• Goodwin T, Demner-Fushman D. Deep Learning from Incomplete Data: Detecting Imminent Risk of Hospital-acquired Pneumonia in ICU Patients. Proceedings of the AMIA 2019 Annual Symposium, Washington, DC, USA, November 17-20, 2019.

  Abstract | pub9980.pdf

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

  Abstract | PMID:  18694041

  Abstract
• Ben Abacha A, Demner-Fushman D. On the role of question summarization and information source restriction in consumer health question answering. In Proceedings of the AMIA 2019 Informatics Summit, San Francisco, CA, USA, 2019.

  Abstract | pub9917.pdf

  AbstractDownload
• Demner-Fushman D, Fung K, Do P, Boyce R, Goodwin T. Overview of the TAC 2018 Drug-Drug Interaction Extraction from Drug Labels Track. Proceedings of the Text Analysis Conference (TAC) 2018, Gaithersburg, MD, USA, November 13-14, 2018.

  Abstract | pub9978.pdf

  AbstractDownload
• 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.

  Abstract

  Abstract
• Edinger T, Demner-Fushman D, Cohen AM, Bedrick S, Hersh W. Evaluation of Clinical Text Segmentation to Facilitate Cohort Retrieval. AMIA Annu Symp Proc. 2018 Apr 16;2017:660-669. eCollection 2017.

  Abstract | PMID:  29854131 | PMCID:  PMC5977655

  Abstract
• Fung K, Xue Z, Ameye F, Gutierrez AR, D'Have A. Achieving Logical Equivalence between SNOMED CT and ICD-10-PCS Surgical Procedures. AMIA Annu Symp Proc. 2018 Apr 16;2017:724-733. eCollection 2017.

  Abstract | PMID:  29854138 | PMCID:  PMC5977651

  Abstract
• 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

  AbstractDownload
• 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

  AbstractDownload
• Lynch P, Wang Y, Kanduru A, Luan X, Mericle L, Lu S, McDonald CJ. On-the-Fly Data Capture Tooling for FHIR/HL7 V2 HL7 January 2018 Working Group Meeting, New Orleans, LA

  Abstract | pub9749.pdf

  AbstractDownload
• McDonald CJ. FHIR Overview Presentation by Clement J. McDonald, MD

  Abstract | pub9747.pdf

  AbstractDownload
• McDonald CJ. Top LOINC Codes – Orders and Observations

  Abstract

  Abstract
• Ben Abacha A, Long LR, Seco de Herrera AG, Antani SK, Wang K, Demner-Fushman D. Named Entity Recognition in Functional Neuroimaging Literature. BIBM 2017

  Abstract | URL:  https://ieeexplore.ieee.org/document/8218002

  AbstractExternal link
• Abhyankar S, Schluter P, Bennett K, Vreeman D, McDonald CJ. Enabling Interoperability between Healthcare Devices and EHR Systems. In 2017 AMIA Symposium. Wasington DC: IEEE.

  Abstract

  Abstract
• 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

  AbstractDownload
• McDonald CJ, Vreeman D, Wang K, Carr C, Colins B, Abhyankar S, Deckard J, Rubin D, Langlotz C. The LOINC/RSNA Radiology Playbook: A unified terminology for radiology procedures. . In 2017 AMIA Symposium. Washington DC.

  Abstract

  Abstract
• Kury F, Baik SH, McDonald CJ. Cardioprotective Drugs and Incident Dementias in Medicare's Big Data. AMIA 2017.

  Abstract

  Abstract
• Fung K, Gutierrez A, Ameye F, D’Have A, Ariel B. Demonstrating the Benefits of Mapping SNOMED CT to ICD-10-PCS through a Prototype Application for End User Implementation. SNOMED Expo Oct 2017, Bratislava, Slovakia pp. 0

  Abstract

  Abstract
• Roberts K, Gururaj A, Chen X, Pournejati S, Cohen T, Hersh WR, Demner-Fushman D. Information Retrieval for Biomedical Datasets. 2016 bioCADDIE Challenge. AMIA 2017.

  Abstract

  Abstract
• 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

  Abstract
• 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

  Abstract
• McDonald CJ, Maglott D, Abhyankar S, Goodwin R, Kanduru A, Lu S, Lynch P, Vreeman D, Wang Y, Wood G. HL7 Version 2.5.1 Implementation Guide: Lab Results Interface (LRI), Release 1, STU Release 4. US Realm, Chapter 5, Clinical Genomics Results Reporting. Published for May 2017 Ballot.

  Abstract

  Abstract
• 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.

  Abstract

  Abstract
• 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

  AbstractDownload
• Ben Abacha A, Demner-Fushman D. Recognizing Question Entailment for Medical Question Answering. AMIA Annu Symp Proc. 2017 Feb 10;2016:310-318. eCollection 2016.

  Abstract | pub9500.pdf | PMID:  28269825 | PMCID:  PMC5333286

  AbstractDownload
• 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

  AbstractDownload
• Roberts K, Rodriguez L, Shooshan SE, Demner-Fushman D. Resource Classification for Medical Questions. AMIA Annu Symp Proc. 2017 Feb 10;2016:1040-1049. eCollection 2016.

  Abstract | PMID:  28269901 | PMCID:  PMC5333297

  Abstract
• 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

  Abstract
• 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

  Abstract
• 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

  Abstract
• Nelsonn SD, Parker J, Lario R, Winnenburg R, Erlbaum MS, Lincoln MJ, Bodenreider O. Interoperability of medication classification systems: Lessons learned mapping estab-lished pharmacologic classes (EPCs) to SNOMED CT. Stud Health Technol Inform. 2017;245:920-924.

  Abstract | PMID:  29295234 | PMCID:  PMC5881380

  Abstract
• 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

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

  Abstract | pub9441.pdf

  AbstractDownload
• Ben Abacha A. NLM_NIH at TREC 2016 Clinical Decision Support Track. Proceedings of TREC 2016, the 25th Text Retrieval Conference, Gaithersburg, MD, USA, November 2016.

  Abstract | pub9489.pdf

  AbstractDownload
• Ben Abacha A, Demner-Fushman D. NLM_NIH at SemEval-2017 Task 3: from Question Entailment to Question Similarity for Community Question Answering. In Proceedings of the 11th International Workshop on Semantic Evaluation (SemEval@ACL) 2017: 349-352.

  Abstract | pub9538.pdf

  AbstractDownload
• Madani S, Henderson J, Fung K. Development of an oncology subset of SNOMED CT based on patient notes. AMIA Annu Symp Proc 2016: 91-92.

  Abstract | pub9465.pdf

  AbstractDownload
• McDonald CJ, Wang Y, Lynch P, Kanduru A. Feeding FHIR with LHC-Forms HL7 Partners in Interoperability Mt. Washington Conference Center, Baltimore, MD

  Abstract | pub9748.pdf

  AbstractDownload
• 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.

  Abstract

  Abstract
• 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

  AbstractDownload
• Roberts K, Demner-Fushman D. Annotating Logical Forms for EHR Questions. Proceedings of the Language Resources and Evaluation Conference, LREC,23-28 May 2016, Portorož.

  Abstract | URL:  http://www.lrec-conf.org/proceedings/lrec2016/pdf/152_Paper.pdf

  AbstractExternal link
• Kilicoglu H. Software: Bio-SCoRes

  Abstract

  Abstract
• Kilicoglu H. Dataset: Sortal Anaphora Dataset

  Abstract

  Abstract
• 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).

  Abstract

  Abstract
• 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.

  Abstract

  Abstract
• Cimino JJ, Huser V. Characterization of the Context of Drug Concepts in Research Protocols: An Empiric Study to Guide Ontology Development. AMIA Annu Symp Proc. 2015 Nov 5;2015:441-7. eCollection 2015.

  Abstract | PMID:  26958176 | PMCID:  PMC4765569

  Abstract
• 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

  AbstractDownload
• 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

  AbstractDownload
• Roberts K, Demner-Fushman D. Toward a Natural Language Interface for EHR Questions. AMIA Jt Summits Transl Sci Proc. 2015 Mar 25;2015:157-61. eCollection 2015.

  Abstract | pub9234.pdf | PMID:  26306260 | PMCID:  PMC4525248

  AbstractDownload
• 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

  AbstractDownload
• 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

  Abstract

Pages