concept representation: the years beyond 2000 [Poster]. Stud Health Technol Inform. 2013;192:1011.

Abstract | PMID: 23920785 | PMCID: PMC4300111

Abstract

Bodenreider O, Nguyen D, Chiang P, Chuang P, Madden M, Winnenburg R, McClure R, Emrick S, D'Souza I. The NLM value set authority center (Poster). Stud Health Technol Inform. 2013;192:1224.

Abstract | PMID: 23920998 | PMCID: PMC4300102

Abstract

Gallagher ME. Improving Software Sustainability: Lessons Learned from Profiles in Science. Archiving. 2013;2013:74-79.

Abstract | a2013001.pdf | PMID: 25267934 | PMCID: PMC4176707

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Jimeno Yepes A, Mork JG, Aronson A. Using the argumentative structure of scientific literature to improve information access [Poster]. BioNLP 2013.

Abstract

Jimeno Yepes AJ, Mork JG, Aronson A. Identifying Publication Types Using Machine Learning. BioASQ Workshop 2013.

Abstract

Maver A, Hristovski D, Rindflesch TC, Peterlin B. Integration of data from omic studies with the literature-based discovery towards identification of novel treatments for neovascularization in diabetic retinopathy. Biomed Res Int. 2013;2013:848952. doi: 10.1155/2013/848952. Epub 2013 Nov 24.

Abstract | PMID: 24350292 | PMCID: PMC3857903

Abstract

Mork JG, Jimeno Yepes A, Aronson A. The NLM Medical Text Indexer System for Indexing Biomedical Literature. BioASQ 2013.

Abstract

Peters L, Mortensen J, Nguyen T, Bodenreider O. Enabling complex queries to drug information sources through functional composition. Stud Health Technol Inform. 2013;192:692-6.

Abstract | PMID: 23920645 | PMCID: PMC4303373

Abstract

Rance B, Snyder M, Lewis J, Bodenreider O. Leveraging terminological resources for mapping between rare disease information sources. Stud Health Technol Inform. 2013;192:529-33.

Abstract | PMID: 23920611 | PMCID: PMC4296515

Abstract

Winnenburg R, Bodenreider O. Exploring pharmacoepidemiologic groupings of drugs from a clinical perspective. Stud Health Technol Inform. 2013;192:827-31.

Abstract | PMID: 23920673 | PMCID: PMC4304656

Abstract

Zhang M, Del Fiol G, Grout RW, Jonnalagadda S, Medlin R, Mishra R, Weir C, Liu H, Mostafa J, Fiszman M. Automatic identification of comparative effectiveness research from medline citations to support clinicians' treatment information needs. Stud Health Technol Inform. 2013;192:846-50.

Abstract | PMID: 23920677 | PMCID: PMC3940695

Abstract

Zhang, H, Fiszman M, Shin D, Wilkowski B, Rindflesch TC. Clustering cliques for graph-based summarization of the biomedical research literature. BMC Bioinformatics 14:182.

Abstract

Gallagher ME, Moffatt C. The Profiles in Science Digital Library: Behind the Scenes. Proc ACM/IEEE Joint Conf Digit Libr. 2012: 433–434. doi: 10.1145/2232817.2232928.

Abstract | pub2012016.pdf | PMCID: PMC3609548

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Kilicoglu H, Shin D, Fiszman M, Rosemblat G, Rindflesch TC. SemMedDB: a PubMed-scale repository of biomedical semantic predications. Bioinformatics. 2012 Dec 1;28(23):3158-60. doi: 10.1093/bioinformatics/bts591. Epub 2012 Oct 8.

Abstract | PMID: 23044550 | PMCID: PMC3509487

Abstract

Morrison SM, Cheh M, Calvo SC, Collins H, Fun J, Greenberg K, Forman-Neall L. Genetics Home Reference, Ten Years In: Where We Are Now [Poster]. American Society of Human Genetics, November 9, 2012, San Francisco, CA.

Abstract

Lu C, Browne AC. Development of Sub-Term Mapping Tools (STMT) AMIA 2012 Annual Symposium, Chicago, IL, November 3-7, 2012

Abstract | pub2012017.pdf

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Huser V, Cimino JJ. Precision and negative predictive value of links between ClinicalTrials.gov and PubMed. AMIA Annu Symp Proc. 2012;2012:400-8. Epub 2012 Nov 3.

Abstract | PMID: 23304310 | PMCID: PMC3540528

Abstract

Lu C, Browne AC. Development of sub-term mapping tools (STMT) [Poster]. AMIA 2012 Annual Symposium, Chicago, IL, November 3-7, 2012, p. 1845 (AMIA, 2012 Distinguished Poster Award) Poster.

Abstract | pub9348.pdf

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Fung KW, Bodenreider O. Knowledge representation and ontologies. Richesson RL, Andrews JE (Eds.). Clinical Research Informatics, Health Informatics, DOI 10.1007/978-1-84882-448-5_14, Springer-Verlag London Limited Publishing 2012.

Abstract | pub2012015.pdf

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Peters L, Nguyen T, Bodenreider O. RxBatch – Batch operations for RxNorm and NDF-RT APIs (Poster). AMIA Annu Symp Proc, 2012: p. 1897.

Abstract

Bodenreider O. API: Prescribable

Abstract

Rance B, Doughty E, Demner-Fushman D, Kann MG, Bodenreider O. A mutation-centric approach to identifying pharmacogenomic relations in text. J Biomed Inform. 2012 Oct;45(5):835-41. doi: 10.1016/j.jbi.2012.05.003. Epub 2012 Jun 7.

Abstract | PMID: 22683993 | PMCID: PMC3438287

Abstract

Huston M, Williams RJ, Bergeris A, Fun J, Tse T. New style and new content for ClinicalTrials.gov. NLM Tech Bull. 2012 Jul-Aug;(387):e5.

Abstract | URL: http://www.nlm.nih.gov/pubs/techbull/ja12/ja12_clinicaltrials.html

Abstract External link

Tse T, Zarin D, Williams R, Ide N. The role and importance of clinical trial registries and results databases In: Gallin JI, Ognibene FP, eds, Principles and Practice of Clinical Research. 3rd ed. Amsterdam: Academic Press; 2012: 171-81.

Abstract

Lu C, McCreedy L, Tormey D, Browne AC. A Systematic Approach for Automatically Generating Derivational Variants in Lexical Tools Based on theSPECIALIST Lexicon IEEE IT Professional Magazine, May/June, 2012;36-42.

Abstract | pub2012018.pdf

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Jimeno-Yepes A, Mork J, Demner-Fushman D, Aronson AR. A one-size-fits-all indexing method does not exist: automatic selection based on meta-learning. JCSE, vol. 6, no. 2, pp.151-160, 2012.

Abstract | pub-2012-048.pdf | URL: http://jcse.kiise.org/PublishedPaper/topic_abstract.asp?idx=134

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Bodenreider O. Web Interface: RxMix

Abstract

Workman TE, Fiszman M, Hurdle JF. Text summarization as a decision support aid. BMC Med Inform Decis Mak. 2012 May 23;12:41. doi: 10.1186/1472-6947-12-41.

Abstract | PMID: 22621674 | PMCID: PMC3461485

Abstract

Califf RM, Zarin DA, Kramer JM, Sherman RE, Aberle LH, Tasneem A. Characteristics of clinical trials registered in ClinicalTrials.gov, 2007-2010. JAMA. 2012 May 2;307(17):1838-47. doi: 10.1001/jama.2012.3424.

Abstract | PMID: 22550198 | URL: http://jama.jamanetwork.com/article.aspx?articleid=1150093

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Lu C, Tormey D, McCreedy L, Browne AC. A Systematic Approach for Automatically Generating Derivational Variants in Lexical Tools Based on the SPECIALIST Lexicon. IEEE IT Professional Magazine, May/June, 2012, p. 36-42.

Abstract

Miller CM, Rindflesch TC, Fiszman M, Hristovski D, Shin D, Rosemblat G, Zhang H, Strohl KP. A closed literature-based discovery technique finds a mechanistic link between hypogonadism and diminished sleep quality in aging men. Sleep. 2012 Feb 1;35(2):279-85. doi: 10.5665/sleep.1640.

Abstract | PMID: 22294819 | PMCID: PMC3250368

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Mougin F, Burgun A, Bodenreider O. Comparing Drug-class Membership in ATC and NDF-RT Proc IHI 2012 2012:437-443

Abstract | pub2012010.pdf

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Jimeno-Yepes A, Aronson AR. Knowledge-based and knowledge-lean methods combined in unsupervised word sense disambiguation. Proc 2nd ACM SIGHIT International Health Informatics (IHI) Symposium 2012, 733-736.

Abstract

Jimeno-Yepes A, Mork JG, Wilkowski B, Demner-Fushman D, Aronson AR. MEDLINE MeSH indexing: lessons learned from machine learning and future directions. Proc IHI 2012, 737-742.

Abstract

Jimeno-Yepes A, Wilkowski B, Mork JG, Demner-Fushman D, Aronson AR. MeSH indexing: machine learning and lessons learned. ACM SIGHIT International Health Informatics Symposium, Miami, FL, USA, 2012.

Abstract | pub2012-064.pdf

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Ross JS, Tse T, Zarin DA, Xu H, Zhou L, Krumholz HM. Publication of NIH funded trials registered in ClinicalTrials.gov: cross sectional analysis. BMJ. 2012 Jan 3;344:d7292. doi: 10.1136/bmj.d7292.

Abstract | bmj.d7292.pdf | PMID: 22214755 | PMCID: PMC3623605

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Del Fiol G, Huser V, Strasberg HR, Maviglia SM, Curtis C, Cimino JJ. Implementations of the HL7 Context-Aware Knowledge Retrieval ("Infobutton") Standard: challenges, strengths, limitations, and uptake. J Biomed Inform. 2012 Aug;45(4):726-35. doi: 10.1016/j.jbi.2011.12.006.. Epub 2012 Jan 2.

Abstract | PMID: 22226933 | PMCID: PMC3334468

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Adamusiak T, Bodenreider O. Quality assurance in LOINC using Description Logic. AMIA Annu Symp Proc. 2012;2012:1099-108. Epub 2012 Nov 3.

Abstract | PMID: 23304386 | PMCID: PMC3540427

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Kayaalp M. ICU Outcome Predictions using Physiologic Trends in the First Two Days. Computing in Cardiology (39)977–980.

Abstract | PMCID: PMC3607431

Abstract

Winnenburg R, Bodenreider O. Issues in creating and maintaining value sets for clinical quality measures. AMIA Annu Symp Proc. 2012;2012:988-96. Epub 2012 Nov 3.

Abstract | PMID: 23304374 | PMCID: PMC3540585

Abstract

Cameron D, Kavuluru R, Bodenreider O, Mendes PN, Sheth AP, Thirunarayan K. Semantic predications for complex information needs in biomedical literature BIBM 2011:512-519.

Abstract | pub2011069.pdf

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Jimeno-Yepes A, Mork J, Demner-Fushman D, Aronson AR. Automatic algorithm selection for MeSH Heading indexing based on meta-learning. International Symposium on Languages in Biology and Medicine, Singapore, December, 2011.

Abstract | pub2011-110.pdf | URL: http://ii.nlm.nih.gov/MTI_ML/index.shtml

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Kilicoglu H, Rosemblat G, Fiszman M, Rindflesch TC. Constructing a semantic predication gold standard from the biomedical literature. BMC Bioinformatics. 2011 Dec 20;12:486. doi: 10.1186/1471-2105-12-486.

Abstract | PMID: 22185221 | PMCID: PMC3281188 | URL: http://www.biomedcentral.com/1471-2105/12/486

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Cairelli M, Rindflesch TC. Identifying Potential Biomarkers for Mild Traumatic Brain Injury by Mining Semantic Relations from MEDLINE Citations [Poster[. 2011 Trauma Spectrum Conference, Bethesda, MD, December 9, 2011.

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Lu C, Browne AC. Converting Unicode Lexicon and Lexical Tools for ASII NLP Applications AMIA Annu Symp Proc 2011:1870.

Abstract | pub2011070.pdf

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Sahoo SS, Nguyen V, Bodenreider O, Parikh P, Minning T, Sheth AP. A unified framework for managing provenance information in translational research. BMC Bioinformatics. 2011 Nov 29;12:461. doi: 10.1186/1471-2105-12-461.

Abstract | pub2011023.pdf | PMID: 22126369 | PMCID: PMC3298549

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Bodenreider O, Peters L, Nguyen T. Browser and application programming interfaces for drug information sources. AMIA Annu Symp Proc, 2011: p. 2129.

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Peters L, Nguyen T, Bodenreider O. An application programming interface for NDF-RT AMIA Annu Symp Proc 2011:1922

Abstract | pub2011021.pdf

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Cairelli M, Rindflesch TC. Hierarchical Summarization of Concepts for Visual Discovery Browsing - a Pilot Study [abstract and demo]. Procedings of the IEEE VisWeek Workshop on Visual Analytics in Healthcare, October 23, 2011, Providence, RI, 37-40.

Abstract | URL: http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CD0QFjAA&url...

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Bodenreider O. API: NDF-RT

Abstract

Altemus AR. Mobile App: Native Voices: Native Peoples' Concepts of Health and Illness

Abstract

Zhang H, Fiszman M, Shin D, Miller CM, Rosemblat G, Rindflesch TC. Degree centrality for semantic abstraction summarization of therapeutic studies. J Biomed Inform. 2011 Oct;44(5):830-8. doi: 10.1016/j.jbi.2011.05.001. Epub 2011 May 8.

Abstract | PMID: 21575741 | PMCID: PMC3170688

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Rindflesch TC, Kilicoglu H, Fiszman M, Rosemblat G, Shin D. Semantic MEDLINE: An advanced information management application for biomedicine. Information Services and Use, 2011, 31(1): 15-21.

Abstract | pub-lhncbc-2011-109.pdf | URL: http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CDUQFjAA&url...

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Bodenreider O, Peters L, Nguyen T. RxNav: Browser and Application Programming Interfaces for Drug Information Sources [Abstract]. AMIA Annu Symp Proc 2011:2129

Abstract | pub2011018.pdf

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Plaza L, Jimeno-Yepes A, Diaz A, Aronson AR. Studying the correlation between different word sense disambiguation methods and summarization effectiveness in biomedical texts. BMC Bioinformatics. 2011 Aug 26;12:355. doi: 10.1186/1471-2105-12-355.

Abstract | PMID: 21871110 | PMCID: PMC3176269

Abstract

Rance B, Demner-Fushman D, Rindflesch TC, Bodenreider O. Exploring Automatic Approaches to Extracting Pharmacogenomic Information from the Biomedical Literature Proceedings of the 2011 PSB Workshop on Mining the Pharmacogenomics Literature 2011

Abstract | pub2011022.pdf

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Nguyen V, Bodenreider O, Minning T, Sheth AP. The knowledge-driven exploration of integrated biomedical knowledge sources facilitates the generation of new hypotheses Proceedings of the First International Workshop on Linked Science (LISC 2011) 2011:(electronic proceedings: http://ceur-ws.org/Vol-783/)

Abstract | pub2011019.pdf

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Jimeno-Yepes A, Aronson AR. Self-training and co-training in biomedical word sense disambiguation. BioNLP 2011 Workshop, June 2011, 182-183.

Abstract | pub-2011-113.pdf | URL: http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CDwQFjAB&url...

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Jimeno-Yepes A, McInnes BT, Aronson AR. Collocation analysis for UMLS knowledge-based word sense disambiguation. BMC Bioinformatics. 2011 Jun 9;12 Suppl 3:S4. doi: 10.1186/1471-2105-12-S3-S4.

Abstract | pub2010056.pdf | PMID: 21658291 | PMCID: PMC3111590

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Jimeno-Yepes A, McInnes BT, Aronson AR. Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation. BMC Bioinformatics. 2011 Jun 2;12:223. doi: 10.1186/1471-2105-12-223.

Abstract | PMID: 21635749 | PMCID: PMC3123611

Abstract

Simpson MS, Demner-Fushman D. Biomedical Text Mining: A Survey of Recent Progress. In Charu C. Aggarwal and ChengXiang Zhai, Editors. Mining Text Data. (Springer) 2011.

Abstract

Luciano JS, Andersson B, Batchelor C, Bodenreider O, Clark T, Denny 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, Schrimi L, Tonellato PJ, Wjetzel JZ, 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. doi: 10.1186/2041-1480-2-S2-S1.

Abstract | pub2011013.pdf | PMID: 21624155 | PMCID: PMC3102889

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Ripple AM, Mork JG, Humphreys BL, Knecht LS. A retrospective cohort study of structured abstracts in MEDLINE, 1992-2006. J Med Libr Assoc. 2011 Apr;99(2):160-3. doi: 10.3163/1536-5050.99.2.009.

Abstract | PMID: 21464855 | PMCID: PMC3066587

Abstract

Mork J, Peters L, Jimeno-Yepes A, Aronson AR, Bodenreider O. MetaMap in the CALBC Workshop II. CALBC Workshop II, March 2011.

Abstract | pub-2011-114.pdf | URL: http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CDUQFjAA&url...

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Zarin DA, Tse T, Williams RJ, Califf RM, Ide NC. The ClinicalTrials.gov results database--update and key issues. N Engl J Med. 2011 Mar 3;364(9):852-60. doi: 10.1056/NEJMsa1012065.

Abstract | PMID: 21366476 | PMCID: PMC3066456

Abstract

Doughty E, Kirk B, Kann MG, Bodenreider O. Integrating Drug-gene Associations Mined from the Literature with Drug Information Sources - A Comparison with PharmGKB Proceedings of the 2011 PSB Workshop on Mining the Pharmacogenomics Literature 2011

Abstract | LHNCBC-2011-002.pdf

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Doughty E, Kertesz-Farkas A, Bodenreider O, Thompson G, Adadey A, Peterson T, Kann MG. Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature. Bioinformatics. 2011 Feb 1;27(3):408-15. doi: 10.1093/bioinformatics/btq667. Epub 2010 Dec 7.

Abstract | pub2011001.pdf | PMID: 21138947 | PMCID: PMC3031038

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Zarin D, Tse T. The effect of funding source on outcome reporting among drug trials [Letter]. Ann Intern Med. 2011 Jan 18;154(2):137-8; author reply 138. doi: 10.7326/0003-4819-154-2-201101180-00020.

Abstract | PMID: 21242372

Abstract

Beaudoin DE, Longo N, Logan RA, Jones JP, Mitchell JA. Using information prescriptions to refer patients with metabolic conditions to the Genetics Home Reference website. J Med Libr Assoc. 2011 Jan;99(1):70-6. doi: 10.3163/1536-5050.99.1.012.

Abstract | pub2011004.pdf | PMID: 21243058 | PMCID: PMC3016649

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Jimeno-Yepes A, Wilkowski B, Mork J, van Lenten E, Demner-Fushman D, Aronson AR. A bottom-up approach to MEDLINE indexing recommendations. AMIA Annu Symp Proc. 2011;2011:1583-92. Epub 2011 Oct 22.

Abstract | PMID: 22195224 | PMCID: PMC3243198

Abstract

Peters L, Kapusnik-Uner JE, Nguyen T, Bodenreider O. An approximate matching method for clinical drug names. AMIA Annu Symp Proc. 2011;2011:1117-26. Epub 2011 Oct 22.

Abstract | pub2011020.pdf | PMID: 22195172 | PMCID: PMC3243188

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Wilkowski B, Fiszman M, Miller CM, Hristovski D, Arabandi S, Rosemblat G, Rindflesch TC. Graph-based methods for discovery browsing with semantic predications. AMIA Annu Symp Proc. 2011;2011:1514-23. Epub 2011 Oct 22.

Abstract | PMID: 22195216 | PMCID: PMC3243228

Abstract

Jimeno-Yepes A, Aronson AR. Query expansion for UMLS Metathesaurus disambiguation based on automatic corpus extraction. ICMLA 2010, Dec 2010.

Abstract | pub2010-089.pdf | URL: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=5708977&c...

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Lu C, Divita G, Browne AC. Development of Visual Tagging Tool AMIA Annu Symp Proc 2010:1156.

Abstract | pub2010065.pdf

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Jimeno-Yepes A, Aronson AR. Knowledge-based biomedical word sense disambiguation: comparison of approaches. BMC Bioinformatics. 2010 Nov 22;11:569. doi: 10.1186/1471-2105-11-569.

Abstract | pub2010057.pdf | PMID: 21092226 | PMCID: PMC3001745

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Bodenreider O, Demner-Fushman D. Investigating drug classes in biomedical terminologies from the perspective of clinical decision support. AMIA Annu Symp Proc. 2010 Nov 13;2010:56-60.

Abstract | pub2010006.pdf | PMID: 21346940 | PMCID: PMC3041355

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Fiszman M, Shin D, Sneiderman CA, Jin H, Rindflesch TC. A Knowledge Intensive Approach to Mapping Clinical Narrative to LOINC. AMIA Annu Symp Proc. 2010 Nov 13;2010:227-31.

Abstract | pub2010029.pdf | PMID: 21346974 | PMCID: PMC3041410

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Mougin F, Bodenreider O, Burgun A. Looking for Anemia (and Other Disorders) in SNOMED CT: Comparison of Three Approaches and Practical Implications. AMIA Annu Symp Proc. 2010 Nov 13;2010:527-31.

Abstract | pub2010010.pdf | PMID: 21347034 | PMCID: PMC3041405

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Peters L, Kapusnik-Uner JE, Bodenreider O. Methods for managing variation in clinical drug names. AMIA Annu Symp Proc. 2010 Nov 13;2010:637-41.

Abstract | pub2010011.pdf | PMID: 21347056 | PMCID: PMC3041346

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Zhang GQ, Bodenreider O. Large-scale, Exhaustive Lattice-based Structural Auditing of SNOMED CT. AMIA Annu Symp Proc. 2010 Nov 13;2010:922-6.

Abstract | pub2010014.pdf | PMID: 21347113 | PMCID: PMC3041382

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Zhang G-Q, Bodenreider O. Using SPARQL to Test for Lattices: Application to Quality Assurance in Biomedical Ontologies In: Patel-Schneider PF, Pan Y, Hitzler P, Mika P, Zhang L, Pan JZ, et al., editors. Proceedings of the 9th International Semantic Web Conference (ISWC 2010), Shanghai, China, November 7-11, 2010. Berlin, Heidelberg: Springer; 2010. p. 273-288.

Abstract

Mork JG, Aronson AR. The Medical Text Indexer (MTI) system for indexing biomedical literature. book chapter submitted to monograph Indexing Specialities: Medicine. Edited by L. Pilar Wyman. Medford, NJ: Information Today, Inc., in association with the American Society of Indexers, Phoenix, AZ. 2010.

Abstract

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. doi: 10.1136/jamia.2009.001149.

Abstract | PMID: 20962136 | PMCID: PMC3000749

Abstract

Willams RJ, Tse T, Harlan WR, Zarin DA. Registration of observational studies: is it time? CMAJ. 2010 Oct 19;182(15):1638-42. doi: 10.1503/cmaj.092252. Epub 2010 Jul 19.

Abstract | PMID: 20643833 | PMCID: PMC2952011

Abstract

Workman TE, Fiszman M, Hurdle JF, Rindflesch TC. Biomedical text summarization to support genetic database curation: using Semantic MEDLINE to create a secondary database of genetic information. J Med Libr Assoc. 2010 Oct;98(4):273-81. doi: 10.3163/1536-5050.98.4.003.

Abstract | PMID: 20936065 | PMCID: PMC2947139

Abstract

Jimeno-Yepes A, Aronson AR. Improving an automatically extracted corpus for UMLS Metathesaurus word sense disambiguation. BioSEPLN 2010, Sept. 2010.

Abstract | pub2010058.pdf

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Mork JG, Bodenreider O, Demner-Fushman D, Dogan RI, Lang FM, Lu Z, Névéol A, Peters L, Shooshan SE, Aronson AR. Extracting Rx information from clinical narrative. J Am Med Inform Assoc. 2010 Sep-Oct;17(5):536-9. doi: 10.1136/jamia.2010.003970.

Abstract | pub2010047.pdf | PMID: 20819859 | PMCID: PMC2995679

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Kilicoglu H, Fiszman M, Rosemblat G, Marimpietri S, Rindflesch TC. Arguments of Nominals in Semantic Interpretation of Biomedical Text BioNLM Workshop Proc, Assoc. for Computational Linguistics 2010

Abstract | pub2010030k.pdf

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Resnick MP, Ripple AM, Auston I, Rindflesch TC. An Ontology for Public Health to Support Enhanced Information Retrieval AMIA Annu Symp Proc. 2010

Abstract | pub2010031.pdf

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Demner-Fushman D, Mork JG, Shooshan SE, Aronson AR. UMLS content views appropriate for NLP processing of the biomedical literature vs. clinical text. J Biomed Inform. 2010 Aug;43(4):587-94. doi: 10.1016/j.jbi.2010.02.005. Epub 2010 Feb 10.

Abstract | pub2009040.pdf | PMID: 20152935 | PMCID: PMC2890296

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Aronson AR, Lang FM. An overview of MetaMap: historical perspective and recent advances. J Am Med Inform Assoc. 2010 May-Jun;17(3):229-36. doi: 10.1136/jamia.2009.002733.

Abstract | pub2010033.pdf | PMID: 20442139 | PMCID: PMC2995713

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Bodenreider O, Mougin F, Burgun A. Automatic Determination of Anti-coagulation Status with NDF-RT Proceedings of the 13th ISMB'2010 SIG meeting Bio-ontologies 2010:140-143

Abstract | pub2010003.pdf

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Cohen T, Widdows D, Schvaneveldt RW, Rindflesch TC. Logical Leaps and Quantum Connectives: Forging Paths through Predication Space AAAI-Fall 2010 Symposium on Quantum Informatics for Cognitive, Social, and Semantic Processes

Abstract | pub2010028.pdf

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Dumontier M, Andersson B, Batchelor C, Domarew C, Jentzsch A, Luciano J, Pichler E, Prud'hommeaux E, Whetzel PL, Bodenreider O, Clark T, Harland L, Kashyap V, Kos P, Kozlovsky J, McGurk J, Ogbuji C, Samwald M, Schriml L, Tonellato PJ, Zhao J, Stephens S. The Translational Medicine Ontology: Driving Personalized Medicine by Bridging the Gap from Bedside to Bench Proceedings of the 13th ISMB'2010 SIG meeting Bio-ontologies 2010:120-123

Abstract | pub2010004.pdf

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Keselman A, Rosemblat G, Kilicoglu H, Fiszman M, Jin H, Shin D, Rindflesch TC. Adapting Semantic Natural Language Processing Technology to Address Information Overload in Influenza Epidemic Management Journal of the American Society for Information Science and Technology (JASIST), 61(12):2531-2543, 2010

Abstract | pub2011005.pdf

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Sahoo SS, Bodenreider O, Hitzler P, Sheth A, Thirunarayan K. Provenance Context Entity (PaCE): Scalable Provenance Tracking for Scientific RDF Data SSDBM: Springer, 2010. p. 461-470

Abstract | pub2010012.pdf

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Cardillo E, Hernandez, Jr G, Bodenreider O. Integrating consumer-oriented vocabularies with selected professional ones from the UMLS using Semantic Web Technologies. Proceedings of the eHealth 2010 conference, 2010: p. (paper 10579 - electronic proceedings).

Abstract

Bodenreider O, Burgun A. A framework for comparing phenotype annotations of orthologous genes. Stud Health Technol Inform. 2010;160(Pt 2):1309-13.

Abstract | pub2010005.pdf | PMID: 20841896

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Erdogan H, Erdem E, Bodenreider O. Exploiting UMLS semantics for checking semantic consistency among UMLS concepts. Stud Health Technol Inform. 2010;160(Pt 1):749-53.

Abstract | pub2010007.pdf | PMID: 20841786

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Fiszman M, Bray B, Shin D, Kilicoglu H, Bennett GC, Bodenreider O, Rindflesch TC. Combining relevance assignment with quality of the evidence to support guideline development. Stud Health Technol Inform. 2010;160(Pt 1):709-13.

Abstract | pub2010008.pdf | PMID: 20841778

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Mortensen J, Bodenreider O. Comparing Pharmacologic Classes in NDF-RT and SNOMED CT. Proc SMBM 2010:119-124.

Abstract

Wei D, Bodenreider O. Using the abstraction network in complement to description logics for quality assurance in biomedical terminologies - a case study in SNOMED CT. Stud Health Technol Inform. 2010;160(Pt 2):1070-4.

Abstract | pub2010013.pdf | PMID: 20841848

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Zeng-Treitler Q, Kim H, Rosemblat G, Kesselman A. Can multilingual machine translation help make medical record content more comprehensible to patients? Stud Health Technol Inform. 2010;160(Pt 1):73-7.

Abstract | PMID: 20841653

Abstract

Mork JG, Bodenreider O, Demner-Fushman D, Doagan RI, Lang F-M, Lu Z, Névéol A, Peters L, Shooshan SE, Aronson AR. NLM's I2B2 tool system description. Third i2b2 Workshop on Natural Language Processing Challenges for Clinical Records, November, San Francisco, 2009

Abstract | pub2010032.pdf

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Williams R, Tse T. ClinicalTrials.gov: A public database of clinical research. Presented at: American Public Health Association 137th Annual Meeting and Expo; November 2009; Philadelphia, PA.

Abstract

Lu C, Humphrey SM, Rogers W, Browne AC. Development of a semantic type based WSD tool [Abstract]. AMIA Annu Symp Proc 2009:943.

Abstract | pub2009067.pdf

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Mougin F, Bodenreider O, Burgun A. Identifying anatomical concepts associated with ICD10 diseases. Proceedings of the 8th Conference on Terminology and Artificial Intelligence (TIA 2009), 2009: p. (electronic proceedings: http://www.irit.fr/TIA09/start_here.htm).

Abstract

Sneiderman C, Rosemblat G, Bray B, Fiszman M, Rindflesch TC. Matching Clinical Observations in Published Cardiology Case Reports to LOINC [Abstract]. AMIA Annu Symp Proc; 2009 Nov 14-18; San Francisco. p. 1036.

Abstract | pub2009056.pdf

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Aronson AR, Lang FM. The Evolution of MetaMap, a Concept Search Program for Biomedical Text AMIA Annu Symp Proc. 2009 Nov:22

Abstract | pub2009041.pdf

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Bodenreider O. Using SNOMED CT in combination with MedDRA for reporting signal detection and adverse drug reactions reporting. AMIA Annu Symp Proc. 2009 Nov 14;2009:45-9.

Abstract | pub2009026.pdf | PMID: 20351820 | PMCID: PMC2815504

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Burgun A, Mougin F, Bodenreider O. Two approaches to integrating phenotype and clinical information. AMIA Annu Symp Proc. 2009 Nov 14;2009:75-9.

Abstract | pub2009027.pdf | PMID: 20351826 | PMCID: PMC2815427

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Cohen T, Schvaneveldt R, Rindflesch TC. Predication-based semantic indexing: permutations as a means to encode predications in semantic space. AMIA Annu Symp Proc. 2009 Nov 14;2009:114-8.

Abstract | pub2009044.pdf | PMID: 20351833 | PMCID: PMC2815384

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Hristovski D, Kastrin A, Peterlin P, Rindflesch TC. Semantic relations for interpreting DNA microarray data. AMIA Annu Symp Proc. 2009 Nov 14;2009:255-9.

Abstract | pub2009045.pdf | PMID: 20351860 | PMCID: PMC2815475

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An L, Obradovic Z, Smith D, Bodenreider O, Megalooikonomou V. Mining Association Rules among Gene Functions in Clusters of Similar Gene Expression Maps. Workshop proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM09) -- Workshop on Data Mining in Functional Genomics 2009: p. 254-259

Abstract | PMID: 25635265 | PMCID: PMC4307020

Abstract

Bodenreider O. Provenance information in biomedical knowledge repositories – A use case. Proceedings of the First International Workshop on the role of Semantic Web in Provenance Management (SWPM 2009), 2009: p. (electronic proceedings: http://ceur-ws.org/Vol-526/).

Abstract

Névéol A, Mork JG, Aronson AR. Comment on 'MeSH-up: effective MeSH text classification for improved document retrieval'. Bioinformatics. 2009 Oct 15;25(20):2770-1; author reply 2772. doi: 10.1093/bioinformatics/btp483. Epub 2009 Aug 11.

Abstract | pub2009039.pdf | PMID: 19671694 | PMCID: PMC2765257

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Fiszman M, Demner-Fushman D, Kilicoglu H, Rindflesch TC. Automatic summarization of MEDLINE citations for evidence-based medical treatment: a topic-oriented evaluation. J Biomed Inform. 2009 Oct;42(5):801-13. doi: 10.1016/j.jbi.2008.10.002. Epub 2008 Nov 5.

Abstract | PMID: 19022398 | PMCID: PMC2776079

Abstract

Névéol A, Shooshan SE, Humphrey SM, Mork JG, Aronson AR. A recent advance in the automatic indexing of the biomedical literature. J Biomed Inform. 2009 Oct;42(5):814-23. doi: 10.1016/j.jbi.2008.12.007. Epub 2008 Dec 30.

Abstract | pub2009038.pdf | PMID: 19166973 | PMCID: PMC2818245

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Williams R, Tse T, Zarin D. Characterizing sponsor-imposed restrictions on disclosing results of clinical trials. Presented at: Sixth International Congress on Peer Review and Biomedical Publication; September 2009; Vancouver, BC, Canada.

Abstract

Zarin D, Tse T, Williams R. Frequency and nature of changes in primary outcome measures. Presented at: Sixth International Congress on Peer Review and Biomedical Publication; September 2009; Vancouver, BC, Canada.

Abstract

Tse T, Williams RJ, Zarin DA. Reporting "basic results" in ClinicalTrials.gov. Chest. 2009 Jul;136(1):295-303. doi: 10.1378/chest.08-3022.

Abstract | PMID: 19584212 | PMCID: PMC2821287

Abstract

Tse T, Williams RJ, Zarin DA. Update on Registration of Clinical Trials in ClinicalTrials.gov. Chest. 2009 Jul;136(1):304-5. doi: 10.1378/chest.09-1219.

Abstract | PMID: 19584213 | PMCID: PMC2821288

Abstract

Bodenreider O, Peters LB. A graph-based approach to auditing RxNorm. J Biomed Inform. 2009 Jun;42(3):558-70. doi: 10.1016/j.jbi.2009.04.004. Epub 2009 Apr 24.

Abstract | PMID: 19394440 | PMCID: PMC2722378

Abstract

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. doi: 10.1016/j.jbi.2008.12.003. Epub 2008 Dec 25.

Abstract | PMID: 19154797 | PMCID: PMC2729758

Abstract

Mougin FL, Bodenreider O, Burgun A. Analyzing polysemous concepts from a clinical perspective: application to auditing concept categorization in the UMLS. J Biomed Inform. 2009 Jun;42(3):440-51. doi: 10.1016/j.jbi.2009.03.008. Epub 2009 Mar 18.

Abstract | PMID: 19303057

Abstract

Vizenor LT, Bodenreider O, McCray AT. Auditing associative relations across two knowledge sources. J Biomed Inform. 2009 Jun;42(3):426-39. doi: 10.1016/j.jbi.2009.01.004.

Abstract | PMID: 19475724 | PMCID: PMC2891883

Abstract

Bodenreider O, Burgun A. Desiderata for an Ontology of Diseases for the Annotation of Biological Datasets Proc ICBO 2009:39-42

Abstract | pub2009023.pdf

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Hristovski D, Kastrin A, Peterlin B, Rindflesch TC. Combining Semantic Relations and DNA Microarray Data for Novel Hypotheses Generation Lecture Notes in Bioinformatics. Springer

Abstract | pub2009060.pdf

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Kilicoglu H, Demner-Fushman D, Rindflesch TC, Wilczynski NL, Haynes RB. Towards Automatic Recognition of Scientifically Rigorous Clinical Research Evidence J Am Med Inform Assoc. 2009 Jan-Feb;16(1):25-31. Epub 2008 Oct 24.

Abstract | PMID: 18952929 | PMCID: PMC2605595

Abstract

Mariño-Ramírez L, Tharakaraman K, Bodenreider O, Spounge J, Landsman D. Identification of cis-regulatory Elements in Gene Co-expression Networks Using A-GLAM. Methods Mol Biol. 2009;541:1-22.

Abstract | PMID: 19381547 | PMCID: PMC2719765

Abstract

Schulz S, Beisswanger, van den Hoek L, Bodenreider O, van Mulligen EM. Alignment of the UMLS Semantic Network with BioTop: Methodology and Assessment Bioinformatics 2009;25(12):i69-i76

Abstract | PMID: 19478019 | PMCID: PMC2687948

Abstract

Tse T, Zarin DA. Clinical Trial Registration and Results Reporting: ClinicalTrials.gov and FDAAA FDLI Update. 2009 Jan/Feb;1:18-22

Abstract

Zweigenbaum P, Demner-Fushman D. Bioinformatics: Tools and Applications. Springer 2009.

Abstract

Bodenreider O. Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support. Geissbuhler A, Kulikowski C, editors. IMIA Yearbook of Medical Informatics 2008. Methods Inf Med, 2008. 47(Suppl 1): p. 67-79.

Abstract | PMID: 18660879 | PMCID: PMC2592252

Abstract

Bodenreider O. Comparing SNOMED CT and the NCI Thesaurus through Semantic Web Technologies Proc. KR-MED 2008

Abstract

Bodenreider O. Ontologies and Data Integration in Biomedicine: Success Stories and Challenging Issues In: Bairoch A, Cohen-Boulakia S, Froidevaux C, editors. Proceedings of the Fifth International Workshop on Data Integration in the Life Sciences (DILS 2008); Berlin Heidelberg New York: Springer; 2008. p. 1-4

Abstract | pub2008024.pdf

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Bodenreider O. Semantic Web for Translational Biomedicine: Two Pilot Experiments [Abstract]. Proc. MIA Summit on Translational Bioinformatics 2008:141

Abstract | pub2008025.pdf

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Burgun A, Bodenreider O. Accessing and Integrating Data and Knowledge for Biomedical Research Yearb Med Inform. 2008:91-101

Abstract | pub2008027.pdf | PMID: 18660883 | PMCID: PMC2553094

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Kilicoglu H, Fiszman M, Rodriguez A, Shin D, Ripple AM, Rindflesch TC. Semantic MEDLINE: A Web Application for Managing the Results of PubMed Searches Proc. Third Int'l Symposium for Semantic Mining in Biomedicine, 69-76

Abstract

Leroy G, Miller T, Rosemblat G, Browne A. A Balanced Approach to Health Information Evaluation: A Vocabulary-based Naive Bayes Classifier and Readability Formulas JASIST, 59(9):1409-1419, 2008

Abstract | pub2008009.pdf

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Mougin F, Burgun A, Bodenreider O, Chabalier J, Loreal O, Le Beux P. Automatic Methods for Integrating Biomedical Data Sources in a Mediator-Based System Proc DILS 2008. Berlin Heidelberg New York: Springer; 2008. p. 61-76

Abstract | pub2008028.pdf

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Peters L, Bodenreider O. Using the RxNorm Web Services API for Quality Assurance Purposes AMIA Annu Symp Proc. 2008 Nov 6:591-5.

Abstract | PMID: 18999038 | PMCID: PMC2656097

Abstract

Rogers J, Bodenreider O. SNOMED CT: Browsing the Browsers Proc of the Third International Conference on Knowledge Representation in Medicine (KR-MED 2008) 2008:30-36

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Zeng K, Bodenreider O, Kilbourne J, Nelson SJ. Standards, Security and Usability: Experience with MyMedicationList [Abstract]. Proc. AMIA Spring Congress 2008

Abstract | pub2008035.pdf

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Bodenreider O, Coban ZH, Doganay MC, Erdem E, Kosucu H. A preliminary report on answering complex queries related to drug discovery using answer set programming. Proceedings of the 3rd International Workshop on Applications of Logic Programming to the (Semantic) Web and Web Services (ALPSWS2008), 2008: p. 85-90 (electronic proceedings: http://ceur-ws.org/Vol-434/).

Abstract

Liu F, Fontelo P, Fiszman M. Clinically-Weighted Terms in the Evaluation of MeSH Translations: BabelMeSH in Portuguese as a Model. AMIA Annu Symp Proc; 2008 Nov 8-12; Washington DC. p. 1027.

Abstract | PMID: 18998783

Abstract

Sneiderman CA, Demner-Fushman D, Fung KW, Bray B. UMLS-based Automatic Image Indexing. AMIA Annu Symp Proc; 2008 Nov 8-12; Washington DC. p. 1141.

Abstract | PMID: 18998868

Abstract

Aronson AR, Mork JG, Neveol A, Shooshan SE, Demner-Fushman D. Methodology for Creating UMLS Content Views Appropriate for Biomedical Natural Language Processing AMIA Annu Symp Proc. 2008 Nov 6:21-5

Abstract | PMID: 18998883 | PMCID: PMC2655934

Abstract

Bodenreider O. Issues in Mapping LOINC Laboratory Tests to SNOMED CT AMIA Annu Symp Proc. 2008 Nov 6:51-5

Abstract | PMID: 18999311 | PMCID: PMC2655945

Abstract

Fiszman M, Ortiz E, Bray BE, Rindflesch TC. Semantic Processing to Support Clinical Guideline Development AMIA Annu Symp Proc. 2008 Nov 6:187-91

Abstract | PMID: 18999127 | PMCID: PMC2656081

Abstract

He Y, Kayaalp M. Biological Entity Recognition with Conditional Random Fields AMIA Annu Symp Proc. 2008 Nov 6:293-7

Abstract | PMID: 18999272 | PMCID: PMC2656029

Abstract

Kilicoglu H, Demner-Fushman D, Rindflesch TC, Wilczynski NL, Haynes RB. Toward Automatic Recognition of High Quality Clinical Evidence. AMIA Annu Symp Proc. 2008 Nov 6:368

Abstract | PMID: 18998881 | PMCID: PMC2656036

Abstract

Lu C, Humphrey SM, Browne AC. A method for verifying a vector-based text classification system AMIA Annu Symp Proc. 2008 Nov 6:1030.

Abstract | pub2008078.pdf | PMID: 18998786

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Lu C, Browne AC, Allen C, Divita G. Using Lexical tools to convert Unicode characters to ASCII AMIA Annu Symp Proc. 2008 Nov 6:1031.

Abstract | pub2008079.pdf | PMID: 18998787

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Mougin F, Bodenreider O. Auditing the NCI Thesaurus with Semantic Web Technologies AMIA Annu Symp Proc. 2008 Nov 6:500-4

Abstract | pub2008026.pdf | PMID: 18999265 | PMCID: PMC2655981

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Nelson SJ, Zeng K, Bodenreider O. MyMedicationList: Integrating Personal Medication Records with Resources AMIA Annu Symp Proc. 2008 Nov 6:1228

Abstract | pub2008029.pdf | PMID: 18998987

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Sharp M, Bodenreider O, Wacholder N. A Framework for Characterizing Drug Information Sources AMIA Annu Symp Proc. 2008 Nov 6:662-6

Abstract | PMID: 18999182 | PMCID: PMC2656044

Abstract

Zeng K, Bodenreider O, Nelson SJ. Design and Implementation of a Personal Medication Record - MyMedicationList AMIA Annu Symp Proc. 2008 Nov 6:844-8

Abstract | pub2008036.pdf | PMID: 18998962 | PMCID: PMC2656100

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Sahoo SS, Bodenreider O, Rutter JL, Skinner KJ, Sheth AP. An Ontology-driven Semantic Mash-up of Gene and Biological pathway information: Application to the domain of nicotine dependence J Biomed Inform. 2008 Oct;41(5):752-65. Epub 2008 Feb 29

Abstract | PMID: 18395495 | PMCID: PMC2766186

Abstract

Kim H, Goryachev S, Rosemblat G, Browne A, Keselman A, Zeng-Treitler Q. Beyond Surface Characteristics: A New Health Text-specific Readability Measurement AMIA Annu Symp Proc. 2007 Oct 11:418-22

Abstract | PMID: 18693870 | PMCID: PMC2655856

Abstract

Neveol A, Deserno TM, Darmoni SJ, Guld MO, Aronson AR. Natural Language Processing Versus Content-BasedImage Analysis for Medical Document Retrieval J Am Soc Inf Sci Technol. 2008 Sep 18;60(1):123-134

Abstract | PMID: 19633735 | PMCID: PMC2714909

Abstract

Sneiderman C, Fontelo P, Ackerman MJ. XO Computer Application to Medical Science Education. J International Assoc of Medical Science Educators: Special Issue Poster Abstracts of the 12th IAMSE Annual Meeting (2008 Jul 25-29; Salt Lake City);18(supplement 2):100.

Abstract | pub2009010.pdf

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Felts RL, Bennett A, Shi D, Freed E, Lifson J, Lowekamp B, Yoo TS, Bliss D, Subramaniam S. 3D Imaging of HIV transmission and entry using electron tomography and ion-abrasion scanning electron microscopy. Three Dimensional Electron Microscopy: Technical Advances and Recent Breakthroughs in 3DEM. Gordon Research Conference; 2008 Jun 15-20; Lucca (Barga), Italy.

Abstract

Tharakaraman K, Bodenreider O, Landsman D, Spouge JL, Marino-Ramirez. The Biological Function of Some Human Transcription Factor Binding Motifs Varies with Position Relative to the Transcription Start Site Nucleic Acids Res. 2008 May;36(8):2777-86. Epub 2008 Mar 26

Abstract | PMID: 18367472 | PMCID: PMC2377430

Abstract

Zarin DA, Tse T. Moving Towards Transparency of Clinical Trials Science. 2008 Mar 7;319(5868):1340-2.

Abstract | PMID: 18323436 | PMCID: PMC2396952

Abstract

Leroy G, Fiszman M, Rindflesch TC. The Impact of Directionality in Predications on Text Mining Hawaii International Conference on System Sciences (HICSS-41), January 2008

Abstract

Demner-Fushman D, Humphrey SM, Ide NC, Loane RF, Mork J, Ruch P, Ruiz ME, Smith LH, Wilbur WJ, Aronson AR. Combining Resources to Find Answers to Biomedical Questions Proc TREC 2007, 205-14

Abstract | pub2007061.pdf

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Rosemblat G, Graham L, Tse T. Extractive Summarization in Clinical Trials Protocol Summaries: A Case Study Proc IICAI-2007, pp. 1824-1837

Abstract | pub2007060.pdf

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Bangalore AK, Divita G, Humphrey SM, Browne AC, Thorn KE. Automatic Categorization of Google Search Results for Medical Queries using JDI Medinfo 2007: Proc. of the 11th World Congress on Health (Medical) Informatics

Abstract

Fung KW, Bodenreider O, Aronson AR, Hole WT, Srinivasan S. Combining Lexical and Semantic Methods of Inter-terminology Mapping Using the UMLS. Stud Health Technol Inform. 2007;129(Pt 1):605-9.

Abstract | pub2007045.pdf | PMID: 17911788 | PMCID: PMC2430093

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Gallagher ME. Keeping the Promises Associated with Your Digital Assets: Is it Possible? In: Archiving 2007 Final Program and Proceedings, pp.146-149, 2007.

Abstract | pub2007007.pdf

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Logan RA, Tse T. A Multidiscipline Conceptual Framework for Consumer Health Informatics Stud Health Technol Inform. 2007;129(Pt 2):1169-73

Abstract | pub2007030.pdf | PMID: 17911899

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Névéol A, Mork JG, Aronson AR. Automatic indexing of specialized documents: using generic vs. domain-specific document representations. Proc 2007 Workshop BioNL'07, 183-92.

Abstract | pub2007036.pdf

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Sahoo SS, Zeng K, Bodenreider O, Sheth A. From 'Glycosyltransferase' to 'Congenital Muscular Dystrophy': Integrating Knowledge from NCBI Entrez Gene and the Gene Ontology Stud Health Technol Inform. 2007;129(Pt 2):1260-4

Abstract | pub2007048.pdf | PMID: 17911917 | PMCID: PMC2562001

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Zeng K, Bodenreider O. Experience in Integrating Large RDF-based Biomedical Knowledge Resources with Oracle [Abstract]. Proc 8th International Oracle Life Sciences User Group Meeting 2007:(electronic proceedings: http://www.olsug.org/wiki/images/d/d1/Kelly_Zheng.pdf)

Abstract | pub2007008.pdf

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Zeng K, Bodenreider O, Kilbourne J, Nelson SJ. RxNav: An Integrated View on Drug Information Proc AMIA Annu Symp; 2007:1202

Abstract | pub2007086.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

Abstract | pub2007041.pdf | PMID: 18974854 | PMCID: PMC2575410

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Zhang S, Bodenreider O. Hybrid Alignment Strategy for Anatomical Ontologies Results of the 2007 Ontology Alignment Contest Proc OAEI 2007:139-149

Abstract | pub2007088.pdf

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Zhang S, Bodenreider O. Lessons Learned from Cross-Validating Alignments Between Large Anatomical Ontologies Stud Health Technol Inform. 2007;129(Pt 1):822-6

Abstract | pub2007049.pdf | PMID: 17911831 | PMCID: PMC2408442

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Rosemblat G, Logan R. The Consumers' Perspective: Text Features and Readability of Consumer Health Text Mednet 2007: Germany. 12 Oct 2007

Abstract

Bashyam V, Divita G, Bennett DB, Browne AC, Taira RK. A normalized lexical lookup approach to identifying UMLS concepts in free text. Stud Health Technol Inform. 2007;129(Pt 1):545-9.

Abstract | PMID: 17911776

Abstract

Zeng K, Bodenreider O, Kilbourne J, Nelson S. RxNav: Towards an Integrated View on Drug Information MEDINFO 2007:386.

Abstract | pub2007046.pdf

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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

Abstract | pub2007084.pdf | PMID: 18693803

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Fiszman M, Rosemblat G, AhlersCB, Rindflesch TC. Identifying Risk Factors for Metabolic Syndrome in Biomedical Text AMIA Annu Symp Proc. 2007 Oct 11:249-53

Abstract | PMID: 18693836 | PMCID: PMC2655815

Abstract

Hurdle JF, Botkin J, Rindflesch TC. Leveraging Semantic Knowledge in IRB Databases to Improve Translation Science AMIA Annu Symp Proc. 2007 Oct 11:349-53

Abstract | PMID: 18693856 | PMCID: PMC2655842

Abstract

Névéol A, Shooshan SE, Mork JG, Aronson AR. Fine-grained indexing of the biomedical literature: MeSH subheading attachment for a MEDLINE indexing tool. AMIA Annu Symp Proc. 2007 Oct 11:553-7.

Abstract | pub2007062.pdf | PMID: 18693897 | PMCID: PMC2655865

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Zeng K, Bodenreider O. Integrating the UMLS into an RDF-Based Biomedical Knowledge Repository AMIA Annu Symp Proc. 2007 Oct 11:1170.

Abstract | pub2007085.pdf | PMID: 18694266

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Zhang S, Bodenreider O. Identifying Mismatches in Alignments of Large Anatomical Ontologies AMIA Annu Symp Proc. 2007 Oct 11:851-5

Abstract | pub2007087.pdf | PMID: 18693957 | PMCID: PMC2655858

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Bodenreider O, Burgun A. Oncologic Pathology in Biomedical Terminologies: Challenges for Data Integration Proc APIII conference on "Anatomic Pathology Informatics and Imaging Support for Translational Medicine", Pittsburgh, Pennsylvania, September 9-12, 2007:Abstract 342.

Abstract | pub2007050.pdf

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Sneiderman CA, Demner-Fushman D, Fiszman M, Ide NC, Rindflesch TC. Knowledge-Based Methods to Help Clinicians Find Answers in MEDLINE. J Am Med Inform Assoc. 2007 Nov-Dec;14(6):772-80. Epub 2007 Aug 21.

Abstract | PMID: 17712086 | PMCID: PMC2213491

Abstract

Ruch P, Geissbuhler A, Gobeill J, Lisacek F, Tbahriti I, Veuthey A, Aronson AR. Using Discourse Analysis to Improve Text Categorization in MEDLINE Stud Health Technol Inform. 2007;129(Pt 1):710-5

Abstract | pub2007034.pdf | PMID: 17911809

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Aronson AR, Bodenreider O, Demner-Fushman D, Fung KW, Lee VK, Mork JG, Névéol A, Peters L, Rogers WJ. From indexing the biomedical literature to coding clinical text: experience with MTI and machine learning approaches. Proc 2007 Workshop BioNL'07, June 2007, pp. 105-112, Prague, Czech Republic.

Abstract | pub2007040.pdf

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Fiszman M, Demner-Fushman D, Lang FM, Goetz P, Rindflesch TC. Interpreting Comparative Constructons in Biomedical Text Proc 2007 Workshop BioNL'07, June 2007, pp. 137-144, Prague, Czech Republic

Abstract | pub2007037.pdf

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Ide NC, Loane RF, Demner-Fushman D. Essie: A Concept-based Search Engine for Structured BiomedicalText J Am Med Inform Assoc. 2007 May-Jun;14(3):253-63. Epub 2007 Feb 28

Abstract | pub2007019.pdf | PMID: 17329729 | PMCID: PMC2244877

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Walker FL, Gallagher ME, Thoma GR. PDF File Migration to PDF/A: Technical Considerations. Proc IS&T Archiving 2007. Arlington, Virginia, May 2007; 6-11.

Abstract | pub2007020.pdf

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Zarin DA, Ide NC, Tse T, Harlan WR, West JC, Lindberg DA. Issues in the registration of clinical trials. JAMA. 2007 May 16;297(19):2112-20

Abstract | pub2007017.pdf | PMID: 17507347

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Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, Doherty D, Forsberg K, Gao Y, Kashyap V, Kinoshita J, Luciano J, Marshall MS, Oqbuji C, Rees J, Stephens S, Wong GT, Wu E, Zaccaqnini D, Hongsermeier T, Neumann E, Herman I, Cheung KH. Advancing Translational Research with the Semantic Web BMC Bioinformatics. 2007 May 9;8 Suppl 3:S2

Abstract | pub2007013.pdf | PMID: 17493285 | PMCID: PMC1892099

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Logan RA. Clinical, Classroom or Personal Education: Attitudes About Health Literacy J Med Libr Assoc. 2007 Apr;95(2):127-37, e48

Abstract | pub2007029.pdf

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Bodenreider O, Smith B, Kumar A, Burgun A. Investigating Subsumption in SNOMED CT: An Exploration into Large Description Logic-based Biomedical Terminologies Artif Intell Med. 2007 Mar;39(3):183-95. Epub 2007 Jan 22

Abstract | pub2007011.pdf | PMID: 17241777 | PMCID: PMC2442845

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Brennan PF, Rindflesch TC. Towards Linking Patients and Clinical Information: Detecting UMLS Concepts in E-mail J Biomed Inform. 2003 Aug-Oct;36(4-5):334-41

Abstract | pub2003070.pdf

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Zarin DA, Keselman A. Registering a Clinical Trial in ClinicalTrials.gov Chest. 2007 Mar;131(3):909-12. Epub 2007 Feb 15

Abstract | pub2007018.pdf | PMID: 17303677

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Zheng S, Mork P, Bodenreider O, Bernstein PA. Comparing Two Approaches for Aligning Representations of Anatomy Artif Intell Med. 2007 Mar;39(3):227-36. Epub 2007 Jan 23

Abstract | pub2007015.pdf | PMID: 17250997 | PMCID: PMC1973160

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Keselman A, Tse T, Crowell J, Browne AC, Ngo L, Zeng Q. Assessing Consumer Health Vocabulary Familiarity: An Exploratory Study J Med Internet Res. 2007 Mar 14;9(1):e5

Abstract | pub2007079.pdf | PMID: 17478414 | PMCID: PMC1874513

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Zeng QT, Tse T, Divita G, Keselman A, Crowell J, Browne AC, Goryachev S, Ngo L. Term Identification Methods for Consumer Health Vocabulary Development J Med Internet Res. 2007 Feb 28;9(1):e4.

Abstract | pub2007080.pdf | PMID: 17478413 | PMCID: PMC1874512

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Ahlers C, Fiszman M, Demner-Fushman D, Lang F, Rindflesch TC. Extracting Semantic Predications from MEDLINE Citations for Pharmacogenomics Pacific Symposium on Biocomputing 2007 12:209-220

Abstract | pub2007002.pdf | PMID: 17990493

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Lussier YA, Bodenreider O. Clinical Ontologies for Discovery Applications In: Baker CJO, Cheung K-H, editors. Semantic Web: Revolutionizing knowledge discovery in the life sciences. New York: Springer; 2007. p. 101-119.

Abstract | pub2007012.pdf

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Sahoo S, Bodenreider O, Zeng K, Sheth AP. An Experiment in Integrationg Large Biomedical Knowledge Resources with RDF: Application to Associating Genotype and Phenotype Information Proc Workshop on Health Care and Life Sciences Data Integration for the Semantic Web at WWW2007 (electronic proceedings: http://www2007.org/workshops/paper_149.pdf)

Abstract | pub2007014.pdf

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Névéol A, Shooshan SE, Humphrey SM, Rindflesch TC, Aronson AR. Multiple approaches to fine-grained indexing of the biomedical literature. Pac Symp Biocomput. 2007:292-303.

Abstract | pub2007003.pdf | PMID: 17990500 | URL: http://psb.stanford.edu/psb-online/proceedings/psb07/abstracts/2007_p292.html

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Azuaje F, Wang H, Zheng H, Bodenreider O, Chesneau A. Predictive Integration of Gene Ontology-Driven Similarity and Functional Interactions Proc ICDM 2006, Workshop on Data Mining in Bioinformatics: IEEE Computer Society Press; 2006. p. 114 - 119

Abstract | pub2006064.pdf

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Fomous C, Miller N. The Role of the National Library of Medicine Web Sites in Newborn Screening Education Ment Retard Dev Disabil Res Rev. 2006;12(4):305-12

Abstract | pub2006062.pdf | PMID: 17183579

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Keselman A, Massengale L, Ngo L, Browne A, Zeng Q. The Effect of User Factors on Consumer Familiarity with Health Terms: Using Gender as a Proxy for Background Knowledge about Gender-Specific Illnesses ISBMDA 2006: 472-481

Abstract | pub2006067.pdf

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Logan RA, Shin JH, Park J. Prevailing Impressions of Social Actors in Korean News Coverage of a Public Health Crisis Science Communication. 25:4:399-418 (June 2004)

Abstract | pub2004074.pdf

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Mougin F, Burgun A, Bodenreider O. Using WordNet to Improve the Mapping of Data Elements to UMLS for Data Sources Integration AMIA Annu Symp Proc. 2006:574-8

Abstract | pub2006055.pdf | PMID: 17238406 | PMCID: PMC1839757

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Siegel ER, Logan RA, Harnsberger RL, Cravedi K, Krause JA, Lyon B, Hajarian K, Uhl J, Ruffin A, Lindberg DA. Information Rx: Evaluation of a New Informatics Tool for Physicians, Patients, and Libraries Inf Serv Use. 2006;26(1):1-10.

Abstract | pub2006068.pdf | PMID: 17060946

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Bodenreider O, Zhang S. Comparing the Representation of Anatomy in the FMA and SNOMED CT AMIA Annu Symp Proc. 2006:46-50

Abstract | pub2006054.pdf | PMID: 17238300 | PMCID: PMC1839313

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Bodenreider O. Lexical, Terminological and Ontological Resources for Biological Text Mining Ananiadou S, McNaught J, editors. Text mining for biology and biomedicine: Artech House; 2006. p. 43-66.

Abstract | pub2006007.pdf

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Divita G, Browne AC, Loanne R. dTagger: A POS Tagger AMIA Annu Symp Proc. 2006:200-3

Abstract | pub2006041.pdf | PMID: 17238331 | PMCID: PMC1839340

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Fomous C, Mitchell JA, McCray A. Genetics Home Reference: Helping Patients Understand the Role of Genetics in Health and Disease Community Genet. 2006;9(4):274-8

Abstract | pub2006027.pdf

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Golbreich C, Zhang S, Bodenreider O. The Foundational Model of Anatomy in OWL: Experience and Perspectives Web Semant. 2006;4(3):181-195

Abstract | pub2006025.pdf | PMID: 18360535 | PMCID: PMC2270940

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He Y, Kayaalp M. Interpretation of Data and Identification of Information are Sine Qua Non for Modern Digital Information Services AMIA Annu Symp Proc. 2006:946

Abstract | pub2006024.pdf | PMID: 17238565 | PMCID: PMC1839285

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Mougin F, Bodenreider O. Comparing Two Approaches to Eliminating Cycles in Terminological Systems Proc RFIA 2006

Abstract | pub2006008.pdf

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Rosemblat G, Tse T. User Study of a Spanish-language ClinicalTrials.gov Prototype System AMIA Annu Symp Proc. 2006:659-63

Abstract | pub2006040.pdf | PMID: 17238423 | PMCID: PMC1839723

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Ruch P, Tbahriti I, Bobeill J, Aronson AR. Argumentative Feedback: A Linguistically-motivated Term Expansion for Information Retrieval Proc COLING/ACL 2006, 675-82

Abstract | pub2006071.pdf

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Sneiderman C, Demner-Fushman D, Fiszman M, Rosemblat G, Lang FM, Norwood D, Rindflesch TC. Semantic Processing to Enhance Retrieval of Diagnosis Citations from Medline AMIA Annu Symp Proc. 2006:1104

Abstract | pub2006039.pdf | PMID: 17238723 | PMCID: PMC1839324

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Vizenor L, Bodenreider O, Peters L, McCray AT. Enhancing Biomedical Ontologies through Alignment of Semantic Relationships: Exploratory Approaches AMIA Annu Symp Proc. 2006:804-8.

Abstract | pub2006059.pdf | PMID: 17238452 | PMCID: PMC1839588

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Vizenor L, Bodenreider O. Using Dependence Relations in MeSH as a Framework for the Analysis of Disease Information in Medline Proc SMBM-2006, 2006:76-83

Abstract | pub2006021.pdf

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Zeng K, Bodenreider O, Kilbourne J, Nelson SJ. RxNav: A Web Service for Standard Drug Information AMIA Annu Symp Proc. 2006:1156

Abstract | pub2006060.pdf | PMID: 17238775 | PMCID: PMC1839335

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Zhang S, Bodenreider O, Golbreich C. Experience in Reasoning with the Foundational Model of Anatomy in OWL DL Pac Symp Biocomput. 2006:200-11

Abstract | pub2006009.pdf | PMID: 17094240

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Zhang S, Bodenreider O. NLM Anatomical Ontology Alignment system: Results of the 2006 ontology alignment contest Proc OAEI 2006 2006:145-156

Abstract | pub2006061.pdf

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Slaughter LA, Soergel D, Rindflesch TC. Semantic Representation of Consumer Questions and Physician Answers Int J Med Inform. 2006 Jul;75(7):513-29. Epub 2005 Aug 24

Abstract | pub2005050.pdf | PMID: 16125448

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Mougin F, Burgun A, Bodenreider O. Data Integration Through Data Elements: Mapping Data Elements to Terminological Resources BMC Bioinformatics. 2006 Nov 24;7 Suppl 3:S6.

Abstract | pub2006019.pdf

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Mougin F, Burgun A, Bodenreider O. Mapping Data Elements to Terminological Resources for Integrating Biomedical Data Sourcse BMC Bioinformatics. 2006 Nov 24;7 Suppl 3:S6

Abstract | pub2006056.pdf | PMID: 17134479 | PMCID: PMC1764450

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Siegel ER, Wood FB, Dutcher GA, Ruffin A, Logan RA, Scott J. Assessment of the National Library of Medicine's Health Disparities Plan: A Focus on Native American Outreach J Med Libr Assoc. 2005 Oct;93(4 Suppl):S10-20

Abstract | pub2005070.pdf | PMID: 16239954 | PMCID: PMC1255749

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Wood FB, Siegel ER, Dutcher GA, Ruffin A, Logan RA. The National Library of Medicine's Native American Outreach Portfolio: A Descriptive Overview J Med Libr Assoc. 2005 Oct;93(4 Suppl):S21-34

Abstract | pub2005069.pdf | PMID: 16239955 | PMCID: PMC1255750

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Rosemblat G, Logan R, Tse T, Graham L. Text Features and Readability: Expert Evaluation of Consumer Health Text Mednet 2006. October 14-16, 2006. Toronto, Canada

Abstract | pub2006029.pdf

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Aronson AR. API: Semantic Knowledge Representation

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Morrison SM. Web Interface: Genetics Home Reference

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Bodenreider O, Stevens R. Bio-ontologies: Current Trends and Future Directions Brief Bioinform. 2006 Sep;7(3):256-74. Epub 2006 Aug 9

Abstract | pub2006053.pdf | PMID: 16899495 | PMCID: PMC1847325

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Tsaparas P, Marino-Ramirez L, Bodenreider O. Global Similarity and Local Divergence in Human and Mouse Gene Co-expression Networks BMC Evol Biol. 2006 Sep 12;6:70

Abstract | pub2006058.pdf | PMID: 16968540 | PMCID: PMC1601971

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Mitchell JA, Fomous C, Fun J. Challenges and strategies of the Genetics Home Reference J Med Libr Assoc. 2006 Jul;94(3):336-42

Abstract | pub2006026.pdf | PMID: 16888669 | PMCID: PMC1525308

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Rosemblat G, Graham L. Cross-Language Search in a Monolingual Health Information System: Flexible Designs and Lexical Processes Proc ISKO, pages 173-182, Vienna, Austria, July 2006.

Abstract | pub2006015.pdf

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Rosemblat G, Graham L. A Pragmatic Approach to Summary Extraction in Clinical Trials Proc HLT-NAACL 06, pages 124-125, New York City, June 2006

Abstract | pub2006012.pdf

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Zhang S, Bodenreider O. Law and Order: Assessing and Enforcing Compliance with Ontological Modeling Principles in the Foundational Model of Anatomy Comput Biol Med. 2006 Jul-Aug;36(7-8):674-93. Epub 2005 Sep 6.

Abstract | pub2006023.pdf | PMID: 16144698 | PMCID: PMC1784072

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Masseroli M, Kilicoglu H, Lang F-M, Rindflesch TC. Argument-predicate Distance as a Filter for Enhancing Precision in Extracting Predications on the Genetic Etiology of Disease. BMC Bioinformatics. 2006 Jun 8;7:291.

Abstract | pub2006073.pdf | PMID: 16762065 | PMCID: PMC1564420

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Hristovski D, Friedman C, Rindflesch TC. Exploiting Semantic Relations for Literature-Based Discovery AMIA Annu Symp Proc. 2006:349-53

Abstract | pub2006074.pdf | PMID: 17238361 | PMCID: PMC1839258

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Fiszman M, Rindflesch TC, Kilicoglu H. Summarizing Drug Information in Medline Citations AMIA Annu Symp Proc. 2006; 254-8

Abstract | pub2006076.pdf | PMID: 17238342 | PMCID: PMC1839479

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Gallagher ME, Moffatt C. Surviving Change: The First Step Toward Sustaining Your Digital Library In: J. Trant and D. Bearman (eds.). Museums and the Web 2006: Proceedings, Toronto: Archives & Museum Informatics, published March 1, 2006.

Abstract | pub2006006.pdf

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Woods JW, Sneiderman CA, Hameed K, Ackerman MJ, Hatton C. Using UMLS Metathesaurus Concepts to Describe Medical Images: Dermatology Vocabulary. Comput Biol Med. 2006 Jan;36(1):89-100.

Abstract | pub2006013.pdf | PMID: 16324910

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Demner-Fushman D, Humphrey SM, Ide NC, Loane RF, Ruch P, Ruiz ME, Smith LH, Tanabe LK, Wilbur WJ, Aronson AR. Finding Relevant Passages in Scientific Articles: Fusion of Automatic Approaches vs. an Interactive Team Effort. Proc TREC 2006, 569-76.

Abstract | pub2006072.pdf

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Graham L, Tse T, Keselman A. Exploring User Navigation during Online Health Information Seeking AMIA Annu Symp Proc. 2006:299-303

Abstract | pub2006065.pdf | PMID: 17238351 | PMCID: PMC1839467

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Zeng QT, Tse T. Exploring and Developing Consumer Health Vocabularies J Am Med Inform Assoc. 2006 Jan-Feb;13(1):24-9. Epub 2005 Oct 12

Abstract | pub2006001.pdf | PMID: 16221948 | PMCID: PMC1380193

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Humphrey SM, Lu C, Rogers W, Browne AC. Journal descriptor indexing tool for categorizing text according to discipline or semantic type. AMIA Annu Symp Proc. 2006:960.

Abstract | pub2006079.pdf | PMID: 17238579 | PMCID: PMC1839325

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Névéol A, Zeng K, Bodenreider O. Besides precision & recall: exploring alternative approaches to evaluating an automatic indexing tool for MEDLINE. AMIA Annu Symp Proc. 2006:589-93.

Abstract | pub2006057.pdf | PMID: 17238409 | PMCID: PMC1839480

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Aronson AR, Demner-Fushman D, Humphrey SM, Lin J, Liu H, Ruch P, Ruiz ME, Smith LH, Tanabe LK, Wilbur WJ. Fusion of Knowledge-intensive and Statistical Approaches for Retrieving and Annotating Textual Genomics Documents Proc TREC 2005, 36-45

Abstract | pub2005072.pdf

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Bakker TA, Ryce AN, Logan RA, Tse T, Hutcherson LY. A Consumer Health Informatics (CHI) Toolbox: Challenges and Implications AMIA Annu Symp Proc. 2005:21-5

Abstract | pub2005071.pdf | PMID: 16778994 | PMCID: PMC1479846

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Beaudoin DE, Rocha RA, Tse T. Enhancing Access to Patient Education Information: A Pilot Usability Study AMIA Annu Symp Proc. 2005:892

Abstract | pub2005045.pdf | PMID: 16779179 | PMCID: PMC1560886

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Bergun A, Bodenreider O. An ontology of chemical entities helps identify dependence relations among Gene Ontology terms Proc SMBM-2005

Abstract | pub2005028.pdf

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Bergun A, Bodenreider O, Mougin F. Classifying diseases with respect to anatomy: a study in SNOMED CT AMIA Annu Symp Proc. 2005:91-5

Abstract | pub2005030.pdf | PMID: 16779008 | PMCID: PMC1560776

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Bernhardt PJ, Humphrey SM, Rindflesch TC. Determining Prominent Subdomains in Medicine. AMIA Annu Symp Proc. 2005:46-50.

Abstract | pub2005052.pdf | PMID: 16778999 | PMCID: PMC1560510

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Bodenreider O, Burgun A. Linking the Gene Ontology to other biological ontologies Proc ISMB'2005 SIG meeting on Bio-ontologies 2005:17-18

Abstract | pub2005026.pdf

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Bodenreider O, Aubry M, Burgun A. Non-Lexical Approaches to Identifying Associative Relations in the Gene Ontology Pac Symp Biocomput. 2005:91-102

Abstract | pub2005006.pdf

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Cantor MN, Sarkar INK, Bodenreider O, Lussier YA. GenesTrace: Phenomic Knowledge Discovery Via Structured Terminologies Pac Symp Biocomput. 2005:103-14.

Abstract | pub2005008.pdf | PMID: 15759618 | PMCID: PMC2894422

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Crowell J, Zeng QT, Tse T. A Web Application to Support Consumer Health Vocabulary Development AMIA Annu Symp Proc. 2005:932

Abstract | pub2005043.pdf

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Fung KW, Bodenreider O. Utilizing the UMLS for Semantic Mapping between Terminologies. AMIA Annu Symp Proc. 2005:266-70.

Abstract | pub2005031.pdf | PMID: 16779043 | PMCID: PMC1560893

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Gay CW, Kayaalp M, Aronson AR. Semi-Automatic Indexing of Full Text Biomedical Articles AMIA Annu Symp Proc. 2005:271-5

Abstract | pub2005074.pdf | PMID: 16779044 | PMCID: PMC1560666

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Kayaalp M. Why Do We Need Probabilistic Approaches to Ontologies and the Associated Data? AMIA Annu Symp Proc. 2005:1005

Abstract | pub2005018.pdf | PMID: 16779292 | PMCID: PMC1560671

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Rindflesch TC, Fiszman M, Bisharah L. Semantic Interpretation for the Biomedical Research Literature In Hsinchun C, Fuller S, Friedman C, Hersh w (eds.) Medical Informatics: Knowledge Management and Data Mining in Biomedicine. Springer: New York, pp. 399-422, 2005.

Abstract | pub2005049.pdf

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Smith LH, Rindflesch TC, Wilbur WJ. The Importance of the Lexicon in Tagging Biological Text Natural Language Engineering 2005.

Abstract | pub2005051.pdf

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Sneiderman C, Demner-Fushman D, Fiszman M, Rindflesch TC. Semantic Characteristics of MEDLINE Citations Useful for Therapeutic Decision-making AMIA Annu Symp Proc. 2005:1117.

Abstract | pub2005048.pdf | PMID: 16779404 | PMCID: PMC1560453

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Zeng K, Bodenreider O, Nelson SJ. RxNav: A Progress Report AMIA Annu Symp Proc 2005:1168

Abstract | pub2005038.pdf | PMID: 16779454 | PMCID: PMC1560640

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Zeng QT, Tse T, Crowell J, Divita G, Roth L, Browne AC. Identifying Consumer-Friendly Display (CFD) Names for Health Concepts AMIA Annu Symp Proc. 2005:859-63

Abstract | pub2005042.pdf | PMID: 16779162 | PMCID: PMC1560732

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Zhang S, Bodenreider O. Alignment of Multiple Ontologies of Anatomy: Deriving Indirect Mappings from Direct Mappings to a Reference AMIA Annu Symp Proc 2005:864-868

Abstract | pub2005039.pdf | PMID: 16779163 | PMCID: PMC1560629

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Zarin DA, Tse T, Ide NC. Trial Registration at ClinicalTrials.gov between May and October 2005 N Engl J Med. 2005 Dec 29;353(26):2779-87

Abstract | pub2005040.pdf | PMID: 16382064 | PMCID: PMC1568386

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Azuaje F, Wang H, Bodenreider O. Ontology-driven Similarity Approaches to Supporting Gene Functional Assessment Proceedings of the ISMB'2005 SIG meeting on Bio-ontologies 2005:9-10

Abstract | pub2005024.pdf

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Backer A, Bodenreider O, Karp P, Kelly H, Loranger S, Musen M, Sriram R, Wroe C. Knowledge Integration for Bio-Threat Response Los Alamos White Paper

Abstract | pub2005035.pdf

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Bergun A, Bodenreider O, Jacquelinet C. Issues in the Classification of Disease Instances with Ontologies Stud Health Technol Inform 2005;116:695-700

Abstract | pub2005029.pdf | PMID: 16160339 | PMCID: PMC1784521

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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.

Abstract | pub2005027.pdf | PMID: 16779002 | PMCID: PMC1560846

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Golbreich C, Zhang S, Bodenreider O. Migrating the FMA from Protege to OWL Proc of the Eighth International Protege Conference 2005:108-111.

Abstract | pub2005032.pdf

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Mougin F, Bodenreider O. Approaches to Eliminating Cycles in the UMLS Metathesaurus: Naive vs. Formal AMIA Annu Symp Proc. 2005:550-4

Abstract | pub2005034.pdf | PMID: 16779100 | PMCID: PMC1560864

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Smith L, Rindflesch TC, Wilbure WJ. MedTag: A Collection of Biomedical Annotations Bioinformatics. 2004 Sep 22;20(14):2320-1.

Abstract | pub2005056.pdf

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Wang H, Azuaje F, Bodenreider O. An Ontology-Driven Clustering Method for Supporting Gene Expression Analysis CBMS’2005. 2005:389-394.

Abstract | pub2005036.pdf

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Zeng K, Bodenreider O, Nelson SJ. Implementing RxNav, a RxNorm Browser Proc of Medical Informatics Europe 2005 (CD-ROM) 2005:1268.

Abstract | pub2005037.pdf

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Zeng Q, Kin E, Crowell J, Tse T. A Text Corpora-Based Estimation of the Familiarity of Health Terminology ISBMD, Aveiro, Portugal, 10-11 November 2005:184-92.

Abstract | pub2005041.pdf

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Rosemblat G, Tse T, Gemoets D, Gillen JE, Ide NC. Supporting Access to Consumer Health Information Across Languages Proc ICML-9, September 20-23, 2005; Salvador, Bahia, Brazil.

Abstract | pub2005017.pdf

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Leroy G, Rindflesch TC. Effects of Information and Machine Learning Algorithms on Word Sense Disambiguation with Small Datasets Int J Med Inform. 2005 Aug;74(7-8):573-85

Abstract | pub2005053.pdf | PMID: 15897005

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McCray AT. Clinicaltrials.gov: Linking Patients to Medical Research Cancer Informatics: Essential Technologies for Clinical Trials. New York: Springer Verlag. 2002;:302-307.

Abstract | pub2002012.pdf

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Mitchell JA, Fun J, McCray AT. Design of Genetics Home Reference: A New NLM Consumer Health Resource Journal of the American Medical Informatics Association. 2004 Nov.;11(6):439-447.

Abstract | pub2004067.pdf

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Névéol A, Mork JG, Aronson AR, Darmoni SJ. Evaluation of French and English MeSH indexing systems with a parallel corpus. AMIA Annu Symp Proc. 2005:565-9.

Abstract | pub2005073.pdf | PMID: 16779103 | PMCID: PMC1560460

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Rindflesch TC, Pakhomov SV, Fiszman M, Kilicoglu H, Sanchez VR. Medical facts to support inferencing in natural language processing. AMIA Annu Symp Proc. 2005:634-8.

Abstract | pub2005054.pdf | PMID: 16779117 | PMCID: PMC1560850

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Kim GR, Aronson AR, Mork JG, Cohen BA, Lehmann CU. Application of a Medical Text Indexer to an Online Dermatology Atlas. MedInfo. 2004 Sept.;2004.

Abstract | pub2004051.pdf

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Bernhardt PJ, Rindflesch TC, Kilicoglu H, Tringali M. Identifying Anatomical Concepts in Biomedical Text for Automatic Selection of Images Medinfo. 2004 Sept.;2004: 1521.

Abstract | pub2004036.pdf

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Bodenreider O, Burgun A. Aligning Knowledge Sources in the UMLS: Methods, Quantitative Results, and Applications Medinfo. 2004 Sept.;2004:327-331.

Abstract | pub2004031.pdf

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Bodenreider O, Nelson SJ. RxNav: A Semantic Navigation Tool for Clinical Drugs Medinfo. 2004 Sept.;2004: 1530.

Abstract | pub2004037.pdf

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Chapman WW, Fiszman M, Dowling JN, Chapman BE, Rindflesch TC. Identifying Respiratory Findings in Emergency Department Reports for Biosurveillance using MetaMap Medinfo. 2004 Sept.;2004: 487-491.

Abstract | pub2004035.pdf

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Divita G, Tse T, Roth L. Failure Analysis of MetaMap Transfer (MMTx) Medinfo. 2004 Sept.;2004:763-7.

Abstract | pub2004024.pdf

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Fiszman M, Rindflesch TC, Kilicoglu H. Summarization of an Online Medical Encyclopedia MedInfo. 2004 Sept.;2004: 506-510.

Abstract | pub2004048.pdf

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Gemoets D, Rosemblat G, Tse T, Logan R. Assessing Readability of Consumer Health Information: An Exploratory Study Medinfo. 2004 Sept.;2004:869-73.

Abstract | pub2004025.pdf

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Gillen JE, Tse T, Ide NC, McCray AT. Design, Implementation and Management of a Web-based Data Entry System for ClinicalTrials.gov Medinfo. 2004 Sept.;2004:1466-70.

Abstract | pub2004028.pdf

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Leroy G, Rindflesch TC. Using Symbolic Knowledge in the UMLS to Disambiguate Words in Small Datasets with a Naive Bayes Classifier Medinfo. 2004 Sept.;2004: 381-385.

Abstract | pub2004034.pdf

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Logan RA. Evaluating Consumer Informatics: Learning from Health Campaign Research Medinfo. 2004;2004:1147-51.

Abstract | pub2004029.pdf

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McCray AT, Ide NC, Loane RR, Tse T. Strategies for Supporting Consumer Health Information Seeking Medinfo. 2004 Sept.;2004:1152-6.

Abstract | pub2004027.pdf

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Sarkar IN, Cantor MN, Bodenreider O, Lussier YA. GenesTraceTM: Biological Knowledge Discovery via Structured Terminology MedInfo.

Abstract | pub2004047.pdf

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Slaughter LA, Rindflesch TC. Development of a Test Collection of Manually Extracted Semantic Relationships in Health Consumer Texts MedInfo. 2004 Sept.;2004: 1865.

Abstract | pub2004042.pdf

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Soergel D, Tse T, Slaughter L. Helping Healthcare Consumers Understand: An "Interpretive Layer" for Finding and Making Sense of Medical Information Medinfo. 2004 Sept.;2004:931-5.

Abstract | pub2004026.pdf

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Tringali M, Rindflesch TC, Kilicoglu H, Fiszman M, Bodenreider O. Strategies for Mapping Concepts in Gastrointestinal Endoscopy Reports to the UMLS Metathesaurus Medinfo. 2004 Sept.;2004: 1885.

Abstract | pub2004040.pdf

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Zhang S, Bodenreider O. Comparing Associative Relationships Among Equivalent Concepts Across Ontologies MedInfo. 2004 Sept.;2004: 459-463.

Abstract | pub2004050.pdf

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Smith L, Rindflesch TC, Wilbure WJ. MedPost: A Part of Speech Tagger for BioMedical Text Bioinformatics. 2004 Sep 22;20(14):2320-1. Epub 2004 Apr 8

Abstract | pub2005055.pdf | PMID: 15073016

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Bodenreider O. Web Interface: RxNav

Abstract

Lord AM. Learning The "Washington Way": The United States Public Health Service and the History of Sex Education

Abstract | pub2004023.pdf

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Kayaalp M. Bayesian Methods for Diagnosing Physiological Conditions of Human Subjects from Multivariate Time Series Biosensor Data Physiological Data Modeling Contest, the Twenty-First International Conference on Machine Learning (ICML), 2004 July.

Abstract | pub2004022.pdf

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Aronson AR, Demner-Fushman D, Humphrey SM, Ide NC, Kim W, Liu H, Loane RF, Mork JG, Smith LH, Tanabe LK, Wilbur WJ, Xie N. Knowledge-intensive and statistical approaches to the retrieval and annotation of genomics MEDLINE citations. The Thirteenth Text Retrieval Conference (TREC 2004). 2004:503-11.

Abstract | pub2004-076.pdf

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Fiszman M, Rindflesch TC, Kilicoglu H. Abstraction Summarization for Managing the Biomedical Research Literature Proceedings of the HLT-NAACL Workshop on Computational Lexical Semantics. 2004;:76-83.

Abstract | pub2004015.pdf

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Libbus B, Kilicoglu H, Rindflesch TC, Mork JG, Aronson AR. Using Natural Languge Processing, Locus Link, and the Gene Ontology to Compare OMIM to MEDLINE Proceedings of the HLT-NAACL Workshop on Linking the Biological Literature, Ontologies and Databases: Tools for Users. 2004;:69-76.

Abstract | pub2004014.pdf

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Rosemblat G, Tse T, Gemoets D. Adapting A Monolingual Consumer Health System for Cross-Language Information Retrieval Advances in Knowledge Organization, Proceedings of the Eighth International ISKO Conference. 2004 July;9:315-321.

Abstract | pub2004013.pdf

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Logan RA, Park J, Shin JH. How Two Korean Newspapers Covered a Public Health Crisis Science Communication. 25:4:365-389 (June 2004)

Abstract | pub2004073.pdf

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Lomax J, McCray AT. Mapping the Gene Ontology Into the Unified Medical Language System Comparative and Functional Genomics

Abstract | pub2004003.pdf

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Rindflesch TC, Fiszman M. The Interaction of Domain Knowledge and Linguistic Structure in Natural Language Processing: Interpreting Hypernymic Propositions in Biomedical Text Journal of Biomedical Informatics. 2003;36(6):462-77.

Abstract | pub2003069.pdf

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Bodenreider O, Aubry M, Burgun A. From Functional Similarity Among Gene Products to Dependence Relations Among Gene Ontology Terms Proc SOFG, 2004:53.

Abstract | pub2004069.pdf

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Sehgal AK, Srinivasan P, Bodenreider O. Gene Terms and English Words: An Ambiguous Mix Proc of the SIGIR 2004 Workshop on Search and Discovery in Bioinformatics 2004.

Abstract | pub2004071.pdf

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Zhang S, Mork P, Bodenreider O. Lessons Learned from Aligning two Representations of Anatomy Proc of the First International Workshop on Formal Biomedical Knowledge Representation (KR-MED 2004); 2004. p. 102-108.

Abstract | pub2004070.pdf

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Bodenreider O, McCray AT. Exploring Semantic Groups Through Visual Approaches J Biomed Inform. 2003 Dec;36(6):414-432.

Abstract | pub2003065.pdf | PMID: 14759816 | PMCID: PMC1997308

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Bodenreider O, Zhang S. Semantic Integration in Biomedicine Proceedings of the Semantic Integration Workshop at the Second International Semantic Web Conference. 2003;: 156-157.

Abstract | pub2003066.pdf

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Bodenreider O. The Unified Medical Language System (UMLS): Integrating Biomedical Terminology Nucleic Acids Res; Database Issue. 2004;32: 267-70.

Abstract | pub2004002.pdf

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Mitchell JA, McCray AT, Bodenreider O. From Phenotype to Genotype: Issues in Navigating the Available Information Resources Methods Inf Med. 2003;42(5):557-63.

Abstract | pub2003067.pdf | PMID: 14654891 | PMCID: PMC1800828

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Zhang S, Bodenreider O. Investigating Implicit Knowledge in Ontologies with Application to the Anatomical Domain Altman RB, Dunker AK, Hunter L, Jung TA, Klein TE, editors. Pacific Symposium on Biocomputing 2004: World Scientific. 2004;: 250-261.

Abstract | pub2004004.pdf

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Zhang S, Bodenreider O. Knowledge Augmentation for Aligning Ontologies: An Evaluation in the Biomedical Domain Proceedings of the Semantic Integration Workshop at the Second International Semantic Web Conference. 2003: 109-114.

Abstract | pub2003068.pdf

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Aronson AR, Mork JG, Gay CW, Humphrey SM, Rogers W. The NLM Indexing Initiative's Medical Text Indexer. Stud Health Technol Inform. 2004;107(Pt 1):268-72.

Abstract | pub2004-077.pdf | PMID: 15360816

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Leroy G, Rindflesch TC, Libbus B, Kilicoglu H, Chen H. A Syntactic Parser with Semantic Filtering for Biomedical Text. Proceedings of Pacific Symposium on Biocomputing.

Abstract

Azuaje FJ, Bodenreider O, Wang H, Dopazo J. Gene Ontology-Driven Similarity for Gene Expression Correlation Analysis Proceedings of the second conference on Standards and Ontologies for Functional Genomics (SOFG 2) 2004:47.

Abstract

Bodenreider O, Azuaje F. Incorporating Ontology-Driven Similarity Knowledge Into Functional Genomics: An Exploratory Study Proceedings of the 2004 IEEE Fourth Symposium on Bioinformatics and Bioengineering (BIBE-2004) 2004:317-324.

Abstract | pub2004066.pdf

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Bodenreider O, Smith B, Burugn A. The Ontology-Epistemology Divide: A Case Study in Medical Terminology Proceedings of the Third International Conference on Formal Ontology in Information Systems (FOIS2004): IOS Press; 2004. p. 185-195.

Abstract | pub2004064.pdf

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Wang H, Azuaje F, Bodenreider O, Dopazo J. Gene Expression Correlation and Gene Ontology-Based Similarity: An Assessment of Quantitative Relationships Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB'2004) 2004:25-31.

Abstract | pub2004065.pdf

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Bangalore A, Thorn KE, Tilley C, Peters L. The UMLS knowledge source server: an object model for delivering UMLS data. AMIA Annu Symp Proc. 2003 Nov;:51-55.

Abstract | pub2003052.pdf | PMID: 14728132 | PMCID: PMC1480045

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Bodenreider O, Mitchell JA. Graphical Visualization and Navigation of Genetic Disease Information AMIA Annu Symp Proc. 2003:792.

Abstract | pub2003054.pdf | PMID: 14728297 | PMCID: PMC1479900

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Bodenreider O. Strength in Numbers: Exploring Redundancy in Hierarchical Relations Across Biomedical Terminologies AMIA Annu Symp Proc. 2003:101-5.

Abstract | pub2003053.pdf | PMID: 14728142 | PMCID: PMC1480297

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Browne AC, Divita Guy, Aronson AR, McCray AT. Language and Vocabulary Tools AMIA Annu Symp Proc. 2003:798.

Abstract | pub2003051.pdf | PMID: 14728303 | PMCID: PMC1480270

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Fiszman M, Rindflesch TC, Kilicoglu H. Integrating a Hypernymic Proposition Interpreter into a Semantic Processor for Biomedical Texts AMIA Annu Symp Proc. 2003:239-43.

Abstract | pub2003055.pdf | PMID: 14728170 | PMCID: PMC1479962

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Fiszman M, Rindflesch TC, Kilicoglu H. Interpreting Hypernymic Propositions in an Online Medical Encyclopedia AMIA Annu Symp Proc. 2003:840.

Abstract | pub2003056.pdf | PMID: 14728345 | PMCID: PMC1480056

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Kashyap V. The UMLS Semantic Network and the Semantic Web. AMIA Annu Symp Proc. 2003:351-5.

Abstract | pub2003061.pdf | PMID: 14728193 | PMCID: PMC1480032

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Kashyap V, Ramakrishan C, Rindflesch TC. Towards Semi-Automatic Generation of Biomedical Ontologies AMIA Annu Symp Proc. 2003 Nov;:886.

Abstract | pub2003062.pdf

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Mitchell JA, Aronson AR, Mork JG, Folk LC, Humphrey SM, Ward JM. Gene Indexing: Characterization and Analysis of NLM's GeneRIFs. AMIA Annu Symp Proc. 2003:460-4.

Abstract | pub2003058.pdf | PMID: 14728215 | PMCID: PMC1480312

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Mitchell JA, McCray AT. The Genetics Home Reference: A New NLM Consumer Health Resource AMIA Annu Symp Proc. 2003:936

Abstract | pub2003059.pdf | PMID: 14728441

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Rindflesch TC, Libbus B, Hristovski D, Aronson AR, Kilicoglu H. Semantic Relations Asserting the Etiology of Genetic Diseases AMIA Annu Symp Proc. 2003:554-8.

Abstract | pub2003060.pdf | PMID: 14728234 | PMCID: PMC1480275

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Zhang S, Bodenreider O. Aligning Representations of Anatomy Using Lexical and Structural Methods AMIA Annu Symp Proc. 2003 Nov;:753-757.

Abstract | pub2003063.pdf | PMID: 14728274 | PMCID: PMC1480279

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McCray AT, Tse T. Search Failures in Consumer Health Information Systems AMIA Annu Symp Proc. 2003:430-4.

Abstract | pub2003049.pdf | PMID: 14728209 | PMCID: PMC1479930

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Ammenwerth E, Wolff AC, Knaup P, Ulmer H, Skonetzki S, Van Bemmel JH, McCray AT, Haux R, Kulikowski C. Developing and Evaluating Criteria to Help Reviewers of Biomedical Informatics Manuscripts: A Case Report J Am Med Inform Assoc. 2003 June.

Abstract | pub2003024.pdf | PMID: 12807814

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Bodenreider O. A Semantic Navigation Tool for the UMLS AMIA Annu Symp Proc. 2000;: 971.

Abstract | pub2000035.pdf

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Bodenreider O, Mitchell JA, McCray AT. Biomedical Ontologies Pacific Symposium on Biocomputing: World Scientific. 2003;:562-564.

Abstract | pub2003030.pdf

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Bodenreider O, Burgun A. Characterizing the Definitions of Anatomical Concepts in WordNet and Specialized Sources Proc. of the First Global WordNet Conference. 2002;:223-230.

Abstract | pub2002023.pdf

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Bodenreider O. Comment les Usagers Accedent a l'Information Medicale Aux USA: l'Exemple de MEDLINEplus [How Consumers Access Health Information in the USA: The MEDLINEplus Example] Innovation et Technologie en Biologie et Medecine. 2000;21(5):286-90.

Abstract | pub2000036.pdf

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Bodenreider O, Burgun A, Mitchell JA. Evaluation of WordNet as a Source of Lay Knowledge for Molecular Biology and Genetic Diseases: A Feasibility Study Stud Health Technol Inform. 2003;95:379-84.

Abstract | pub2003029.pdf | PMID: 14664016 | PMCID: PMC1893008

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Bodenreider O. Experiences in Visualizing and Navigating Biomedical Ontologies and Knowledge Bases Proc. of the ISMB'SIG meeting; Bio-ontologies. 2002;:29-32.

Abstract | pub2002022.pdf

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Bodenreider O, Pakhomov S. Exploring Adjectival Modification in Biomedical Discourse Across Two Genres Proc. of the ACL, 2003 Workshop, Natural Language Processing in Biomedicine. 2003;:105-112.

Abstract | pub2003031.pdf

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Bodenreider O, Burgun A, Rindflesch TC. Lexically-Suggested Hyponymic Relations Among Medical Terms and Their Representation in the UMLS Proc. of TIA'2001; Terminology and Artificial Intelligence. 2001;:11-21.

Abstract | pub2001025.pdf

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Bodenreider O, Zweigenbaum P. Strategies d'Identification des Noms Propres a Partir de Nomenclatures Medicales Paralleles Traitement Automatique des Langues. 2000;41(3):727-757.

Abstract | pub2000037.pdf

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Bodenreider O, Rindflesch TC, Burgun A. Unsupervised, Corpus-Based Method for Extending a Biomedical Terminology Proc. of the ACL Workshop; Natural Language Processing in the Biomedical Domain. 2002;:53-60.

Abstract | pub2002027.pdf

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Botti G, Bodenreider O, Burgun A, Le Beux P, Fieschi M. De la Classification à la Connaissance des Maladies: Une Réflexion à Partir de la Classification Internationale des Maladies [From Classification to Knowledge About Diseases: Thoughts about the International Classification of Diseases] Innovation et Technologie en Biologie et Médecine. 2000;21(5):291-97.

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Burgun A, Bodenreider O. Aspects of the Taxonomic Relation in the Biomedical Domain FOIS. 2001;: 222-233

Abstract | pub2001028.pdf

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Burgun A, Bodenreider O. Comparing Terms, Concepts and Semantic Classes in WordNet and the Unified Medical Language System Proc. of the NAACL'2001 Workshop; WordNet and Other Lexical Resources: Applications, Extensions and Customizations. 2001;:77-82.

Abstract | pub2001027.pdf

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Cantor MN, SI N, Hartel F, Bodenreider O, Lussier YA. An Evaluation of Hybrid Methods for Matching Biomedical Terminologies: Mapping the Gene Ontology to the UMLS Stud Health Technol Inform. 2003;:62-67.

Abstract | pub2003032.pdf

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Griffenhagen GB, Brushwood D, Parascandola J, Schondelmeyer S. Trends and Events in American Pharmacy, 1852-2002 J Am Pharm Assoc (Wash). 2002 Sep-Oct;42(5 Suppl 1):S24-5.

Abstract | pub2002041.pdf

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Hersh WJ, Velterop J, McCray AT, Eynsenbach G, Boguski M. Overcoming Impediments to Effective Health and Biomedical Digital Libraries, JCDL JCDL. 2002;: 360.

Abstract | pub2002043.pdf

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Humphrey S, Rindflesch TC, Aronson AR. Automatic Journal Descriptor Indexing Extended to Indexing by UMLS Semantic Type Using the Cosine Document Similarity Measure. Proc. of the 11th SIG/CR Classification Research Workshop. 2000;103-16.

Abstract | pub2000056.pdf

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Jacquelinet C, Bodenreider O, Burgun A. Modelling Syllepse in Medical Knowledge Bases with Application in the Domain of Organ Failure and Transplantation Proc. of OntoLex; Workshop on Ontologies and Lexical Knowledge Bases 2000.

Abstract | pub2000040.pdf

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Lederberg J, McCray AT. 'Ome Sweet 'Omics - A Genealogical Treasury of Words Genealogical Treasury of Words. Scientist. 2001;15(7):8.

Abstract | pub2001047.pdf

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McCray AT, Bodenreider O. A Conceptual Framework for the Biomedical Domain The Semantics of Relationships: An Interdisciplinary Perspective. Boston: Kluwer Academic Publishers. 2002;:181-198.

Abstract | pub2002029.pdf

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McCray AT, Gallagher ME. Principles for Digital Library Development Communications of the ACM. 2001 May; 44(5): 48-54.

Abstract | pub2001017.pdf

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Moore SR, Parascandola J. The Other Pharmacists in the American Civil War Am J Health Syst Pharm. 2000 Jul 1;57(13):1276.

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Parascandola J. Alice Catherine Evans (1881-1975) J Public Health Policy. 2001 ;22(1):105-11.

Abstract | URL: http://www.jstor.org/stable/3343557

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Parascandola J. Chaulmoogra Oil and the Treatment of Leprosy Pharm Hist. 2003 ;45(2):47-57.

Abstract | pub2003048.pdf

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Parascandola J. From Cards to Computers: The National Library of Medicine and the Transmission of Medical Knowledge Medicina nei Secoli. 2002;:14.

Abstract | pub2002033.pdf

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Parascandola J. From Germs to Genes: Trends in Drug Therapy, 1852-2002 Pharm Hist. 2002 ;44(1):3-11.

Abstract | pub2002042.pdf

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Parascandola J. John Mahoney and the Introduction of Penicillin to Treat Syphilis Pharmacy in History. 2001; 43: 3-13.

Abstract | pub2001051.pdf

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Parascandola J. Public Health Service, Militarization of the PHS Commissioned Corps Militarization of the PHS Commissioned Corps. 2001 Sept.

Abstract | pub2001060.pdf

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Parascandola J. The Contributions of David L. Cowen Publ Am Inst Hist Pharm. 2001;19:1-3.

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Parascandola J. To Bond or Not to Bond: Chemical Versus Physical Theories of Drug Action Bulletin for the History of Chemistry. 2003;28: 1-8.

Abstract | pub2003045.pdf

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Ray J, Dale R, Moore R, Reich V, Underwood W, McCray AT. Panel on Digital Preservation, JCDL Panel on Digital Preservation, JCDL. 2002;: 365-367.

Abstract | pub2002044.pdf

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Rindflesch TC, Rajan J, Hunter L. Extracting Molecular Binding Relationships from Biomedical Text Proc. of the 6th Applied Natural Language Processing Conference. 2000;: 188-95.

Abstract | pub2000016.pdf

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Rindflesch TC, Aronson AR. Semantic Processing for Enhanced Access to Biomedical Knowledge Real World Semantic Web Applications, IOS Press. 2002;:157-72.

Abstract | pub2002019.pdf

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Rosemblat G, Gemoets D, Browne AC, Tse T. Machine Translation-Supported Cross Language Information Retrieval for a Consumer Health Resource AMIA Annu Symp Proc. 2003:564-8.

Abstract | pub2003028.pdf | PMID: 14728236 | PMCID: PMC1480254

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Shin DW. Towards Efficient XML Query Processing, XML Developer Day in XML 2000: Graphic Communications Association. 2000;:1-45.

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Srinivasan P, Mitchell JA, Bodenreider O, Pant G, Menczer F. Web Crawling Agents for Retrieving Biomedical Information Proc. of the International Workshop on Bioinformatics and Multi-Agent Systems (BIXMAS). 2002 Jul.

Abstract | pub2002032.pdf

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Tse T, Soergel D. Exploring Medical Expressions Used by Consumers and the Media: An Emerging View of Consumer Health Vocabularies AMIA Annu Symp Proc. 2003:674-8

Abstract | pub2003025.pdf

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Tse T, Soergel D. Procedures for Mapping Vocabularies from Non-Professional Discourse and a Case Study from the Medical Domain ASIST Annual Meeting. 2003.

Abstract | pub2003027.pdf

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Xiaocheng L, Prettyman M, Antonucci R. System Expansion and Integration with Agents in HSTAT Proc. of the World Multiconference on Systemics, Cybernetics, and Informatics. 2000 Jul.

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Kayaalp M, Aronson AR, Humphrey SM, Ide NC, Tanabe LK, Smith LH, Demner-Fushman D, Loane RF, Mork JG, Bodenreider O. Methods for accurate retrieval of MEDLINE citations in functional genomics. The Twelfth Text Retrieval Conference (TREC 2003). 2003:441-50.

Abstract | pub2003-077.pdf | URL: http://trec.nist.gov/pubs/trec12/t12_proceedings.html

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Lord AM. Models of Masculinity: Sex Education, the United States Public Health Service, and the YMCA, 1919-1924 J Hist Med Allied Sci. 2003 Apr ;58(2):123-52.

Abstract | pub2003041.pdf | PMID: 12776436

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Weeber M, Vos R, Klein H, De Jong-Van Den Berg LT, Aronson AR, Molema G. Generating Hypotheses by Discovering Implicit Associations in the Literature: A Case Report of a Search for New Potential Therapeutic Uses for Thalidomide J Am Med Inform Assoc. 2003 May-Jun;10(3):252-9. Epub 2003 Jan 28.

Abstract | pub2003034.pdf | PMID: 12626374 | PMCID: PMC342048

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Locatis C, Fontelo P, Sneiderman C, Ackerman MJ, Uijtdehaage S, Candler C, Stensaas S, Dennis S. Webcasting videoconferences over IP: a synchronous communication experiment. J Am Med Inform Assoc. 2003 Mar-Apr;10(2):150-3. DOI: 10.1197/jamia.M1170.

Abstract | PMID: 12595404 | PMCID: PMC150368

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Bodenreider O, Burgun A, Rindflesch TC. Assessing the Consistency of a Biomedical Terminology Through Lexical Knowledge Int J Med Inf. 2002 Dec 4;67(1-3):85-95.

Abstract | pub2002024.pdf | PMID: 12460634

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Burgun A, Bodenreider O, Le Duff F, Moussouni F, Loreal O. Representation of roles in biomedical ontologies: a case study in functional genomics. Proc AMIA Symp. 2002:86-90.

Abstract | pub2002028.pdf | PMID: 12463792 | PMCID: PMC2244301

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Libbus B, Rindflesch TC. NLP-Based Information Extraction for Managing the Molecular Biology Literature Proc AMIA Symp. 2002:445-9.

Abstract | pub2002016.pdf | PMID: 12463863 | PMCID: PMC2244458

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Liu H, Aronson AR, Friedman C. A Study of Abbreviations in MEDLINE Abstracts AMIA Annu Symp. 2002 ;():464-8.

Abstract | pub2002051.pdf | PMID: 12463867 | PMCID: PMC2244212

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Sarkar IN, Rindflesch TC. Discovering Protein Similarity Using Natural Language Processing Proc AMIA Symp. 2002:677-81.

Abstract | pub2002015.pdf | PMID: 12463910 | PMCID: PMC2244512

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Srinivasan P, Rindflesch T. Exploring Text Mining from MEDLINE Proc AMIA Symp. 2002:722-6.

Abstract | pub2002017.pdf | PMID: 12463919 | PMCID: PMC2244226

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Srinivasan S, Rindflesch TC, Hole WT, Aronson AR, Mork JG. Finding UMLS Metathesaurus Concepts in MEDLINE. Proc AMIA Symp. 2002:727-31.

Abstract | pub2002018.pdf | PMID: 12463920 | PMCID: PMC2244184

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Locatis C, Fontelo P, Ackerman MJ, Sneiderman C. Feasibility Studies in IP Videoconferencing, Streaming, and Wireless Communication. AMIA Annu Symp Proc [Proceedings of the American Medical Informatics Association Annual Symposium]; 2002 Nov 9-13; San Antonio, Texas. p. 1090.

Abstract | pub2002047.pdf

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Buchanan BG, Chapman W, Cooper GF, Hanbury P, Kayaalp M, Ramachandran M, Saul M. Creating a Software Tool for the Clinical Researcher -- the IPS System Proc AMIA Symp. 2002: : 1210.

Abstract | PMCID: PMC2244346

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Aronson AR. Effective Mapping of Biomedical Text to the UMLS Metathesaurus: The MetaMap Program Proc AMIA Symp. 2001:17-21.

Abstract | pub2001032.pdf | PMID: 11825149 | PMCID: PMC2243666

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Burgun A, Bodenreider O. Mapping the UMLS Semantic Network into General Ontologies Proc AMIA Symp. 2001:81-5.

Abstract | pub2001029.pdf | PMID: 11833483 | PMCID: PMC2243467

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Kim W, Aronson AR, Wilbur WJ. Automatic MeSH Term Assignment and Quality Assessment Proc AMIA Symp. 2001:319-23.

Abstract | pub2001045.pdf | PMID: 11825203 | PMCID: PMC2243528

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McCray AT, Bodenreider O, Malley JD, Browne AC. Evaluating UMLS Strings for Natural Language Processing AMIA Annu Symp Proc. 2001;():448-52.

Abstract | pub2001018.pdf | PMID: 11825228 | PMCID: PMC2243606

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Bodenreider O. An Object-Oriented Model for Representing Semantic Locality in the UMLS Medinfo. 2001 ;10(Pt 1):161-5.

Abstract | pub2001022.pdf | PMID: 11604725

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Burgun A, Bodenreider O. Methods for Exploring the Semantics of the Relationships Between Co-Occurring UMLS Concepts Medinfo. 2001 ;10(Pt 1):171-5.

Abstract | pub2001026.pdf | PMID: 11604727

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McCray AT, Burgun A, Bodenreider O. Aggregating UMLS Semantic Types for Reducing Conceptual Complexity Medinfo. 2001 ;10(Pt 1):216-20.

Abstract | pub2001031.pdf | PMID: 11604736

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Bodenreider O. Circular hierarchical relationships in the UMLS: etiology, diagnosis, treatment, complications and prevention. Proc AMIA Symp. 2001:57-61.

Abstract | pub2001023.pdf | PMID: 11825155 | PMCID: PMC2243677

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Bodenreider O, Zweigenbaum P. Identifying Proper Names in Parallel Medical Terminologies Stud Health Technol Inform. 2000;77:443-7

Abstract | pub2000038.pdf | PMID: 11187591 | PMCID: PMC1790050

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Cooper GF, Buchanan BG, Chapman W, Hanbury P, Kayaalp M, Saul M. IPS: A System That Uses Machine Learning to Help Locate Patient Records for Clinical Research. Proc AMIA Symp. 2001: : 813.

Abstract | PMCID: PMC2243522

Abstract

Humphrey SM, Rindflesch TC, Aronson AR. Automatic Indexing by Discipline and High-Level Categories: Methodology and Potential Applications Advances in classification research. Proc. of the 11th ASIST SIG/CR Classification Research Workshop. 2001.

Abstract | pub2001044.pdf

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Weeber M, Mork JG, Aronson AR. Developing a Test Collection for Biomedical Word Sense Disambiguation Proc AMIA Symp. 2001:746-50.

Abstract | pub2001054.pdf | PMID: 11825285 | PMCID: PMC2243574

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Bodenreider O, Bean CA. Relationships Among Knowledge Structures: Vocabulary Integration Within a Subject Domain. In: Bean A, Green R, editors. Relationships in the organization of knowledge. Springer; 2001. pp. 81-98.

Abstract | pub2001024.pdf

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Bodenreider O. Using UMLS semantics for classification purposes. Proc AMIA Symp. 2000:86-90.

Abstract | pub2000034.pdf | PMID: 11079850 | PMCID: PMC2243905

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McCray AT, Dorfman E, Ripple A, Ide NC, Jha M, Katz DG, Loane RF, Tse T. Usability Issues in Developing a Web-Based Consumer Health Site Proc AMIA Symp. 2000:556-60.

Abstract | pub2000022.pdf | PMID: 11079945 | PMCID: PMC2244083

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Rindflesch TC, Bean CA, Sneiderman CA. Argument Identification for Arterial Branching Predications Asserted in Cardiac Catheterization Reports Proc AMIA Symp. 2000:704-8.

Abstract | pub2000018.pdf | PMID: 11079975 | PMCID: PMC2243725

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Weeber M, Klein H, Aronson AR, Mork JG, de Jong-van den Berg LT, Vos R. Text-Based Discovery in Biomedicine: The Architecture of the DAD-System AMIA Annu Symp Proc. 2000 ;():903-7.

Abstract | pub2000061.pdf | PMID: 11080015 | PMCID: PMC2243779

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Rindflesch TC, Tanabe L, Weinstein JN, Hunter L. EDGAR: extraction of drugs, genes and relations from the biomedical literature. Pac Symp Biocomput. 2000:517-28.

Abstract | pub2000017.pdf | PMID: 10902199 | PMCID: PMC2709525

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Kayaalp M, Cooper GF, Clemont G. Predicting ICU mortality: a comparison of stationary and nonstationary temporal models. Proc AMIA Symp. 2000:418-22.

Abstract | PMID: 11079917 | PMCID: PMC2243937

Abstract

Aronson AR, Bodenreider O, Chang HF, Humphrey SM, Mork JG, Nelson SJ, Rindflesch TC, Wilbur WJ. The NLM Indexing Initiative. Proc AMIA Symp. 2000:17-21.

Abstract | pub2000033.pdf | PMID: 11079836 | PMCID: PMC2243970

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McCray AT. Better access to information about clinical trials. Ann Intern Med. 2000 Oct 17;133(8):609-14.

Abstract | pub2000020.pdf | PMID: 11033590

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Lu CJ, Bangalore A, Tse T. Developing Web Browser Recording Tools Using Server-Side Programming Technology. Proc. of WebNet 2000, World conference on WWW and Internet: Association for the Advancement of Computing in Education. 2000;:372-7.

Abstract | pub2000053.pdf

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Weeber M, Vos R. Extracting the Lowest-Frequency Words: Pitfalls and Possibilities Computational Linguistics. 2000;26(3):301-17.

Abstract | pub2000060.pdf

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McCray AT, Ide NC. Design and implementation of a national clinical trials registry. J Am Med Inform Assoc. 2000 May-Jun;7(3):313-23.

Abstract | pub2000019.pdf | PMID: 10833169 | PMCID: PMC61435

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Aronis JM, Cooper GF, Kayaalp M, Buchanan BG. Identifying patient subgroups with simple Bayes'. Proc AMIA Symp. 1999:658-62.

Abstract | PMID: 10566441 | PMCID: PMC2232601

Abstract

McCray AT, Gallagher ME, Flannick MA. Extending the role of metadata in a digital library system. In: Proceedings of the IEEE Forum on Research and Technology Advances in Digital Libraries, pp. 190-9, 1999.

Abstract | A1999001.pdf

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Cooper GF, Buchanan BG, Kayaalp M, Saul M, Vries JK. Using computer modeling to help identify patient subgroups in clinical data repositories. Proc AMIA Symp. 1998:180-4.

Abstract | PMID: 9929206 | PMCID: PMC2232142

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