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1.  Human Factors Engineering in HI: So What? Who Cares? and What's in It for You? 
Healthcare Informatics Research  2012;18(4):237-241.
Human factors engineering is a discipline that deals with computer and human systems and processes and provides a methodology for designing and evaluating systems as they interact with human beings. This review article reviews important current and past efforts in human factors engineering in health informatics in the context of the current trends in health informatics.
The methodology of human factors engineering and usability testing in particular were reviewed in this article.
This methodology arises from the field of human factors engineering, which uses principles from cognitive science and applies them to implementations such as a computer-human interface and user-centered design.
Patient safety and best practice of medicine requires a partnership between patients, clinicians and computer systems that serve to improve the quality and safety of patient care. People approach work and problems with their own knowledge base and set of past experiences and their ability to use systems properly and with low error rates are directly related to the usability as well as the utility of computer systems. Unusable systems have been responsible for medical error and patient harm and have even led to the death of patients and increased mortality rates. Electronic Health Record and Computerized Physician Order Entry systems like any medical device should come with a known safety profile that minimizes medical error and harm. This review article reviews important current and past efforts in human factors engineering in health informatics in the context of the current trends in health informatics.
PMCID: PMC3548152  PMID: 23346473
Health Informatics; Human Factors Engineering; Usability Testing; User-Centered Design; Patient Safety
2.  geneCBR: a translational tool for multiple-microarray analysis and integrative information retrieval for aiding diagnosis in cancer research 
BMC Bioinformatics  2009;10:187.
Bioinformatics and medical informatics are two research fields that serve the needs of different but related communities. Both domains share the common goal of providing new algorithms, methods and technological solutions to biomedical research, and contributing to the treatment and cure of diseases. Although different microarray techniques have been successfully used to investigate useful information for cancer diagnosis at the gene expression level, the true integration of existing methods into day-to-day clinical practice is still a long way off. Within this context, case-based reasoning emerges as a suitable paradigm specially intended for the development of biomedical informatics applications and decision support systems, given the support and collaboration involved in such a translational development. With the goals of removing barriers against multi-disciplinary collaboration and facilitating the dissemination and transfer of knowledge to real practice, case-based reasoning systems have the potential to be applied to translational research mainly because their computational reasoning paradigm is similar to the way clinicians gather, analyze and process information in their own practice of clinical medicine.
In addressing the issue of bridging the existing gap between biomedical researchers and clinicians who work in the domain of cancer diagnosis, prognosis and treatment, we have developed and made accessible a common interactive framework. Our geneCBR system implements a freely available software tool that allows the use of combined techniques that can be applied to gene selection, clustering, knowledge extraction and prediction for aiding diagnosis in cancer research. For biomedical researches, geneCBR expert mode offers a core workbench for designing and testing new techniques and experiments. For pathologists or oncologists, geneCBR diagnostic mode implements an effective and reliable system that can diagnose cancer subtypes based on the analysis of microarray data using a CBR architecture. For programmers, geneCBR programming mode includes an advanced edition module for run-time modification of previous coded techniques.
geneCBR is a new translational tool that can effectively support the integrative work of programmers, biomedical researches and clinicians working together in a common framework. The code is freely available under the GPL license and can be obtained at .
PMCID: PMC2703634  PMID: 19538727
3.  MED34/448: The Networked Health-Care Environment of the Future: Requirements for new human abilities 
The implications of the Internet for health care are increasingly understood as scientists, health workers, patients, and health administrators envision new applications, new means for communicating about health issues, and new ways of accessing pertinent health information at the point of care. It is important to study not only the new technologies themselves, but also to recognize that the optimal use of these technologies requires new skills by users. Not only must both patients and health professionals be taught the basic skills related to use of networking technologies, but those who develop future systems must understand the new human abilities that are implied by the remarkable changes that are envisioned. We describe the results of research that have implications for effectively exploiting networking technology in order to enhance creativity, collaboration, and communication. The development and implementation of enabling tools and methods that provide ready access to knowledge and information are among the central goals of medical informatics. Given the immensity of this challenge, the need for multi-institutional collaboration is increasingly being recognized. Collaboration has typically involved individuals who work together at the same location. With the evolution of electronic communication modalities, workers at Harvard, Columbia, McGill, and Stanford Universities jointly investigated the role that networking technologies can play in supporting research collaboration at a distance. All communications among the workers from the other three institutions were observed in order to gain insights into the limitations and successes of communications technology in supporting this distributed creative process. We analyzed the activities of the Intermed team as they sought to develop a common representation for clinical guidelines, known as the GuideLine Interchange Format (GLIF). These activities can be described as a process of computer-mediated collaborative design. We report here on the cognitive, socio-cultural, and logistical issues encountered when scientists from diverse organizations and backgrounds use communications technologies while designing and implementing shared products. Results demonstrate that the effectiveness of communication modalities is predicated on the specific objectives of the task. We identify suitable uses of email, conference calls, and face-to-face meetings. The leaders play an integral role in guiding and facilitating the group activities across modalities. Most important was the proper use of technology to support the evolution of a shared vision of group goals and methods, an element that is clearly necessary before successful collaborative designs can proceed. We interpret these research findings as they relate to the scientific collaboration via the Internet with specific focus on changes in skills required with these new media of communication.
PMCID: PMC1761787
Communication; Internet-based Collaboration; Cognition; Medical Education
4.  Active Assistance Technology for Health-Related Behavior Change: An Interdisciplinary Review 
Information technology can help individuals to change their health behaviors. This is due to its potential for dynamic and unbiased information processing enabling users to monitor their own progress and be informed about risks and opportunities specific to evolving contexts and motivations. However, in many behavior change interventions, information technology is underused by treating it as a passive medium focused on efficient transmission of information and a positive user experience.
To conduct an interdisciplinary literature review to determine the extent to which the active technological capabilities of dynamic and adaptive information processing are being applied in behavior change interventions and to identify their role in these interventions.
We defined key categories of active technology such as semantic information processing, pattern recognition, and adaptation. We conducted the literature search using keywords derived from the categories and included studies that indicated a significant role for an active technology in health-related behavior change. In the data extraction, we looked specifically for the following technology roles: (1) dynamic adaptive tailoring of messages depending on context, (2) interactive education, (3) support for client self-monitoring of behavior change progress, and (4) novel ways in which interventions are grounded in behavior change theories using active technology.
The search returned 228 potentially relevant articles, of which 41 satisfied the inclusion criteria. We found that significant research was focused on dialog systems, embodied conversational agents, and activity recognition. The most covered health topic was physical activity. The majority of the studies were early-stage research. Only 6 were randomized controlled trials, of which 4 were positive for behavior change and 5 were positive for acceptability. Empathy and relational behavior were significant research themes in dialog systems for behavior change, with many pilot studies showing a preference for those features. We found few studies that focused on interactive education (3 studies) and self-monitoring (2 studies). Some recent research is emerging in dynamic tailoring (15 studies) and theoretically grounded ontologies for automated semantic processing (4 studies).
The potential capabilities and risks of active assistance technologies are not being fully explored in most current behavior change research. Designers of health behavior interventions need to consider the relevant informatics methods and algorithms more fully. There is also a need to analyze the possibilities that can result from interaction between different technology components. This requires deep interdisciplinary collaboration, for example, between health psychology, computer science, health informatics, cognitive science, and educational methodology.
PMCID: PMC3415065  PMID: 22698679
Behavior change; consumer health informatics; health communication; health promotion; personalization
5.  Delivering patient decision aids on the Internet: definitions, theories, current evidence, and emerging research areas 
In 2005, the International Patient Decision Aids Standards Collaboration identified twelve quality dimensions to guide assessment of patient decision aids. One dimension—the delivery of patient decision aids on the Internet—is relevant when the Internet is used to provide some or all components of a patient decision aid. Building on the original background chapter, this paper provides an updated definition for this dimension, outlines a theoretical rationale, describes current evidence, and discusses emerging research areas.
An international, multidisciplinary panel of authors examined the relevant theoretical literature and empirical evidence through 2012.
The updated definition distinguishes Internet-delivery of patient decision aids from online health information and clinical practice guidelines. Theories in cognitive psychology, decision psychology, communication, and education support the value of Internet features for providing interactive information and deliberative support. Dissemination and implementation theories support Internet-delivery for providing the right information (rapidly updated), to the right person (tailored), at the right time (the appropriate point in the decision making process). Additional efforts are needed to integrate the theoretical rationale and empirical evidence from health technology perspectives, such as consumer health informatics, user experience design, and human-computer interaction.
Despite Internet usage ranging from 74% to 85% in developed countries and 80% of users searching for health information, it is unknown how many individuals specifically seek patient decision aids on the Internet. Among the 86 randomized controlled trials in the 2011 Cochrane Collaboration’s review of patient decision aids, only four studies focused on Internet-delivery. Given the limited number of published studies, this paper particularly focused on identifying gaps in the empirical evidence base and identifying emerging areas of research.
As of 2012, the updated theoretical rationale and emerging evidence suggest potential benefits to delivering patient decision aids on the Internet. However, additional research is needed to identify best practices and quality metrics for Internet-based development, evaluation, and dissemination, particularly in the areas of interactivity, multimedia components, socially-generated information, and implementation strategies.
PMCID: PMC4043476  PMID: 24625064
6.  Enhancing participant safety through electronically-generated medication order sets in a clinical research environment: A medical informatics initiative 
While clinical medicine is often well-supported by health system information technology infrastructure, clinical research may need to create strategies to use clinical medicine informational technology tools. The authors describe a medication safety initiative that was carried out in a National Institutes of Health (NIH) Clinical and Translational Science Award (CTSA)-sponsored clinical research environment. A Web-based, medical informatics application was designed and implemented which allowed research groups to build protocol-specific, electronic medication templates that were subsequently used to create participant-specific medication order sets for conductance of clinical research activities in the CTSA-sponsored clinical research environment. The medical informatics initiative eliminated typewritten or handwritten medication orders, created research protocol-specific templates meeting institutional order-writing requirements, and formalized a rigorous review and approval process. Enhancing safety in medication ordering and prescribing practices in a clinical research environment provided the background for multi-disciplinary cooperation in medical informatics.
PMCID: PMC3076285  PMID: 21167008
7.  Metropolis redux: the unique importance of library skills in informatics 
Objectives: The objective is to highlight the important role that librarians have in teaching within a successful medical informatics program. Librarians regularly utilize skills that, although not technology dependent, are essential to conducting computer-based research. The Metropolis analogy is used to introduce the part librarians play as informatics partners. Science fiction is a modern mythology that, beyond a technical exterior, has lasting value in its ability to reflect the human condition. The teaching of medical informatics, an intersection of technology and knowledge, is also most relevant when it transcends the operation of databases and systems. Librarians can teach students to understand, research, and utilize information beyond specific technologies.
Methods: A survey of twenty-six informatics programs was conducted during 2002, with specific emphasis on the role of the library service.
Results: The survey demonstrated that librarians currently do have a central role in informatics instruction, and that library-focused skills form a significant part of the curriculum in many of those programs. In addition, librarians have creative opportunities to enhance their involvement in informatics training. As a sample program in the study, the development of the informatics course at the Massachusetts College of Pharmacy and Health Sciences is included.
Conclusions: Medical informatics training is a wonderful opportunity for librarians to collaborate with professionals from the sciences and other information disciplines. Librarians' unique combination of human research and technology skills provides a valuable contribution to any program.
PMCID: PMC385302  PMID: 15098050
8.  E-Learning as New Method of Medical Education 
Acta Informatica Medica  2008;16(2):102-117.
Distance learning refers to use of technologies based on health care delivered on distance and covers areas such as electronic health, tele-health (e-health), telematics, telemedicine, tele-education, etc. For the need of e-health, telemedicine, tele-education and distance learning there are various technologies and communication systems from standard telephone lines to the system of transmission digitalized signals with modem, optical fiber, satellite links, wireless technologies, etc. Tele-education represents health education on distance, using Information Communication Technologies (ICT), as well as continuous education of a health system beneficiaries and use of electronic libraries, data bases or electronic data with data bases of knowledge. Distance learning (E-learning) as a part of tele-education has gained popularity in the past decade; however, its use is highly variable among medical schools and appears to be more common in basic medical science courses than in clinical education. Distance learning does not preclude traditional learning processes; frequently it is used in conjunction with in-person classroom or professional training procedures and practices. Tele-education has mostly been used in biomedical education as a blended learning method, which combines tele-education technology with traditional instructor-led training, where, for example, a lecture or demonstration is supplemented by an online tutorial. Distance learning is used for self-education, tests, services and for examinations in medicine i.e. in terms of self-education and individual examination services. The possibility of working in the exercise mode with image files and questions is an attractive way of self education. Automated tracking and reporting of learners’ activities lessen faculty administrative burden. Moreover, e-learning can be designed to include outcomes assessment to determine whether learning has occurred. This review article evaluates the current status and level of tele-education development in Bosnia and Herzegovina outlining its components, faculty development needs for implementation and the possibility of its integration as official learning standard in biomedical curricula in Bosnia and Herzegovina. Tele-education refers to the use of information and communication technologies (ICT) to enhance knowledge and performance. Tele-education in biomedical education is widely accepted in the medical education community where it is mostly integrated into biomedical curricula forming part of a blended learning strategy. There are many biomedical digital repositories of e-learning materials worldwide, some peer reviewed, where instructors or developers can submit materials for widespread use. First pilot project with the aim to introduce tele-education in biomedical curricula in Bosnia and Herzegovina was initiated by Department for Medical Informatics at Medical Faculty in Sarajevo in 2002 and has been developing since. Faculty member’s skills in creating tele-education differ from those needed for traditional teaching and faculty rewards must recognize this difference and reward the effort. Tele-education and use of computers will have an impact of future medical practice in a life long learning. Bologna process, which started last years in European countries, provide us to promote and introduce modern educational methods of education at biomedical faculties in Bosnia and Herzegovina. Cathedra of Medical informatics and Cathedra of Family medicine at Medical Faculty of University of Sarajevo started to use Web based education as common way of teaching of medical students. Satisfaction with this method of education within the students is good, but not yet suitable for most of medical disciplines at biomedical faculties in Bosnia and Herzegovina.
PMCID: PMC3789161  PMID: 24109154
Medical education; Distance learning; Bosnia and Herzegovina
9.  Informatics and the Clinical Laboratory 
The Clinical Biochemist Reviews  2014;35(3):177-192.
The nature of pathology services is changing under the combined pressures of increasing workloads, cost constraints and technological advancement. In the face of this, laboratory systems need to meet new demands for data exchange with clinical electronic record systems for test requesting and results reporting. As these needs develop, new challenges are emerging especially with respect to the format and content of the datasets which are being exchanged. If the potential for the inclusion of intelligent systems in both these areas is to be realised, the continued dialogue between clinicians and laboratory information specialists is of paramount importance. Requirements of information technology (IT) in pathology, now extend well beyond the provision of purely analytical data. With the aim of achieving seamless integration of laboratory data into the total clinical pathway, ‘Informatics’ – the art and science of turning data into useful information – is becoming increasingly important in laboratory medicine. Informatics is a powerful tool in pathology – whether in implementing processes for pathology modernisation, introducing new diagnostic modalities (e.g. proteomics, genomics), providing timely and evidence-based disease management, or enabling best use of limited and often costly resources. Providing appropriate information to empowered and interested patients – which requires critical assessment of the ever-increasing volume of information available – can also benefit greatly from appropriate use of informatics in enhancing self-management of long term conditions. The increasing demands placed on pathology information systems in the context of wider developmental change in healthcare delivery are explored in this review. General trends in medical informatics are reflected in current priorities for laboratory medicine, including the need for unified electronic records, computerised order entry, data security and recovery, and audit. We conclude that there is a need to rethink the architecture of pathology systems and in particular to address the changed environment in which electronic patient record systems are maturing rapidly. The opportunity for laboratory-based informaticians to work collaboratively with clinical systems developers to embed clinically intelligent decision support systems should not be missed.
PMCID: PMC4204239  PMID: 25336763
10.  Cornell University Life Sciences Core Laboratories Center 
The Cornell University Life Sciences Core Laboratories Center (CLC) provides an array of genomics, proteomics, imaging and informatics shared research resources and services to the university community and to outside investigators. The CLC includes fee-for-service research, technology testing and development, and educational components. The Center has nine core facilities, including DNA sequencing and genotyping, microarrays, epigenomics, proteomics and mass spectrometry, high throughput screening, microscopy and imaging, mouse transgenics, bioinformatics, and bio-IT. The CLC is part of a New York State designated Center for Advanced Technology in Life Science Enterprise. The mission of the CLC is to promote research in the life sciences with advanced technologies in a shared resource environment. Use of the CLC resources and services is steadily increasing due to the growth in the number and types of cores in the center, to the expansion of exiting services and the implementation of new core technologies, and to the coordinated integration and synergy of services between the CLC cores. Multidisciplinary support for multi-functional instrument platforms is implemented by coordinated operations of the CLC core facilities. CLC core users are offered coordinated project consultations with the directors and staff of all relevant cores during the design, data production and analysis phases of their projects. The CLC is also involved in establishing and supporting multidisciplinary research projects that involve both intercampus initiatives and multi-institutional collaborations. With a concentration of advanced instrumentation and expertise in their applications, the CLC is a key resource for life sciences basic research and medical research for investigators at Cornell University and at other academic institutions and commercial enterprises.
PMCID: PMC2918124
11.  Using informatics to capture older adults’ wellness 
The aim of this paper is to demonstrate how informatics applications can support the assessment and visualization of older adults’ wellness. A theoretical framework is presented that informs the design of a technology enhanced screening platform for wellness. We highlight an ongoing pilot demonstration in an assisted living facility where a community room has been converted into a living laboratory for the use of diverse technologies (including a telehealth component to capture vital signs and customized questionnaires, a gait analysis component and cognitive assessment software) to assess the multiple aspects of wellness of older adults.
A demonstration project was introduced in an independent retirement community to validate our theoretical framework of informatics and wellness assessment for older adults. Subjects are being recruited to attend a community room and engage in the use of diverse technologies to assess cognitive performance, physiological and gait variables as well as psychometrics pertaining to social and spiritual components of wellness for a period of eight weeks. Data are integrated from various sources into one study database and different visualization approaches are pursued to efficiently display potential correlations between different parameters and capture overall trends of wellness.
Preliminary findings indicate that older adults are willing to participate in technology-enhanced interventions and embrace different information technology applications given appropriate and customized training and hardware and software features that address potential functional limitations and inexperience with computers.
Informatics can advance health care for older adults and support a holistic assessment of older adults’ wellness. The described framework can support decision making, link formal and informal caregiving networks and identify early trends and patterns that if addressed could reduce adverse health events.
PMCID: PMC4061974  PMID: 21482182
Health promotion; Aging; Informatics; Wellness; Function
12.  A Nursing Informatics Research Agenda for 2008–18: Contextual Influences and Key Components 
Nursing outlook  2008;56(5):206-214.e3.
The context for nursing informatics research has changed significantly since the National Institute of Nursing Research-funded Nursing Informatics Research Agenda was published in 1993 and the Delphi study of nursing informatics research priorities reported a decade ago. The authors focus on three specific aspects of context - genomic health care, shifting research paradigms, and social (Web 2.0) technologies - that must be considered in formulating a nursing informatics research agenda. These influences are illustrated using the significant issue of healthcare associated infections (HAI). A nursing informatics research agenda for 2008–18 must expand users of interest to include interdisciplinary researchers; build upon the knowledge gained in nursing concept representation to address genomic and environmental data; guide the reengineering of nursing practice; harness new technologies to empower patients and their caregivers for collaborative knowledge development; develop user-configurable software approaches that support complex data visualization, analysis, and predictive modeling; facilitate the development of middle-range nursing informatics theories; and encourage innovative evaluation methodologies that attend to human-computer interface factors and organizational context.
PMCID: PMC2613178  PMID: 18922269
13.  Case-based medical informatics 
The "applied" nature distinguishes applied sciences from theoretical sciences. To emphasize this distinction, we begin with a general, meta-level overview of the scientific endeavor. We introduce the knowledge spectrum and four interconnected modalities of knowledge. In addition to the traditional differentiation between implicit and explicit knowledge we outline the concepts of general and individual knowledge. We connect general knowledge with the "frame problem," a fundamental issue of artificial intelligence, and individual knowledge with another important paradigm of artificial intelligence, case-based reasoning, a method of individual knowledge processing that aims at solving new problems based on the solutions to similar past problems.
We outline the fundamental differences between Medical Informatics and theoretical sciences and propose that Medical Informatics research should advance individual knowledge processing (case-based reasoning) and that natural language processing research is an important step towards this goal that may have ethical implications for patient-centered health medicine.
We focus on fundamental aspects of decision-making, which connect human expertise with individual knowledge processing. We continue with a knowledge spectrum perspective on biomedical knowledge and conclude that case-based reasoning is the paradigm that can advance towards personalized healthcare and that can enable the education of patients and providers.
We center the discussion on formal methods of knowledge representation around the frame problem. We propose a context-dependent view on the notion of "meaning" and advocate the need for case-based reasoning research and natural language processing. In the context of memory based knowledge processing, pattern recognition, comparison and analogy-making, we conclude that while humans seem to naturally support the case-based reasoning paradigm (memory of past experiences of problem-solving and powerful case matching mechanisms), technical solutions are challenging.
Finally, we discuss the major challenges for a technical solution: case record comprehensiveness, organization of information on similarity principles, development of pattern recognition and solving ethical issues.
Medical Informatics is an applied science that should be committed to advancing patient-centered medicine through individual knowledge processing. Case-based reasoning is the technical solution that enables a continuous individual knowledge processing and could be applied providing that challenges and ethical issues arising are addressed appropriately.
PMCID: PMC544898  PMID: 15533257
14.  Safer electronic health records: Using the science of informatics to develop safety assessment guides 
Following the IOM report, “Health IT and Patient Safety: Building Safer Systems for Better Care,” the Office of the National Coordinator for Health Information Technology sponsored a project to address safety concerns in electronic health record-enabled (EHR) healthcare systems. To address the complexity of EHR-related errors and the difficulty in eliminating them, we designed the SAFER project (Safety Assurance Factors for EHR Resilience) to proactively identify potential safety issues and best practices for addressing them. We take into account the full sociotechnical context of EHR implementation and use. Our iterative work is grounded in several recently developed informatics-based scientific methods including: Review of scientific clinical informatics literatureUse of Rapid Assessment Process mixed-methods approaches developed for evaluating EHR-enabled healthcare systems in contextA semantic wiki for asynchronous collaborationAn 8-dimension socio-technical model of safe and effective EHR use
We are developing and piloting self-assessment “checklist-type” tools using a unique mix of methods based on the science of biomedical informatics. As the country continues its rapid EHR deployment, we believe that these tools are essential to ensure that the safety of the “EHR-enabled healthcare system” continues to improve.
PMCID: PMC3540559
15.  A Primer on Aspects of Cognition for Medical Informatics 
As a multidisciplinary field, medical informatics draws on a range of disciplines, such as computer science, information science, and the social and cognitive sciences. The cognitive sciences can provide important insights into the nature of the processes involved in human– computer interaction and help improve the design of medical information systems by providing insight into the roles that knowledge, memory, and strategies play in a variety of cognitive activities. In this paper, the authors survey literature on aspects of medical cognition and provide a set of claims that they consider to be important in medical informatics.
PMCID: PMC130077  PMID: 11418539
16.  An Overview of the CERC ARTEMIS Project 
The basic premise of this effort is that health care can be made more effective and affordable by applying modern computer technology to improve collaboration among diverse and distributed health care providers.
Information sharing, communication, and coordination are basic elements of any collaborative endeavor. In the health care domain, collaboration is characterized by cooperative activities by health care providers to deliver total and real-time care for their patients. Communication between providers and managed access to distributed patient records should enable health care providers to make informed decisions about their patients in a timely manner. With an effective medical information infrastructure in place, a patient will be able to visit any health care provider with access to the network, and the provider will be able to use relevant information from even the last episode of care in the patient record. Such a patient-centered perspective is in keeping with the real mission of health care providers.
Today, an easy-to-use, integrated health care network is not in place in any community, even though current technology makes such a network possible. Large health care systems have deployed partial and disparate systems that address different elements of collaboration. But these islands of automation have not been integrated to facilitate cooperation among health care providers in large communities or nationally.
CERC and its team members at Valley Health Systems, Inc., St. Marys Hospital and Cabell Huntington Hospital form a consortium committed to improving collaboration among the diverse and distributed providers in the health care arena. As the first contract recipient of the multi-agency High Performance Computing and Communications (HPCC) Initiative, this team of computer system developers, practicing rural physicians, community care groups, health care researchers, and tertiary care providers are using research prototypes and commercial off-the-shelf technologies to develop an open collaboration environment for the health care domain. This environment is called ARTEMIS — Advanced Research TEstbed for Medical InformaticS.
PMCID: PMC2579046  PMID: 8563249
17.  Bioinformatics and Medical Informatics: Collaborations on the Road to Genomic Medicine? 
In this report, the authors compare and contrast medical informatics (MI) and bioinformatics (BI) and provide a viewpoint on their complementarities and potential for collaboration in various subfields. The authors compare MI and BI along several dimensions, including: (1) historical development of the disciplines, (2) their scientific foundations, (3) data quality and analysis, (4) integration of knowledge and databases, (5) informatics tools to support practice, (6) informatics methods to support research (signal processing, imaging and vision, and computational modeling, (7) professional and patient continuing education, and (8) education and training. It is pointed out that, while the two disciplines differ in their histories, scientific foundations, and methodologic approaches to research in various areas, they nevertheless share methods and tools, which provides a basis for exchange of experience in their different applications. MI expertise in developing health care applications and the strength of BI in biological “discovery science” complement each other well. The new field of biomedical informatics (BMI) holds great promise for developing informatics methods that will be crucial in the development of genomic medicine. The future of BMI will be influenced strongly by whether significant advances in clinical practice and biomedical research come about from separate efforts in MI and BI, or from emerging, hybrid informatics subdisciplines at their interface.
PMCID: PMC264428  PMID: 12925552
18.  Using computer decision support systems in NHS emergency and urgent care: ethnographic study using normalisation process theory 
Information and communication technologies (ICTs) are often proposed as ‘technological fixes’ for problems facing healthcare. They promise to deliver services more quickly and cheaply. Yet research on the implementation of ICTs reveals a litany of delays, compromises and failures. Case studies have established that these technologies are difficult to embed in everyday healthcare.
We undertook an ethnographic comparative analysis of a single computer decision support system in three different settings to understand the implementation and everyday use of this technology which is designed to deal with calls to emergency and urgent care services. We examined the deployment of this technology in an established 999 ambulance call-handling service, a new single point of access for urgent care and an established general practice out-of-hours service. We used Normalization Process Theory as a framework to enable systematic cross-case analysis.
Our data comprise nearly 500 hours of observation, interviews with 64 call-handlers, and stakeholders and documents about the technology and settings. The technology has been implemented and is used distinctively in each setting reflecting important differences between work and contexts. Using Normalisation Process Theory we show how the work (collective action) of implementing the system and maintaining its routine use was enabled by a range of actors who established coherence for the technology, secured buy-in (cognitive participation) and engaged in on-going appraisal and adjustment (reflexive monitoring).
Huge effort was expended and continues to be required to implement and keep this technology in use. This innovation must be understood both as a computer technology and as a set of practices related to that technology, kept in place by a network of actors in particular contexts. While technologies can be ‘made to work’ in different settings, successful implementation has been achieved, and will only be maintained, through the efforts of those involved in the specific settings and if the wider context continues to support the coherence, cognitive participation, and reflective monitoring processes that surround this collective action. Implementation is more than simply putting technologies in place – it requires new resources and considerable effort, perhaps on an on-going basis.
PMCID: PMC3614561  PMID: 23522021
Computer technology; CDSS; Urgent care; Emergency care; Normalisation process theory
19.  Consumer Informatics in Chronic Illness 
Objective: To explore the informatic requirements in the home care of chronically ill patients.
Design: A number of strategies were deployed to help evoke a picture of home care informatics needs: A detailed questionnaire evaluating informational needs and assessing programmable technologies was distributed to a clinic population of parents of children with cancer. Open ended questionnaires were distributed to medical staff and parents soliciting a list of questions asked of medical staff. Parent procedure training was observed to evaluate the training dialog, and parents were observed interacting with a prototype information and education computer offering.
Results: Parents' concerns ranged from the details of managing day to day, to conceptual information about disease and treatment, to management of psychosocial problems. They sought information to solve problems and to provide emotional support, which may create conflicts of interest when the material is threatening. Whether they preferred to be informed by a doctor, nurse, or another parent depended on the nature of the information. Live interaction was preferred to video, which was preferred to text for all topics. Respondents used existing technologies in a straightforward way but were enthusiastic about the proposed use of computer technology to support home care. Multimedia solutions appear to complement user needs and preferences.
Conclusion: Consumers appear positively disposed toward on-line solutions. On-line systems can offer breadth, depth and timeliness currently unattainable. Patients should be involved in the formation and development process in much the same way that users are involved in usercentered computer interface design. A generic framework for patient content is presented that could be applied across multiple disorders.
PMCID: PMC61246  PMID: 9223035
20.  What Is eHealth (4): A Scoping Exercise to Map the Field 
Lack of consensus on the meaning of eHealth has led to uncertainty among academics, policymakers, providers and consumers. This project was commissioned in light of the rising profile of eHealth on the international policy agenda and the emerging UK National Programme for Information Technology (now called Connecting for Health) and related developments in the UK National Health Service.
To map the emergence and scope of eHealth as a topic and to identify its place within the wider health informatics field, as part of a larger review of research and expert analysis pertaining to current evidence, best practice and future trends.
Multiple databases of scientific abstracts were explored in a nonsystematic fashion to assess the presence of eHealth or conceptually related terms within their taxonomies, to identify journals in which articles explicitly referring to eHealth are contained and the topics covered, and to identify published definitions of the concept. The databases were Medline (PubMed), the Cumulative Index of Nursing and Allied Health Literature (CINAHL), the Science Citation Index (SCI), the Social Science Citation Index (SSCI), the Cochrane Database (including Dare, Central, NHS Economic Evaluation Database [NHS EED], Health Technology Assessment [HTA] database, NHS EED bibliographic) and ISTP (now known as ISI proceedings).We used the search query, “Ehealth OR e-health OR e*health”. The timeframe searched was 1997-2003, although some analyses contain data emerging subsequent to this period. This was supplemented by iterative searches of Web-based sources, such as commercial and policy reports, research commissioning programmes and electronic news pages. Definitions extracted from both searches were thematically analyzed and compared in order to assess conceptual heterogeneity.
The term eHealth only came into use in the year 2000, but has since become widely prevalent. The scope of the topic was not immediately discernable from that of the wider health informatics field, for which over 320000 publications are listed in Medline alone, and it is not explicitly represented within the existing Medical Subject Headings (MeSH) taxonomy. Applying eHealth as narrative search term to multiple databases yielded 387 relevant articles, distributed across 154 different journals, most commonly related to information technology and telemedicine, but extending to such areas as law. Most eHealth articles are represented on Medline. Definitions of eHealth vary with respect to the functions, stakeholders, contexts and theoretical issues targeted. Most encompass a broad range of medical informatics applications either specified (eg, decision support, consumer health information) or presented in more general terms (eg, to manage, arrange or deliver health care). However the majority emphasize the communicative functions of eHealth and specify the use of networked digital technologies, primarily the Internet, thus differentiating eHealth from the field of medical informatics. While some definitions explicitly target health professionals or patients, most encompass applications for all stakeholder groups. The nature of the scientific and broader literature pertaining to eHealth closely reflects these conceptualizations.
We surmise that the field – as it stands today – may be characterized by the global definitions suggested by Eysenbach and Eng.
PMCID: PMC1550637  PMID: 15829481
eHealth; Internet; telemedicine; medical informatics
21.  Educational Technologies in Problem-Based Learning in Health Sciences Education: A Systematic Review 
As a modern pedagogical philosophy, problem-based learning (PBL) is increasingly being recognized as a major research area in student learning and pedagogical innovation in health sciences education. A new area of research interest has been the role of emerging educational technologies in PBL. Although this field is growing, no systematic reviews of studies of the usage and effects of educational technologies in PBL in health sciences education have been conducted to date.
The aim of this paper is to review new and emerging educational technologies in problem-based curricula, with a specific focus on 3 cognate clinical disciplines: medicine, dentistry, and speech and hearing sciences. Analysis of the studies reviewed focused on the effects of educational technologies in PBL contexts while addressing the particular issue of scaffolding of student learning.
A comprehensive computerized database search of full-text articles published in English from 1996 to 2014 was carried out using 3 databases: ProQuest, Scopus, and EBSCOhost. Eligibility criteria for selection of studies for review were also determined in light of the population, intervention, comparison, and outcomes (PICO) guidelines. The population was limited to postsecondary education, specifically in dentistry, medicine, and speech and hearing sciences, in which PBL was the key educational pedagogy and curriculum design. Three types of educational technologies were identified as interventions used to support student inquiry: learning software and digital learning objects; interactive whiteboards (IWBs) and plasma screens; and learning management systems (LMSs).
Of 470 studies, 28 were selected for analysis. Most studies examined the effects of learning software and digital learning objects (n=20) with integration of IWB (n=5) and LMS (n=3) for PBL receiving relatively less attention. The educational technologies examined in these studies were seen as potentially fit for problem-based health sciences education. Positive outcomes for student learning included providing rich, authentic problems and/or case contexts for learning; supporting student development of medical expertise through the accessing and structuring of expert knowledge and skills; making disciplinary thinking and strategies explicit; providing a platform to elicit articulation, collaboration, and reflection; and reducing perceived cognitive load. Limitations included cumbersome scenarios, infrastructure requirements, and the need for staff and student support in light of the technological demands of new affordances.
This literature review demonstrates the generally positive effect of educational technologies in PBL. Further research into the various applications of educational technology in PBL curricula is needed to fully realize its potential to enhance problem-based approaches in health sciences education.
PMCID: PMC4275485  PMID: 25498126
systematic review; educational technologies; problem-based learning; medical education; health sciences; software; digital learning object; interactive whiteboard; learning management system
22.  Towards human-computer synergetic analysis of large-scale biological data 
BMC Bioinformatics  2013;14(Suppl 14):S10.
Advances in technology have led to the generation of massive amounts of complex and multifarious biological data in areas ranging from genomics to structural biology. The volume and complexity of such data leads to significant challenges in terms of its analysis, especially when one seeks to generate hypotheses or explore the underlying biological processes. At the state-of-the-art, the application of automated algorithms followed by perusal and analysis of the results by an expert continues to be the predominant paradigm for analyzing biological data. This paradigm works well in many problem domains. However, it also is limiting, since domain experts are forced to apply their instincts and expertise such as contextual reasoning, hypothesis formulation, and exploratory analysis after the algorithm has produced its results. In many areas where the organization and interaction of the biological processes is poorly understood and exploratory analysis is crucial, what is needed is to integrate domain expertise during the data analysis process and use it to drive the analysis itself.
In context of the aforementioned background, the results presented in this paper describe advancements along two methodological directions. First, given the context of biological data, we utilize and extend a design approach called experiential computing from multimedia information system design. This paradigm combines information visualization and human-computer interaction with algorithms for exploratory analysis of large-scale and complex data. In the proposed approach, emphasis is laid on: (1) allowing users to directly visualize, interact, experience, and explore the data through interoperable visualization-based and algorithmic components, (2) supporting unified query and presentation spaces to facilitate experimentation and exploration, (3) providing external contextual information by assimilating relevant supplementary data, and (4) encouraging user-directed information visualization, data exploration, and hypotheses formulation. Second, to illustrate the proposed design paradigm and measure its efficacy, we describe two prototype web applications. The first, called XMAS (Experiential Microarray Analysis System) is designed for analysis of time-series transcriptional data. The second system, called PSPACE (Protein Space Explorer) is designed for holistic analysis of structural and structure-function relationships using interactive low-dimensional maps of the protein structure space. Both these systems promote and facilitate human-computer synergy, where cognitive elements such as domain knowledge, contextual reasoning, and purpose-driven exploration, are integrated with a host of powerful algorithmic operations that support large-scale data analysis, multifaceted data visualization, and multi-source information integration.
The proposed design philosophy, combines visualization, algorithmic components and cognitive expertise into a seamless processing-analysis-exploration framework that facilitates sense-making, exploration, and discovery. Using XMAS, we present case studies that analyze transcriptional data from two highly complex domains: gene expression in the placenta during human pregnancy and reaction of marine organisms to heat stress. With PSPACE, we demonstrate how complex structure-function relationships can be explored. These results demonstrate the novelty, advantages, and distinctions of the proposed paradigm. Furthermore, the results also highlight how domain insights can be combined with algorithms to discover meaningful knowledge and formulate evidence-based hypotheses during the data analysis process. Finally, user studies against comparable systems indicate that both XMAS and PSPACE deliver results with better interpretability while placing lower cognitive loads on the users. XMAS is available at: PSPACE is available at:
PMCID: PMC3851181  PMID: 24267485
23.  Applications of the pipeline environment for visual informatics and genomics computations 
BMC Bioinformatics  2011;12:304.
Contemporary informatics and genomics research require efficient, flexible and robust management of large heterogeneous data, advanced computational tools, powerful visualization, reliable hardware infrastructure, interoperability of computational resources, and detailed data and analysis-protocol provenance. The Pipeline is a client-server distributed computational environment that facilitates the visual graphical construction, execution, monitoring, validation and dissemination of advanced data analysis protocols.
This paper reports on the applications of the LONI Pipeline environment to address two informatics challenges - graphical management of diverse genomics tools, and the interoperability of informatics software. Specifically, this manuscript presents the concrete details of deploying general informatics suites and individual software tools to new hardware infrastructures, the design, validation and execution of new visual analysis protocols via the Pipeline graphical interface, and integration of diverse informatics tools via the Pipeline eXtensible Markup Language syntax. We demonstrate each of these processes using several established informatics packages (e.g., miBLAST, EMBOSS, mrFAST, GWASS, MAQ, SAMtools, Bowtie) for basic local sequence alignment and search, molecular biology data analysis, and genome-wide association studies. These examples demonstrate the power of the Pipeline graphical workflow environment to enable integration of bioinformatics resources which provide a well-defined syntax for dynamic specification of the input/output parameters and the run-time execution controls.
The LONI Pipeline environment provides a flexible graphical infrastructure for efficient biomedical computing and distributed informatics research. The interactive Pipeline resource manager enables the utilization and interoperability of diverse types of informatics resources. The Pipeline client-server model provides computational power to a broad spectrum of informatics investigators - experienced developers and novice users, user with or without access to advanced computational-resources (e.g., Grid, data), as well as basic and translational scientists. The open development, validation and dissemination of computational networks (pipeline workflows) facilitates the sharing of knowledge, tools, protocols and best practices, and enables the unbiased validation and replication of scientific findings by the entire community.
PMCID: PMC3199760  PMID: 21791102
24.  RES6/466: Toward a Discovery Support System Based on Medical and Health Unifying Principles to Formulate Recombinant Hypotheses through Internet Online Databases 
Since the 17-century, scientists have been enquiring for the logical scientific principles of medicine and informatics, among other disciplines, encouraged by the instance of Newtonian physics. In the 20-century, the main principles of informatics were found making possible the development of present computers & Internet. However, very little research has been done seeking medical & health scientific principles, allowing among other functions, assistance in scientific hypotheses formation beside empirical data. One important effort on hypothesis formulation, has been the running of the Arrowsmith system of software and database search strategies at (Swanson & Smalheiser, 1997), which evokes hypothesis using the relational structure of the NCBI PubMed Internet on-line database (1966-). Nevertheless, although it uses a powerful logical mathematical method, it does not include any logical scientific principle from experimental or clinical medicine, & public health sciences. The aim of this paper is to give an outline of the design & rationale of an international collaborative research, complementary to Arrowsmith system, whose outcomes would be the logical basis of content seeking a more rational discovery support system.
Crucial fragmented information of multiple specialities and cognitive levels, synthesised by an international cross-disciplinary team or teams of experts, through a complex inductive method using Internet research facilities.
Expected Results:
Medical & health unifying principles that would perfect Arrowsmith target search strategies or other formal discovery computer-assisted systems to formulate recombinant hypotheses, using PubMed on-line database, and even in the future, the NCBI E-Biomed Internet on-line database proposed at (Varmus, Lipman & Brown, 1999). The perfected system will complete then, the premises to receive the benefits of Artificial Intelligence concepts & tools, to continue its improving.
PMCID: PMC1761764
Unifying Principles; Inductive Method; Hypothesis Formulation; Internet; Discover Support System
25.  A collaborative design method to support integrated care. An ICT development method containing continuous user validation improves the entire care process and the individual work situation 
Integrated care involves different professionals, belonging to different care provider organizations and requires immediate and ubiquitous access to patient-oriented information, supporting an integrated view on the care process [1].
To present a method for development of usable and work process-oriented information and communication technology (ICT) systems for integrated care.
Theory and method
Based on Human-computer Interaction Science and in particular Participatory Design [2], we present a new collaborative design method in the context of health information systems (HIS) development [3]. This method implies a thorough analysis of the entire interdisciplinary cooperative work and a transformation of the results into technical specifications, via user validated scenarios, prototypes and use cases, ultimately leading to the development of appropriate ICT for the variety of occurring work situations for different user groups, or professions, in integrated care.
Results and conclusions
Application of the method in homecare of the elderly resulted in an HIS that was well adapted to the intended user groups. Conducted in multi-disciplinary seminars, the method captured and validated user needs and system requirements for different professionals, work situations, and environments not only for current work; it also aimed to improve collaboration in future (ICT supported) work processes. A holistic view of the entire care process was obtained and supported through different views of the HIS for different user groups, resulting in improved work in the entire care process as well as for each collaborating profession [4].
PMCID: PMC2807103
ICT development method; participatory design; interdisciplinary cooperative work; user validation

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