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Getting the foot out of the pelvis: modeling problems affecting use of SNOMED CT hierarchies in practical applications

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JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 2011年第4期18卷 432-440页

作者： Rector, Alan L. Brandt, Sam Schneider, Thomas Univ Manchester Sch Comp Sci Manchester M13 9PL Lancs England Siemens Hlth Serv Malvern PA USA

Objectives (a) To determine the extent and range of errors and issues in the Systematised Nomenclature of Medicine Clinical Terms (SNOMED CT) hierarchies as they affect two practical projects. (b) To determine the origin of issues raised and propose methods to address them. methods The hierarchies for concepts in the Core Problem List Subset published by the Unified Medical Language System were examined for their appropriateness in two applications. Anomalies were traced to their source to determine whether they were simple local errors, systematic inferences propagated by SNOMED's classification process, or the result of problems with SNOMED's schemas. Conclusions were confirmed by showing that altering the root cause and reclassifying had the intended effects, and not others. Main results Major problems were encountered, involving concepts central to medicine including myocardial infarction, diabetes, and hypertension. Most of the issues raised were systematic. Some exposed fundamental errors in SNOMED's schemas, particularly with regards to anatomy. In many cases, the root cause could only be identified and corrected with the aid of a classifier. Limitations This is a preliminary 'experiment of opportunity.' The results are not exhaustive;nor is consensus on all points definitive. Conclusions The SNOMED CT hierarchies cannot be relied upon in their present state in our applications. However, systematic quality assurance and correction are possible and practical but require sound techniques analogous to software engineering and combined lexical and semantic techniques. Until this is done, anyone using SNOMED codes should exercise caution. Errors in the hierarchies, or attempts to compensate for them, are likely to compromise interoperability and meaningful use.

关键词： Knowledge bases knowledge representations methods for integration of information from disparate sources knowledge acquisition and knowledge management developing and refining EHR data standards (including image standards) data models data exchange controlled terminologies and vocabularies communication integration across care settings (inter- and intraenterprise) ontologies terminology EHRs

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User perspectives on the usability of a regional health information exchange

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JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 2011年第5期18卷 711-716页

作者： Gadd, Cynthia S. Ho, Yun-Xian Cala, Cather Marie Blakemore, Dana Chen, Qingxia Frisse, Mark E. Johnson, Kevin B. Vanderbilt Univ Dept Biomed Informat Eskind Lib Nashville TN 37203 USA Vanderbilt Univ Dept Biostat Nashville TN 37203 USA

Objective We assessed the usability of a health information exchange (HIE) in a densely populated metropolitan region. This grant-funded HIE had been deployed rapidly to address the imminent needs of the patient population and the need to draw wider participation from regional entities. Design We conducted a cross-sectional survey of individuals given access to the HIE at participating organizations and examined some of the usability and usage factors related to the technology acceptance model. Measurements We probed user perceptions using the Questionnaire for User Interaction Satisfaction, an author-generated Trust scale, and user characteristic questions (eg, age, weekly system usage time). Results Overall, users viewed the system favorably (ratings for all usability items were greater than neutral (one-sample Wilcoxon test, p<0.0014, Bonferroni-corrected for 35 tests). System usage was regressed on usability, trust, and demographic and user characteristic factors. Three usability factors were positively predictive of system usage: overall reactions (p<0 0.01), learning (p<0.05), and system functionality (p<0.01). Although trust is an important component in collaborative relationships, we did not find that user trust of other participating healthcare entities was significantly predictive of usage. An analysis of respondents' comments revealed ways to improve the HIE. Conclusion We used a rapid deployment model to develop an HIE and found that perceptions of system usability were positive. We also found that system usage was predicted well by some aspects of usability. Results from this study suggest that a rapid development approach may serve as a viable model for developing usable HIEs serving communities with limited resources.

关键词： information dissemination medical records system regional health planning usability usage biomedical informatics evaluation Qualitative/ethnographic field study Improving the education and skills training of health professionals System implementation and management issues Social/organizational study Collaborative technologies methods for integration of information from disparate sources Demonstrating return on IT investment distributed systems agents Software engineering: architecture Supporting practice at a distance (telehealth) Data exchange communication and integration across care settings (inter- and intra-enterprise) Visualization of data and knowledge policy Legal historical ethical study methods clinical informatics biomedical informatics pediatrics e-prescribing human factors

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The TOKEn project: knowledge synthesis for in silico science

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JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 2011年第Sup1期18卷 I125-I131页

作者： Payne, Philip R. O. Borlawsky, Tara B. Lele, Omkar James, Stephen Greaves, Andrew W. Ohio State Univ Dept Biomed Informat Columbus OH 43210 USA Moores UCSD Canc Ctr CLL Res Consortium La Jolla CA USA

Objective The conduct of investigational studies that involve large-scale data sets presents significant challenges related to the discovery and testing of novel hypotheses capable of supporting in silico discovery science. The use of what are known as Conceptual Knowledge Discovery in Databases (CKDD) methods provides a potential means of scaling hypothesis discovery and testing approaches for large data sets. Such methods enable the high-throughput generation and evaluation of knowledge-anchored relationships between complexes of variables found in targeted data sets. methods The authors have conducted a multipart model formulation and validation process, focusing on the development of a methodological and technical approach to using CKDD to support hypothesis discovery for in silico science. The model the authors have developed is known as the Translational Ontology-anchored Knowledge Discovery Engine (TOKEn). This model utilizes a specific CKDD approach known as Constructive Induction to identify and prioritize potential hypotheses related to the meaningful semantic relationships between variables found in large-scale and heterogeneous biomedical data sets. Results The authors have verified and validated TOKEn in the context of a translational research data repository maintained by the NCI-funded Chronic Lymphocytic Leukemia Research Consortium. Such studies have shown that TOKEn is: (1) computationally tractable;and (2) able to generate valid and potentially useful hypotheses concerning relationships between phenotypic and biomolecular variables in that data collection. Conclusions The TOKEn model represents a potentially useful and systematic approach to knowledge synthesis for in silico discovery science in the context of large-scale and multidimensional research data sets.

关键词： Computing methodologies knowledge bases information theory research design phenotype biological markers visualization of data and knowledge translational research—application of biological knowledge to clinical care linking the genotype and phenotype methods for integration of information from disparate sources knowledge acquisition and knowledge management data modeling and integration knowledge representations data models methods for integration of information from disparate sources informatics

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Collaborative search in electronic health records

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JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 2011年第3期18卷 282-291页

作者： Zheng, Kai Mei, Qiaozhu Hanauer, David A. Univ Michigan Sch Publ Hlth Dept Hlth Management & Policy Sch Informat Ann Arbor MI 48109 USA Univ Michigan Dept Elect Engn & Comp Sci Ann Arbor MI 48109 USA Univ Michigan Dept Pediat Ann Arbor MI 48109 USA Univ Michigan Ctr Comprehens Canc Ann Arbor MI 48109 USA

Objective A full-text search engine can be a useful tool for augmenting the reuse value of unstructured narrative data stored in electronic health records (EHR). A prominent barrier to the effective utilization of such tools originates from users' lack of search expertise and/or medical-domain knowledge. To mitigate the issue, the authors experimented with a 'collaborative search' feature through a homegrown EHR search engine that allows users to preserve their search knowledge and share it with others. This feature was inspired by the success of many social information-foraging techniques used on the web that leverage users' collective wisdom to improve the quality and efficiency of information retrieval. Design The authors conducted an empirical evaluation study over a 4-year period. The user sample consisted of 451 academic researchers, medical practitioners, and hospital administrators. The data were analyzed using a social-network analysis to delineate the structure of the user collaboration networks that mediated the diffusion of knowledge of search. Results The users embraced the concept with considerable enthusiasm. About half of the EHR searches processed by the system (0.44 million) were based on stored search knowledge;0.16 million utilized shared knowledge made available by other users. The social-network analysis results also suggest that the user-collaboration networks engendered by the collaborative search feature played an instrumental role in enabling the transfer of search knowledge across people and domains. Conclusion Applying collaborative search, a social information-foraging technique popularly used on the web, may provide the potential to improve the quality and efficiency of information retrieval in healthcare.

关键词： Collaborative technologies personal health records and self-care systems developing/using clinical decision support (other than diagnostic) and guideline systems systems supporting patient-provider interaction human–computer interaction and human-centered computing improving healthcare workflow and process efficiency system implementation and management issues social/organizational study qualitative/ethnographic field study cognitive study (including experiments emphasizing verbal protocol analysis and usability) methods for integration of information from disparate sources information storage and retrieval (text and images) data exchange communication integration across care settings (inter- and intraenterprise) visualization of data and knowledge developing/using computerized provider order entry

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A secure protocol for protecting the identity of providers when disclosing data for disease surveillance

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JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 2011年第3期18卷 212-217页

作者： El Emam, Khaled Hu, Jun Mercer, Jay Peyton, Liam Kantarcioglu, Murat Malin, Bradley Buckeridge, David Samet, Saeed Earle, Craig Childrens Hosp Eastern Ontario Res Inst Ottawa ON K1H 8L1 Canada Univ Ottawa Sch Informat Technol & Engn Ottawa ON Canada Univ Texas Dallas Dallas TX 75230 USA Vanderbilt Univ Nashville TN USA McGill Univ Dept Epidemiol & Biostat Montreal PQ Canada Ontario Inst Canc Res Toronto ON Canada Inst Clin Evaluat Sci Toronto ON Canada

Background Providers have been reluctant to disclose patient data for public-health purposes. Even if patient privacy is ensured, the desire to protect provider confidentiality has been an important driver of this reluctance. methods Six requirements for a surveillance protocol were defined that satisfy the confidentiality needs of providers and ensure utility to public health. The authors developed a secure multi-party computation protocol using the Paillier cryptosystem to allow the disclosure of stratified case counts and denominators to meet these requirements. The authors evaluated the protocol in a simulated environment on its computation performance and ability to detect disease outbreak clusters. Results Theoretical and empirical assessments demonstrate that all requirements are met by the protocol. A system implementing the protocol scales linearly in terms of computation time as the number of providers is increased. The absolute time to perform the computations was 12.5 s for data from 3000 practices. This is acceptable performance, given that the reporting would normally be done at 24 h intervals. The accuracy of detection disease outbreak cluster was unchanged compared with a non-secure distributed surveillance protocol, with an F-score higher than 0.92 for outbreaks involving 500 or more cases. Conclusion The protocol and associated software provide a practical method for providers to disclose patient data for sentinel, syndromic or other indicator-based surveillance while protecting patient privacy and the identity of individual providers.

关键词： Privacy reidentification de-identification consent ethics integration across care settings (inter- and intraenterprise) languages computational methods advanced algorithms personal health records and self-care systems assuring information system security and personal privacy anonymization other methods for security and policy enforcement cryptography data exchange communication ethical study methods statistical analysis of large datasets methods for integration of information from disparate sources distributed systems agents software engineering: architecture detecting disease outbreaks and biological threats policy legal historical simulation of complex systems (at all levels: molecules to work groups to organizations) monitoring the health of populations privacy and security machine learning health data standards vocabulary ontology scientific information and health data policy consumer health/patient education information information retrieval NLP public-health informatics clinical trials syndromic surveillance secure computation

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Targeted screening for pediatric conditions with the CHICA system

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JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 2011年第4期18卷 485-490页

作者： Carroll, Aaron E. Biondich, Paul G. Anand, Vibha Dugan, Tamara M. Sheley, Meena E. Xu, Shawn Z. Downs, Stephen M. Indiana Univ Sch Med Childrens Hlth Serv Res Indianapolis IN 46202 USA Indiana Univ Sch Med Regenstrief Inst Hlth Care Indianapolis IN 46202 USA

Objective The Child Health Improvement through Computer Automation (CHICA) system is a decision-support and electronic-medical-record system for pediatric health maintenance and disease management. The purpose of this study was to explore CHICA's ability to screen patients for disorders that have validated screening criteria specifically tuberculosis (TB) and iron-deficiency anemia. Design Children between 0 and 11 years were randomized by the CHICA system. In the intervention group, parents were asked about TB and iron-deficiency risk, and physicians received a tailored prompt. In the control group, no screens were performed, and the physician received a generic prompt about these disorders. Results 1123 participants were randomized to the control group and 1116 participants to the intervention group. Significantly more people reported positive risk factors for iron-deficiency anemia in the intervention group (17.5% vs 3.1%, OR 6.6, 95% CI 4.5 to 9.5). In general, far fewer parents reported risk factors for TB than for iron-deficiency anemia. Again, there were significantly higher detection rates of positive risk factors in the intervention group (1.8% vs 0.8%, OR 2.3, 95% CI 1.0 to 5.0). Limitations It is possible that there may be more positive screens without improving outcomes. However, the guidelines are based on studies that have evaluated the questions the authors used as sensitive and specific, and there is no reason to believe that parents misunderstood them. Conclusions Many screening tests are risk-based, not universal, leaving physicians to determine who should have a further workup. This can be a time-consuming process. The authors demonstrated that the CHICA system performs well in assessing risk automatically for TB and iron-deficiency anemia.

关键词： Tuberculosis iron-deficiency anemia CHICA screening computer decision-support system visualization of data and knowledge knowledge representations communications networking methods mobility uncertain reasoning and decision theory languages computational methods advanced algorithms methods for integration of information from disparate sources distributed systems agents software engineering: architecture data models automated learning developing/using clinical decision support (other than diagnostic) and guideline systems discovery text and data mining methods

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Health information exchange usage in emergency departments and clinics: the who, what, and why

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JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 2011年第5期18卷 690-697页

作者： Johnson, Kevin B. Unertl, Kim M. Chen, Qingxia Lorenzi, Nancy M. Nian, Hui Bailey, James Frisse, Mark Vanderbilt Univ Sch Med Dept Biomed Informat Nashville TN 37232 USA Vanderbilt Univ Sch Med Dept Pediat Nashville TN 37232 USA Vanderbilt Univ Sch Med Dept Biostat Nashville TN 37232 USA Univ Tennessee Hlth Sci Ctr Div Gen Internal Med Nashville TN USA

Objective Health information exchange (HIE) systems are being developed across the nation. Understanding approaches taken by existing successful exchanges can help new exchange efforts determine goals and plan implementations. The goal of this study was to explore characteristics of use and users of a successful regional HIE. Design We used a mixed-method analysis, consisting of cross-sectional audit log data, semi-structured interviews, and direct observation in a sample of emergency departments and ambulatory safety net clinics actively using HIE. For each site, we measured overall usage trends, user logon statistics, and data types accessed by users. We also assessed reasons for use and outcomes of use. Results Overall, users accessed HIE for 6.8% of all encounters, with higher rates of access for repeat visits, for patients with comorbidities, for patients known to have data in the exchange, and at sites providing HIE access to both nurses and physicians. Discharge summaries and test reports were the most frequently accessed data in the exchange. Providers consistently noted retrieving additional history, preventing repeat tests, comparing new results to retrieved results, and avoiding hospitalizations as a consequence of HIE access. Conclusion HIE use in emergency departments and ambulatory clinics was focused on patients where missing information was believed to be present in the exchange and was related to factors including the roles of people with access, the setting, and other site-specific issues that impacted the overall breadth of routine system use. These data should form an important foundation as other sites embark upon HIE implementation.

关键词： Health information exchange usage clinical informatics biomedical informatics pediatrics e-prescribing human factors qualitative/ethnographic field study designing usable (responsive) resources and systems improving healthcare workflow and process efficiency system implementation and management issues surveys and needs analysis social/organizational study health information exchange collaborative technologies methods for integration of information from disparate sources demonstrating return on IT investment distributed systems agents software engineering: architecture supporting practice at a distance (telehealth) data exchange communication and integration across care settings (inter- and intra-enterprise) visualization of data and knowledge policy legal historical ethical study methods

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Computationally translating molecular discoveries into tools for medicine: translational bioinformatics articles now featured in JAMIA

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JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 2011年第4期18卷 352-353页

作者： Butte, Atul J. Shah, Nigam H. Stanford Univ Sch Med Dept Pediat Div Syst Med Stanford CA 94305 USA Lucile Packard Childrens Hosp Palo Alto CA USA Stanford Univ Sch Med Stanford Ctr Biomed Informat Res Stanford CA 94305 USA

This year marks the 15th anniversary of the invention of the gene expression microarray. As mRNA transcripts serve as the blueprint within cells for making proteins, measuring mRNA levels was seen as an accurate and manageable way to investigate cell and tissue processes. Those earliest microarrays in 1995 could measure 48 transcripts in parallel in plants,1but within 1 year were scaled up to measure more than 1000 transcripts including those in human tissues. Today, these microarrays are essentially commodity items, commonly used to study human health and disease in hospitals and academic institutions, as well as in the biotechnology and pharmaceutical industry.

关键词： Modeling physiologic and disease processes Linking the genotype and phenotype identifying genome and protein structure and function visualization of data and knowledge collaborative technologies applications that link biomedical knowledge from diverse primary sources (includes automated indexing) knowledge representations statistical analysis of large datasets methods for integration of information from disparate sources discovery and text and data mining methods automated learning ontologies knowledge bases

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Enabling distributed electronic research data collection for a rural Appalachian tobacco cessation study

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JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 2011年第Sup1期18卷 I140-I143页

作者： Borlawsky, Tara B. Lele, Omkar Jensen, Daniel Hood, Nancy E. Wewers, Mary Ellen Ohio State Univ Dept Biomed Informat Columbus OH 43210 USA Ohio State Univ Coll Publ Hlth Columbus OH 43210 USA

Tobacco use is increasingly prevalent among vulnerable populations, such as people living in rural Appalachian communities. Owing to limited access to a reliable internet service in such settings, there is no widespread adoption of electronic data capture tools for conducting community-based research. By integrating the REDCap data collection application with a custom synchronization tool, the authors have enabled a workflow in which field research staff located throughout the Ohio Appalachian region can electronically collect and share research data. In addition to allowing the study data to be exchanged in near-real-time among the geographically distributed study staff and centralized study coordinator, the system architecture also ensures that the data are stored securely on encrypted laptops in the field and centrally behind the Ohio State University Medical Center enterprise firewall. The authors believe that this approach can be easily applied to other analogous study designs and settings.

关键词： Data collection community-based participatory research medical informatics software data modeling and integration machine learning predictive modeling statistical learning privacy technology visualization of data and knowledge knowledge representations methods for integration of information from disparate sources data models data exchange

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EliXR: an approach to eligibility criteria extraction and representation

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JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 2011年第Sup1期18卷 I116-I124页

作者： Weng, Chunhua Wu, Xiaoying Luo, Zhihui Boland, Mary Regina Theodoratos, Dimitri Johnson, Stephen B. Columbia Univ Dept Biomed Informat New York NY 10032 USA New Jersey Inst Technol Dept Comp Sci Newark NJ 07102 USA

Objective To develop a semantic representation for clinical research eligibility criteria to automate semistructured information extraction from eligibility criteria text. Materials and methods An analysis pipeline called eligibility criteria extraction and representation (EliXR) was developed that integrates syntactic parsing and tree pattern mining to discover common semantic patterns in 1000 eligibility criteria randomly selected from http://***. The semantic patterns were aggregated and enriched with unified medical language systems semantic knowledge to form a semantic representation for clinical research eligibility criteria. Results The authors arrived at 175 semantic patterns, which form 12 semantic role labels connected by their frequent semantic relations in a semantic network. Evaluation Three raters independently annotated all the sentence segments (N=396) for 79 test eligibility criteria using the 12 top-level semantic role labels. Eight-six per cent (339) of the sentence segments were unanimously labelled correctly and 13.8% (55) were correctly labelled by two raters. The Fleiss' kappa was 0.88, indicating a nearly perfect interrater agreement. Conclusion This study present a semi-automated data-driven approach to developing a semantic network that aligns well with the top-level information structure in clinical research eligibility criteria text and demonstrates the feasibility of using the resulting semantic role labels to generate semistructured eligibility criteria with nearly perfect interrater reliability.

关键词： AMTB analytical processing clinical research eligibility criteria clinical research informatics collaborative technologies databases data exchange data integration data mining data models data warehousing knowledge acquisition knowledge acquisition and knowledge management knowledge representations linking the genotype and phenotype machine learning methods for integration of information from disparate sources natural-language processing predictive modelling privacy technology semantic network semantics social/organizational study statistical learning text-based ontology learning visualization of data and knowledge

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