Journal: Journal of Biomedical Informatics

Volume 45, Issue 6

1021 -- 1034Farzaneh Tatari, Mohammad R. Akbarzadeh-Totonchi, Ahmad Sabahi. Fuzzy-probabilistic multi agent system for breast cancer risk assessment and insurance premium assignment
1035 -- 1041Won Kim, Lana Yeganova, Donald C. Comeau, W. John Wilbur. Identifying well-formed biomedical phrases in MEDLINE® text
1042 -- 1048Huanying Gu, Gai Elhanan, Yehoshua Perl, George Hripcsak, James J. Cimino, Julia Xu, Yan Chen, James Geller, C. Paul Morrey. A study of terminology auditors' performance for UMLS semantic type assignments
1049 -- 1065Trevor Cohen, Dominic Widdows, Roger W. Schvaneveldt, Peter Davies, Thomas C. Rindflesch. Discovering discovery patterns with predication-based Semantic Indexing
1066 -- 1074Jose Salavert Torres, J. Damiàn Segrelles Quilis, Ignacio Blanquer Espert, Vicente Hernández. Improving knowledge management through the support of image examination and data annotation using DICOM structured reporting
1075 -- 1083Hua Xu, Yonghui Wu, Noemie Elhadad, Peter D. Stetson, Carol Friedman. A new clustering method for detecting rare senses of abbreviations in clinical notes
1084 -- 1107Xuan Hung Le, Terry Doll, Monica Barbosu, Amneris E. Luque, Dongwen Wang. An enhancement of the Role-Based Access Control model to facilitate information access management in context of team collaboration and workflow
1108 -- 1119F. Stella, Y. Amer. Continuous time Bayesian network classifiers
1120 -- 1136Fabio Grandi, Federica Mandreoli, Riccardo Martoglia. Efficient management of multi-version clinical guidelines
1137 -- 1150Rachel M. Satter, Trevor Cohen, Pierina Ortiz, Kanav Kahol, James Mackenzie, Carol Olson, Mina Johnson, Vimla L. Patel. Avatar-based simulation in the evaluation of diagnosis and management of mental health disorders in primary care
1151 -- 1163Alla Keselman, Catherine Arnott-Smith. A classification of errors in lay comprehension of medical documents
1164 -- 1174Chih-Lin Chi, W. Nick Street, Jennifer G. Robinson, Matthew A. Crawford. Individualized patient-centered lifestyle recommendations: An expert system for communicating patient specific cardiovascular risk information and prioritizing lifestyle options
1175 -- 1184Hanen Borchani, Concha Bielza, Pablo Martínez-Martín, Pedro Larrañaga. Markov blanket-based approach for learning multi-dimensional Bayesian network classifiers: An application to predict the European Quality of Life-5 Dimensions (EQ-5D) from the 39-item Parkinson's Disease Questionnaire (PDQ-39)
1185 -- 1190Loubna Bouarfa, Jenny Dankelman. Workflow mining and outlier detection from clinical activity logs
1191 -- 1198Do Kyoon Kim, Hyunjung Shin, Young-Soo Song, Ju Han Kim. Synergistic effect of different levels of genomic data for cancer clinical outcome prediction
1199 -- 1201Yves A. Lussier, Haiquan Li. Breakthroughs in genomics data integration for predicting clinical outcome
1202 -- 1216Jan Horsky, Gordon D. Schiff, Douglas Johnston, Lauren Mercincavage, Douglas S. Bell, Blackford Middleton. Interface design principles for usable decision support: A targeted review of best practices for clinical prescribing interventions
1217 -- 0Himali Saitwal, David Qing, Stephen Jones, Elmer V. Bernstam, Christopher G. Chute, Todd R. Johnson. Erratum to "Cross-terminology mapping challenges: A demonstration using medication terminological systems" [J. Biomed. Inform. (2012) 613-625]

Volume 45, Issue 5

825 -- 826Adrien Coulet, K. Bretonnel Cohen, Russ B. Altman. The state of the art in text mining and natural language processing for pharmacogenomics
827 -- 834Rong Xu, QuanQiu Wang. A knowledge-driven conditional approach to extract pharmacogenomics specific drug-gene relationships from free text
835 -- 841Bastien Rance, Emily Doughty, Dina Demner-Fushman, Maricel G. Kann, Olivier Bodenreider. A mutation-centric approach to identifying pharmacogenomic relations in text
842 -- 850Jörg Hakenberg, Dmitry Voronov, Nguyen Ha Vo, Shanshan Liang, Saadat Anwar, Barry Lumpkin, Robert Leaman, Luis Tari, Chitta Baral. A SNPshot of PubMed to associate genetic variants with drugs, diseases, and adverse reactions
851 -- 861Fabio Rinaldi, Gerold Schneider, Simon Clematide. Relation mining experiments in the pharmacogenomics domain
862 -- 869Sergey V. Pakhomov, Bridget T. McInnes, J. Lamba, Y. Liu, Genevieve B. Melton, Y. Ghodke, N. Bhise, V. Lamba, Angela K. Birnbaum. Using PharmGKB to train text mining approaches for identifying potential gene targets for pharmacogenomic studies
870 -- 878Jiao Li, Zhiyong Lu. Systematic identification of pharmacogenomics information from clinical trials
879 -- 884Erik M. van Mulligen, Annie Fourrier-Réglat, David Gurwitz, Mariam Molokhia, Ainhoa Nieto, Gianluca Trifirò, Jan A. Kors, Laura Inés Furlong. The EU-ADR corpus: Annotated drugs, diseases, targets, and their relationships
885 -- 892Harsha Gurulingappa, Abdul Mateen Rajput, Angus Roberts, Juliane Fluck, Martin Hofmann-Apitius, Luca Toldo. Development of a benchmark corpus to support the automatic extraction of drug-related adverse effects from medical case reports
893 -- 900Murat Sariyar, Andreas Borg, Klaus Pommerening. Active learning strategies for the deduplication of electronic patient data using classification trees
901 -- 912Philip Gooch, Abdul V. Roudsari. Lexical patterns, features and knowledge resources for coreference resolution in clinical notes
913 -- 921Xiao Hu, Monica Sapo, Valeriy Nenov, Tod Barry, Sunghan Kim, Duc H. Do, Noel Boyle, Neil Martin. Predictive combinations of monitor alarms preceding in-hospital code blue events
922 -- 930Tai-Chun Wang, Javid Taheri, Albert Y. Zomaya. Using genetic algorithm in reconstructing single individual haplotype with minimum error correction
931 -- 937Bo Liao, Xiong Li, Wen Zhu, Renfa Li, Shulin Wang. Multiple ant colony algorithm method for selecting tag SNPs
938 -- 949María Adela Grando, David Glasspool, Aziz A. Boxwala. Argumentation logic for the flexible enactment of goal-based medical guidelines
950 -- 957Pamela M. Neri, Stephanie E. Pollard, Lynn A. Volk, Lisa P. Newmark, Matthew Varugheese, Samantha Baxter, Samuel J. Aronson, Heidi L. Rehm, David W. Bates. Usability of a novel clinician interface for genetic results
958 -- 974Siddika Parlak, Aleksandra Sarcevic, Ivan Marsic, Randall S. Burd. Introducing RFID technology in dynamic and time-critical medical settings: Requirements and challenges
975 -- 991James F. Brinkley, Landon Detwiler. A Query Integrator and Manager for the Query Web
992 -- 998Vijay Garla, Cynthia Brandt. Ontology-guided feature engineering for clinical text classification
999 -- 1008Chang Sik Son, Yoon Nyun Kim, Hyung-Seop Kim, Hyoung-Seob Park, Min-Soo Kim. Decision-making model for early diagnosis of congestive heart failure using rough set and decision tree approaches
1009 -- 1017Arun Sen, Amarnath Banerjee, Atish P. Sinha, Manish Bansal. Clinical decision support: Converging toward an integrated architecture
1018 -- 1019Vojtech Huser. Process Mining: Discovery, Conformance and Enhancement of Business Processes

Volume 45, Issue 4

609 -- 612Elizabeth S. Chen, Genevieve B. Melton, Indra Neil Sarkar. Translating standards into practice: Experiences and lessons learned in biomedicine and health care
613 -- 625Himali Saitwal, David Qing, Stephen Jones, Elmer V. Bernstam, Christopher G. Chute, Todd R. Johnson. Cross-terminology mapping challenges: A demonstration using medication terminological systems
626 -- 633Li Zhou, Joseph M. Plasek, Lisa M. Mahoney, Frank Y. Chang, Dana DiMaggio, Roberto A. Rocha. Mapping Partners Master Drug Dictionary to RxNorm using an NLP-based approach
634 -- 641Casey Bennett. Utilizing RxNorm to support practical computing applications: Capturing medication history in live electronic health records
642 -- 650Swapna Abhyankar, Dina Demner-Fushman, Clement J. McDonald. Standardizing clinical laboratory data for secondary use
651 -- 657Hyeoneui Kim, Robert E. El-Kareh, Anupam Goel, F. N. U. Vineet, Wendy Webber Chapman. An approach to improve LOINC mapping through augmentation of local test names
658 -- 666M.-C. Lin, Daniel J. Vreeman, Clement J. McDonald, Stanley M. Huff. Auditing consistency and usefulness of LOINC use among three large institutions - Using version spaces for grouping LOINC codes
667 -- 673Daniel J. Vreeman, Maria Teresa Chiaravalloti, John Hook, Clement J. McDonald. Enabling international adoption of LOINC through translation
674 -- 682Philip J. Kroth, Shamsi Daneshvari, Edward F. Harris, Daniel J. Vreeman, Heather J. H. Edgar. Using LOINC to link 10 terminology standards to one unified standard in a specialized domain
683 -- 688Susan Matney, Judith J. Warren, Jonathan L. Evans, Tae Youn Kim, Amy Coenen, Vivian A. Auld. Development of the nursing problem list subset of SNOMED CT®
689 -- 696Christian G. Reich, Patrick B. Ryan, Paul E. Stang, Mitra Rocca. Evaluation of alternative standardized terminologies for medical conditions within a network of observational healthcare databases
697 -- 702Philip Scott, Robert Worden. Semantic mapping to simplify deployment of HL7 v3 Clinical Document Architecture
703 -- 710Stéphane M. Meystre, Sanghoon Lee, Chai Young Jung, Raphaël D. Chevrier. Common data model for natural language processing based on two existing standard information models: CDA+GrAF
711 -- 718Matthias Samwald, Karsten Fehre, Jeroen S. de Bruin, Klaus-Peter Adlassnig. The Arden Syntax standard for clinical decision support: Experiences and directions
719 -- 725Karen A. Monsen, Claire Neely, Gary Oftedahl, Madeleine J. Kerr, Pam Pietruszewski, Oladimeji Farri. Feasibility of encoding the Institute for Clinical Systems Improvement Depression Guideline using the Omaha System
726 -- 735Guilherme Del Fiol, Vojtech Huser, Howard R. Strasberg, Saverio M. Maviglia, Clayton Curtis, James J. Cimino. Implementations of the HL7 Context-Aware Knowledge Retrieval ("Infobutton") Standard: Challenges, strengths, limitations, and uptake
736 -- 745Fulvio Barbarito, Francesco Pinciroli, John Mason, Sara Marceglia, Luca Mazzola, Stefano Bonacina. Implementing standards for the interoperability among healthcare providers in the public regionalized Healthcare Information System of the Lombardy Region
746 -- 762José Alberto Maldonado, Catalina Martínez-Costa, David Moner, Marcos Menárguez Tortosa, Diego Boscá, José Antonio Miñarro-Giménez, Jesualdo Tomás Fernández-Breis, Montserrat Robles. Using the ResearchEHR platform to facilitate the practical application of the EHR standards
763 -- 771Susan Rea, Jyotishman Pathak, Guergana K. Savova, Thomas A. Oniki, Les Westberg, Calvin E. Beebe, Cui Tao, Craig G. Parker, Peter J. Haug, Stanley M. Huff, Christopher G. Chute. Building a robust, scalable and standards-driven infrastructure for secondary use of EHR data: The SHARPn project
772 -- 781Paul C. Fu Jr., Daniel Rosenthal, Joshua M. Pevnick, Floyd Eisenberg. The impact of emerging standards adoption on automated quality reporting
782 -- 794Helena F. Deus, Eric Prud'hommeaux, Michael Miller, Jun Zhao, James Malone, Tomasz Adamusiak, Jim McCusker, Sudeshna Das, Philippe Rocca-Serra, Ronan Fox, M. Scott Marshall. Translating standards into practice - One Semantic Web API for Gene Expression
795 -- 812Jorien van der Peijl, Jan Klein 0002, Christian Grass, Adinda Freudenthal. Design for risk control: The role of usability engineering in the management of use-related risks
813 -- 823Omar Bouhaddou, Tim Cromwell, Mike Davis, Sarah Maulden, Nelson Hsing, David Carlson, Jennifer Cockle, Catherine Hoang, Linda Fischetti. Translating standards into practice: Experience and lessons learned at the Department of Veterans Affairs

Volume 45, Issue 3

401 -- 407Mohammad A. Tabatabai, Wayne M. Eby, Zoran Bursac. Oscillabolastic model, a new model for oscillatory dynamics, applied to the analysis of Hes1 gene expression and Ehrlich ascites tumor growth
408 -- 418Sheng Yu, Damon Berry, Jesus Bisbal. Clinical coverage of an archetype repository over SNOMED-CT
419 -- 422Daniel R. Masys, Gail P. Jarvik, Neil F. Abernethy, Nicholas R. Anderson, George J. Papanicolaou, Dina N. Paltoo, Mark A. Hoffman, Isaac S. Kohane, Howard P. Levy. Technical desiderata for the integration of genomic data into Electronic Health Records
423 -- 428Ning Kang, Zubair Afzal, Bharat Singh, Erik M. van Mulligen, Jan A. Kors. Using an ensemble system to improve concept extraction from clinical records
429 -- 446David Riaño 0001, Francis Real, Joan Albert López-Vallverdú, Fabio Campana, Sara Ercolani, Patrizia Mecocci, Roberta Annicchiarico, Carlo Caltagirone. An ontology-based personalization of health-care knowledge to support clinical decisions for chronically ill patients
447 -- 459Jonathan M. Garibaldi, Shang Ming Zhou, Xiao-Ying Wang, Robert Ivor John, Ian O. Ellis. Incorporation of expert variability into breast cancer treatment recommendation in designing clinical protocol guided fuzzy rule system models
460 -- 470David Juckett. A method for determining the number of documents needed for a gold standard corpus
471 -- 481Rimma Pivovarov, Noemie Elhadad. A hybrid knowledge-based and data-driven approach to identifying semantically similar concepts
482 -- 494C. Maria Keet. Transforming semi-structured life science diagrams into meaningful domain ontologies with DiDOn
495 -- 506Vassilis Koutkias, Vassilis Kilintzis, George Stalidis, Katerina Lazou, Julie Niès, Ludovic Durand-Texte, Peter McNair, Régis Beuscart, Nicos Maglaveras. Knowledge engineering for adverse drug event prevention: On the design and development of a uniform, contextualized and sustainable knowledge-based framework
507 -- 521Wendy Webber Chapman, Guergana K. Savova, Jiaping Zheng, Melissa Tharp, Rebecca S. Crowley. Anaphoric reference in clinical reports: Characteristics of an annotated corpus
522 -- 527Shane Steinert-Threlkeld, Siamak Ardekani, José L. V. Mejino Jr., Landon Detwiler, James F. Brinkley, Michael Halle, Ron Kikinis, Raimond L. Winslow, Michael I. Miller, J. Tilak Ratnanather. Ontological labels for automated location of anatomical shape differences
528 -- 534Mohamed Mysara, Mahmoud ElHefnawi, Jonathan M. Garibaldi. MysiRNA: Improving siRNA efficacy prediction using a machine-learning model combining multi-tools and whole stacking energy (ΔG)
535 -- 543Longhua Qian, Guodong Zhou. Tree kernel-based protein-protein interaction extraction from biomedical literature
544 -- 556Pravin Pawar, Val Jones, Bert-Jan van Beijnum, Hermie Hermens. A framework for the comparison of mobile patient monitoring systems
557 -- 565Hameedullah Kazi, Peter Haddawy, Siriwan Suebnukarn. Employing UMLS for generating hints in a tutoring system for medical problem-based learning
566 -- 579Vassilios P. Aggelidis, Prodromos D. Chatzoglou. Hospital information systems: Measuring end user computing satisfaction (EUCS)
580 -- 590Atish Rajkomar, Ann Blandford. Understanding infusion administration in the ICU through Distributed Cognition
591 -- 597Beilei Zhang, Liz Youngblood, Gerald D. Murphy, Michael Ramsay, Yan Xiao. System engineering approach to documentation: An evaluation of the documentation process in a gastroenterology laboratory
598 -- 607Sarah A. Collins, Leanne M. Currie, Suzanne Bakken, David K. Vawdrey, Patricia W. Stone. Health literacy screening instruments for eHealth applications: A systematic review

Volume 45, Issue 2

199 -- 209Alan L. Rector, Luigi Iannone. Lexically suggest, logically define: Quality assurance of the use of qualifiers and expected results of post-coordination in SNOMED CT
210 -- 223Yaqiang Wang, Zhonghua Yu, Yongguang Jiang, Yongchao Liu, Li Chen, Yiguang Liu. A framework and its empirical study of automatic diagnosis of traditional Chinese medicine utilizing raw free-text clinical records
224 -- 230Xiaoyi Wang, Jiying Ling. Multiple valued logic approach for matching patient records in multiple databases
231 -- 239Stefania Rubrichi, Silvana Quaglini. Summary of Product Characteristics content extraction for a safe drugs usage
240 -- 254Joanna Abraham, Thomas George Kannampallil, Vimla L. Patel. Bridging gaps in handoffs: A continuity of care based approach
255 -- 264Germain Forestier, Florent Lalys, Laurent Riffaud, Brivael Trelhu, Pierre Jannin. Classification of surgical processes using dynamic time warping
265 -- 272Yukun Chen, Subramani Mani, Hua Xu. Applying active learning to assertion classification of concepts in clinical text
273 -- 291Carlo Combi, Giuseppe Pozzi, Rosalba Rossato. Querying temporal clinical databases on granular trends
292 -- 306Jon Patrick, Min Li. An ontology for clinical questions about the contents of patient notes
307 -- 315Sarah A. Collins, Lena Mamykina, Desmond Jordan, Daniel M. Stein, Alisabeth Shine, Paul Reyfman, David R. Kaufman. In search of common ground in handoff documentation in an Intensive Care Unit
316 -- 322Dairong Wang, Henry P. Parkman, Michael R. Jacobs, Anurag K. Mishra, Evgeny Krynetskiy, Zoran Obradovic. DNA microarray SNP associations with clinical efficacy and side effects of domperidone treatment for gastroparesis
323 -- 336Yang Xiang, Kewei Lu, Stephen L. James, Tara Borlawsky, Kun Huang, Philip R. O. Payne. k-Neighborhood decentralization: A comprehensive solution to index the UMLS for large scale knowledge discovery
337 -- 349Watson Wei Khong Chua, Jung-jae Kim. BOAT: Automatic alignment of biomedical ontologies using term informativeness and candidate selection
350 -- 362Farzana Kabir Ahmad, Safaai Deris, N. H. Othman. The inference of breast cancer metastasis through gene regulatory networks
363 -- 371Sachin Mathur, Deendayal Dinakarpandian. Finding disease similarity based on implicit semantic similarity
372 -- 387Mary F. McGuire, M. Sriram Iyengar, David W. Mercer. Data driven linear algebraic methods for analysis of molecular pathways: Application to disease progression in shock/trauma
388 -- 389David L. Buckeridge. Infectious Disease Informatics: Syndromic Surveillance for Public Health and Bio-Defense, Hsinchun Chen, Daniel Zeng, Ping Yan. Springer (2010)
390 -- 397Leila Eadie, Paul Taylor, Adam P. Gibson. Recommendations for research design and reporting in computer-assisted diagnosis to facilitate meta-analysis

Volume 45, Issue 1

1 -- 14Yue Wang, Michael Halper, Duo Wei, Huanying Gu, Yehoshua Perl, Junchuan Xu, Gai Elhanan, Yan Chen, Kent A. Spackman, James T. Case, George Hripcsak. Auditing complex concepts of SNOMED using a refined hierarchical abstraction network
15 -- 29Yue Wang, Michael Halper, Duo Wei, Yehoshua Perl, James Geller. Abstraction of complex concepts with a refined partial-area taxonomy of SNOMED
30 -- 36Zi-hui Li, Yu-Feng Liu, Ke-ning Li, Hui-zi DuanMu, Zhi-Qiang Chang, Zhen-qi Li, Shan-zhen Zhang, Yan Xu. Analysis of functional and pathway association of differential co-expressed genes: A case study in drug addiction
37 -- 44Lilian Minne, Saeid Eslami, Nicolette de Keizer, Evert de Jonge, Sophia E. de Rooij, Ameen Abu-Hanna. Statistical process control for validating a classification tree model for predicting mortality - A novel approach towards temporal validation
45 -- 60Elpiniki I. Papageorgiou, Jos De Roo, Csaba Huszka, Dirk Colaert. Formalization of treatment guidelines using Fuzzy Cognitive Maps and semantic web tools
61 -- 70Yan Chen, Huanying Gu, Yehoshua Perl, James Geller. Overcoming an obstacle in expanding a UMLS semantic type extent
71 -- 81Danielle Mowery, Janyce Wiebe, Shyam Visweswaran, Henk Harkema, Wendy Webber Chapman. Building an automated SOAP classifier for emergency department reports
82 -- 92Xia Jing, Stephen Kay, Tom Marley, Nicholas R. Hardiker, James J. Cimino. Incorporating personalized gene sequence variants, molecular genetics knowledge, and health knowledge into an EHR prototype based on the Continuity of Care Record standard
93 -- 100Tae Youn Kim, Amy Coenen, Nicholas R. Hardiker. Semantic mappings and locality of nursing diagnostic concepts in UMLS
101 -- 106Ketan K. Mane, Chris Bizon, Charles Schmitt, Phillips Owen, Bruce Burchett, Ricardo Pietrobon, Kenneth Gersing. VisualDecisionLinc: A visual analytics approach for comparative effectiveness-based clinical decision support in psychiatry
107 -- 119Merlijn Sevenster, Rob C. van Ommering, Yuechen Qian. Algorithmic and user study of an autocompletion algorithm on a large medical vocabulary
120 -- 128Tiffani J. Bright, E. Yoko Furuya, Gilad J. Kuperman, James J. Cimino, Suzanne Bakken. Development and evaluation of an ontology for guiding appropriate antibiotic prescribing
129 -- 140Siddhartha Jonnalagadda, Trevor Cohen, Stephen Tze-Inn Wu, Graciela Gonzalez. Enhancing clinical concept extraction with distributional semantics
141 -- 155David Sánchez 0001, Albert Solé-Ribalta, Montserrat Batet, Francesc Serratosa. Enabling semantic similarity estimation across multiple ontologies: An evaluation in the biomedical domain
156 -- 164Lishuang Li, Wenting Fan, Degen Huang, Yanzhong Dang, Jing Sun. Boosting performance of gene mention tagging system by hybrid methods
165 -- 172Anna Ferrante, James Boyd. A transparent and transportable methodology for evaluating Data Linkage software
173 -- 183Anas A. Abu-Doleh, Omar M. Al-Jarrah, Asem Alkhateeb. Protein contact map prediction using multi-stage hybrid intelligence inference systems
184 -- 198Predrag V. Klasnja, Wanda Pratt. Healthcare in the pocket: Mapping the space of mobile-phone health interventions