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PubMed2005

KEGG as a glycome informatics resource.

Bioinformatics approaches to carbohydrate research have recently begun using large amounts of protein and carbohydrate data. In this field called glycome informatics, the foremost necessity is a comprehensive resource for genome-scale bioinformatics analysis of glycan data. Although the accumulation of experimental data may be useful as a reference of biological and biochemical information on carbohydrates, this is insufficient for bioinformatics analysis. Thus, we have developed a glycome informatics resource (http://www.genome.jp/kegg/glycan/) in KEGG (Kyoto Encyclopedia of Genes and Genomes), an integrated knowledge base of protein networks, genomic information, and chemical information. This review describes three noteworthy features: (1) GLYCAN, a database of carbohydrate structures; (2) glycan-related pathways; and (3) Composite Structure Map (CSM), a map illustrating all possible variations of carbohydrate structures within organisms. GLYCAN includes two useful tools: an intuitive drawing tool called KegDraw, and an efficient glycan search and alignment tool called KEGG Carbohydrate Matcher (KCaM). KEGG's glycan biosynthesis and metabolism pathways, integrating carbohydrate structures, proteins, and reactions, are also a pivotal resource. CSM is constructed as a bridge between carbohydrate functions and structures. CSM is able to display, for example, expression data of glycosyltransferases in a compact manner. In all the KEGG resources, various objects including KEGG pathways, chemical compounds, as well as carbohydrate structures are commonly represented as graphs, which are widely studied and utilized in the computer science field.

Carbohydrates↗

PubMed1999

Home care nursing informatic guidelines.

Technology presents benefits and special challenges to home care nurses in their attempt to safeguard patients' rights. This article presents a set of home care informatic standards that can assist nurses in managing patient-sensitive information in computer networks and suggests ways to avoid risks while using informatics.

Community Health Nursing↗

PubMed1997

Re-engineering intensive care: the role of informatics.

Managed care and quality improvement are two driving forces in the current health care environment. The pressure of capitation and the recent focus on outcomes of care have generated new incentives to restructure care delivery to control costs. Intensive care units, once revenue centers, are becoming cost centers. Re-engineering, or redesigning, the process of care entails examining premises for ability to provide services as well as considering how to do things more efficiently. The assumption is that all aspects of a process are legitimately subject to examination and restructuring. Information systems provide a powerful tool to support re-engineering. Nursing informatics, which pertains to nursing data, information, and knowledge has major implications for hospital information systems. This article explores possible changes in intensive care and the role of informatics in a changing health care environment.

Hospital Information Systems↗

PubMed1989

The study of nursing informatics.

A framework for organizing the study of nursing informatics is presented. The management and processing of nursing data, information science and nursing science is proposed as an area for study. The premises for such study and the key concepts and relationships are discussed. Nursing informatics would support the practice of nursing and delivery of nursing care.

Education, Nursing↗

PubMed2003

Informatics and quantitative analysis in biological imaging.

Biological imaging is now a quantitative technique for probing cellular structure and dynamics and is increasingly used for cell-based screens. However, the bioinformatics tools required for hypothesis-driven analysis of digital images are still immature. We are developing the Open Microscopy Environment (OME) as an informatics solution for the storage and analysis of optical microscope image data. OME aims to automate image analysis, modeling, and mining of large sets of images and specifies a flexible data model, a relational database, and an XML-encoded file standard that is usable by potentially any software tool. With this design, OME provides a first step toward biological image informatics.

Algorithms↗

PubMedDate not supplied

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 user-centered computer interface design. A generic framework for patient content is presented that could be applied across multiple disorders.

Adaptation, Psychological↗

PubMedDate not supplied

The Unified Medical Language System: an informatics research collaboration.

In 1986, the National Library of Medicine (NLM) assembled a large multidisciplinary, multisite team to work on the Unified Medical Language System (UMLS), a collaborative research project aimed at reducing fundamental barriers to the application of computers to medicine. Beyond its tangible products, the UMLS Knowledge Sources, and its influence on the field of informatics, the UMLS project is an interesting case study in collaborative research and development. It illustrates the strengths and challenges of substantive collaboration among widely distributed research groups. Over the past decade, advances in computing and communications have minimized the technical difficulties associated with UMLS collaboration and also facilitated the development, dissemination, and use of the UMLS Knowledge Sources. The spread of the World Wide Web has increased the visibility of the information access problems caused by multiple vocabularies and many information sources which are the focus of UMLS work. The time is propitious for building on UMLS accomplishments and making more progress on the informatics research issues first highlighted by the UMLS project more than 10 years ago.

Computer Communication Networks↗

PubMed2003

Initiating informatics and GIS support for a field investigation of Bioterrorism: The New Jersey anthrax experience.

BACKGROUND: The investigation of potential exposure to anthrax spores in a Trenton, New Jersey, mail-processing facility required rapid assessment of informatics needs and adaptation of existing informatics tools to new physical and information-processing environments. Because the affected building and its computers were closed down, data to list potentially exposed persons and map building floor plans were unavailable from the primary source. RESULTS: Controlling the effects of anthrax contamination required identification and follow-up of potentially exposed persons. Risk of exposure had to be estimated from the geographic relationship between work history and environmental sample sites within the contaminated facility. To assist in establishing geographic relationships, floor plan maps of the postal facility were constructed in ArcView Geographic Information System (GIS) software and linked to a database of personnel and visitors using Epi Info and Epi Map 2000. A repository for maintaining the latest versions of various documents was set up using Web page hyperlinks. CONCLUSIONS: During public health emergencies, such as bioterrorist attacks and disease epidemics, computerized information systems for data management, analysis, and communication may be needed within hours of beginning the investigation. Available sources of data and output requirements of the system may be changed frequently during the course of the investigation. Integrating data from a variety of sources may require entering or importing data from a variety of digital and paper formats. Spatial representation of data is particularly valuable for assessing environmental exposure. Written documents, guidelines, and memos important to the epidemic were frequently revised. In this investigation, a database was operational on the second day and the GIS component during the second week of the investigation.

Journal Article↗

PubMed2005

On geography and medical journalology: a study of the geographical distribution of articles published in a leading medical informatics journal between 1999 and 2004.

BACKGROUND: Studying the contribution of individual countries to leading journals in a given discipline can highlight which countries have the most impact on that discipline, and also give some idea about the geographical outreach of those journals. This paper examines the number of countries that contributed articles to one leading medical informatics journal, Medical Informatics & the Internet in Medicine, and the amount of their contributions between 1999 and the first half of 2004. METHODS: The PubMed citations of all indexed articles from the chosen journal (n = 128) were retrieved online (up to Volume 29, Number 2/June 2004 issue, the latest indexed issue as at 28 January 2005). The country of corresponding author's affiliation for each retrieved citation was recorded. The five-year-and-half corpus of abstracts retrieved from PubMed was further explored using MetaCarta Geographic Text Search http://www.metacarta.com/. RESULTS: The examined journal has an international outreach, with authors from 24 countries, spanning four continents, contributing to the journal during the studied period. The journal is dominated by a very large number of articles from Europe (81.25% of all articles counted in this study), and in particular from the UK (15.63%) and Greece (15.63%). There were no contributions from Africa or South America. CONCLUSION: A detailed discussion and interpretation of these results and ideas for future analyses are provided. MetaCarta can prove very useful as a bibliometric research tool.

Journal Article↗

PubMed2003

Integration of telemedicine in graduate medical informatics education.

An essential part of health informatics is telemedicine, the use of advanced telecommunications technologies to bridge distance and support health care delivery and education. This report discusses the integration of telemedicine into a medical informatics curriculum and, specifically, a framework for a telemedicine course. Within this framework, the objectives and exit competencies are presented and course sections are described: definitions, introduction to technical aspects of telemedicine, evolution of telemedicine and its impact on health care delivery, success and failure factors, and legal and ethical issues. The emphasis is on literature review tools, practical exposure to products and applications, and problem-based learning. Given the rapid advances in the telecommunication field, keeping the course material up to date becomes a challenge for the instructor who at the same time aims to equip students with the knowledge and tools they will need in their future role as decision makers to detect a need for, design, implement, maintain, or evaluate a telemedicine application.

Cost Savings↗

PubMed2003

Informatics tools and medical communication: patient perspectives of "knowledge coupling" in primary care.

The use of various "informatics tools" for routine patient care promises to radically alter the ways whereby medical knowledge and information are processed and applied. In so doing, it can also change the nature of the information exchange and relational communication that occurs between patients and caregivers. This investigation examines how patients view "knowledge coupling" (KC) tools as they are routinely used in a "coupler-centered" family practice (CCP). How do patients view these tools as influencing information exchange and their relationship with caregivers? Based upon close- and open-ended questions of a random sample of patients in the CCP, this study found that most respondents viewed KC informatics tools as elevating the information exchange that occurs between patients and caregivers-increasing the extent to which patients are "heard and understood" by caregivers and come to "know and understand" what is ailing them. Many respondents report being empowered by the use of the tools, and having greater confidence in the care and advice caregivers offer. A few others, however, suggest diminished confidence in care and a more "impersonal" environment, resulting specifically from the use of the computer in the office. The article concludes by suggesting ways whereby such deficiencies might be remedied.

Adult↗

PubMed2004

Quantitative signature for architectural organization of regulatory factors using intranuclear informatics.

Regulatory machinery for replication and gene expression is punctately organized in supramolecular complexes that are compartmentalized in nuclear microenvironments. Quantitative approaches are required to understand the assembly of regulatory machinery within the context of nuclear architecture and to provide a mechanistic link with biological control. We have developed 'intranuclear informatics' to quantify functionally relevant parameters of spatially organized nuclear domains. Using this informatics strategy we have characterized post-mitotic reestablishment of focal subnuclear organization of Runx (AML/Cbfa) transcription factors in progeny cells. By analyzing point mutations that abrogate fidelity of Runx intranuclear targeting, we establish molecular determinants for the spatial order of Runx domains. Our novel approach provides evidence that architectural organization of Runx factors may be fundamental to their tissue-specific regulatory function.

Animals↗

PubMed2006

Applied medical informatics for the chest physician: information you can use!

The world of applied medical informatics is changing rapidly. This is the first of a three-part series of articles on applied medical informatics that will bring the practicing chest physician up to date on the structure, function, benefits, and drawbacks of the electronic medical record and all of its components, including the virtual ICU and the daily practice of medicine.

Decision Support Systems, Clinical↗

PubMed2003

How could primary care meet the informatics needs of UK Biobank? A Scottish proposal.

UK Biobank is an ambitious post-genomic project involving the recruitment and follow-up of 500 000 volunteers aged 45 to 69 years. Many primary care teams will be involved in the study directly or indirectly. The programme of research will use at least five data sources: paper-based questionnaires, blood samples, genotype information derived from the bloods, clinical/prescribing data from the medical records, and data on deaths. We describe three of the key challenges to primary care informatics posed by this project: patient recruitment, confidentiality, and data management. We then describe solutions proposed in Scotland, based on existing technologies. Some of these may be applicable elsewhere in the other Regional Collaborating Centres and other large-scale collaborative projects which rely on primary care informatics.

Aged↗

PubMed2004

Biomedical informatics: development of a comprehensive data warehouse for clinical and genomic breast cancer research.

The Windber Research Institute is an integrated high-throughput research center employing clinical, genomic and proteomic platforms to produce terabyte levels of data. We use biomedical informatics technologies to integrate all of these operations. This report includes information on a multi-year, multi-phase hybrid data warehouse project currently under development in the Institute. The purpose of the warehouse is to host the terabyte-level of internal experimentally generated data as well as data from public sources. We have previously reported on the phase I development, which integrated limited internal data sources and selected public databases. Currently, we are completing phase II development, which integrates our internal automated data sources and develops visualization tools to query across these data types. This paper summarizes our clinical and experimental operations, the data warehouse development, and the challenges we have faced. In phase III we plan to federate additional manual internal and public data sources and then to develop and adapt more data analysis and mining tools. We expect that the final implementation of the data warehouse will greatly facilitate biomedical informatics research.

Breast Neoplasms↗

PubMedDate not supplied

Medical image informatics infrastructure design and applications.

Picture archiving and communication systems (PACS) is a system integration of multimodality images and health information systems designed for improving the operation of a radiology department. As it evolves, PACS becomes a hospital image document management system with a voluminous image and related data file repository. A medical image informatics infrastructure can be designed to take advantage of existing data, providing PACS with add-on value for health care service, research, and education. A medical image informatics infrastructure (MIII) consists of the following components: medical images and associated data (including PACS database), image processing, data/knowledge base management, visualization, graphic user interface, communication networking, and application oriented software. This paper describes these components and their logical connection, and illustrates some applications based on the concept of the MIII.

Age Determination by Skeleton↗

PubMedDate not supplied

The new informatics of national healthcare reform.

The President's Health Security Act has succeeded in attracting America's attention. Several of its initiatives have been well-publicized and hotly debated in Congress. The act also includes a number of implications for healthcare informatics, and devotes an entire chapter to this subject, although this area has not received as much publicity. Every behavioral healthcare provider's information system would be significantly affected by enactment of the Health Security Act. Selected forms and data elements for the management and delivery of behavioral healthcare services would need to be standardized. Organizations of behavioral healthcare providers, managed care companies and purchasers would increasingly share selected patient and subscriber information in aggregated form, for a variety of purposes. As a result, tougher laws to protect patient data privacy will likely be forthcoming. The following article gives an overview of the informatics needs of the soon-to-be reformed American healthcare system, into which behavioral healthcare will be integrated. As part of the larger system, behavioral healthcare services and information systems will need to comply with the same guidelines and requirements, outlined below, as other healthcare providers. Preparation to meet the information demands of the evolving healthcare system will require adaptation of existing computerized information systems, utilization of new technology, consultation with the system's major shareholders and attention to continuous quality improvement processes.

Computer Communication Networks↗

PubMed1995

Capitation and informatics.

When physicians, hospitals, and allied health professionals bill for services they render, their information processing requirements are relatively simple, at least compared to those of capitated organizations. When payers (insurers or employers) accept financial risk for the health care services of beneficiaries, they have usually invested in claims processing, membership tracking, and, under managed care, utilization review and provider profiling systems. But payers, for the most part, have not invested in electronic collection of clinical information about beneficiaries, nor have they tended to keep all claims they have processed in electronic form for study after accounts are settled and payments disbursed. In this article, we will explore why informatics is so important to capitated organizations and why payers that have traditionally taken financial risk for insuring the health care costs of populations are also learning about the importance of informatics.

Capitation Fee↗