TY - STD TI - Ford E, Nicholson A, Koeling R, Tate AR, Carroll J, Axelrod L, et al. Optimising the use of electronic health records to estimate the incidence of rheumatoid arthritis in primary care: what information is hidden in free text? BMC Med Res Methodol. 2013;13. ID - ref1 ER - TY - JOUR AU - Rosenbloom, S. T. AU - Denny, J. C. AU - Xu, H. AU - Lorenzi, N. AU - Stead, W. W. AU - Johnson, K. B. PY - 2011 DA - 2011// TI - Data from clinical notes: a perspective on the tension between structure and flexible documentation JO - J Am Med Informatics Assoc VL - 18 UR - https://doi.org/10.1136/jamia.2010.007237 DO - 10.1136/jamia.2010.007237 ID - Rosenbloom2011 ER - TY - JOUR AU - Coorevits, P. AU - Sundgren, M. AU - Klein, G. O. AU - Bahr, A. AU - Claerhout, B. AU - Daniel, C. PY - 2013 DA - 2013// TI - Electronic health records: new opportunities for clinical research JO - J Intern Med VL - 274 UR - https://doi.org/10.1111/joim.12119 DO - 10.1111/joim.12119 ID - Coorevits2013 ER - TY - JOUR AU - Danciu, I. AU - Cowan, J. D. AU - Basford, M. AU - Wang, X. AU - Saip, A. AU - Osgood, S. PY - 2014 DA - 2014// TI - Secondary use of clinical data: the Vanderbilt approach JO - J Biomed Inform VL - 52 UR - https://doi.org/10.1016/j.jbi.2014.02.003 DO - 10.1016/j.jbi.2014.02.003 ID - Danciu2014 ER - TY - STD TI - Price SJ, Stapley SA, Shephard E, Barraclough K, Hamilton WT. Is omission of free text records a possible source of data loss and bias in clinical practice research Datalink studies? A case-control study. BMJ Open. 2016;6. ID - ref5 ER - TY - JOUR AU - Gruber, T. R. PY - 1993 DA - 1993// TI - A translation approach to portable ontology specifications JO - Knowl Acquis VL - 5 UR - https://doi.org/10.1006/knac.1993.1008 DO - 10.1006/knac.1993.1008 ID - Gruber1993 ER - TY - STD TI - SNOMED International. SNOMED CT http://www.snomed.org/snomed-ct/five-step-briefing. Accessed 29 Jun 2020. UR - http://www.snomed.org/snomed-ct/five-step-briefing ID - ref7 ER - TY - JOUR AU - Köhler, S. AU - Carmody, L. AU - Vasilevsky, N. AU - Jacobsen, J. O. B. AU - Danis, D. AU - Gourdine, J. P. PY - 2019 DA - 2019// TI - Expansion of the human phenotype ontology (HPO) knowledge base and resources JO - Nucleic Acids Res VL - 47 UR - https://doi.org/10.1093/nar/gky1105 DO - 10.1093/nar/gky1105 ID - Köhler2019 ER - TY - JOUR AU - Krasowski, M. AU - Schriever, A. AU - Mathur, G. AU - Blau, J. AU - Stauffer, S. AU - Ford, B. PY - 2015 DA - 2015// TI - Use of a data warehouse at an academic medical center for clinical pathology quality improvement, education, and research JO - J Pathol Inform VL - 6 UR - https://doi.org/10.4103/2153-3539.161615 DO - 10.4103/2153-3539.161615 ID - Krasowski2015 ER - TY - JOUR AU - Wu, H. AU - Toti, G. AU - Morley, K. I. AU - Ibrahim, Z. M. AU - Folarin, A. AU - Jackson, R. PY - 2018 DA - 2018// TI - SemEHR: a general-purpose semantic search system to surface semantic data from clinical notes for tailored care, trial recruitment, and clinical research JO - J Am Med Inf Assoc VL - 25 UR - https://doi.org/10.1093/jamia/ocx160 DO - 10.1093/jamia/ocx160 ID - Wu2018 ER - TY - JOUR AU - Shivade, C. AU - Malewadkar, P. AU - Fosler-Lussier, E. AU - Lai, A. M. PY - 2015 DA - 2015// TI - Comparison of UMLS terminologies to identify risk of heart disease using clinical notes JO - J Biomed Inform VL - 58 UR - https://doi.org/10.1016/j.jbi.2015.08.025 DO - 10.1016/j.jbi.2015.08.025 ID - Shivade2015 ER - TY - JOUR AU - Lingren, T. AU - Thaker, V. AU - Brady, C. AU - Namjou, B. AU - Kennebeck, S. AU - Bickel, J. PY - 2016 DA - 2016// TI - Developing an algorithm to detect early childhood obesity in two tertiary pediatric medical centers JO - Appl Clin Inform VL - 7 UR - https://doi.org/10.4338/ACI-2016-01-RA-0015 DO - 10.4338/ACI-2016-01-RA-0015 ID - Lingren2016 ER - TY - JOUR AU - Ni, Y. AU - Kennebeck, S. AU - Dexheimer, J. W. AU - McAneney, C. M. AU - Tang, H. AU - Lingren, T. PY - 2015 DA - 2015// TI - Automated clinical trial eligibility prescreening: increasing the efficiency of patient identification for clinical trials in the emergency department JO - J Am Med Informatics Assoc. VL - 22 UR - https://doi.org/10.1136/amiajnl-2014-002887 DO - 10.1136/amiajnl-2014-002887 ID - Ni2015 ER - TY - JOUR AU - Sun, H. AU - Depraetere, K. AU - Roo, J. AU - Mels, G. AU - Vloed, B. AU - Twagirumukiza, M. PY - 2015 DA - 2015// TI - Semantic processing of EHR data for clinical research JO - J Biomed Inform VL - 58 UR - https://doi.org/10.1016/j.jbi.2015.10.009 DO - 10.1016/j.jbi.2015.10.009 ID - Sun2015 ER - TY - JOUR AU - Kreimeyer, K. AU - Foster, M. AU - Pandey, A. AU - Arya, N. AU - Halford, G. AU - Jones, S. F. PY - 2017 DA - 2017// TI - Natural language processing systems for capturing and standardizing unstructured clinical information: a systematic review JO - J Biomed Inf VL - 73 UR - https://doi.org/10.1016/j.jbi.2017.07.012 DO - 10.1016/j.jbi.2017.07.012 ID - Kreimeyer2017 ER - TY - JOUR AU - Gonzalez-Hernandez, G. AU - Sarker, A. AU - O’Connor, K. AU - Savova, G. PY - 2017 DA - 2017// TI - Capturing the Patient’s perspective: a review of advances in natural language processing of health-related text JO - Yearb Med Inf VL - 26 UR - https://doi.org/10.15265/IY-2017-029 DO - 10.15265/IY-2017-029 ID - Gonzalez-Hernandez2017 ER - TY - JOUR AU - Jovanovic, J. AU - Bagheri, E. AU - Jovanović, J. AU - Bagheri, E. AU - Jovanovic, J. AU - Bagheri, E. PY - 2017 DA - 2017// TI - Semantic annotation in biomedicine: the current landscape JO - J Biomed Semant VL - 8 UR - https://doi.org/10.1186/s13326-017-0153-x DO - 10.1186/s13326-017-0153-x ID - Jovanovic2017 ER - TY - STD TI - UK EQUATOR Centre. The EQUATOR Network. https://www.equator-network.org/. Accessed 29 Jun 2020. UR - https://www.equator-network.org/ ID - ref18 ER - TY - JOUR AU - Ford, E. AU - Carroll, J. A. AU - Smith, H. E. AU - Scott, D. AU - Cassell, J. A. PY - 2016 DA - 2016// TI - Extracting information from the text of electronic medical records to improve case detection: a systematic review JO - J Am Med Informatics Assoc. VL - 23 UR - https://doi.org/10.1093/jamia/ocv180 DO - 10.1093/jamia/ocv180 ID - Ford2016 ER - TY - JOUR AU - Vuokko, R. AU - Makela-Bengs, P. AU - Hypponen, H. AU - Lindqvist, M. AU - Doupi, P. AU - Mäkelä-Bengs, P. PY - 2017 DA - 2017// TI - Impacts of structuring the electronic health record: results of a systematic literature review from the perspective of secondary use of patient data JO - Int J Med Inform VL - 97 UR - https://doi.org/10.1016/j.ijmedinf.2016.10.004 DO - 10.1016/j.ijmedinf.2016.10.004 ID - Vuokko2017 ER - TY - JOUR AU - Collins, G. S. AU - Reitsma, J. B. AU - Altman, D. G. AU - Moons, K. G. M. PY - 2015 DA - 2015// TI - Transparent reporting of a multivariable prediction model for individual prognosis or diagnosis (TRIPOD): the TRIPOD statement JO - TRIPOD Group Circ VL - 131 ID - Collins2015 ER - TY - JOUR AU - Elm, E. AU - Altman, D. G. AU - Egger, M. AU - Pocock, S. J. AU - Gøtzsche, P. C. AU - Vandenbroucke, J. P. PY - 2008 DA - 2008// TI - The strengthening the reporting of observational studies in epidemiology (STROBE) statement: guidelines for reporting observational studies JO - J Clin Epidemiol VL - 61 UR - https://doi.org/10.1016/j.jclinepi.2007.11.008 DO - 10.1016/j.jclinepi.2007.11.008 ID - Elm2008 ER - TY - STD TI - Benchimol EI, Smeeth L, Guttmann A, Harron K, Moher D, Peteresen I et al. The REporting of studies Conducted using Observational Routinely-collected health Data (RECORD) Statement. PLoS Med. 2015;12:1–22. ID - ref23 ER - TY - STD TI - Bossuyt PM, Reitsma JB, Bruns DE, Gatsonis CA, Glasziou PP, Irwig L, et al. STARD 2015: an updated list of essential items for reporting diagnostic accuracy studies. BMJ. 2015;351:h5527. ID - ref24 ER - TY - STD TI - Moher D, Liberati A, Tetzlaff J, Altman DG, Altman D, Antes G et al. Preferred reporting items for systematic reviews and meta-analyses: The PRISMA statement. PLoS Med. 2009;6:1–6. ID - ref25 ER - TY - STD TI - The EndNote Team. EndNote. Philadelphia: Clarivate; 2013. ID - ref26 ER - TY - STD TI - Ouzzani M, Hammady H, Fedorowicz Z, Elmagarmid A. Rayyan—a web and mobile app for systematic reviews. Syst Rev. 2016;5:210. ID - ref27 ER - TY - STD TI - Veritas Health Innovation. Covidence systematic review software. Melbourne: Veritas Health Innovation; 2020. ID - ref28 ER - TY - JOUR AU - Afshar, M. AU - Dligach, D. AU - Sharma, B. AU - Cai, X. AU - Boyda, J. AU - Birch, S. PY - 2019 DA - 2019// TI - Development and application of a high throughput natural language processing architecture to convert all clinical documents in a clinical data warehouse into standardized medical vocabularies JO - J Am Med Inform Assoc VL - 26 UR - https://doi.org/10.1093/jamia/ocz068 DO - 10.1093/jamia/ocz068 ID - Afshar2019 ER - TY - JOUR AU - Alnazzawi, N. AU - Thompson, P. AU - Ananiadou, S. PY - 2016 DA - 2016// TI - Mapping Phenotypic Information in Heterogeneous Textual Sources to a Domain-Specific Terminological Resource JO - PLoS One VL - 11 UR - https://doi.org/10.1371/journal.pone.0162287 DO - 10.1371/journal.pone.0162287 ID - Alnazzawi2016 ER - TY - JOUR AU - Atutxa, A. AU - Perez, A. AU - Casillas, A. PY - 2018 DA - 2018// TI - Machine Learning Approaches on Diagnostic Term Encoding with the ICD for Clinical Documentation JO - IEEE J Biomed Heal Informatics VL - 22 UR - https://doi.org/10.1109/JBHI.2017.2743824 DO - 10.1109/JBHI.2017.2743824 ID - Atutxa2018 ER - TY - JOUR AU - Barrett, N. AU - Weber-Jahnke, J. H. AU - Thai, V. PY - 2013 DA - 2013// TI - Engineering natural language processing solutions for structured information from clinical text: extracting sentinel events from palliative care consult letters JO - Stud Health Technol Inform VL - 192 ID - Barrett2013 ER - TY - JOUR AU - Becker, M. AU - Bockmann, B. PY - 2016 DA - 2016// TI - Extraction of UMLS(R) Concepts Using Apache cTAKES for German Language JO - Stud Health Technol Inform VL - 223 ID - Becker2016 ER - TY - JOUR AU - Becker, M. AU - Kasper, S. AU - Böckmann, B. AU - Jöckel, K. -. H. AU - Virchow, I. PY - 2019 DA - 2019// TI - Natural language processing of German clinical colorectal cancer notes for guideline-based treatment evaluation JO - Int J Med Inform VL - 127 UR - https://doi.org/10.1016/j.ijmedinf.2019.04.022 DO - 10.1016/j.ijmedinf.2019.04.022 ID - Becker2019 ER - TY - JOUR AU - Bejan, C. A. AU - Wei, W. Q. AU - Denny, J. C. PY - 2015 DA - 2015// TI - Assessing the role of a medication-indication resource in the treatment relation extraction from clinical text JO - J Am Med Informatics Assoc VL - 22 UR - https://doi.org/10.1136/amiajnl-2014-002954 DO - 10.1136/amiajnl-2014-002954 ID - Bejan2015 ER - TY - BOOK AU - Castro, E. AU - Iglesias, A. AU - Martínez, P. AU - Castaño, L. PY - 2010 DA - 2010// TI - Automatic Identification of Biomedical Concepts in Spanish-language Unstructured Clinical Texts. German Research Cent for Artificial, Intelligence - DFKI GmbH, Kaiserslautern, Germany Seattle, WA, USA: ACM ID - Castro2010 ER - TY - JOUR AU - Catling, F. AU - Spithourakis, G. P. AU - Riedel, S. PY - 2018 DA - 2018// TI - Towards automated clinical coding JO - Int J Med Inform VL - 120 UR - https://doi.org/10.1016/j.ijmedinf.2018.09.021 DO - 10.1016/j.ijmedinf.2018.09.021 ID - Catling2018 ER - TY - JOUR AU - Chapman, W. W. AU - Fiszman, M. AU - Dowling, J. N. AU - Chapman, B. E. AU - Rindflesch, T. C. PY - 2004 DA - 2004// TI - Identifying respiratory findings in emergency department reports for biosurveillance using MetaMap JO - Medinfo VL - 11 ID - Chapman2004 ER - TY - JOUR AU - Chen, J. AU - Zheng, J. AU - Yu, H. PY - 2016 DA - 2016// TI - Finding Important Terms for Patients in Their Electronic Health Records: A Learning-to-Rank Approach Using Expert Annotations JO - JMIR Med informatics VL - 4 UR - https://doi.org/10.2196/medinform.6373 DO - 10.2196/medinform.6373 ID - Chen2016 ER - TY - JOUR AU - Chiaramello, E. AU - Pinciroli, F. AU - Bonalumi, A. AU - Caroli, A. AU - Tognola, G. PY - 2016 DA - 2016// TI - Use of “off-the-shelf” information extraction algorithms in clinical informatics: A feasibility study of MetaMap annotation of Italian medical notes JO - J Biomed Inform VL - 63 UR - https://doi.org/10.1016/j.jbi.2016.07.017 DO - 10.1016/j.jbi.2016.07.017 ID - Chiaramello2016 ER - TY - CHAP AU - Chodey, K. P. AU - Hu, G. PY - 2016 DA - 2016// TI - Clinical text analysis using machine learning methods BT - 2016 IEEE/ACIS 15th International Conference on Computer and Information Science (ICIS) ID - Chodey2016 ER - TY - STD TI - Chung J, Murphy S. Concept-value pair extraction from semi-structured clinical narrative: a case study using echocardiogram reports. AMIA Annu Symp Proc. 2005:131–5. ID - ref42 ER - TY - JOUR AU - Combi, C. AU - Zorzi, M. AU - Pozzani, G. AU - Moretti, U. AU - Arzenton, E. PY - 2018 DA - 2018// TI - From narrative descriptions to MedDRA: automagically encoding adverse drug reactions JO - J Biomed Inform VL - 84 UR - https://doi.org/10.1016/j.jbi.2018.07.001 DO - 10.1016/j.jbi.2018.07.001 ID - Combi2018 ER - TY - JOUR AU - Bruijn, B. AU - Cherry, C. AU - Kiritchenko, S. AU - Martin, J. AU - Zhu, X. PY - 2011 DA - 2011// TI - Machine-learned solutions for three stages of clinical information extraction: The state of the art at i2b2 2010 JO - J Am Med Informatics Assoc VL - 18 UR - https://doi.org/10.1136/amiajnl-2011-000150 DO - 10.1136/amiajnl-2011-000150 ID - Bruijn2011 ER - TY - JOUR AU - Deisseroth, C. A. AU - Birgmeier, J. AU - Bodle, E. E. AU - Kohler, J. N. AU - Matalon, D. R. AU - Nazarenko, Y. PY - 2019 DA - 2019// TI - ClinPhen extracts and prioritizes patient phenotypes directly from medical records to expedite genetic disease diagnosis JO - Genet Med VL - 21 UR - https://doi.org/10.1038/s41436-018-0381-1 DO - 10.1038/s41436-018-0381-1 ID - Deisseroth2019 ER - TY - JOUR AU - Demner-Fushman, D. AU - Rogers, W. J. AU - Aronson, A. R. PY - 2017 DA - 2017// TI - MetaMap Lite: An evaluation of a new Java implementation of MetaMap JO - J Am Med Informatics Assoc VL - 24 UR - https://doi.org/10.1093/jamia/ocw177 DO - 10.1093/jamia/ocw177 ID - Demner-Fushman2017 ER - TY - JOUR AU - Divita, G. AU - Zeng, Q. T. AU - Gundlapalli, A. V. AU - Duvall, S. AU - Nebeker, J. AU - Samore, M. H. PY - 2014 DA - 2014// TI - Sophia: A Expedient UMLS Concept Extraction Annotator JO - AMIA Annu Symp Proc VL - 2014 ID - Divita2014 ER - TY - JOUR AU - Duarte, F. AU - Martins, B. AU - Pinto, C. S. AU - Silva, M. J. PY - 2018 DA - 2018// TI - Deep neural models for ICD-10 coding of death certificates and autopsy reports in free-text JO - J Biomed Inform VL - 80 UR - https://doi.org/10.1016/j.jbi.2018.02.011 DO - 10.1016/j.jbi.2018.02.011 ID - Duarte2018 ER - TY - BOOK AU - Falis, M. AU - Pajak, M. AU - Lisowska, A. AU - Schrempf, P. AU - Deckers, L. AU - Mikhael, S. PY - 2019 DA - 2019// TI - Ontological attention ensembles for capturing semantic concepts in ICD code prediction from clinical text ID - Falis2019 ER - TY - CHAP AU - Ferrão, J. C. AU - Janela, F. AU - Oliveira, M. D. AU - HMG, M. PY - 2013 DA - 2013// TI - Using Structured EHR Data and SVM to Support ICD-9-CM Coding BT - 2013 IEEE International Conference on Healthcare Informatics UR - https://doi.org/10.1109/ICHI.2013.79 DO - 10.1109/ICHI.2013.79 ID - Ferrão2013 ER - TY - STD TI - Gerbier S, Yarovaya O, Gicquel Q, Millet A-L, Smaldore V, Pagliaroli V, et al. Evaluation of natural language processing from emergency department computerized medical records for intra-hospital syndromic surveillance. BMC Med Inform Decis Mak. 2011;11:50. ID - ref51 ER - TY - JOUR AU - Goicoechea Salazar, J. A. AU - Nieto García, M. A. AU - Laguna Téllez, A. AU - Canto Casasola, V. D. AU - Rodríguez Herrera, J. AU - Murillo, C. F. PY - 2013 DA - 2013// TI - Development of an automated coding system to retrieve and analyze diagnostic information stored in hospital emergency department records JO - Emergencias VL - 25 ID - Goicoechea Salazar2013 ER - TY - JOUR AU - Hamid, H. AU - Fodeh, S. J. AU - Lizama, A. G. AU - Czlapinski, R. AU - Pugh, M. J. AU - LaFrance, W. C. PY - 2013 DA - 2013// TI - Validating a natural language processing tool to exclude psychogenic nonepileptic seizures in electronic medical record-based epilepsy research JO - Epilepsy Behav VL - 29 UR - https://doi.org/10.1016/j.yebeh.2013.09.025 DO - 10.1016/j.yebeh.2013.09.025 ID - Hamid2013 ER - TY - JOUR AU - Hassanzadeh, H. AU - Kholghi, M. AU - Nguyen, A. AU - Chu, K. PY - 2018 DA - 2018// TI - Clinical document classification using labeled and unlabeled data across hospitals JO - AMIA . Annu Symp proceedings AMIA Symp VL - 2018 ID - Hassanzadeh2018 ER - TY - BOOK AU - Helwe, C. AU - Elbassuoni, S. AU - Geha, M. AU - Hitti, E. AU - Makhlouf, O. C. PY - 2017 DA - 2017// TI - CCS Coding of Discharge Diagnoses via Deep Neural Networks. German Research Cent for Artificial, Intelligence - DFKI GmbH, Kaiserslautern, Germany Seattle, WA, USA: ACM ID - Helwe2017 ER - TY - JOUR AU - Hersh, W. AU - Mailhot, M. AU - Arnott-Smith, C. AU - Lowe, H. PY - 2001 DA - 2001// TI - Selective automated indexing of findings and diagnoses in radiology reports JO - J Biomed Inform VL - 34 UR - https://doi.org/10.1006/jbin.2001.1025 DO - 10.1006/jbin.2001.1025 ID - Hersh2001 ER - TY - JOUR AU - Hoogendoorn, M. AU - Szolovits, P. AU - Moons, L. M. G. AU - Numans, M. E. PY - 2015 DA - 2015// TI - Utilizing uncoded consultation notes from electronic medical records for predictive modeling of colorectal cancer JO - Artif Intell Med. VL - 69 UR - https://doi.org/10.1016/j.artmed.2016.03.003 DO - 10.1016/j.artmed.2016.03.003 ID - Hoogendoorn2015 ER - TY - JOUR AU - Jindal, P. AU - Roth, D. PY - 2013 DA - 2013// TI - Extraction of events and temporal expressions from clinical narratives JO - J Biomed Inform VL - 46 UR - https://doi.org/10.1016/j.jbi.2013.08.010 DO - 10.1016/j.jbi.2013.08.010 ID - Jindal2013 ER - TY - JOUR AU - Kang, B. Y. AU - Kim, D. W. AU - Kim, H. G. PY - 2009 DA - 2009// TI - Two-phase chief complaint mapping to the UMLS metathesaurus in Korean Electronic Medical Records JO - IEEE Trans Inf Technol Biomed VL - 13 UR - https://doi.org/10.1109/TITB.2008.2007103 DO - 10.1109/TITB.2008.2007103 ID - Kang2009 ER - TY - JOUR AU - Kersloot, M. G. M. G. AU - Lau, F. AU - Abu-Hanna, A. AU - Arts, D. L. D. L. AU - Cornet, R. PY - 2019 DA - 2019// TI - Automated SNOMED CT concept and attribute relationship detection through a web-based implementation of cTAKES JO - J Biomed Semantics. VL - 10 UR - https://doi.org/10.1186/s13326-019-0207-3 DO - 10.1186/s13326-019-0207-3 ID - Kersloot2019 ER - TY - JOUR AU - König, M. AU - Sander, A. AU - Demuth, I. AU - Diekmann, D. AU - Steinhagen-Thiessen, E. PY - 2019 DA - 2019// TI - Knowledge-based best of breed approach for automated detection of clinical events based on German free text digital hospital discharge letters JO - PLoS One VL - 14 UR - https://doi.org/10.1371/journal.pone.0224916 DO - 10.1371/journal.pone.0224916 ID - König2019 ER - TY - STD TI - Li Q, Spooner SA, Kaiser M, Lingren N, Robbins J, Lingren T, et al. An end-to-end hybrid algorithm for automated medication discrepancy detection. BMC Med Inform Decis Mak. 2015;15:37. ID - ref62 ER - TY - JOUR AU - Li, F. AU - Jin, Y. AU - Liu, W. AU - Rawat, B. P. S. AU - Cai, P. AU - Yu, H. PY - 2019 DA - 2019// TI - Fine-tuning bidirectional encoder representations from transformers (BERT)-based models on large-scale electronic health record notes: an empirical study JO - JMIR Med informatics VL - 7 UR - https://doi.org/10.2196/14830 DO - 10.2196/14830 ID - Li2019 ER - TY - JOUR AU - Liu, C. AU - Ta, C. N. AU - Rogers, J. R. AU - Li, Z. AU - Lee, J. AU - Butler, A. M. PY - 2019 DA - 2019// TI - Ensembles of natural language processing systems for portable phenotyping solutions JO - J Biomed Inform VL - 100 UR - https://doi.org/10.1016/j.jbi.2019.103318 DO - 10.1016/j.jbi.2019.103318 ID - Liu2019 ER - TY - JOUR AU - Lowe, H. J. AU - Huang, Y. AU - Regula, D. P. PY - 2009 DA - 2009// TI - Using a statistical natural language Parser augmented with the UMLS specialist lexicon to assign SNOMED CT codes to anatomic sites and pathologic diagnoses in full text pathology reports JO - AMIA Annu Symp Proc VL - 2009 ID - Lowe2009 ER - TY - JOUR AU - Luo, Y. AU - Sohani, A. R. AU - Hochberg, E. P. AU - Szolovits, P. PY - 2014 DA - 2014// TI - Automatic lymphoma classification with sentence subgraph mining from pathology reports JO - J Am Med Informatics Assoc VL - 21 UR - https://doi.org/10.1136/amiajnl-2013-002443 DO - 10.1136/amiajnl-2013-002443 ID - Luo2014 ER - TY - JOUR AU - Meystre, S. AU - Haug, P. J. PY - 2006 DA - 2006// TI - Natural language processing to extract medical problems from electronic clinical documents: performance evaluation JO - J Biomed Inform VL - 39 UR - https://doi.org/10.1016/j.jbi.2005.11.004 DO - 10.1016/j.jbi.2005.11.004 ID - Meystre2006 ER - TY - JOUR AU - Meystre, S. M. AU - Thibault, J. AU - Shen, S. AU - Hurdle, J. F. AU - South, B. R. PY - 2010 DA - 2010// TI - Automatically detecting medications and the reason for their prescription in clinical narrative text documents JO - Stud Health Technol Inform. VL - 160 ID - Meystre2010 ER - TY - JOUR AU - Minard, A. L. AU - Ligozat, A. L. AU - Abacha, A. B. AU - Bernhard, D. AU - Cartoni, B. AU - Deléger, L. PY - 2011 DA - 2011// TI - Hybrid methods for improving information access in clinical documents: Concept, assertion, and relation identification JO - J Am Med Informatics Assoc VL - 18 UR - https://doi.org/10.1136/amiajnl-2011-000154 DO - 10.1136/amiajnl-2011-000154 ID - Minard2011 ER - TY - JOUR AU - Mishra, R. AU - Burke, A. AU - Gitman, B. AU - Verma, P. AU - Engelstad, M. AU - Haendel, M. A. PY - 2019 DA - 2019// TI - Data-driven method to enhance craniofacial and oral phenotype vocabularies JO - J Am Dent Assoc VL - 150 UR - https://doi.org/10.1016/j.adaj.2019.05.029 DO - 10.1016/j.adaj.2019.05.029 ID - Mishra2019 ER - TY - JOUR AU - Nguyen, A. N. AU - Truran, D. AU - Kemp, M. AU - Koopman, B. AU - Conlan, D. AU - O’Dwyer, J. PY - 2018 DA - 2018// TI - Computer-assisted diagnostic coding: effectiveness of an NLP-based approach using SNOMED CT to ICD-10 mappings JO - AMIA . Annu Symp proceedings AMIA Symp VL - 2018 ID - Nguyen2018 ER - TY - JOUR AU - Oellrich, A. AU - Collier, N. AU - Smedley, D. AU - Groza, T. PY - 2015 DA - 2015// TI - Generation of silver standard concept annotations from biomedical texts with special relevance to phenotypes JO - PLoS One VL - 10 UR - https://doi.org/10.1371/journal.pone.0116040 DO - 10.1371/journal.pone.0116040 ID - Oellrich2015 ER - TY - JOUR AU - Patrick, J. D. AU - Nguyen, D. H. M. AU - Wang, Y. AU - Li, M. PY - 2011 DA - 2011// TI - A knowledge discovery and reuse pipeline for information extraction in clinical notes JO - J Am Med Informatics Assoc VL - 18 UR - https://doi.org/10.1136/amiajnl-2011-000302 DO - 10.1136/amiajnl-2011-000302 ID - Patrick2011 ER - TY - JOUR AU - Pérez, A. AU - Atutxa, A. AU - Casillas, A. AU - Gojenola, K. AU - Sellart, Á. PY - 2018 DA - 2018// TI - Inferred joint multigram models for medical term normalization according to ICD JO - Int J Med Inform VL - 110 UR - https://doi.org/10.1016/j.ijmedinf.2017.12.007 DO - 10.1016/j.ijmedinf.2017.12.007 ID - Pérez2018 ER - TY - JOUR AU - Reátegui, R. AU - Ratté, S. PY - 2018 DA - 2018// TI - Comparison of MetaMap and cTAKES for entity extraction in clinical notes JO - BMC Med Inform Decis Mak VL - 18 UR - https://doi.org/10.1186/s12911-018-0654-2 DO - 10.1186/s12911-018-0654-2 ID - Reátegui2018 ER - TY - JOUR AU - Roberts, K. AU - Harabagiu, S. M. PY - 2011 DA - 2011// TI - A flexible framework for deriving assertions from electronic medical records JO - J Am Med Informatics Assoc VL - 18 UR - https://doi.org/10.1136/amiajnl-2011-000152 DO - 10.1136/amiajnl-2011-000152 ID - Roberts2011 ER - TY - JOUR AU - Rousseau, J. F. AU - Ip, I. K. AU - Raja, A. S. AU - Valtchinov, V. I. AU - Cochon, L. AU - Schuur, J. D. PY - 2019 DA - 2019// TI - Can automated retrieval of data from emergency department physician notes enhance the imaging order entry process? JO - Appl Clin Inform VL - 10 UR - https://doi.org/10.1055/s-0039-1679927 DO - 10.1055/s-0039-1679927 ID - Rousseau2019 ER - TY - JOUR AU - Savova, G. K. AU - Masanz, J. J. AU - Ogren, P. V. AU - Zheng, J. AU - Sohn, S. AU - Kipper-Schuler, K. C. PY - 2010 DA - 2010// TI - Mayo clinical text analysis and knowledge extraction system (cTAKES): architecture, component evaluation and applications JO - J Am Med Informatics Assoc. VL - 17 UR - https://doi.org/10.1136/jamia.2009.001560 DO - 10.1136/jamia.2009.001560 ID - Savova2010 ER - TY - STD TI - Shoenbill K, Song Y, Gress L, Johnson H, Smith M, Mendonca EA. Natural language processing of lifestyle modification documentation. Health Informatics J. 2019:1460458218824742. ID - ref79 ER - TY - JOUR AU - Sohn, S. AU - Clark, C. AU - Halgrim, S. R. AU - Murphy, S. P. AU - Chute, C. G. AU - Liu, H. PY - 2014 DA - 2014// TI - MedXN: An open source medication extraction and normalization tool for clinical text JO - J Am Med Informatics Assoc VL - 21 UR - https://doi.org/10.1136/amiajnl-2013-002190 DO - 10.1136/amiajnl-2013-002190 ID - Sohn2014 ER - TY - STD TI - Solti I, Aaronson B, Fletcher G, Solti M, Gennari JH, Cooper M, et al. Building an automated problem list based on natural language processing: lessons learned in the early phase of development. AMIA Annu Symp Proc. 2008;2008:687–91. ID - ref81 ER - TY - CHAP AU - Soriano, I. M. AU - Peña, J. L. C. AU - Breis, J. T. F. AU - Román, I. S. AU - Barriuso, A. A. AU - Baraza, D. G. PY - 2019 DA - 2019// TI - Snomed2Vec: Representation of SNOMED CT Terms with Word2Vec BT - 2019 IEEE 32nd International Symposium on Computer-Based Medical Systems (CBMS) UR - https://doi.org/10.1109/CBMS.2019.00138 DO - 10.1109/CBMS.2019.00138 ID - Soriano2019 ER - TY - JOUR AU - Soysal, E. AU - Wang, J. AU - Jiang, M. AU - Wu, Y. AU - Pakhomov, S. AU - Liu, H. PY - 2018 DA - 2018// TI - CLAMP - a toolkit for efficiently building customized clinical natural language processing pipelines JO - J Am Med Informatics Assoc VL - 25 UR - https://doi.org/10.1093/jamia/ocx132 DO - 10.1093/jamia/ocx132 ID - Soysal2018 ER - TY - JOUR AU - Spasić, I. AU - Zhao, B. AU - Jones, C. B. AU - Button, K. PY - 2015 DA - 2015// TI - KneeTex: An ontology-driven system for information extraction from MRI reports JO - J Biomed Semantics VL - 6 UR - https://doi.org/10.1186/s13326-015-0033-1 DO - 10.1186/s13326-015-0033-1 ID - Spasić2015 ER - TY - JOUR AU - Strauss, J. A. AU - Chao, C. R. AU - Kwan, M. L. AU - Ahmed, S. A. AU - Schottinger, J. E. AU - Quinn, V. P. PY - 2013 DA - 2013// TI - Identifying primary and recurrent cancers using a SAS-based natural language processing algorithm JO - J Am Med Informatics Assoc VL - 20 UR - https://doi.org/10.1136/amiajnl-2012-000928 DO - 10.1136/amiajnl-2012-000928 ID - Strauss2013 ER - TY - JOUR AU - Sung, S. F. AU - Chen, K. AU - Wu, D. P. AU - Hung, L. C. AU - Su, Y. H. AU - Hu, Y. H. PY - 2018 DA - 2018// TI - Applying natural language processing techniques to develop a task-specific EMR interface for timely stroke thrombolysis: A feasibility study JO - Int J Med Inform VL - 112 UR - https://doi.org/10.1016/j.ijmedinf.2018.02.005 DO - 10.1016/j.ijmedinf.2018.02.005 ID - Sung2018 ER - TY - JOUR AU - Tchechmedjiev, A. AU - Abdaoui, A. AU - Emonet, V. AU - Zevio, S. AU - Jonquet, C. PY - 2018 DA - 2018// TI - SIFR annotator: ontology-based semantic annotation of French biomedical text and clinical notes JO - BMC Bioinformatics VL - 19 UR - https://doi.org/10.1186/s12859-018-2429-2 DO - 10.1186/s12859-018-2429-2 ID - Tchechmedjiev2018 ER - TY - JOUR AU - Ternois, I. AU - Escudie, J. -. B. AU - Benamouzig, R. AU - Duclos, C. PY - 2018 DA - 2018// TI - Development of an automatic coding system for digestive endoscopies JO - Stud Health Technol Inform VL - 255 ID - Ternois2018 ER - TY - JOUR AU - Travers, D. A. AU - Haas, S. W. PY - 2004 DA - 2004// TI - Evaluation of Emergency Medical Text Processor, a system for cleaning chief complaint text data JO - Acad Emerg Med VL - 11 UR - https://doi.org/10.1197/j.aem.2004.08.012 DO - 10.1197/j.aem.2004.08.012 ID - Travers2004 ER - TY - JOUR AU - Tulkens, S. AU - Šuster, S. AU - Daelemans, W. PY - 2019 DA - 2019// TI - Unsupervised concept extraction from clinical text through semantic composition JO - J Biomed Inform VL - 91 UR - https://doi.org/10.1016/j.jbi.2019.103120 DO - 10.1016/j.jbi.2019.103120 ID - Tulkens2019 ER - TY - JOUR AU - Usui, M. AU - Aramaki, E. AU - Iwao, T. AU - Wakamiya, S. AU - Sakamoto, T. AU - Mochizuki, M. PY - 2018 DA - 2018// TI - Extraction and standardization of patient complaints from electronic medication histories for Pharmacovigilance: natural language processing analysis in Japanese JO - JMIR Med informatics. VL - 6 UR - https://doi.org/10.2196/11021 DO - 10.2196/11021 ID - Usui2018 ER - TY - JOUR AU - Valtchinov, V. I. AU - Lacson, R. AU - Wang, A. AU - Khorasani, R. PY - 2019 DA - 2019// TI - Comparing Artificial Intelligence Approaches to Retrieve Clinical Reports Documenting Implantable Devices Posing MRI Safety Risks JO - J Am Coll Radiol VL - S1546–1440 ID - Valtchinov2019 ER - TY - JOUR AU - Wadia, R. AU - Akgun, K. AU - Brandt, C. AU - Fenton, B. T. AU - Levin, W. AU - Marple, A. H. PY - 2018 DA - 2018// TI - Comparison of natural language processing and manual coding for the identification of cross-sectional imaging reports suspicious for lung Cancer JO - JCO Clin cancer informatics VL - 2 UR - https://doi.org/10.1200/CCI.17.00069 DO - 10.1200/CCI.17.00069 ID - Wadia2018 ER - TY - JOUR AU - Walker, G. AU - Soysal, E. AU - Xu, H. PY - 2019 DA - 2019// TI - Development of a natural language processing tool to extract radiation treatment sites JO - Cureus. VL - 11 ID - Walker2019 ER - TY - BOOK AU - Xie, X. AU - Xiong, Y. AU - Yu, P. S. AU - Zhu, Y. PY - 2019 DA - 2019// TI - EHR Coding with Multi-scale Feature Attention and Structured Knowledge Graph Propagation. ACM ID - Xie2019 ER - TY - JOUR AU - Xu, H. AU - Fu, Z. AU - Shah, A. AU - Chen, Y. AU - Peterson, N. B. AU - Chen, Q. PY - 2011 DA - 2011// TI - Extracting and integrating data from entire electronic health records for detecting colorectal cancer cases JO - AMIA Annu Symp Proc VL - 2011 ID - Xu2011 ER - TY - JOUR AU - Yadav, K. AU - Sarioglu, E. AU - Smith, M. AU - Choi, H. A. PY - 2013 DA - 2013// TI - Automated outcome classification of emergency department computed tomography imaging reports JO - Acad Emerg Med VL - 20 UR - https://doi.org/10.1111/acem.12174 DO - 10.1111/acem.12174 ID - Yadav2013 ER - TY - JOUR AU - Yao, L. AU - Mao, C. AU - Luo, Y. PY - 2019 DA - 2019// TI - Clinical text classification with rule-based features and knowledge-guided convolutional neural networks JO - BMC Med Inform Decis Mak VL - 19 UR - https://doi.org/10.1186/s12911-019-0781-4 DO - 10.1186/s12911-019-0781-4 ID - Yao2019 ER - TY - JOUR AU - Zeng, Z. AU - Espino, S. AU - Roy, A. AU - Li, X. AU - Khan, S. A. AU - Clare, S. E. PY - 2018 DA - 2018// TI - Using natural language processing and machine learning to identify breast cancer local recurrence JO - BMC Bioinformatics VL - 19 UR - https://doi.org/10.1186/s12859-018-2466-x DO - 10.1186/s12859-018-2466-x ID - Zeng2018 ER - TY - JOUR AU - Zhang, S. AU - Elhadad, N. PY - 2013 DA - 2013// TI - Unsupervised biomedical named entity recognition: Experiments with clinical and biological texts JO - J Biomed Inform VL - 46 UR - https://doi.org/10.1016/j.jbi.2013.08.004 DO - 10.1016/j.jbi.2013.08.004 ID - Zhang2013 ER - TY - CHAP AU - Zhou, X. AU - Han, H. AU - Chankai, I. AU - Prestrud, A. AU - Brooks, A. PY - 2006 DA - 2006// TI - Approaches to Text Mining for Clinical Medical Records BT - German Research Cent for Artificial, Intelligence - DFKI GmbH, Kaiserslautern, Germany Seattle, WA, USA: ACM ID - Zhou2006 ER - TY - JOUR AU - Zhou, L. AU - Plasek, J. M. AU - Mahoney, L. M. AU - Karipineni, N. AU - Chang, F. AU - Yan, X. PY - 2011 DA - 2011// TI - Using Medical Text Extraction, Reasoning and Mapping System (MTERMS) to process medication information in outpatient clinical notes JO - AMIA Annu Symp Proc VL - 2011 ID - Zhou2011 ER - TY - JOUR AU - Zhou, L. AU - Lu, Y. AU - Vitale, C. J. AU - Mar, P. L. AU - Chang, F. AU - Dhopeshwarkar, N. PY - 2014 DA - 2014// TI - Representation of information about family relatives as structured data in electronic health records JO - Appl Clin Inform VL - 5 UR - https://doi.org/10.4338/ACI-2013-10-RA-0080 DO - 10.4338/ACI-2013-10-RA-0080 ID - Zhou2014 ER - TY - BOOK AU - Hassanzadeh, H. AU - Nguyen, A. AU - Koopman, B. PY - 2016 DA - 2016// TI - Evaluation of Medical Concept Annotation Systems on Clinical Records ID - Hassanzadeh2016 ER - TY - JOUR AU - Matentzoglu, N. AU - Malone, J. AU - Mungall, C. AU - Stevens, R. PY - 2018 DA - 2018// TI - MIRO: guidelines for minimum information for the reporting of an ontology JO - J Biomed Semantics VL - 9 UR - https://doi.org/10.1186/s13326-017-0172-7 DO - 10.1186/s13326-017-0172-7 ID - Matentzoglu2018 ER - TY - JOUR AU - Beleites, C. AU - Neugebauer, U. AU - Bocklitz, T. AU - Krafft, C. AU - Popp, J. PY - 2013 DA - 2013// TI - Sample size planning for classification models JO - Anal Chim Acta VL - 760 UR - https://doi.org/10.1016/j.aca.2012.11.007 DO - 10.1016/j.aca.2012.11.007 ID - Beleites2013 ER - TY - JOUR AU - Yang, Q. AU - Liu, Y. AU - Chen, T. AU - Tong, Y. PY - 2019 DA - 2019// TI - Federated machine learning: concept and applications JO - ACM Trans Intell Syst Technol VL - 10 ID - Yang2019 ER - TY - JOUR AU - Sokolova, M. AU - Lapalme, G. PY - 2009 DA - 2009// TI - A systematic analysis of performance measures for classification tasks JO - Inf Process Manag VL - 45 UR - https://doi.org/10.1016/j.ipm.2009.03.002 DO - 10.1016/j.ipm.2009.03.002 ID - Sokolova2009 ER -