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PubMed2003

BioWareDB: the biomedical software and database search engine.

UNLABELLED: A wealth of bioinformatics tools and databases has been created over the last decade and most are freely available to the general public. However, these valuable resources live a shadow existence compared to experimental results and methods that are widely published in journals and relatively easily found through publication databases such as PubMed. For the general scientist as well as bioinformaticists, these tools can deliver great value to the design and analysis of biological and medical experiments, but there is no inventory presenting an up-to-date and easily searchable index of all these resources. To remedy this, the BioWareDB search engine has been created. BioWareDB is an extensive and current catalog of software and databases of relevance to researchers in the fields of biology and medicine, and presently consists of 2800 validated entries. AVAILABILITY: BioWareDB is freely available over the Internet at http://www.biowaredb.org/

Abstracting and Indexing↗
PubMed2003

Cross-language MeSH indexing using morpho-semantic normalization.

We consider three alternative procedures for the automatic indexing of medical documents using MeSH thesaurus identifiers as target units (document descriptors). Rather than considering complete words as the starting point of the indexing procedure, we here propose morphologically plausible subwords as basic units from which MeSH terms are derived. We describe the morphological segmentation and normalization procedures, as well as the mappings from subwords to MeSH terms, and discuss results from an evaluation carried out on a German-language corpus.

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PubMed2000

Mapping access to food in a deprived area: the development of price and availability indices.

OBJECTIVE: To develop and map indices to illustrate variation in the cost and availability of healthy food. DESIGN: Two contiguous wards in London were selected by virtue of their high Carstairs deprivation scores. A 2-km area was defined around a randomly chosen central point. All retail outlets selling food within the area were visited and their location recorded. A list of foods, acceptable to the local ethnically diverse population, which met current dietary guidelines, was devised. Data on the availability and price of 71 food items were collected. Indices were developed using SPSS and mapped using Geographic Information System (GIS) software. RESULTS: Information on availability and prices were collected from 199 outlets. The mean price index shows how expensive a shop is relative to other shops in the area. The least cost index shows the relative expense of a shop using the cheapest ways of buying their range of foods. Shorthand indices were tested, using data on 19 of the 71 prices. Availability indices are also discussed, including a green availability index and a fresh green availability index. Illustrative maps of the shop locations and the mean price index and fresh green availability index are shown. CONCLUSIONS: Data can be collected and indices developed which indicate geographic variation in shop 'expensiveness', and in the price and availability of healthy food. GIS software can be used to map these indices, to identify areas with high food prices or low availability.

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PubMed1986

How to construct a subjective index.

We present a method of constructing quantitative indices, which is based on the subjective opinions of a panel of experts, and discuss how a Bayesian probability model and panel opinions can be used together to produce an index. Among the advantages of the method are its face validity and ease of construction. Research shows that when expert opinions are solicited according to certain guidelines, subjective methods may be as accurate as the more objective ones. Guidelines along with a brief report of a recent application are also discussed.

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PubMed1995

A quantitative ranking of the Biomedical Informatics serials.

We have developed a quantitative serial ranking system based on multiple citation analysis techniques, library use statistics, expert opinion, and selected distinguishing publication characteristics. Evaluation criteria categories include: average Science Citation Index (Impact Factor, Immediacy Index, Total citations) rankings from 1987 to 1992; citation source counts of multiple "core" biomedical informatics publications; a questionnaire sent to American College of Medical Informatics Fellows; publication delay; distinguishing characteristics (e.g., subscription cost, total circulation, year established, places indexed, affiliation with a professional society, major biomedical resource library holdings); and the total number of interlibrary loan requests to the U. S. National Library of Medicine. The top serials were Computers and Biomedical Research, MD Computing, Methods of Information in Medicine, Medical Decision Making and Computers in Biology and Medicine.

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PubMed1994

An evaluation of computer assisted clinical classification algorithms.

The Mayo Clinic has a long tradition of indexing patient records in high resolution and volume. Several algorithms have been developed which promise to help human coders in the classification process. We evaluate variations on code browsers and free text indexing systems with respect to their speed and error rates in our production environment. The more sophisticated indexing systems save measurable time in the coding process, but suffer from incompleteness which requires a back-up system or human verification. Expert Network does the best job of rank ordering clinical text, potentially enabling the creation of thresholds for the pass through of computer coded data without human review.

Abstracting and Indexing↗
PubMed1994

MENELAS: an access system for medical records using natural language.

The overall goal of MENELAS is to provide better access to the information contained in natural language patient discharge summaries, through the design and implementation of a pilot system able to access medical reports through natural languages. A first, experimental version of the MENELAS indexing prototype for French has been assembled. Its function is to encode free text PDSs into both an internal representation and ICD-9-CM nomenclature codes. A preliminary evaluation shows the potential for reasonable coverage and precision. The MENELAS prototype will be enhanced and extended into a pilot system which will be tested in two hospital sites.

Abstracting and Indexing↗
PubMed2001

SIR: a simple indexing and retrieval system for biological flat file databases.

SUMMARY: SIR is a Simple Indexing and Retrieval tool for indexing and searching biological flat file databases. SIR is a cross-platform solution entirely written in Python. Since the package is very small and installation is trivial, this would be an ideal solution for database providers to provide a custom retrieval tool to access them. AVAILABILITY: The modules will be made available at http://www.EMBLHeidelberg.de/~chenna/PySAT/sir.html

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PubMed2006

Mapping the literature of nursing education.

OBJECTIVES: As part of a project to map the literature of nursing, sponsored by the Nursing and Allied Health Resources Section of the Medical Library Association, this study identifies core journals cited in nursing education journals and the indexing services that cover the cited journals. METHODS: Three nursing education source journals were subjected to a citation analysis of articles from 1997 to 1999, followed by an analysis of database access to the most frequently cited journal titles. RESULTS: Cited formats included journals (62.4%), books (31.3%), government documents (1.4%), Internet (0.3%), and miscellaneous (4.6%). Cited references were relatively older than other studies, with just 58.6% published in the 1990s. One-third of the citations were found in a core of just 6 journal titles; one-third were dispersed among a middle zone of 53 titles; the remaining third were scattered in a larger zone of 762 titles. Indexing coverage for the core titles was most comprehensive in CINAHL, followed by PubMed/MEDLINE and Social Sciences Citation Index. CONCLUSIONS: Citation patterns in nursing education show more reliance on nursing and education literature than biomedicine. Literature searches need to include CINAHL and PubMed/MEDLINE, as well as education and social sciences databases. Likewise, library collections need to include education and social sciences resources to complement works developed for nurse educators.

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PubMed1972

In-depth indexing of monograph literature for an on-line retrieval system: a pilot project.

One of the unique features of the State University of New York (SUNY) Biomedical Communication Network is the availability of depth-indexed monograph information for on-line retrieval. Approximately 8,000 titles from the Upstate Medical Center Library collection in Syracuse, New York, were indexed in depth, chapter-by-chapter, as to subject content using the control vocabulary Medical Subject Headings. Detailed indexing of monographic conference proceedings was considered of particular importance to the project. This attempt to make monograph literature more readily accessible to medical library patrons is interesting from both a philosophical and a technical point of view. This paper will discuss both of these aspects, giving an overall description of the nature of this innovative project.

Abstracting and Indexing↗
PubMed1980

Prestel: flaws in the indexing tree.

Viewdata is a generic name for a system that links people to computer-based data through an adapted TV set and the telephone. It is expensive; information providers can spend hundreds of thousands of pounds a year on information frames that still have limited use. In Britain the main system is called Prestel. Pauline Drummond examines its relevance for the health service, particularly in the light of recent experiments.

Abstracting and Indexing↗
PubMed1985

Early dental journalism: a mirror of the development of dentistry as a profession.

The rise of dentistry from a mechanical trade to a profession has often been attributed to the so-called "triumvirate" of organization, education, and journal literature. This essay focuses on one part of the triumvirate, examining the role of journals in the growth of dentistry as a profession, from the appearance of the first journal in 1839 to the publication of the Index to Dental Literature in 1921. Rather than discussing the history of individual titles, it identifies some of the broader issues and problems that confronted early dental journalism. The evolution of dental journals from trade house publications to independent scientific literature mirrored the movement toward professional status in dentistry during the late 19th and early 20th centuries.

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PubMed1986

Tests of methods for evaluating bibliographic databases: an analysis of the National Library of Medicine's handling of literatures in the medical behavioral sciences.

This article reports on five separate studies designed for the National Library of Medicine (NLM) to develop and test methodologies for evaluating the products of large databases. The methodologies were tested on literatures of the medical behavioral sciences (MBS). One of these studies examined how well NLM covered MBS monographic literature using CATLINE and OCLC. Another examined MBS journal and serial literature coverage in MEDLINE and other MBS-related databases available through DIALOG. These two studies used 1010 items derived from the reference lists of sixty-one journals, and tested for gaps and overlaps in coverage in the various databases. A third study examined the quality of the indexing NLM provides to MBS literatures and developed a measure of indexing as a system component. The final two studies explored how well MEDLINE retrieved documents on topics submitted by MBS professionals and how online searchers viewed MEDLINE (and other systems and databases) in handling MBS topics. The five studies yielded both broad research outcomes and specific recommendations to NLM.

Abstracting and Indexing↗
PubMed2002

Improving access to the international coverage of reports of controlled trials in electronic databases: a search of the Australasian Medical Index.

INTRODUCTION: Locating reports of trials from journals not indexed in the major databases presents difficulties to systematic reviewers, and may be a factor in improving the reliability of the reviews. OBJECTIVES: To identify and make available reports of controlled trials from the Australasian Medical Index (AMI). To measure the quality of indexing of trials in AMI. METHODS: Using a highly sensitive search strategy consisting of methodology indexing and free-text terms, records from AMI were read for reports of controlled trials. Trials meeting the criteria were submitted for inclusion in The Cochrane Controlled Trials Register (CCTR) and assessed for the quality of their indexing. RESULTS: 3621 records were downloaded, of which 512 were identified as reports of controlled trials (317 RCTs; 195 CCTs) and submitted to CCTR. The precision of methodology indexing terms was 60%, but sensitivity just 18%. The quality of indexing of trials was generally poor with only 50 tagged with the RCT/CCT publication type term. 453 reports (88%) were not previously available in CCTR. CONCLUSIONS: The large proportion of trials found to be unique to the AMI database increases the pool of studies available to systematic reviewers, and helps ensure CCTR remains the most comprehensive source of trials.

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PubMed1999

Mapping the literature of perfusion.

Perfusionists select and operate the equipment necessary for monitoring, supporting, or temporarily replacing the patient's circulatory or respiratory function. There are over 3,000 perfusionists working in U.S. hospitals, medical and perfusionist groups, and as independent contractors. The purpose of this study was to identify the core literature of perfusion and to determine which major databases provide the most thorough access to this literature. This paper is part of the Medical Library Association Nursing and Allied Health Resource Section's project to map the literature of the allied health professions. It uses a bibliometric methodology to identify core journals. A group of forty-three journals was determined to make up the core journal literature of perfusion. MEDLINE provided the best overall indexing coverage for these journals, but librarians and perfusionists will wish to supplement its use with the Cumulative Index to Nursing and Allied Health Literature in order to access the journals written primarily for perfusionists. The study results can guide purchasing and database searching decisions of collection development and reference librarians, encourage the database producer to increase coverage of titles that are unindexed or underindexed, and advise perfusionists of the best access to their core literature.

Abstracting and Indexing↗
PubMed1992

An evaluation of the source selection elements of the prototype UMLS Information Sources Map.

The Information Sources Map (ISM) is a component of the National Library of Medicine's Unified Medical Language System (UMLS) project. The ISM is intended to provide both human-readable and machine-interpretable information about the content, scope, and access conditions for various information sources such as databases, expert systems, and the organizations which make these information sources available. Automated source selection is supported by three types of indexing in the ISM: Medical Subject Heading (MeSH) terms and subheadings; Semantic Types from the UMLS Semantic Network; and Semantic Type Relations, which depict pairs of semantic types joined by a relationship chosen from the Semantic Network. This paper reports a study of the recall and precision of the source selection elements in the prototype version of the ISM.

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PubMed1995

Building a medical multimedia database system to integrate clinical information: an application of high-performance computing and communications technology.

The rapid growth of diagnostic-imaging technologies over the past two decades has dramatically increased the amount of nontextual data generated in clinical medicine. The architecture of traditional, text-oriented, clinical information systems has made the integration of digitized clinical images with the patient record problematic. Systems for the classification, retrieval, and integration of clinical images are in their infancy. Recent advances in high-performance computing, imaging, and networking technology now make it technologically and economically feasible to develop an integrated, multimedia, electronic patient record. As part of The National Library of Medicine's Biomedical Applications of High-Performance Computing and Communications program, we plan to develop Image Engine, a prototype microcomputer-based system for the storage, retrieval, integration, and sharing of a wide range of clinically important digital images. Images stored in the Image Engine database will be indexed and organized using the Unified Medical Language System Metathesaurus and will be dynamically linked to data in a text-based, clinical information system. We will evaluate Image Engine by initially implementing it in three clinical domains (oncology, gastroenterology, and clinical pathology) at the University of Pittsburgh Medical Center.

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PubMed1990

Managing journal references with JREF, an IBM-compatible program to simplify manuscript preparation.

JREF is a program which stores, manages and converts journal references. It is intended for the writer of articles and reviews, to simplify the task of keeping card indexes. Entries can be made from downloaded literature searches or from the keyboard. When writing, selections are made from the archival files, for conversion into the specific style of the chosen Journal. All files are ASCII text, accessible to most word processing programs. Once the accuracy of entries has been confirmed, these can be transformed into a perfectly punctuated bibliography.

Abstracting and Indexing↗