Imagene: an integrated computer environment for sequence annotation and analysis.
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MOTIVATION: To be fully and efficiently exploited, data coming from sequencing projects together with specific sequence analysis tools need to be integrated within reliable data management systems. Systems designed to manage genome data and analysis tend to give a greater importance either to the data storage or to the methodological aspect, but lack a complete integration of both components. RESULTS: This paper presents a co-operative computer environment (called Imagenetrade mark) dedicated to genomic sequence analysis and annotation. Imagene has been developed by using an object-based model. Thanks to this representation, the user can directly manipulate familiar data objects through icons or lists. Imagene also incorporates a solving engine in order to manage analysis tasks. A global task is solved by successive divisions into smaller sub-tasks. During program execution, these sub-tasks are graphically displayed to the user and may be further re-started at any point after task completion. In this sense, Imagene is more transparent to the user than a traditional menu-driven package. Imagene also provides a user interface to display, on the same screen, the results produced by several tasks, together with the capability to annotate these results easily. In its current form, Imagene has been designed particularly for use in microbial sequencing projects. AVAILABILITY: Imagene best runs on SGI (Irix 6.3 or higher) workstations. It is distributed free of charge on a CD-ROM, but requires some Ilog licensed software to run. Some modules also require separate license agreements. Please contact the authors for specific academic conditions and other Unix platforms. CONTACT: imagene home page: http://wwwabi.snv.jussieu.fr/imagene (+info)
A model for enhancing Internet medical document retrieval with "medical core metadata".
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OBJECTIVE: Finding documents on the World Wide Web relevant to a specific medical information need can be difficult. The goal of this work is to define a set of document content description tags, or metadata encodings, that can be used to promote disciplined search access to Internet medical documents. DESIGN: The authors based their approach on a proposed metadata standard, the Dublin Core Metadata Element Set, which has recently been submitted to the Internet Engineering Task Force. Their model also incorporates the National Library of Medicine's Medical Subject Headings (MeSH) vocabulary and MEDLINE-type content descriptions. RESULTS: The model defines a medical core metadata set that can be used to describe the metadata for a wide variety of Internet documents. CONCLUSIONS: The authors propose that their medical core metadata set be used to assign metadata to medical documents to facilitate document retrieval by Internet search engines. (+info)
Incompleteness and retrieval of case notes in a case note audit of colorectal cancer.
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Hospital case notes are a crucial source of data but are subject to two major biases: incompleteness of data and non-retrieval. To assess these biases in relation to colorectal cancer a study was performed of all cases of colorectal cancer listed in the Thames cancer registry in patients resident in one of four districts in South Thames regions with a diagnosis in 1988. Five medical record sites were involved. Retrieval rate for all case notes for districts combined was 80%. In two districts the rates were too high for further investigation; in the other two respectively patient survival and whether treatment was given were positively associated with retrieval. Among the four districts incompleteness of notes ranged from 38% to 62% for staging, 8% to 40% for treatment, and 70% to 25% for diagnostic tests. Information about treatment was missing in 3% to 20%; survival data were omitted in less than 5%. In all districts completeness of case notes was inadequate and in some non-retrieval compounded the problem. Missing data reduce the quality of cancer registry data and potentially undermine interpretation of epidemiological studies and evaluation of care. Further research is warranted into the standards and resourcing of medical records departments and their effects on retrieval and data quality. Structured proformas could be applied across specialties to identify missing items in case notes, to identify areas where standards are required, or to audit notes where standards have already been agreed. A staging protocol to set standards for colorectal cancer has been adopted in one district, and a prospective audit is being established. (+info)
Comparative hospital databases: value for management and quality.
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OBJECTIVES: To establish an accurate and reliable comparative database of discharge abstracts and to appraise its value for assessments of quality of care. DESIGN: Retrospective review of case notes by trained research abstractors and comparison with matched information as routinely collected by the hospitals' own information systems. SETTING: Three district general hospitals and two major London teaching hospitals. PATIENTS: The database included 3905 medical and surgical cases and 2082 obstetric cases from 1990 and 1991. MAIN MEASURES: Accessibility of case notes; measures of reliability between reviewers and of validity of case note content; application of high level quality indicators. RESULTS: The existing hospital systems extracted insufficient detail from case notes to conduct clinical comparative analyses for medical and surgical cases. The research abstractors at least doubled the diagnostic codes extracted. Interabstractor agreement of about 70% was obtained for primary diagnosis and assignment to diagnosis related group. These data were sufficient to create a comparative database and apply high level quality indicators designed to flag topics for further study. For obstetric-specific indicators the rates were comparable for abstractors and the hospital information systems, which in each case was a departmentally based system (SMMIS) producing more detailed and accessible data. CONCLUSIONS: Current methods of extracting and coding diagnostic and procedural data from case notes in this sample of hospitals is unsatisfactory: notes were difficult to access and recording is unacceptably incomplete. IMPLICATIONS: Improvements as piloted in this project, are readily available should the NHS, hospital managers, and clinicians see the value of these data in their clinical and managerial activities. (+info)
Conducting a literature review on the effectiveness of health care interventions.
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The dramatic increase in the volume of research based information means that effective policy makers must be able to conduct and interpret literature reviews. This article sets out the steps that should be followed in doing so. They are: explicitly defining the question; locating relevant literature; assessing the quality of studies and deciding whether they should be included; synthesizing and re-analyzing the results; and presenting them in a clear and concise manner. The article identifies the leading sources of information, including electronic databases and useful Internet addresses and describes briefly how each stage should be conducted, highlighting the strengths and weaknesses of different approaches and the ways in which bias may be introduced. (+info)
Searching for information on outcomes: do you need to be comprehensive?
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The concepts of evidence-based practice and clinical effectiveness are reliant on up to date, accurate, high quality, and relevant information. Although this information can be obtained from a range of sources, computerised databases such as MEDLINE offer a fast, effective means of bringing up to date information to clinicians, as well as health service and information professionals. Common problems when searching for information from databases include missing important relevant papers or retrieving too much information. Effective search strategies are therefore necessary to retrieve a manageable amount of relevant information. This paper presents a range of strategies which can be used to locate information on MEDLINE efficiently and effectively. (+info)
The ability to search bibliographic databases effectively is now an essential skill for anyone undertaking research in health. This article discusses the way in which databases are constructed and some of the important steps in planning and carrying out a search. Consideration is given to some of the advantages and limitations of searching using both thesaurus and natural language (textword) terms. A selected list of databases in health and medicine is included. (+info)
Tracing the evolution of critical evaluation skills in students' use of the Internet.
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This paper documents the evolving uses of the Internet made by public health graduate students and traces the development of their search methods and critical evaluative criteria. Early in the first semester and again six months later, twenty-four graduate students in a problem-based learning curriculum, which emphasizes evidence-based critical thinking skills, were required to describe their most helpful resources and to evaluate these resources critically. The answers were coded for the types of resources the students used, how frequently they were used, and why they were used. Student perception of the usefulness of resources, especially the Internet, and ability to evaluate these resources critically changed greatly. Initially, 96% of the students stated that the Internet was their most helpful resource. Six months later, these students continued to use the Internet; however, it was not their most useful source. At the later point, students had very specific uses for the Internet. Their most frequently used evaluation criterion was the reliability and objectivity of the source of the information. By the end of the first year of study, the majority of the students demonstrated an understanding of the principles of evidence-based practice and applied them to their research and analysis of information resources. (+info)