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ORCIDJournal of Biomedical Informatics, Volume 45
Volume 45, Number 1, February 2012
- Yue Wang, Michael Halper, Duo Helen 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. 1-14 - Yue Wang, Michael Halper, Duo Helen Wei, Yehoshua Perl, James Geller:
Abstraction of complex concepts with a refined partial-area taxonomy of SNOMED. 15-29 - Zi-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. 30-36 - Lilian 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. 37-44 - Elpiniki I. Papageorgiou, Jos De Roo, Csaba Huszka, Dirk Colaert:
Formalization of treatment guidelines using Fuzzy Cognitive Maps and semantic web tools. 45-60 - Yan Chen, Huanying Gu, Yehoshua Perl, James Geller:
Overcoming an obstacle in expanding a UMLS semantic type extent. 61-70 - Danielle L. Mowery, Janyce Wiebe, Shyam Visweswaran, Henk Harkema, Wendy Webber Chapman:
Building an automated SOAP classifier for emergency department reports. 71-81 - Xia 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. 82-92 - Tae Youn Kim, Amy Coenen, Nicholas R. Hardiker:
Semantic mappings and locality of nursing diagnostic concepts in UMLS. 93-100 - Ketan 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. 101-106 - Merlijn Sevenster, Rob C. van Ommering, Yuechen Qian:
Algorithmic and user study of an autocompletion algorithm on a large medical vocabulary. 107-119 - Tiffani J. Bright, E. Yoko Furuya, Gilad J. Kuperman, James J. Cimino, Suzanne Bakken:
Development and evaluation of an ontology for guiding appropriate antibiotic prescribing. 120-128 - Siddhartha Jonnalagadda, Trevor Cohen, Stephen T. Wu, Graciela Gonzalez:
Enhancing clinical concept extraction with distributional semantics. 129-140 - David Sánchez, Albert Solé-Ribalta, Montserrat Batet, Francesc Serratosa:
Enabling semantic similarity estimation across multiple ontologies: An evaluation in the biomedical domain. 141-155 - Lishuang Li, Wenting Fan, Degen Huang, Yanzhong Dang, Jing Sun:
Boosting performance of gene mention tagging system by hybrid methods. 156-164 - Anna M. Ferrante, James H. Boyd:
A transparent and transportable methodology for evaluating Data Linkage software. 165-172 - Anas A. Abu-Doleh, Omar M. Al-Jarrah, Asem Alkhateeb:
Protein contact map prediction using multi-stage hybrid intelligence inference systems. 173-183
- Predrag V. Klasnja, Wanda Pratt:
Healthcare in the pocket: Mapping the space of mobile-phone health interventions. 184-198
Volume 45, Number 2, April 2012
- Alan L. Rector, Luigi Iannone:
Lexically suggest, logically define: Quality assurance of the use of qualifiers and expected results of post-coordination in SNOMED CT. 199-209 - Yaqiang 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. 210-223 - Xiaoyi Wang, Jiying Ling:
Multiple valued logic approach for matching patient records in multiple databases. 224-230 - Stefania Rubrichi, Silvana Quaglini:
Summary of Product Characteristics content extraction for a safe drugs usage. 231-239 - Joanna Abraham, Thomas George Kannampallil, Vimla L. Patel:
Bridging gaps in handoffs: A continuity of care based approach. 240-254 - Germain Forestier, Florent Lalys, Laurent Riffaud, Brivael Trelhu, Pierre Jannin:
Classification of surgical processes using dynamic time warping. 255-264 - Yukun Chen, Subramani Mani, Hua Xu:
Applying active learning to assertion classification of concepts in clinical text. 265-272 - Carlo Combi, Giuseppe Pozzi, Rosalba Rossato:
Querying temporal clinical databases on granular trends. 273-291 - Jon David Patrick, Min Li:
An ontology for clinical questions about the contents of patient notes. 292-306 - Sarah A. Collins, Lena Mamykina, Desmond A. Jordan, Daniel M. Stein, Alisabeth Shine, Paul Reyfman, David R. Kaufman:
In search of common ground in handoff documentation in an Intensive Care Unit. 307-315 - Dairong 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. 316-322 - Yang 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. 323-336 - Watson Wei Khong Chua, Jung-Jae Kim:
BOAT: Automatic alignment of biomedical ontologies using term informativeness and candidate selection. 337-349 - Farzana Kabir Ahmad, Safaai Deris, N. H. Othman:
The inference of breast cancer metastasis through gene regulatory networks. 350-362 - Sachin Mathur, Deendayal Dinakarpandian:
Finding disease similarity based on implicit semantic similarity. 363-371 - Mary 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. 372-387
- David L. Buckeridge:
Infectious Disease Informatics: Syndromic Surveillance for Public Health and Bio-Defense, Hsinchun Chen, Daniel Zeng, Ping Yan. Springer (2010). 388-389
- Leila Eadie, Paul Taylor, Adam P. Gibson:
Recommendations for research design and reporting in computer-assisted diagnosis to facilitate meta-analysis. 390-397
Volume 45, Number 3, June 2012
- Mohammad 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. 401-407 - Sheng Yu, Damon Berry, Jesus Bisbal:
Clinical coverage of an archetype repository over SNOMED-CT. 408-418 - Daniel 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. 419-422 - Ning Kang, Zubair Afzal, Bharat Singh, Erik M. van Mulligen, Jan A. Kors:
Using an ensemble system to improve concept extraction from clinical records. 423-428 - David Riaño, 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. 429-446 - Jonathan 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. 447-459 - David Juckett:
A method for determining the number of documents needed for a gold standard corpus. 460-470 - Rimma Pivovarov, Noemie Elhadad:
A hybrid knowledge-based and data-driven approach to identifying semantically similar concepts. 471-481 - C. Maria Keet:
Transforming semi-structured life science diagrams into meaningful domain ontologies with DiDOn. 482-494 - Vassilis 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. 495-506 - Wendy Webber Chapman, Guergana K. Savova, Jiaping Zheng, Melissa Tharp, Rebecca S. Crowley:
Anaphoric reference in clinical reports: Characteristics of an annotated corpus. 507-521 - Shane 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. 522-527 - Mohamed Mysara, Mahmoud ElHefnawi, Jonathan M. Garibaldi:
MysiRNA: Improving siRNA efficacy prediction using a machine-learning model combining multi-tools and whole stacking energy (ΔG). 528-534 - Longhua Qian, Guodong Zhou:
Tree kernel-based protein-protein interaction extraction from biomedical literature. 535-543 - Pravin Pawar, Val Jones, Bert-Jan van Beijnum, Hermie J. Hermens:
A framework for the comparison of mobile patient monitoring systems. 544-556 - Hameedullah Kazi, Peter Haddawy, Siriwan Suebnukarn:
Employing UMLS for generating hints in a tutoring system for medical problem-based learning. 557-565 - Vassilios P. Aggelidis, Prodromos D. Chatzoglou:
Hospital information systems: Measuring end user computing satisfaction (EUCS). 566-579 - Atish Rajkomar, Ann Blandford:
Understanding infusion administration in the ICU through Distributed Cognition. 580-590 - Beilei 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. 591-597
- Sarah A. Collins, Leanne M. Currie, Suzanne Bakken, David K. Vawdrey, Patricia W. Stone:
Health literacy screening instruments for eHealth applications: A systematic review. 598-607
Volume 45, Number 4, August 2012
- Elizabeth S. Chen, Genevieve B. Melton, Indra Neil Sarkar:
Translating standards into practice: Experiences and lessons learned in biomedicine and health care. 609-612 - Himali Saitwal, David Qing, Stephen Jones, Elmer V. Bernstam, Christopher G. Chute, Todd R. Johnson:
Cross-terminology mapping challenges: A demonstration using medication terminological systems. 613-625 - Li 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. 626-633 - Casey Bennett:
Utilizing RxNorm to support practical computing applications: Capturing medication history in live electronic health records. 634-641 - Swapna Abhyankar, Dina Demner-Fushman, Clement J. McDonald:
Standardizing clinical laboratory data for secondary use. 642-650 - Hyeoneui 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. 651-657 - M. 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. 658-666 - Daniel J. Vreeman, Maria Teresa Chiaravalloti, John Hook, Clement J. McDonald:
Enabling international adoption of LOINC through translation. 667-673 - Philip 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. 674-682 - Susan 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®. 683-688 - Christian 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. 689-696 - Philip J. Scott, Robert Worden:
Semantic mapping to simplify deployment of HL7 v3 Clinical Document Architecture. 697-702 - Stéphane 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. 703-710 - Matthias Samwald, Karsten Fehre, Jeroen S. de Bruin, Klaus-Peter Adlassnig:
The Arden Syntax standard for clinical decision support: Experiences and directions. 711-718 - Karen 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. 719-725 - Guilherme 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. 726-735 - Fulvio 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. 736-745 - José 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. 746-762 - Susan 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. 763-771 - Paul C. Fu Jr., Daniel Rosenthal, Joshua M. Pevnick, Floyd Eisenberg:
The impact of emerging standards adoption on automated quality reporting. 772-781 - Helena F. Deus, Eric Prud'hommeaux, Michael Miller, Jun Zhao, James Malone, Tomasz Adamusiak, Jamie P. McCusker, Sudeshna Das, Philippe Rocca-Serra, Ronan Fox, M. Scott Marshall:
Translating standards into practice - One Semantic Web API for Gene Expression. 782-794 - Jorien van der Peijl, Jan Klein, Christian Grass, Adinda Freudenthal:
Design for risk control: The role of usability engineering in the management of use-related risks. 795-812 - Omar Bouhaddou, Tim Cromwell, Mike Davis, Sarah A. 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. 813-823
Volume 45, Number 5, October 2012
- Adrien Coulet, K. Bretonnel Cohen, Russ B. Altman:
The state of the art in text mining and natural language processing for pharmacogenomics. 825-826 - Rong Xu, QuanQiu Wang:
A knowledge-driven conditional approach to extract pharmacogenomics specific drug-gene relationships from free text. 827-834 - Bastien Rance, Emily Doughty, Dina Demner-Fushman, Maricel G. Kann, Olivier Bodenreider:
A mutation-centric approach to identifying pharmacogenomic relations in text. 835-841 - Jörg 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. 842-850 - Fabio Rinaldi, Gerold Schneider, Simon Clematide:
Relation mining experiments in the pharmacogenomics domain. 851-861 - Sergey V. Pakhomov, Bridget T. McInnes, J. Lamba, Y. Liu, Genevieve B. Melton, Yogita Ghodke, N. Bhise, V. Lamba, Angela K. Birnbaum:
Using PharmGKB to train text mining approaches for identifying potential gene targets for pharmacogenomic studies. 862-869 - Jiao Li, Zhiyong Lu:
Systematic identification of pharmacogenomics information from clinical trials. 870-878 - Erik 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. 879-884 - Harsha 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. 885-892
- Murat Sariyar, Andreas Borg, Klaus Pommerening:
Active learning strategies for the deduplication of electronic patient data using classification trees. 893-900 - Philip Gooch, Abdul V. Roudsari:
Lexical patterns, features and knowledge resources for coreference resolution in clinical notes. 901-912 - Xiao Hu, Monica Sapo, Valeriy Nenov, Tod Barry, Sunghan Kim, Duc H. Do, Noel G. Boyle, Neil Martin:
Predictive combinations of monitor alarms preceding in-hospital code blue events. 913-921 - Tai-Chun Wang, Javid Taheri, Albert Y. Zomaya:
Using genetic algorithm in reconstructing single individual haplotype with minimum error correction. 922-930 - Bo Liao, Xiong Li, Wen Zhu, Renfa Li, Shulin Wang:
Multiple ant colony algorithm method for selecting tag SNPs. 931-937 - María Adela Grando, David Glasspool, Aziz A. Boxwala:
Argumentation logic for the flexible enactment of goal-based medical guidelines. 938-949 - Pamela 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. 950-957 - Siddika Parlak, Aleksandra Sarcevic, Ivan Marsic, Randall S. Burd:
Introducing RFID technology in dynamic and time-critical medical settings: Requirements and challenges. 958-974 - James F. Brinkley, Landon Detwiler:
A Query Integrator and Manager for the Query Web. 975-991 - Vijay Garla, Cynthia Brandt:
Ontology-guided feature engineering for clinical text classification. 992-998 - Chang 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. 999-1008 - Arun Sen, Amarnath Banerjee, Atish P. Sinha, Manish Bansal:
Clinical decision support: Converging toward an integrated architecture. 1009-1017 - Vojtech Huser:
Process Mining: Discovery, Conformance and Enhancement of Business Processes. 1018-1019
Volume 45, Number 6, December 2012
- Farzaneh Tatari, Mohammad R. Akbarzadeh-Totonchi, Ahmad Sabahi:
Fuzzy-probabilistic multi agent system for breast cancer risk assessment and insurance premium assignment. 1021-1034 - Won Kim, Lana Yeganova, Donald C. Comeau, W. John Wilbur:
Identifying well-formed biomedical phrases in MEDLINE® text. 1035-1041 - Huanying 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. 1042-1048 - Trevor Cohen, Dominic Widdows, Roger W. Schvaneveldt, Peter Davies, Thomas C. Rindflesch:
Discovering discovery patterns with predication-based Semantic Indexing. 1049-1065 - José Salavert Torres, J. Damian Segrelles Quilis, Ignacio Blanquer Espert, Vicente Hernández:
Improving knowledge management through the support of image examination and data annotation using DICOM structured reporting. 1066-1074 - Hua Xu, Yonghui Wu, Noemie Elhadad, Peter D. Stetson, Carol Friedman:
A new clustering method for detecting rare senses of abbreviations in clinical notes. 1075-1083 - Xuan 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. 1084-1107 - Fabio Stella, Y. Amer:
Continuous time Bayesian network classifiers. 1108-1119 - Fabio Grandi, Federica Mandreoli, Riccardo Martoglia:
Efficient management of multi-version clinical guidelines. 1120-1136 - Rachel 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. 1137-1150 - Alla Keselman, Catherine Arnott-Smith:
A classification of errors in lay comprehension of medical documents. 1151-1163 - Chih-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. 1164-1174 - Hanen 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). 1175-1184 - Loubna Bouarfa, Jenny Dankelman:
Workflow mining and outlier detection from clinical activity logs. 1185-1190 - Do Kyoon Kim, Hyunjung Shin, Young Soo Song, Ju Han Kim:
Synergistic effect of different levels of genomic data for cancer clinical outcome prediction. 1191-1198 - Yves A. Lussier, Haiquan Li:
Breakthroughs in genomics data integration for predicting clinical outcome. 1199-1201
- Jan Horsky, Gordon D. Schiff, Douglas Johnston, Lauren M. Mercincavage, Douglas S. Bell, Blackford Middleton:
Interface design principles for usable decision support: A targeted review of best practices for clinical prescribing interventions. 1202-1216
- Himali 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]. 1217
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