Journal of Biomedical Informatics, Volume 46

Volume 46, Number 1, February 2013

Special Section: Community-Driven Curation of Ontologies and Knowledge Bases

• 
  Tudor Groza, Tania Tudorache, Michel Dumontier:
  State of the art and open challenges in community-driven knowledge curation. 1-4
• 
  James Malone, Robert Stevens:
  Measuring the level of activity in community built bio-ontologies. 5-14
• 
  Michael Hartung, Anika Groß, Erhard Rahm:
  COnto-Diff: generation of complex evolution mappings for life science ontologies. 15-32

Original Research Articles

• 
  Zhihui Luo, Riccardo Miotto, Chunhua Weng:
  A human-computer collaborative approach to identifying common data elements in clinical trial eligibility criteria. 33-39
• 
  Radhakrishnan Nagarajan, Alex T. Kalinka, William R. Hogan:
  Evidence of community structure in Biomedical Research Grant Collaborations. 40-46
• 
  Milos Hauskrecht, Iyad Batal, Michal Valko, Shyam Visweswaran, Gregory F. Cooper, Gilles Clermont:
  Outlier detection for patient monitoring and alerting. 47-55
• 
  Jean-Baptiste Lamy, Lina Fatima Soualmia, Gaétan Kerdelhué, Alain Venot, Catherine Duclos:
  Validating the semantics of a medical iconic language using ontological reasoning. 56-67
• 
  Cosmin Adrian Bejan, Lucy Vanderwende, Fei Xia, Meliha Yetisgen-Yildiz:
  Assertion modeling and its role in clinical phenotype identification. 68-74
• 
  Tânia F. G. G. Cova, Jorge Luis G. C. Pereira, Alberto A. C. C. Pais:
  Is standard multivariate analysis sufficient in clinical and epidemiological studies? 75-86
• 
  Dennis Lee, Ronald Cornet, Francis Y. Lau, Nicolette de Keizer:
  A survey of SNOMED CT implementations. 87-96
• 
  James Geller, Zhe He, Yehoshua Perl, C. Paul Morrey, Julia Xu:
  Rule-based support system for multiple UMLS semantic type assignments. 97-110
• 
  Zhengxing Huang, Xudong Lu, Huilong Duan, Wu Fan:
  Summarizing clinical pathways from event logs. 111-127
• 
  Cui Tao, Jyotishman Pathak, Harold R. Solbrig, Wei-Qi Wei, Christopher G. Chute:
  Terminology representation guidelines for biomedical ontologies in the semantic web notations. 128-138
• 
  David K. Vawdrey, George Hripcsak:
  Publication bias in clinical trials of electronic health records. 139-141
• 
  Óscar Jesús Rubio Martí, Álvaro Alesanco Iglesias, José García:
  A robust and simple security extension for the medical standard SCP-ECG. 142-151
• 
  Stefan Franke, Jürgen Meixensberger, Thomas Neumuth:
  Intervention time prediction from surgical low-level tasks. 152-159
• 
  Tien-Tuan Dao, Tuan Nha Hoang, Xuan Hien Ta, Marie Christine Ho Ba Tho:
  Knowledge-based personalized search engine for the Web-based Human Musculoskeletal System Resources (HMSR) in biomechanics. 160-173
• 
  Lorenzo Beretta, Alessandro Santaniello:
  Extension of the survival dimensionality reduction algorithm to detect epistasis in competing risks models (SDR-CR). 174-180

Methodological Review

• 
  Jan Maarten Schraagen, Fenne Verhoeven:
  Methods for studying medical device technology and practitioner cognition: The case of user-interface issues with infusion pumps. 181-195

Volume 46, Number 2, April 2013

Methodological Reviews

• 
  Fei Zhu, Preecha Patumcharoenpol, Cheng Zhang, Yang Yang, Jonathan H. Chan, Asawin Meechai, Wanwipa Vongsangnak, Bairong Shen:
  Biomedical text mining and its applications in cancer research. 200-211
• 
  Thomas Lippincott, Laura Rimell, Karin Verspoor, Anna Korhonen:
  Approaches to verb subcategorization for biomedicine. 212-227

Original Research

• 
  Laura Rimell, Thomas Lippincott, Karin Verspoor, Helen L. Johnson, Anna Korhonen:
  Acquisition and evaluation of verb subcategorization resources for biomedicine. 228-237
• 
  Delroy Cameron, Olivier Bodenreider, Hima Yalamanchili, Tu Danh, Sreeram Vallabhaneni, Krishnaprasad Thirunarayan, Amit P. Sheth, Thomas C. Rindflesch:
  A graph-based recovery and decomposition of Swanson's hypothesis using semantic predications. 238-251
• 
  Xin Sun, Yanheng Liu, Da Wei, Mantao Xu, Hui-Ling Chen, Jiawei Han:
  Selection of interdependent genes via dynamic relevance analysis for cancer diagnosis. 252-258
• 
  Jihad S. Obeid, Catherine A. McGraw, Brenda L. Minor, Jose G. Conde, Robert Pawluk, Michael Lin, Janey Wang, Sean R. Banks, Sheree A. Hemphill, Robert Taylor, Paul A. Harris:
  Procurement of shared data instruments for Research Electronic Data Capture (REDCap). 259-265
• 
  Yuanxi Li, Stephen Swift, Allan Tucker:
  Modelling and analysing the dynamics of disease progression from cross-sectional studies. 266-274
• 
  Xiaodan Zhu, Colin Cherry, Svetlana Kiritchenko, Joel D. Martin, Berry de Bruijn:
  Detecting concept relations in clinical text: Insights from a state-of-the-art model. 275-285
• 
  Qian Zhu, Robert R. Freimuth, Zonghui Lian, Scott Bauer, Jyotishman Pathak, Cui Tao, Matthew J. Durski, Christopher G. Chute:
  Harmonization and semantic annotation of data dictionaries from the Pharmacogenomics Research Network: A case study. 286-293
• 
  Sergio Martínez, David Sánchez, Aïda Valls:
  A semantic framework to protect the privacy of electronic health records with non-numerical attributes. 294-303
• 
  Marcos Menárguez Tortosa, Jesualdo Tomás Fernández-Breis:
  OWL-based reasoning methods for validating archetypes. 304-317
• 
  Sylvie M. N. Ngouongo, Matthias Löbe, Jürgen Stausberg:
  The ISO/IEC 11179 norm for metadata registries: Does it cover healthcare standards in empirical research? 318-327
• 
  Ilhan Ilhan, Gülay Tezel:
  A genetic algorithm-support vector machine method with parameter optimization for selecting the tag SNPs. 328-340
• 
  Szymon Wilk, Wojtek Michalowski, Martin Michalowski, Ken Farion, Marisela Mainegra Hing, Subhra Mohapatra:
  Mitigation of adverse interactions in pairs of clinical practice guidelines using constraint logic programming. 341-353
• 
  Meliha Yetisgen-Yildiz, Martin L. Gunn, Fei Xia, Thomas H. Payne:
  A text processing pipeline to extract recommendations from radiology reports. 354-362
• 
  Luca Anselma, Alessio Bottrighi, Stefania Montani, Paolo Terenziani:
  Managing proposals and evaluations of updates to medical knowledge: Theory and applications. 363-376

Volume 46, Number 3, June 2013

Commentary

• 
  David Riaño, John A. Bohada, Antoni Collado, Joan Albert López-Vallverdú:
  MPM: A knowledge-based functional model of medical practice. 379-387

Original Research

• 
  José Luis Iglesias Allones, Maria Taboada, Diego Martínez, Raimund Lozano, María Jesús Sobrido:
  SNOMED CT module-driven clinical archetype management. 388-400
• 
  Jörn Kretschmer, Christoph Schranz, Christian Knöbel, J. Wingender, Edmund Koch, Knut Möller:
  Efficient computation of interacting model systems. 401-409
• 
  Andrew R. Post, Tahsin M. Kurç, Sharath R. Cholleti, Jingjing Gao, Xia Lin, William Bornstein, Dedra Cantrell, David Levine, Sam Hohmann, Joel H. Saltz:
  The Analytic Information Warehouse (AIW): A platform for analytics using electronic health record data. 410-424
• 
  Andrea Esuli, Diego Marcheggiani, Fabrizio Sebastiani:
  An enhanced CRFs-based system for information extraction from radiology reports. 425-435
• 
  Samah Jamal Fodeh, Cynthia Brandt, Thaibinh Luong, Ali Haddad, Martin H. Schultz, Terrence Murphy, Michael Krauthammer:
  Complementary ensemble clustering of biomedical data. 436-443
• 
  Ricardo Villamarín-Salomón, Gregory F. Cooper, Michael M. Wagner, Fu-Chiang Tsui, Jeremy U. Espino:
  A method for estimating from thermometer sales the incidence of diseases that are symptomatically similar to influenza. 444-457
• 
  Maarten van der Heijden, Peter J. F. Lucas, Bas Lijnse, Yvonne F. Heijdra, Tjard R. J. Schermer:
  An autonomous mobile system for the management of COPD. 458-469
• 
  Frank Weichert, Christoph Mertens, Lars Walczak, Gabriele Kern-Isberner, Mathias Wagner:
  A novel approach for connecting temporal-ontologies with blood flow simulations. 470-479
• 
  Shuang Wang, Xiaoqian Jiang, Yuan Wu, Lijuan Cui, Samuel Cheng, Lucila Ohno-Machado:
  EXpectation Propagation LOgistic REgRession (EXPLORER): Distributed privacy-preserving online model learning. 480-496
• 
  Lingyun Luo, José L. V. Mejino Jr., Guo-Qiang Zhang:
  An analysis of FMA using structural self-bisimilarity. 497-505
• 
  Md. Faisal Mahbub Chowdhury, Pierre Zweigenbaum:
  A controlled greedy supervised approach for co-reference resolution on clinical text. 506-515
• 
  Nelia Lasierra, Álvaro Alesanco Iglesias, S. Guillén, José García:
  A three stage ontology-driven solution to provide personalized care to chronic patients at home. 516-529
• 
  Kornel Skalkowski, Krzysztof Zielinski:
  Applying formalized rules for treatment procedures to data delivered by personal medical devices. 530-540

Methodological Reviews

• 
  José Luis Fernández-Alemán, Inmaculada Carrión Señor, Pedro Ángel Oliver Lozoya, Ambrosio Toval:
  Security and privacy in electronic health records: A systematic literature review. 541-562
• 
  Dimitris Kleftogiannis, Aigli Korfiati, Konstantinos A. Theofilatos, Spiros Likothanassis, Athanasios K. Tsakalidis, Seferina Mavroudi:
  Where we stand, where we are moving: Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role. 563-573

Volume 46, Number 4, August 2013

Original Research

• 
  Anne M. Turner, Blaine Reeder, Judith Ramey:
  Scenarios, personas and user stories: User-centered evidence-based design representations of communicable disease investigations. 575-584
• 
  Rong Xu, QuanQiu Wang:
  A semi-supervised approach to extract pharmacogenomics-specific drug-gene pairs from biomedical literature for personalized medicine. 585-593
• 
  Zhiyi Mao, Wensheng Cai, Xueguang Shao:
  Selecting significant genes by randomization test for cancer classification using gene expression data. 594-601
• 
  Vivekanand Sharma, Indra Neil Sarkar:
  Leveraging concept-based approaches to identify potential phyto-therapies. 602-614
• 
  Kate Button, Robert W. van Deursen, Larisa N. Soldatova, Irena Spasic:
  TRAK ontology: Defining standard care for the rehabilitation of knee conditions. 615-625
• 
  Martin Schmettow, Wendy Vos, Jan Maarten Schraagen:
  With how many users should you test a medical infusion pump? Sampling strategies for usability tests on high-risk systems. 626-641
• 
  Chunhua Weng, Yu Li, Solomon Berhe, Mary Regina Boland, Junfeng Gao, Gregory William Hruby, Richard C. Steinman, Carlos Lopez-Jimenez, Linda Busacca, George Hripcsak, Suzanne Bakken, J. Thomas Bigger:
  An Integrated Model for Patient Care and Clinical Trials (IMPACT) to support clinical research visit scheduling workflow for future learning health systems. 642-652
• 
  Óscar Jesús Rubio Martí, Álvaro Alesanco Iglesias, José García:
  Secure information embedding into 1D biomedical signals based on SPIHT. 653-664
• 
  Todd R. Johnson, Eliz Markowitz, Elmer V. Bernstam, Jorge R. Herskovic, Harold Thimbleby:
  SYFSA: A framework for Systematic Yet Flexible Systems Analysis. 665-675
• 
  Mar Marcos, José Alberto Maldonado, Begoña Martínez-Salvador, Diego Boscá, Montserrat Robles:
  Interoperability of clinical decision-support systems and electronic health records using archetypes: A case study in clinical trial eligibility. 676-689
• 
  Qian Zhu, Robert R. Freimuth, Jyotishman Pathak, Matthew J. Durski, Christopher G. Chute:
  Disambiguation of PharmGKB drug-disease relations with NDF-RT and SPL. 690-696
• 
  Arief Gusnanto, Alexander Ploner, Farag Shuweihdi, Yudi Pawitan:
  Partial least squares and logistic regression random-effects estimates for gene selection in supervised classification of gene expression data. 697-709
• 
  Pablo Gay, Beatriz López, Albert Pla, Jordi Saperas, Carles Pous:
  Enabling the use of hereditary information from pedigree tools in medical knowledge-based systems. 710-720
• 
  Joseph Cooley, Sean W. Smith:
  Privacy-preserving screen capture: Towards closing the loop for health IT usability. 721-733

Methodological Reviews

• 
  Mike Conway, John N. Dowling, Wendy Webber Chapman:
  Using chief complaints for syndromic surveillance: A review of chief complaint based classifiers in North America. 734-743
• 
  Mor Peleg:
  Computer-interpretable clinical guidelines: A methodological review. 744-763

Volume 46, Number 5, October 2013

Special Report

• 
  Carol Friedman, Thomas C. Rindflesch, Milton Corn:
  Natural language processing: State of the art and prospects for significant progress, a workshop sponsored by the National Library of Medicine. 765-773

Commentary

• 
  Aisling O'Driscoll, Jurate Daugelaite, Roy D. Sleator:
  'Big data', Hadoop and cloud computing in genomics. 774-781

Book Review

• 
  Kenneth W. Goodman:
  Handbook of Analytic Philosophy of Medicine Series: Philosophy and Medicine, Vol 113. Kazem Sadegh-Zadeh (2012). XXXII, 1133 pp. 782-783

Original Research

• 
  Ali Anil Sinaci, Gokce Banu Laleci Erturkmen:
  A federated semantic metadata registry framework for enabling interoperability across clinical research and care domains. 784-794
• 
  Brent I. Fox, Joshua C. Hollingsworth, Michael D. Gray, Michael L. Hollingsworth, Juan Gao, Richard A. Hansen:
  Developing an expert panel process to refine health outcome definitions in observational data. 795-804
• 
  Sanmitra Bhattacharya, Michael N. Cantor:
  Analysis of eligibility criteria representation in industry-standard clinical trial protocols. 805-813
• 
  Kevin B. Johnson, Yun-Xian Ho, Stephen Andrew Spooner, Marvin Palmer, Stuart T. Weinberg:
  Assessing the reliability of an automated dose-rounding algorithm. 814-821
• 
  Germain Forestier, Florent Lalys, Laurent Riffaud, D. Louis Collins, Jürgen Meixensberger, Shafik N. Wassef, Thomas Neumuth, Benoît Goulet, Pierre Jannin:
  Multi-site study of surgical practice in neurosurgery based on surgical process models. 822-829
• 
  Nicole Gray Weiskopf, George Hripcsak, Sushmita Swaminathan, Chunhua Weng:
  Defining and measuring completeness of electronic health records for secondary use. 830-836
• 
  Michael J. Rothman, Steven I. Rothman, Joseph Beals IV:
  Development and validation of a continuous measure of patient condition using the Electronic Medical Record. 837-848
• 
  Prashanti Manda, Fiona M. McCarthy, Susan M. Bridges:
  Interestingness measures and strategies for mining multi-ontology multi-level association rules from gene ontology annotations for the discovery of new GO relationships. 849-856
• 
  Thusitha De Silva Mabotuwana, Michael C. Lee, Eric Cohen-Solal:
  An ontology-based similarity measure for biomedical data - Application to radiology reports. 857-868
• 
  Vijay Garla, Caroline Taylor, Cynthia Brandt:
  Semi-supervised clinical text classification with Laplacian SVMs: An application to cancer case management. 869-875
• 
  Francesca Vitali, Francesca Mulas, Pietro Marini, Riccardo Bellazzi:
  Network-based target ranking for polypharmacological therapies. 876-881
• 
  Cui Tao, Dezhao Song, Deepak K. Sharma, Christopher G. Chute:
  Semantator: Semantic annotator for converting biomedical text to linked data. 882-893
• 
  Patrizia F. Stifanelli, Teresa Maria Creanza, Roberto Anglani, Vania C. Liuzzi, Sayan Mukherjee, Francesco P. Schena, Nicola Ancona:
  A comparative study of covariance selection models for the inference of gene regulatory networks. 894-904
• 
  Barbara Sheehan, Lise E. Nigrovic, Peter S. Dayan, Nathan Kuppermann, Dustin W. Ballard, Evaline Alessandrini, Lalit Bajaj, Howard Goldberg, Jeffrey Hoffman, Steven R. Offerman, Dustin G. Mark, Marguerite Swietlik, Eric Tham, Leah Tzimenatos, David R. Vinson, Grant S. Jones, Suzanne Bakken:
  Informing the design of clinical decision support services for evaluation of children with minor blunt head trauma in the emergency department: A sociotechnical analysis. 905-913
• 
  María Herrero-Zazo, Isabel Segura-Bedmar, Paloma Martínez, Thierry Declerck:
  The DDI corpus: An annotated corpus with pharmacological substances and drug-drug interactions. 914-920
• 
  Jörn Lötsch, Alfred Ultsch:
  A machine-learned knowledge discovery method for associating complex phenotypes with complex genotypes. Application to pain. 921-928
• 
  Myungjae Kwak, Gondy Leroy, Jesse D. Martinez, Jeffrey Harwell:
  Development and evaluation of a biomedical search engine using a predicate-based vector space model. 929-939
• 
  Ke-Chun Huang, I-Jen Chiang, Furen Xiao, Chun-Chih Liao, Charles Chih-Ho Liu, Jau-Min Wong:
  PICO element detection in medical text without metadata: Are first sentences enough? 940-946

Methodological Review

• 
  Jonathan Joe, George Demiris:
  Older adults and mobile phones for health: A review. 947-954

Volume 46, Number 6, December 2013

Special Section: Social Media Environments

• 
  Alejandro Rodríguez González, Miguel Angel Mayer, Jesualdo Tomás Fernández-Breis:
  Biomedical information through the implementation of social media environments. 955-956
• 
  Mark Merolli, Kathleen Gray, Fernando Martín-Sánchez:
  Health outcomes and related effects of using social media in chronic disease management: A literature review and analysis of affordances. 957-969
• 
  Jacob B. Weiss, Eta S. Berner, Kevin B. Johnson, Dario A. Giuse, Barbara A. Murphy, Nancy M. Lorenzi:
  Recommendations for the design, implementation and evaluation of social support in online communities, networks, and groups. 970-976
• 
  Alicia Martinez-García, Alberto Moreno-Conde, Francisco Jódar-Sánchez, Sandra Leal, Carlos Parra:
  Sharing clinical decisions for multimorbidity case management using social network and open-source tools. 977-984
• 
  Delroy Cameron, Gary A. Smith, Raminta Daniulaityte, Amit P. Sheth, Drashti Dave, Lu Chen, Gaurish Anand, Robert Carlson, Kera Z. Watkins, Russel Falck:
  PREDOSE: A semantic web platform for drug abuse epidemiology using social media. 985-997
• 
  Jina Huh, Meliha Yetisgen-Yildiz, Wanda Pratt:
  Text classification for assisting moderators in online health communities. 998-1005
• 
  Laia Subirats, Luigi Ceccaroni, Raquel Lopez-Blazquez, Felip Miralles, Alejandro García-Rudolph, José María Tormos:
  Circles of Health: Towards an advanced social network about disabilities of neurological origin. 1006-1029

Regular Research Papers

• 
  Dorota Formanowicz, Adam Kozak, Tomasz Glowacki, Marcin Radom, Piotr Formanowicz:
  Hemojuvelin-hepcidin axis modeled and analyzed using Petri nets. 1030-1043
• 
  Christopher E. Gillies, Mohammad-Reza Siadat, Nilesh V. Patel, George D. Wilson:
  A simulation to analyze feature selection methods utilizing gene ontology for gene expression classification. 1044-1059
• 
  Riccardo Miotto, Silis Y. Jiang, Chunhua Weng:
  eTACTS: A method for dynamically filtering clinical trial search results. 1060-1067
• 
  Rasmus Rasmussen, André Kushniruk:
  Digital video analysis of health professionals' interactions with an electronic whiteboard: A longitudinal, naturalistic study of changes to user interactions. 1068-1079
• 
  William Brown III, Po-Yin Yen, Marlene Rojas, Rebecca Schnall:
  Assessment of the Health IT Usability Evaluation Model (Health-ITUEM) for evaluating mobile health (mHealth) technology. 1080-1087
• 
  Shaodian Zhang, Noemie Elhadad:
  Unsupervised biomedical named entity recognition: Experiments with clinical and biological texts. 1088-1098
• 
  Graciela Rosemblat, Dongwook Shin, Halil Kilicoglu, Charles Sneiderman, Thomas C. Rindflesch:
  A methodology for extending domain coverage in SemRep. 1099-1107
• 
  Pedro Lopes, José Luís Oliveira:
  An innovative portal for rare genetic diseases research: The semantic Diseasecard. 1108-1115
• 
  Bridget T. McInnes, Ted Pedersen:
  Evaluating measures of semantic similarity and relatedness to disambiguate terms in biomedical text. 1116-1124
• 
  Hamed Valizadegan, Quang Nguyen, Milos Hauskrecht:
  Learning classification models from multiple experts. 1125-1135
• 
  Oladimeji Farri, Karen A. Monsen, Serguei V. S. Pakhomov, David S. Pieczkiewicz, Stuart M. Speedie, Genevieve B. Melton:
  Effects of time constraints on clinician-computer interaction: A study on information synthesis from EHR clinical notes. 1136-1144
• 
  Riccardo Miotto, Chunhua Weng:
  Unsupervised mining of frequent tags for clinical eligibility text indexing. 1145-1151

Volume 46, Supplement, December 2013

2012 i2b2 NLP Challenge on Temporal Relations in Clinical Data
Guest Editorial

• 
  Özlem Uzuner, Amber Stubbs, Weiyi Sun:
  Chronology of your health events: Approaches to extracting temporal relations from medical narratives. S1-S4

Methodological Review

• 
  Weiyi Sun, Anna Rumshisky, Özlem Uzuner:
  Annotating temporal information in clinical narratives. S5-S12

Original Research

• 
  Prateek Jindal, Dan Roth:
  Extraction of events and temporal expressions from clinical narratives. S13-S19
• 
  Yu-Kai Lin, Hsinchun Chen, Randall A. Brown:
  MedTime: A temporal information extraction system for clinical narratives. S20-S28
• 
  Jennifer D'Souza, Vincent Ng:
  Classifying temporal relations in clinical data: A hybrid, knowledge-rich approach. S29-S39
• 
  Azadeh Nikfarjam, Ehsan Emadzadeh, Graciela Gonzalez-Hernandez:
  Towards generating a patient's timeline: Extracting temporal relationships from clinical notes. S40-S47
• 
  Yao Cheng, Peter Anick, Pengyu Hong, Nianwen Xue:
  Temporal relation discovery between events and temporal expressions identified in clinical narrative. S48-S53
• 
  Yung-Chun Chang, Hong-Jie Dai, Johnny Chi-Yang Wu, Jian-Ming Chen, Richard Tzong-Han Tsai, Wen-Lian Hsu:
  TEMPTING system: A hybrid method of rule and machine learning for temporal relation extraction in patient discharge summaries. S54-S62