Showing papers on "Translational research informatics published in 2013"

Biomedical Informatics for Computer-Aided Decision Support Systems: A Survey

Abstract: The volumes of current patient data as well as their complexity make clinical decision making more challenging than ever for physicians and other care givers. This situation calls for the use of biomedical informatics methods to process data and form recommendations and/or predictions to assist such decision makers. The design, implementation, and use of biomedical informatics systems in the form of computer-aided decision support have become essential and widely used over the last two decades. This paper provides a brief review of such systems, their application protocols and methodologies, and the future challenges and directions they suggest.

Evidence Based Health Informatics: 10 Years of Efforts to Promote the Principle. Joint Contribution of IMIA WG EVAL and EFMI WG EVAL.

Abstract: Objectives: To present the importance of Evidence-based Health Informatics (EBHI) and the ethical imperative of this approach; to highlight the work of the IMIA Working Group on Technology Assessment and Quality Improvement and the EFMI Working Group on Assessment of Health Information Systems; and to introduce the further important evaluation and evidence aspects being addressed. Methods: Reviews of IMIA, EFMA and other initiatives, together with literature reviews on evaluation methods and on published systematic reviews. Results: Presentation of the rationale for the health informatics domain to adopt a scientific approach by assessing impact, avoiding harm, and empirically demonstrating benefit and best use; reporting of the origins and rationale of the IMIA- and EQUATOR-endorsed Statement on Reporting of Evaluation Studies in Health Informatics (STARE-HI) and of the IMIA WG's Guideline for Good Evaluation Practice in Health Informatics (GEP-HI); presentation of other initiatives for objective evaluation; and outlining of further work in hand on usability and indicators; together with the case for development of relevant evaluation methods in newer applications such as telemedicine. The focus is on scientific evaluation as a reliable source of evidence, and on structured presentation of results to enable easy retrieval of evidence. Conclusions: EBHI is feasible, necessary for efficiency and safety, and ethically essential. Given the significant impact of health informatics on health systems, care delivery and personal health, it is vital that cultures change to insist on evidence-based policies and investment, and that emergent global moves for this are supported.

Evolution of human factors research and studies of health information technologies: the role of patient safety.

Abstract: Evolution of Human Factors Research and Studies of Health Information Technologies: The Role of Patient Safety -

Health Care Transformation Through Collaboration on Open-Source Informatics Projects: Integrating a Medical Applications Platform, Research Data Repository, and Patient Summarization

Abstract: Background: The Strategic Health IT Advanced Research Projects (SHARP) program seeks to conquer well-understood challenges in medical informatics through breakthrough research. Two SHARP centers have found alignment in their methodological needs: (1) members of the National Center for Cognitive Informatics and Decision-making (NCCD) have developed knowledge bases to support problem-oriented summarizations of patient data, and (2) Substitutable Medical Apps, Reusable Technologies (SMART), which is a platform for reusable medical apps that can run on participating platforms connected to various electronic health records (EHR). Combining the work of these two centers will ensure wide dissemination of new methods for synthesized views of patient data. Informatics for Integrating Biology and the Bedside (i2b2) is an NIH-funded clinical research data repository platform in use at over 100 sites worldwide. By also working with a co-occurring initiative to SMART-enabling i2b2, we can confidently write one app that can be used extremely broadly.

Mathematical models for translational and clinical oncology

Abstract: In the context of translational and clinical oncology, mathematical models can provide novel insights into tumor-related processes and can support clinical oncologists in the design of the treatment regime, dosage, schedule, toxicity and drug-sensitivity. In this review we present an overview of mathematical models in this field beginning with carcinogenesis and proceeding to the different cancer treatments. By doing so we intended to highlight recent developments and emphasize the power of such theoretical work.

State of the art in clinical informatics: evidence and examples.

Abstract: Objective The field of clinical informatics has expanded substantially in the six decades since its inception. Early research focused on simple demonstrations that health information technology (HIT) such as electronic health records (EHRs), computerized provider order entry (CPOE), and clinical decision support (CDS) systems were feasible and potentially beneficial in clinical practice. Methods In this review, we present recent evidence on clinical informatics in the United States covering three themes: 1) clinical informatics systems and interventions for providers, including EHRs, CPOE, CDS, and health information exchange; 2) consumer health informatics systems, including personal health records and web-based and mobile HIT; and 3) methods and governance for clinical informatics, including EHR usability; data mining, text mining, natural language processing, privacy, and security. Results Substantial progress has been made in demonstrating that various clinical informatics methodologies and applications improve the structure, process, and outcomes of various facets of the healthcare system. Conclusion Over the coming years, much more will be expected from the field. As we move past the "early adopters" in Rogers' diffusion of innovations' curve through the "early majority" and into the "late majority," there will be a crucial need for new research methodologies and clinical applications that have been rigorously demonstrated to work (i.e., to improve health outcomes) in multiple settings with different types of patients and clinicians.

Global informetric perspective studies on translational medical research

Abstract: Translational medical research literature has increased rapidly in the last few decades and played a more and more important role during the development of medicine science. The main aim of this study is to evaluate the global performance of translational medical research during the past few decades. Bibliometric, social network analysis, and visualization technologies were used for analyzing translational medical research performance from the aspects of subject categories, journals, countries, institutes, keywords, and MeSH terms. Meanwhile, the co-author, co-words and cluster analysis methods were also used to trace popular topics in translational medical research related work. Research output suggested a solid development in translational medical research, in terms of increasing scientific production and research collaboration. We identified the core journals, mainstream subject categories, leading countries, and institutions in translational medical research. There was an uneven distribution of publications at authorial, institutional, and national levels. The most commonly used keywords that appeared in the articles were “translational research”, “translational medicine”, “biomarkers”, “stroke”, “inflammation”, “cancer”, and “breast cancer”. The subject categories of “Research & Experimental Medicine”, “Medical Laboratory Technology”, and “General & Internal Medicine” play a key role in translational medical research both in production and in its networks. Translational medical research and CTS, etc. are core journals of translational research. G7 countries are the leading nations for translational medical research. Some developing countries, such as P.R China, also play an important role in the communication of translational research. The USA and its institutions play a dominant role in the production, collaboration, citations and high quality articles. The research trends in translational medical research involve drug design and development, pathogenesis and treatment of disease, disease model research, evidence-based research, and stem and progenitor cells.

Survey of Clinical Data Mining Applications on Big Data in Health Informatics

Abstract: Every piece of information learned in human health has the potential to improve the length and quality of life for patients. However, the search for more knowledge in the domain of Health Informatics has led to vast quantities of data, far more than can be easily processed by researchers. Fortunately, Justas this problem of Big Data has begun to challenge advances in Health Informatics, so too can the data mining and machine learning techniques used for the general study of Big Data be brought to bear on the these problems. This paper will discuss recent studies done on Big Data Analytics in the field of Health Informatics which sought to answer various clinical questions, using data acquired from the molecular, tissue, and patient levels of Health Informatics. We also consider what work remains to be done in this area.

Evaluating various areas of process improvement in an effort to improve clinical research: discussions from the 2012 Clinical Translational Science Award (CTSA) Clinical Research Management workshop.

Abstract: Emphasis has been placed on assessing the efficiency of clinical and translational research as part of the National Institutes of Health (NIH) goal to "improve human health." Improvements identified and implemented by individual organizations cannot address the research infrastructure needs of all clinical and translational research conducted. NIH's National Center for Advancing Translational Sciences (NCATS) has brought together 61 Clinical and Translational Science Award (CTSA) sites creating a virtual national laboratory that reflects the diversity and breadth of academic medical centers to collectively improve clinical and translational science. The annual Clinical Research Management workshop is organized by the CTSA consortium with participation from CTSA awardees, NIH, and others with an interest in clinical research management. The primary objective of the workshop is to disseminate information that improves clinical research management although the specific objectives of each workshop evolve within the consortium. The fifth annual workshop entitled "Learning by doing; applying evidence-based tools to re-engineer clinical research management" took place in June 2012. The primary objective of the 2012 workshop was to utilize data to evaluate, modify, and improve clinical research management. This report provides a brief summary of the workshop proceedings and the major themes discussed among the participants.

Editorial: Special Issue on Health Informatics and Personalized Medicine

Abstract: The increasingly aging population, prevalence of chronic diseases and rising costs have brought about some unique healthcare challenges to our global society. In response to these unmet healthcare needs, researchers are actively seeking for innovative solutions that target for 1) prevention of diseases and 2) personalized diagnosis and treatment. It is envisaged that by taking preventive measures for health monitoring and diagnosing and treating patients with a personalized approach at an early stage of disease development, healthcarewill be more cost effective and sustainable. Engineers, computer scientists, as well as information and communication technologists all have their respective unique roles in this future health model. The authors provide an overview of the advancements in information and communication technologies (ICT), and explain how some innovative health solutions can now be delivered to individuals at a relatively low cost.

Epilepsy informatics and an ontology-driven infrastructure for large database research and patient care in epilepsy.

Abstract: The epilepsy community increasingly recognizes the need for a modern classification system that can also be easily integrated with effective informatics tools. The 2010 reports by the United States President's Council of Advisors on Science and Technology (PCAST) identified informatics as a critical resource to improve quality of patient care, drive clinical research, and reduce the cost of health services. An effective informatics infrastructure for epilepsy, which is underpinned by a formal knowledge model or ontology, can leverage an ever increasing amount of multimodal data to improve (1) clinical decision support, (2) access to information for patients and their families, (3) easier data sharing, and (4) accelerate secondary use of clinical data. Modeling the recommendations of the International League Against Epilepsy (ILAE) classification system in the form of an epilepsy domain ontology is essential for consistent use of terminology in a variety of applications, including electronic health records systems and clinical applications. In this review, we discuss the data management issues in epilepsy and explore the benefits of an ontology-driven informatics infrastructure and its role in adoption of a “data-driven” paradigm in epilepsy research.

Biomedical Informatics: We Are What We Publish

Abstract: Introduction: This article is part of a For-Discussion-Section of Methods of Information in Medicine on “Biomedical Informatics: We are what we publish“. It is introduced by an editorial and followed by a commentary paper with invited comments. In subsequent issues the discussion may continue through letters to the editor. Objective: Informatics experts have attempted to define the field via consensus projects which has led to consensus statements by both AMIA. and by IMIA. We add to the output of this process the results of a study of the Pubmed publications with abstracts from the field of Biomedical Informatics. Methods: We took the terms from the AMIA consensus document and the terms from the IMIA definitions of the field of Biomedical Informatics and combined them through human review to create the Health Informatics Ontology. We built a terminology server using the Intelligent Natural Language Processor (iNLP). Then we downloaded the entire set of articles in Medline identified by searching the literature by “Medical Informatics” OR “Bioinformatics”. The articles were parsed by the joint AMIA / IMIA terminology and then again using SNOMED CT and for the Bioinformatics they were also parsed using HGNC Ontology. Results: We identified 153,580 articles using “Medical Informatics” and 20,573 articles using “Bioinformatics”. This resulted in 168,298 unique articles and an overlap of 5,855 articles. Of these 62,244 articles (37%) had titles and abstracts that contained at least one concept from the Health Informatics Ontology. SNOMED CT indexing showed that the field interacts with most all clinical fields of medicine. Conclusions: Further defining the field by what we publish can add value to the consensus driven processes that have been the mainstay of the efforts to date. Next steps should be to extract terms from the literature that are uncovered and create class hierarchies and relationships for this content. We should also examine the high occurring of MeSH terms as markers to define Biomedical Informatics. Greater understanding of the Biomedical Informatics Literature has the potential to lead to improved self-awareness for our field.

Implementation of the CDC translational informatics platform - from genetic variants to the national Swedish Rheumatology Quality Register

Abstract: Background Sequencing of the human genome and the subsequent analyses have produced immense volumes of data. The technological advances have opened new windows into genomics beyond the DNA sequence. In parallel, clinical practice generate large amounts of data. This represents an underused data source that has much greater potential in translational research than is currently realized. This research aims at implementing a translational medicine informatics platform to integrate clinical data (disease diagnosis, diseases activity and treatment) of Rheumatoid Arthritis (RA) patients from Karolinska University Hospital and their research database (biobanks, genotype variants and serology) at the Center for Molecular Medicine, Karolinska Institutet.

Clinical research informatics: survey of recent advances and trends in a maturing field.

Abstract: Objectives To provide a survey of the field of clinical research informatics (CRI), focusing in particular on significant developments over the past 3 years and the insights they provide about the progress and state of the field. Methods An iterative "scoping review" of the literature published in scientific journals and conference proceedings that are relevant to CRI, from late 2009 to early 2013. Results 212 articles were identified, and 64 were selected to illustrate recent advances in the field. Based on those, six categories of CRI activity were identified: Data and Knowledge Management, Discovery and Standards; Clinical Data Re-Use for Research; Researcher Support and Resources; Participant Recruitment; Patients/Consumers and CRI; Policy, Regulatory and Fiscal Matters. Conclusions This survey demonstrates that the field of CRI has matured and is now well established. The ongoing work is essential to overcome many of the challenges the clinical research enterprise is facing and more work is needed. Even as work continues to establish necessary infrastructure, methods, and best practices, CRI researchers should strive for more rigorous study designs to evaluate the impacts of the work in the field. There is little doubt that the field is poised for rapid growth, and that the CRI literature will continue to reflect that growth in years to come.

Health Informatics and its practice: Emerging Domain of Information Science - Indian Scenario

Abstract: Health informatics is actually an integration of informatics and health or medical systems. Health informatics alternatively also referred as health information system. Informatics and health integration means application and utilization of informatics, computer and technological systems in health and medical systems, hospital, clinical houses, nursing home, pharmacy lab, clinical research lab and so on. Health information systems promotes the information transfer cycle chain and also boost the overall computerization and electronic documents. This paper deals with health computation and informatics. Here, we discuss the role, values and emerging challenges and opportunities of health information practice in India in contemporary scenario.

Library-based clinical and translational research support

Abstract: There has been a shift in the workflow at academic biomedical research and clinical care centers to promote more efficient clinical and community implementation of bench discoveries. Strong financial support for this effort is provided by the Clinical and Translational Science Awards (CTSAs) from the National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), awarded to about sixty biomedical research institutions constituting the CTSA Consortium [1]. CTSAs offer an opportunity to speed the translation of bench discoveries to improved human health by transforming the

Challenges facing translational research organizations in China: a qualitative multiple case study

Abstract: Translational medicine is attracting much attention worldwide and many translational research organizations (TROs) have been established. In China, translational medicine has developed rapidly, but faces many challenges. This study was aimed at exploring these challenges faced by emerging TROs in China. A qualitative, multiple case study approach was used to assess the challenges faced by TROs in China. Data were collected between May and August 2012. Eight cases were identified. Overall, four themes that characterized TROs in China emerged from analyses: 1. objectives, organizer, and funding resources, 2. participating partners and research teams, 3. management, and 4. achievements. All TROs had objectives related to translating basic discovery to clinic treatment and cultivating translational researchers. In terms of organizer and funding resources, 7 out of 8 TROs were launched only by universities and/or hospitals, and funded mostly through research grants. As for participating partners and multidisciplinary research teams, all but one of the TROs only involved biomedical research institutions who were interested in translational research, and characterized as clinical research centers; 7 out of 8 TROs involved only researchers from biomedicine and clinical disciplines and none involved disciplines related to education, ethnicity, and sociology, or engaged the community. Current management of the TROs were generally nested within the traditional research management paradigms, and failed to adapt to the tenets of translational research. Half of the TROs were at developmental stages defined as infrastructure construction and recruitment of translational researchers. TROs in China face the challenge of attracting sustainable funding sources, widening multidisciplinary cooperation, cultivating multi-disciplinary translational researchers and adapting current research management to translational research. Greater emphasis should be placed on increasing multidisciplinary cooperation, and innovating in education programs to cultivate of translational researchers. Efforts should be made to reform research management in TROs, and establish sustainable funding resources.

Usability Methods for Ensuring Health Information Technology Safety: Evidence-Based Approaches

Abstract: Usability Methods for Ensuring Health Information Technology Safety: Evidence-Based Approaches -

Knowledge management and informatics considerations for comparative effectiveness research: a case-driven exploration.

Abstract: BACKGROUND As clinical data are increasingly collected and stored electronically, their potential use for comparative effectiveness research (CER) grows. Despite this promise, challenges face those wishing to leverage such data. In this paper we aim to enumerate some of the knowledge management and informatics issues common to such data reuse. DESIGN After reviewing the current state of knowledge regarding biomedical informatics challenges and best practices related to CER, we then present 2 research projects at our institution. We analyze these and highlight several common themes and challenges related to the conduct of CER studies. Finally, we represent these emergent themes. RESULTS The informatics challenges commonly encountered by those conducting CER studies include issues related to data information and knowledge management (eg, data reuse, data preparation) as well as those related to people and organizational issues (eg, sociotechnical factors and organizational factors). Examples of these are described in further detail and a formal framework for describing these findings is presented. CONCLUSIONS Significant challenges face researchers attempting to use often diverse and heterogeneous datasets for CER. These challenges must be understood in order to be dealt with successfully and can often be overcome with the appropriate use of informatics best practices. Many research and policy questions remain to be answered in order to realize the full potential of the increasingly electronic clinical data available for such research.

Evidence-based Biomedical Informatics. The Long Way from Pioneer to Science.

Abstract: OBJECTIVES: An overview of current trends and achievements in building more evidence of using information sciences technologies in biomedical informatics. METHODS: Extensive search using PubMed for published papers in this field in 2012. A selection process organized in three steps: a) identification and first selection of papers; b) international peer-review by at least 4 reviewers for each paper; c) final selection of five papers by the editorial board of the Yearbook based on the international reviewing results and a balanced coverage of the topics. RESULTS: Synopsis of the articles selected for the IMIA Yearbook 2012 and an invited opinion paper written by leading scientists in this field. CONCLUSION: Evidence based health informatics is an important and ubiquitous trend in biomedical informatics. However, this research field has to be enhanced even further and, more importantly, achievements have to be put in practice.

A Systematic Literature Review Approach To Clinical Trial Informatics Systems: Case of caBIG and its Clinical Trial Management System

Abstract: An increased usage of clinical trial informatics systems will promote scientific institutions, benefit the worldwide research community, and assist in the rising trend of personalized medicine. This paper undertakes a systematic review to gain insight into existing studies on the Clinical Trial Informatics Systems (CTIS). In particular, we will focus on those articles that have worked on a special type of CTIS called the Cancer Biomedical Informatics Grid (caBIG), developed by the National Cancer Institute, and its Clinical Trial Management System (CTMS) workspace which uses Clinical Trials Suite software. Based on the 67 extracted studies from 2001-2011, we classified the literature into the 3 broad categories of product description, analysis of options, and user behaviour, each containing some subcategories, and provided insight into each category. Moreover, this paper presents insightful recommendations for health institutions to enable them ensure that the adoption and implementation of a clinical trials informatics systems such as caBIG/CTMS will be satisfactory. Finally, this article presents 5 important gaps in the literature and calls for future research to fill those gaps.

From genome sequencing to bedside. Findings from the section on bioinformatics and translational informatics.

Abstract: OBJECTIVES To summarize excellent current research in the field of Bioinformatics and Translational Informatics with application in the health domain and evidence-based medicine. METHOD We provide a synopsis of the articles selected for the IMIA Yearbook 2013, from which we attempt to derive a synthetic overview of current and future activities in the field. Three steps of selection were performed by querying PubMed and Web of Science. A first set of 5,549 articles was refined into a second set of 1,272 articles from which 15 articles were retained for peer-review. RESULTS The selection and evaluation process of this Yearbook's section on Bioinformatics and Translational Informatics yielded four excellent articles regarding the Human Genome and Medicine. Exploiting genomic data depends on having the appropriate reference annotation available. In the first article, the goal of the GENCODE Consortium is to produce and publish The GENCODE human reference gene set. As a result it is composed by merged manual and automatic annotations, which are frequently updated from public experimental databases. The quality of genome sequencing is platform-dependant. In the second article, a generic database independent from the sequencing technologies, Huvariome, can help to identify errors and inconsistencies in sequencing. To understand complex diseases of patients it will be of great importance to detect rare gene variants. This is the aim of the third study. Finally, in the last article, the plasma's DNA of healthy individual and patients suffering from cancer is compared. CONCLUSIONS The current research activities attest to the continuous convergence of Bioinformatics and Medical Informatics for clinical practice. For instance, a direct use of high throughput sequencing technologies for patients could aid the diagnosis of complex diseases (such as cancer) without invasive surgery (such as biopsy) but only with blood analysis. However, ongoing genomic tests will generate massive amounts of data and will imply new trends in the near future: "Big Data" and smart health management.

crcTRP: a translational research platform for colorectal cancer.

Abstract: Colorectal cancer is a leading cause of cancer mortality in both developed and developing countries. Transforming basic research results into clinical practice is one of the key tasks of translational research, which will greatly improve the diagnosis and treatments of colorectal cancer. In this paper, a translational research platform for colorectal cancer, named crcTRP, is introduced. crcTRP serves the colorectal cancer translational research by providing various types of biomedical information related with colorectal cancer to the community. The information, including clinical data, epidemiology data, individual omics data, and public omics data, was collected through a multisource biomedical information collection solution and then integrated in a clinic-omics database, which was constructed with EAV-ER model for flexibility and efficiency. A preliminary exploration of conducting translational research on crcTRP was implemented and worked out a set of clinic-genomic relations, linking clinical data with genomic data. These relations have also been applied to crcTRP to make it more conductive for cancer translational research.

Health informatics: Introduction

Abstract: T his issue of the Bulletin contains a suite of articles grounded in the emerging field of health informatics. While an earlier issue of the Bulletin contained a definition and introduction to the field

The patient-centric translational health record

Abstract: Challenges Current healthcare information technologies (HITs) do not provide electronic health records (EHRs) that are longitudinal and crossinstitutional, rather they attempt to federate medical records scattered across various healthcare providers where a patient was seen. HIT efforts regarding health records are focused on providing an ad hoc EHR, which often consists of sparse and semantically inconsistent clinical data, thus making it hard to achieve two of the main objectives of HITs; that is, to analyze the data in a meaningful way and to enable their semantic interoperability across disparate health-related information systems in both the clinical and research worlds [1].

Comment on “Time to Integrate Clinical and Research Informatics”

Abstract: The same code standards should be used in both research and clinical care to facilitate data integration across domains.