Field Of Biomedical Informatics Research Articles

Silver Anniversary: 25 Editions of the IMIA Yearbook.

To provide an editorial introduction into the special 25th anniversary edition of the IMIA Yearbook of Medical Informatics with discussion of the significance of the Yearbook, past and current editorial teams, and a look into the future. A brief overview of the 2016 anniversary edition of the Yearbook allows for a discussion of the significance and value of the Yearbook to the Biomedical Informatics community as well as a review of changes in Yearbook team and format over time. The IMIA Yearbook celebrates its 25th edition bearing witness to the quality of the IMIA brand, the Yearbook content, as well as to the dedication of and the inordinate amount of labor from the authors and editors of the Yearbook. Editorial teams are to be applauded for their hard work and for their foresight in steering the Yearbook from a paperback to an open access online publication. The special edition provides reviews of past editorials with the knowledge of today. The IMIA Yearbook celebrates a remarkable milestone providing a testament to the maturity of the Biomedical Informatics field. Informaticians across the world are encouraged to thank past editorial teams and celebrate with IMIA.

Developing new pathways into the biomedical informatics field: the AMIA High School Scholars Program.

Increasing access to biomedical informatics experiences is a significant need as the field continues to face workforce challenges. Looking beyond traditional medical school and graduate school pathways into the field is crucial for expanding the number of individuals and increasing diversity in the field. This case report provides an overview of the development and initial implementation of the American Medical Informatics Association (AMIA) High School Scholars Program. Initiated in 2014, the program's primary goal was to provide dissemination opportunities for high school students engaged in biomedical informatics research. We discuss success factors including strong cross-institutional, cross-organizational collaboration and the high quality of high school student submissions to the program. The challenges encountered, especially around working with minors and communicating program expectations clearly, are also discussed. Finally, we present the path forward for the continued evolution of the AMIA High School Scholars Program.

Developing the FARSEEING Taxonomy of Technologies: Classification and description of technology use (including ICT) in falls prevention studies

BackgroundRecent Cochrane reviews on falls and fall prevention have shown that it is possible to prevent falls in older adults living in the community and in care facilities. Technologies aimed at fall detection, assessment, prediction and prevention are emerging, yet there has been no consistency in describing or reporting on interventions using technologies. With the growth of eHealth and data driven interventions, a common language and classification is required. ObjectiveThe FARSEEING Taxonomy of Technologies was developed as a tool for those in the field of biomedical informatics to classify and characterise components of studies and interventions. MethodsThe Taxonomy Development Group (TDG) comprised experts from across Europe. Through face-to-face meetings and contributions via email, five domains were developed, modified and agreed: Approach; Base; Components of outcome measures; Descriptors of technologies; and Evaluation. Each domain included sub-domains and categories with accompanying definitions. The classification system was tested against published papers and further amendments undertaken, including development of an online tool. Six papers were classified by the TDG with levels of consensus recorded. ResultsTesting the taxonomy with papers highlighted difficulties in definitions across international healthcare systems, together with differences of TDG members’ backgrounds. Definitions were clarified and amended accordingly, but some difficulties remained. The taxonomy and manual were large documents leading to a lengthy classification process. The development of the online application enabled a much simpler classification process, as categories and definitions appeared only when relevant. Overall consensus for the classified papers was 70.66%. Consensus scores increased as modifications were made to the taxonomy. ConclusionThe FARSEEING Taxonomy of Technologies presents a common language, which should now be adopted in the field of biomedical informatics. In developing the taxonomy as an online tool, it has become possible to continue to develop and modify the classification system to incorporate new technologies and interventions.

A Survey of the Job Profiles of Biomedical Informatics Graduates.

In 2003, the University of São Paulo established the first Biomedical Informatics (BMI) undergraduate course in Brazil. Our mission is to provide undergraduate students with formal education on the fundamentals of BMI and its applied methods. This undergraduate course offers theoretical aspects, practical knowledge and scientifically oriented skills in the area of BMI, enab- ling students to contribute to research and methodical development in BMI. Course coordinators, professors and students frequently evaluate the BMI course and the curriculum to ensure that alumni receive quality higher education. This study investigates (i) the main job activities undertake by USP BMI graduates, (ii) subjects that are fundamental important for graduates to pursue a career in BMI, and (iii) the course quality perceived by the alumni. Use of a structured questionnaire to conduct a survey involving all the BMI graduates who received their Bachelor degree before July, 2015 (attempted n = 205). One hundred and forty-five graduates (71 %) answered the questionnaire. Nine out of ten of our former students currently work as informaticians. Seventy-six graduates (52 %) work within the biomedical informatics field. Fifty-five graduates (38 %) work outside the biomedical informatics field, but they work in other IT areas. Ten graduates (7 %) do not work with BMI or any other informatics activities, and four (3 %) are presently unemployed. Among the 145 surveyed BMI graduates, 46 (32 %) and seven (5 %) hold a Master's degree and a PhD degree, respectively. Database Systems, Software Engineering, Introduction to Computer Science, Object-Oriented Programming, and Data Structures are regarded as the most important subjects during the higher education course. The majority of the graduates (105 or 72 %) are satisfied with the BMI education and training they received during the undergraduate course. More than half of the graduates from our BMI course work in their primary education area. Besides technical adequacy, the diverse job profiles, and the high level of satisfaction of our graduates indicate the importance of undergraduate courses specialized in the BMI domain are of utmost importance.

Use of genetic algorithm for the selection of EEG features

Genetic Algorithm (GA) is a popular optimization technique that can detect the global optimum of a multivariable function containing several local optima. GA has been widely used in the field of biomedical informatics, especially in the context of designing decision support systems that classify biomedical signals or images into classes of interest. The aim of this paper is to present a methodology, based on GA, for the selection of the optimal subset of features that can be used for the efficient classification of Event Related Potentials (ERPs), which are recorded during the observation of correct or incorrect actions. In our experiment, ERP recordings were acquired from sixteen (16) healthy volunteers who observed correct or incorrect actions of other subjects. The brain electrical activity was recorded at 47 locations on the scalp. The GA was formulated as a combinatorial optimizer for the selection of the combination of electrodes that maximizes the performance of the Fuzzy C Means (FCM) classification algorithm. In particular, during the evolution of the GA, for each candidate combination of electrodes, the well-known (Σ, Φ, Ω) features were calculated and were evaluated by means of the FCM method. The proposed methodology provided a combination of 8 electrodes, with classification accuracy 93.8%. Thus, GA can be the basis for the selection of features that discriminate ERP recordings of observations of correct or incorrect actions.

Developing an Open-Source Bibliometric Ranking Website Using Google Scholar Citation Profiles for Researchers in the Field of Biomedical Informatics.

We developed the Biomedical Informatics Researchers ranking website (rank.informatics-review.com) to overcome many of the limitations of previous scientific productivity ranking strategies. The website is composed of four key components that work together to create an automatically updating ranking website: (1) list of biomedical informatics researchers, (2) Google Scholar scraper, (3) display page, and (4) updater. The site has been useful to other groups in evaluating researchers, such as tenure and promotions committees in interpreting the various citation statistics reported by candidates. Creation of the Biomedical Informatics Researchers ranking website highlights the vast differences in scholarly productivity among members of the biomedical informatics research community.

Note on Friedman's ‘what informatics is and isn't’: Figure 1

Friedman's article ‘What informatics is and isn't’,1 presents a necessary and timely analysis of the field of informatics. After defining some of its characteristics, training needs and also examples of what it isn't, the author re-introduces what he has called ‘the fundamental theorem of informatics’1—originally formulated for biomedical informatics—‘that persons supported by information technology will be better than the same persons performing the same task unassisted’. Figure 1 shows it graphically. Figure 1 Friedman's ‘fundamental theorem of informatics’.1 Both the theorem and the picture have become well known in the biomedical informatics field. However, while an interesting, thought-provoking exercise, this proposal about ‘what informatics is and isn't’ faces several scientific vulnerabilities, as noted below. The term ‘informatics’ derives from the German ‘Informatik’, the Russian ‘Informatika’ and the French ‘informatique’, which combines ‘information’ with ‘automatique’. One concept lies at its core: information. While it is clear how ‘informatics’ is semantically linked to ‘information’, what is meant by information is not so obvious: it can convey a wide range of meanings:

Biomedical Informatics: We Are What We Publish

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. 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. 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. 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. 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.

President's column: Informatics professionals—leading the way?

It was a proverbial shout out ! The October 2012 issue of Harvard Business Review literally screamed at me as I turned to page 70. The title of the article? ‘Data scientist: the sexiest job of the 21st century’1 (emphasis added). It appears that the geeks have come of age. I smiled. We have entered the decade of informatics for the healthcare field, and the data scientist phenomenon is nowhere more evident than in the field of biomedical informatics. Developments across the field have allowed us to reach a critical point of confluence which could radically alter the future direction of healthcare—at the intersection of incentives and data. Regardless of who wins the US presidential election, President Obama or Governor Romney, the Patient Protection and Affordable Care Act represents a remarkable piece of legislation that will no doubt change the incentives related to cost, quality, and service in care delivery. As a result of the legislation, we are moving in …

Biomedical Informatics Revolutionizing Changes in Health Care Delivery

The Symposium on Biomedical Informatics: Confluence of Multiple Disciplines held in Heidelberg, Germany at the University of Heidelberg s Internationales Wissenschaftsforum in 2011 reflected opportunities, challenges and priorities of organizing, representing and analyzing data, information and knowledge in biomedicine and health care. As an outcome of the symposium, five manuscripts were published in the journal Methods of Information in Medicine, Volume 50, No. 6, 2011. Biomedical Informatics is a discipline that has a great impact on many other fields and is also influenced by them. For this reasons biomedical informatics based on collaborative research brings new opportunities for revolutionizing changes in health care delivery. The aim of the editorial board of the European Journal for Biomedical Informatics (EJBI) is to reach the highest scientific level of the journal and to show the best practices of biomedical informatics applications to wide readership. It has been often important for health professionals to have the possibility to read important articles not only in English but also in their native language. For this reason EJBI publishes accepted peer-reviewed papers in English and other languages simultaneously. This opens new possibilities for faster transfer of scientific-research pieces of knowledge to a large international community of biomedical researches, physicians, other health personnel and citizens. Since 2012 (Volume 8) the European Journal for Biomedical Informatics begins to implement several changes, which will bring new opportunities for authors and readers. The journal publishes peer-reviewed original articles, review articles, reports, opinions papers and editorials in the field of biomedical informatics and applications in health care. EJBI provides immediate open access to peer-reviewed papers, which will be published in the running first issue of EJBI during each calendar year. The other issues of EJBI in each calendar year are EJBI approved special issues related to different biomedical informatics topics. Authors do not pay an article processing fee for the immediate release of peer-reviewed articles, but a small financial support is required in case that the support of projects or sponsors is acknowledged (see instructions to authors and ejbi-template). However, for further development of EJBI and its multilingual objectives we offer the possibility of sponsorship of single issues of EJBI (see more information here) to support dissemination of new information and knowledge in other languages than in English. Topics for special issues can be proposed to the editor-inchief of EJBI using the Proposal of EJBI special issue form for further processing. The topic for special issue is specified by an open call or by a special event. In the year 2012 we will publish two special issues based on open calls with special topics Support of eHealth Applications by Legal Systems in Europe and Standards and Solutions for eHealth Interoperability. The other special issues in 2012 will be directly connected with different events, e.g. conferences, symposia, workshops etc. We plan to prepare special issues connected with the MIE 2012 conference (Pisa, Italy, August 28-31, 2012) and with the Ph.D. students conference Semantic Interoperability in Biomedicine and Health Care (First Faculty of Medicine of Charles University in Prague, November 22, 2012). In the year 2013 we plan to have a special issue connected with the forthcoming EFMI special topic conference Data and Knowledge for Medical Decision Support (Prague, April 17-19, 2013). We invite you to propose special topics that would help to accelerate needed changes in health care by easy transfer of a new information and knowledge for health care delivery.

Computerized provider-order entry: challenges, achievements, and opportunities

The Merriam-Webster dictionary defines ‘traction’ as the adhesive friction of a body on a surface on which it moves.1 Within the field of biomedical informatics, we have updated that definition so that the ‘body’ may refer to a technological advance, and the ‘surface’ to a person, group, or environment in which the technological advance has been introduced. In this context, traction implies not just adoption, but adherence, or the ‘state of steady or faithful attachment’. By any measure, the past 5 years has witnessed the attainment of traction by computerized provider order entry (CPOE). Certainly, the work undertaken by the Institute of Medicine to position CPOE as the most critical component of a safe decision-making environment,2–5 leading to the eventual mandates for CPOE as a part of certified health information technology,6 justifies this assertion. The early efforts of informatics researchers such as McDonald,7 Miller et al ,8 Geissbuhler and Miller9 and Warner et … Correspondence to Dr Kevin Johnson, Biomedical Informatics, Vanderbilt University, 2209 Garland Avenue, Nashville, TN 37232, USA; kevin.johnson{at}vanderbilt.edu

Biomedical Informatics Techniques for Processing and Analyzing Web Blogs of Military Service Members

IntroductionWeb logs (“blogs”) have become a popular mechanism for people to express their daily thoughts, feelings, and emotions. Many of these expressions contain health care-related themes, both physical and mental, similar to information discussed during a clinical interview or medical consultation. Thus, some of the information contained in blogs might be important for health care research, especially in mental health where stress-related conditions may be difficult and expensive to diagnose and where early recognition is often key to successful treatment. In the field of biomedical informatics, techniques such as information retrieval (IR) and natural language processing (NLP) are often used to unlock information contained in free-text notes. These methods might assist the clinical research community to better understand feelings and emotions post deployment and the burden of symptoms of stress among US military service members.MethodsIn total, 90 military blog posts describing deployment situations and 60 control posts of Operation Enduring Freedom/Operation Iraqi Freedom (OEF/OIF) were collected. After “stop” word exclusion and stemming, a “bag-of-words” representation and term weighting was performed, and the most relevant words were manually selected out of the high-weight words. A pilot ontology was created using Collaborative Protégé, a knowledge management application. The word lists and the ontology were then used within General Architecture for Text Engineering (GATE), an NLP framework, to create an automated pipeline for recognition and analysis of blogs related to combat exposure. An independent expert opinion was used to create a reference standard and evaluate the results of the GATE pipeline.ResultsThe 2 dimensions of combat exposure descriptors identified were: words dealing with physical exposure and the soldiers’ emotional reactions to it. GATE pipeline was able to retrieve blog texts describing combat exposure with precision 0.9, recall 0.75, and F-score 0.82.DiscussionNatural language processing and automated information retrieval might potentially provide valuable tools for retrieving and analyzing military blog posts and uncovering military service members’ emotions and experiences of combat exposure.

Biomedical informatics and outcomes research: enabling knowledge-driven health care.

At its core, the practice of medicine is an information-intensive endeavor. Most of what physicians do involves the collection, review, and management of information. Examples of such activities include obtaining and recording patient information, consulting colleagues, reading the scientific literature, planning diagnostic procedures, devising strategies for patient care, interpreting tests, and conducting research. The ever-increasing biomedical knowledge base that must be considered to deliver optimal patient care only adds to the challenges facing medicine today. Successfully addressing these challenges to deliver the best health care possible requires not only the existence of valid and generalizable data sets derived from systematic basic, clinical, and epidemiological research efforts but also the ability to apply the knowledge derived from these research efforts at the point of care. It is easy to understand, therefore, why the field of biomedical informatics, a field that is concerned with collecting, managing, and optimally using information in health care and biomedicine, is critical to the current and future practice of medicine and the study of healthcare outcomes that result from such practice.1,2 Biomedical informatics approaches and related health information technology (health IT) platforms are key to enabling knowledge-driven healthcare and practice improvement initiatives based on a solid research foundation. Similar biomedical informatics approaches and resources are also critical to advancing outcomes research. Indeed, such technologies such as electronic health records (EHRs), clinical data repositories, and research-specific data management systems are already transforming the way we practice medicine and conduct research. This transformation is being further advanced by federally directed funding and research infrastructure development efforts.3,4 In the sections that follow, we provide an overview of how biomedical informatics and health IT processes and tools can affect the conduct of research and the delivery of evidence-based health care from our perspective. Given the current state of development …

Closing the Loops in Biomedical Informatics. Editorial

Summary Objectives To provide an editorial introduction to the 2009 IMIA Yearbook of Medical Informatics with an overview of its contents and contributors. Methods A brief overview of the main theme, and an outline of the purposes, contents, format, and acknowledgment of contributions for the 2009 IMIA Yearbook. Results This 2009 issue of the IMIA Yearbook highlights important, beneficial loops which, if closed, could lead to considerable advances in the field of biomedical informatics and, indirectly, in healthcare and biomedical research. Progress towards closing the loops and remaining gaps are identified from the recent literature, illustrated by selected papers published during the past 12 months. Conclusion Reviews and Surveys of the main research sub-fields in biomedical informatics in the Yearbook provide an overview of progress and current challenges across the spectrum of the discipline.

Inspiring Vanguards

Twice a year, the National Library of Medicine and Marine Biological Laboratory co-sponsor a fellowship in Biomedical Informatics for librarians, clinicians, and other health professionals in Woods Hole, MA. The fellowship is designed to inspire participants to become “agents of change” at their institution and to broaden their scope of knowledge for biomedical informatics. This paper discusses the field of biomedical informatics and explores the results of an informal survey from the librarians who participated in the fall session of 2005.

Biomedical Informatics Research and Education at the EuroMISE Center

In the paper we described the partial achievements reached by the EuroMISE Center in research and higher education, supporting better healthcare in future information society. Through the research cooperation, the EuroMISE Centre suggests publicly available tools and methods that allow the application of new technologies for various healthcare organizations and citizens, with a special focus on the national environment of the Czech Republic. It provides a platform for a greater level of research cooperation with the usage of the most up-to-date information and communication technologies and a wide spectrum of clinical and genetic data and knowledge. Results of research and higher education of the EuroMISE Centre in the field of Biomedical Informatics are described in outputs of national and European projects. Further results have been published and/or presented at national and international meetings and incorporated in education and healthcare practice. The long-term effect of postgraduate doctoral education in the field of biomedical informatics consists in the rapid increase of scientists that are needed in the Czech Republic to reach the goals of information society in health care. The multidisciplinary research at the EuroMISE Center moves towards direct usage in the informational support of diagnostics and therapy, mining of the medical databases, and in the customization of healthcare based on the clinical and genetic profile of a patient.

An information technology emphasis in biomedical informatics education

Unprecedented growth in the interdisciplinary domain of biomedical informatics reflects the recent advancements in genomic sequence availability, high-content biotechnology screening systems, as well as the expectations of computational biology to command a leading role in drug discovery and disease characterization. These forces have moved much of life sciences research almost completely into the computational domain. Importantly, educational training in biomedical informatics has been limited to students enrolled in the life sciences curricula, yet much of the skills needed to succeed in biomedical informatics involve or augment training in information technology curricula. This manuscript describes the methods and rationale for training students enrolled in information technology curricula in the field of biomedical informatics, which augments the existing information technology curriculum and provides training on specific subjects in Biomedical Informatics not emphasized in bioinformatics courses offered in life science programs, and does not require prerequisite courses in the life sciences.

Medical Informatics and Bioinformatics: Integration or Evolution through Scientific Crises?

To contribute a new perspective on recent investigations into the scientific foundations of medical informatics (MI) and bioinformatics (BI). To support efforts that could generate synergies and new research directions. MI and BI are compared and contrasted from a philosophy of science perspective. Historical examples from MI and BI are analyzed based on contrasting viewpoints about the evolution of scientific disciplines. Our analysis suggests that the scientific approaches of MI and BI involve different assumptions and foundations, which, together with largely non-overlapping communities of researchers for the two disciplines, have led to different courses of development. We indicate how their respective application domains, medicine, and biology may have contributed to these differences in development. An analysis from the point of view of the philosophy of science is characteristic of established scientific disciplines. From a Kuhnian perspective, both disciplines may be entering a period of scientific crisis, where their foundations are questioned and where new ideas (or paradigm shifts) and a progressive research programme are needed to advance them scientifically. We discuss research directions and trends both supporting and challenging integration of the subdisciplines of MI and BI into a unified field of biomedical informatics (BMI), centered around the evolution of information cybernetics.

The Full Spectrum of Biomedical Informatics Research and Education at OHSU

Although the biomedical informatics field is small relative to others in the life and health sciences, the breadth of subject domains, types of research, and occupations is vast. The biomedical informatics program at Oregon Health & Science University exemplifies the breadth in the field. At the center of our full spectrum of activities in informatics, however, is a core philosophy of the discipline that drives our research, educational, and other programs.

Clinical Informatics: Supporting the Use of Evidence in Practice and Relevance to Physical Therapy Education

Background. Clinical informatics is the subdiscipline of biomedical informatics that focuses on the representation, collection, retrieval, and use of health information in clinical practice. Purpose. This paper provides a general introduction to the field of biomedical informatics and recommends specific facets of clinical informatics that are germane to education programs in physical therapy. Position and Rationale. In light of the growing importance of information technology in health care, an understanding of clinical informatics is needed for physical therapy practitioners. Discussion. Many avenues and examples are available for incorporating clinical informatics training into the core curriculum of allied health programs. Conclusion. Instruction regarding applied aspects of clinical informatics needs to be considered as a component of a well-rounded education in physical therapy.