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Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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PubMed2003

Informatics systems to assess and apply clinical research on dental restorative materials.

Dental biomaterials are used clinically for one or more of the following purposes: to restore function, to enhance esthetics, and to prevent or arrest demineralization of tooth structure. Studies of the clinical performance of restorations and prostheses made from these materials have generally focused on quality assessment and survival statistics. Data from these studies should provide probabilities of specific treatment outcomes that are useful for practicing dentists. However, the utility of these data is limited by the lack of national and international standards for assessing these clinical outcomes. Standardized approaches toward clinical informatics and treatment-decision analysis are urgently needed to minimize the variability of clinical outcomes reported in publications associated with direct and indirect restorative materials used for dental restorations and prostheses.

Clinical Trials as Topic↗
PubMed2003

Integrating computationally assembled mouse transcript sequences with the Mouse Genome Informatics (MGI) database.

Databases of experimentally generated and computationally derived transcript sequences are valuable resources for genome analysis and annotation. The utility of such databases is enhanced when the sequences they contain are integrated with such biological information as genomic location, gene function, gene expression and phenotypic variation. We present the analysis and results of a semi-automated process of connecting transcript assemblies with highly curated biological information for mouse genes that is available through the Mouse Genome Informatics (MGI) database.

Animals↗
PubMed2005

The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging.

The Open Microscopy Environment (OME) defines a data model and a software implementation to serve as an informatics framework for imaging in biological microscopy experiments, including representation of acquisition parameters, annotations and image analysis results. OME is designed to support high-content cell-based screening as well as traditional image analysis applications. The OME Data Model, expressed in Extensible Markup Language (XML) and realized in a traditional database, is both extensible and self-describing, allowing it to meet emerging imaging and analysis needs.

Computational Biology↗
PubMed2004

Relational databases: a transparent framework for encouraging biology students to think informatically.

We discuss how relational databases constitute an ideal framework for representing and analyzing large-scale genomic data sets in biology. As a case study, we describe a Drosophila splice-site database that we recently developed at Wesleyan University for use in research and teaching. The database stores data about splice sites computed by a custom algorithm using Drosophila cDNA transcripts and genomic DNA and supports a set of procedures for analyzing splice-site sequence space. A generic Web interface permits the execution of the procedures with a variety of parameter settings and also supports custom structured query language queries. Moreover, new analytical procedures can be added by updating special metatables in the database without altering the Web interface. The database provides a powerful setting for students to develop informatic thinking skills.

Algorithms↗
PubMedDate not supplied

Design and analysis of controlled trials in naturally clustered environments: implications for medical informatics.

In medical informatics research, study questions frequently involve individuals who are grouped into clusters. For example, an intervention may be aimed at a clinician (who treats a cluster of patients) with the intention of improving the health of individual patients. Correlation among individuals within a cluster can lead to incorrect estimates of the sample size required to detect an effect and inappropriate estimates of the confidence intervals and the statistical significance of the intervention effects. Contamination, which is the spread of the effect of an intervention or control treatment to the opposite group, often occurs between individuals within clusters. It leads to an attenuation of the effect of the intervention and reduced power to detect a difference. If individuals are randomized in a clinical trial (individual-randomized trial), then correlation must be taken into account in the analysis, and the sample size may need to be increased to compensate for contamination. Randomizing clusters rather than individuals (cluster-randomized trials) can eliminate contamination and may be preferred for logistical reasons. Cluster-randomized trials are generally less efficient than individual-randomized trials, so the tradeoffs must be assessed. Correlation must be taken into account in the analysis and in the sample-size calculations for cluster-randomized trials.

Cluster Analysis↗
PubMedDate not supplied

Does national regulatory mandate of provider order entry portend greater benefit than risk for health care delivery? The 2001 ACMI debate. The American College of Medical Informatics.

The 2001 debate of the American College of Medical Informatics focused on the proposition that national regulatory mandate of computer-based provider order entry (CPOE), to take effect by the end of 2005, portends greater benefit than risk for health care delivery. Both sides accepted that provider order entry offers potential benefit. Those supporting the proposition emphasized public safety, noting that payers have little economic incentive to pay for quality and that a mandate would force vendors to improve the usability and value of their systems. They argued that the mandate would align the economic incentives to finally allow CPOE to be widely adopted. Those opposing the proposition emphasized the risks resulting from a mandate, including the direct implementation costs, the logistic issues of implementation, and the cost of failed implementations. They also noted the potential for errors introduced by the systems themselves and the fact that the safety and utility of commercially available CPOE products have yet to be proved.

Delivery of Health Care↗
PubMed2004

Toxicogenomics through the eyes of informatics: conference overview and recommendations.

Virginia Bioinformatics Institute, in conjunction with National Institutes of Environmental Health Sciences, hosted a conference, "Toxicogenomics through the Eyes of Informatics," in Bethesda, Maryland, USA, on 12-13 May 2003. Researchers around the world met to discuss how the application of bioinformatics tools, methodologies, and technologies will enhance our understanding of how cells and organisms respond to toxins. Conference topics included statistical methods, quantitative molecular data sets, computational algorithms for data analysis, computational modeling and simulation, challenges and opportunities in computational biology, and information technology infrastructure for data and tool management. This meeting report is a summary of conference presentations, survey results, current toxicogenomics concerns, and future directions of the toxicogenomics community. In conclusion this report discusses toxicogenomics as related to environmental agents, cell-chemical reactions, and gene-environment interactions.

Algorithms↗
PubMed2006

Applied medical informatics for the chest physician: information you can use!--Part 3.

In this third and last part in our series on applied medical informatics (AMI), we will examine the following: (1) a concise wrap-up of the practice steps necessary to achieve the benefits from AMI in your practice; (2) an introduction to the patient health-care record and why it is important to physicians; and (3) a look at some of the latest developments in AMI that are of interest to the chest physician.

Humans↗
PubMed2004

Gene expression informatics.

There are many methodologies for performing gene expression profiling on transcripts, and through their use scientists have been generating vast amounts of experimental data. Turning the raw experimental data into meaningful biological observation requires a number of processing steps; to remove noise, to identify the "true" expression value, normalize the data, compare it to reference data, and to extract patterns, or obtain insight into the underlying biology of the samples being measured. In this chapter we give a brief overview of how the raw data is processed, provide details on several data-mining methods, and discuss the future direction of expression informatics.

Animals↗
PubMed2003

The informatics of a C57BL/6J mouse brain atlas.

The Mouse Atlas Project (MAP) aims to produce a framework for organizing and analyzing the large volumes of neuroscientific data produced by the proliferation of genetically modified animals. Atlases provide an invaluable aid in understanding the impact of genetic manipulations by providing a standard for comparison. We use a digital atlas as the hub of an informatics network, correlating imaging data, such as structural imaging and histology, with text-based data, such as nomenclature, connections, and references. We generated brain volumes using magnetic resonance microscopy (MRM), classical histology, and immunohistochemistry, and registered them into a common and defined coordinate system. Specially designed viewers were developed in order to visualize multiple datasets simultaneously and to coordinate between textual and image data. Researchers can navigate through the brain interchangeably, in either a text-based or image-based representation that automatically updates information as they move. The atlas also allows the independent entry of other types of data, the facile retrieval of information, and the straight-forward display of images. In conjunction with centralized servers, image and text data can be kept current and can decrease the burden on individual researchers' computers. A comprehensive framework that encompasses many forms of information in the context of anatomic imaging holds tremendous promise for producing new insights. The atlas and associated tools can be found at http://www.loni.ucla.edu/MAP.

Anatomy, Artistic↗
PubMed2004

Informatics approaches to functional MRI odor mapping of the rodent olfactory bulb: OdorMapBuilder and OdorMapDB.

The present study applies informatics tools to aid and extend fMRI analysis of the coding mechanism of neural signals in the rodent olfactory system. Odor stimulation evokes unique spatial patterns of activity in the glomerular layer of the mammalian olfactory bulb (OB). An open-source software program, OdorMap-Builder, has been developed to process the high resolution anatomical and functional MRI images of the OB and to generate single two-dimensional flat maps, called odor maps, that describe the spatial activity patterns in the entire glomerular layer. Odor maps help identify the spatial activity patterns from the tremendous amount of fMRI data and they serve as ideal representation of space coding for the olfactory signals in the OB in response to a given odor stimulation. Based on the fMRI technology, OdorMapBuilder provides comparable odor maps on the intra-subject basis, a significant step towards the detailed analyses of the effects of odor types and/or concentrations. In addition, a new database, OdorMapDB, is developed to provide a repository for the generated odor maps. Web interfaces to the database are provided for the data entry, modification and retrieval. OdorMapDB is based on the EAV/CR (entity-attribute-value with classes and relationships) architecture and it is integrated with two other SenseLab olfactory databases: the olfactory receptor and odor databases. Both OdorMapBuilder and OdorMapDB should serve as useful tools and resources for the field and help facilitate experimental research in understanding the olfactory system and the mechanism for smell perception.

Animals↗
PubMed2003

Health informatics and modernisation: bridging the gap.

This pilot initiative uses an approach that focuses on improving the whole business of primary care, its processes and its people. The Health Informatics Programme for Coronary Heart Disease (HIP for CHD) addresses the two faces of clinical governance but has a prime focus on the development of learning organisations. The project has developed a methodology and an associated set of tools that it has tested and evaluated in a small number of pilot sites. The work of HIP for CHD is focused on coronary heart disease but the methodology is equally applicable to other clinical areas. In particular, HIP for CHD provides an approach that allows the diverse strands of all of the National Service Frameworks to be handled in a joined-up way in primary care.

Coronary Disease↗
PubMed2003

Applying new thinking from the linked and emerging fields of digital identity and privacy to information governance in health informatics.

Recent work in the emerging field of network or digital identity suggests a new approach to the design of informatics systems, in which the individual becomes the guardian of their own personal data, and is assisted in controlling access to it by an infrastructure that is aware of roles, such as 'doctor', and relationships, such as 'doctor-patient'.For these purposes, an 'identity' is defined as the history of a relationship between two entities, and thus encompasses not only name and address but also data that would usually be regarded as part of an electronic patient or health record. This paper presents a description of how such a true person-centric architecture might work, and shows how it can be seen as an evolution of current plans in the NHS for a national patient data spine. One application, the electronic transmission of prescriptions, is described in detail. Other applications, both within and without the healthcare field, are described in outline. The implementation of such a person-centric system requires a modest degree of technical innovation, but significant change in organisational and business models. It is suggested that there is a need for one or more not-for-profit trusts, each with a remit to act as host for an individual's digital identity, and as the individual's true agent. Service providers - such as healthcare organisations - will pay the trust for provision of authentication, and for the storage and transmission of a patient's data; the trust in turn will pay implementation partners, such as smart card issuers and providers of communication channels, acting on behalf of the individual.

Access to Information↗
PubMed2006

The optimum granularity for coding diagnostic data in primary care: report of a workshop of the EFMI Primary Care Informatics Working Group at MIE 2005.

INTRODUCTION: The EFMI Primary Care Informatics Working Group held a workshop to explore interventions used across Europe to improve the data quality in primary care computerised medical records. METHOD: A plenary session reviewed the UK literature about improving data quality and then the session split into three small groups. Fifteen delegates from nine countries contributed to the workshop. These groups reported back at the end of the session. RESULTS: The groups defined what they meant by data quality. The principal requirement was that data must be 'fit for purpose'. The participants felt this was particularly important for diagnostic data, while recognising that the purpose might not be known at the point of data recording. They also described the barriers to recording structured and coded data. The most important were an inappropriate interface with the coding system and inappropriate granularity of codes. There was a wide range of suggestions as to how to overcome these barriers, including providing feedback, links to expert systems, education and training, use of the data for care elsewhere in the health system and mandation of electronic data recording. CONCLUSIONS: The workshop developed a new characteristic of data quality: 'fit for purpose'. This is different from definitions that focus on completeness, accuracy, currency, or its positive predictive value and sensitivity. The group also highlighted the importance of data quality of diagnoses, as these data are important throughout the health system as well as acting as a prompt for other interventions within the individual consultation. More research is needed into appropriate levels of granularity for diagnostic recording in primary care.

Diagnostic Tests, Routine↗
PubMed2004

[Being a nursing teacher in an informatized world].

The social phenomenology approach allowed us to understand that informatics projects are based on the biographic situation and the educational experiences of each teacher and their adoption happens voluntarily, in a reflection process on the favorable and unfavorable alternatives implied in the social context. Thus, we conjecture about the construction of teachers' technological and pedagogical competences and pro-active institutional policies that adhere to the contemporary society, seeking to integrate the new technologies with the needs of the profession and the human dimension of nursing.

Computer-Assisted Instruction↗
PubMed2006

Taxonomic informatics tools for the electronic Nomenclator Zoologicus.

Given the current trends, it seems inevitable that all biological documents will eventually exist in a digital format and be distributed across the internet. New network services and tools need to be developed to increase retrieval rates for documents and to refine data recovery. Biological data have traditionally been well managed using taxonomic principles. As part of a larger initiative to build an array of names-based network services that emulate taxonomic principles for managing biological information, we undertook the digitization of a major taxonomic reference text, Nomenclator Zoologicus. The process involved replicating the text to a high level of fidelity, parsing the content for inclusion within a database, developing tools to enable expert input into the product, and integrating the metadata and factual content within taxonomic network services. The result is a high-quality and freely available web application (http://uio.mbl.edu/NomenclatorZoologicus/) capable of being exploited in an array of biological informatics services.

Animals↗