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PubMed1995

The SAPHIRE server: a new algorithm and implementation.

SAPHIRE is an experimental information retrieval system implemented to test new approaches to automated indexing and retrieval of medical documents. Due to limitations in its original concept-matching algorithm, a modified algorithm has been implemented which allows greater flexibility in partial matching and different word order within concepts. With the concomitant growth in client-server applications and the Internet in general, the new algorithm has been implemented as a server that can be accessed via other applications on the Internet.

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PubMed2004

PARIS: a proteomic analysis and resources indexation system.

UNLABELLED: We developed a system for managing data from two-dimensional electrophoresis-based proteomic experiments. Named PARIS, the system stores gel image and information about experiments and analysis procedures, allows the user to search and navigate in genomic and proteomic data, supports visual verification and validation of the analysis results, and provides tools for cross multi-experiment and multi-experimenter data validation and exploration. AVAILABILITY: The software is freely available from http://www.inra.fr/bia/J/imaste/Projets/PARIS/index.html

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PubMed2006

The use of PubMed/Medline in psychiatry. 1: Presentation of NLM and PubMed.

A comprehensive view of the available literature on a psychiatric problem can be found in the large electronic databases. Medline at the National Library of Medicine (NLM) in USA is the largest medical database. PubMed is the searchable database at the NLM, having Medline as its major content. PubMed is free of charge, barrier-free and always accessible via the Internet. This paper describes the NLM, Medline and PubMed. The indexing of scientific papers in Medline is based on Medical Subject Headings, the MeSH terms. The hierarchic tree structure of MeSH is the basis of the search and retrieval system. The present paper is the first in a series of three, intended as a tutorial on the use of PubMed for inexperienced users. Information and examples on the MeSH system, together with exercises in its use, are presented in an appendix.

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PubMed1998

An analysis of 5 years of medical informatics publications.

This study describes an analysis of 1520 papers that were published in six medical informatics journals from 1992 through 1996, and indexed in NLM's MEDLINE. Of retrieved publications the countries of origin were determined, and insight in the subject of the publication was obtained by analysing the used MeSH terms. The main conclusion is that despite the fact that publications in medical informatics stem from a wide international community, scientific recognition can still not be demonstrated by high impact factors of journals.

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PubMed2002

In focus. Life after BioethicsLine: a reply to Joyce Plaza.

The recent closure and removal of BioethicsLine led many researchers to wonder where to turn for their research needs. Joyce Plaza wrote that the closure is a mistake. In this essay I maintain, contra Plaza, that due to its cross-disciplinary nature researchers can find bioethics literature in other databases. In developing the search strategy the researcher needs to consider what the problem is about. If the researcher has a philosophical approach in mind, a wise choice would be to use Philosopher's Index; a legal approach suggests using Academic Universe, Westlaw, Lexis or legal databases freely available through state and federal websites. Further, in so far as the National Library of Medicine is integrating citations in BioethicsLine into the NLM Gateway databases (PubMed and LOCATORplus) I point out suggestions on using the latter databases effectively. There is a wealth of information readily available and researchers have much to learn by trying the alternatives.

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PubMedDate not supplied

Quantification of the scientific research in the United States about popular herbal remedies referenced on PubMed.

Herbal supplements are among the most popular complementary and alternative therapies used in the US, yet many healthcare providers report having inadequate knowledge about herbs. It also has been reported that many healthcare providers want to have a better understanding of herbs so that they may recommend or discourage their use. In this report, we attempt to determine whether a significant body of research has been indexed in PubMed on the most widely used herbs in the US. These data also prove useful in determining whether the scientific community in the US is focusing investigations on herbs that are widely used domestically. In addition, many clinicians in the US use data from clinical trials performed in the US to inform their practice, so we wanted to determine whether significant clinical data on these herbs were available.

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PubMed1995

Retrieving research studies: a comparison of bibliographic and full-text versions of the New England Journal of Medicine.

It has been established that subject searches of medical full-text databases obtain higher recall than subject searches in a bibliographic database. In this study we attempted to determine if the same rule might apply when searching for a non-subject parameter such as study design. A simultaneous search of bibliographic and full-text records from the New England Journal of Medicine provided data on the number of items retrieved by each kind of search. Filtering strategies were created for 5 different study types: randomized controlled trials, other clinical trials and prospective studies, cohort studies, longitudinal and follow-up studies, and multicenter studies. The point of the study was to compare the numbers of items retrieved from the bibliographic database, MEDLINE, and those retrieved from the full-text version of NEJM, and to examine the unique access points available in each file. For all the study types the full-text file retrieved a larger number of records than MEDLINE, most of which were retrieved because of methodology terms found in the text but not in the title or abstract. In MEDLINE, descriptors and publication types, two value-added fields supplied by indexers, retrieved 11-89% more than title and abstract alone.

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PubMed1991

Medicare program; Medicare Economic Index update for 1991--HCFA. Notice.

This notice updates the Medicare Economic Index (MEI), which is used to calculate the prevailing charge levels that help to determine reasonable charges for certain physician services under the Medicare Supplementary Medical Insurance (part B) program. As mandated by section 4105 of Public Law 101-508, for physician services furnished on or after January 1, 1991, and before January 1, 1992, the increase for primary care services will be 2 percent. There will be no increase for all other physician services.

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PubMed1987

Bibliography of Bioethics and Index Medicus: comparison of coverage, publication delay, and ease of recall for journal articles on bioethics.

Citations selected from the bibliographies of recent texts, a specialized subject bibliography, and review articles were checked in both Cumulated Index Medicus (IM) and the Bibliography of Bioethics (BB) to compare coverage, publication delay, probable causes of indexing and retrieval failure, and the ease with which relevant citations were retrieved. The study also attempted to determine whether BB included appropriate articles from the MEDLINE database in a timely and systematic manner. While 98% of the IM citations appeared within a year of publication, 79% of the BB citations appeared two to three years after their publication dates. The average citation appeared twice as frequently in IM as in BB.

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PubMed1981

[Need for scientific medical information by internists working in the therapeutic and prophylactic system].

A study was carried out on the necessity of scientific medical information (SMI) among the internists, engaged in the practical public health care according to the methods: inquiry, collective expert evaluation and entropic. The results revealed that the scientific medical periodicals, books and drug catalogues are preferred as a source of SMI, whereas the secondary sources indexes, surveys, congress materials are less known and used. Of occupational and scientific interest is the scientific information on the fresh news of the methods about: a) diagnostics; b) treatment and c) new drugs. The inquired physicians gave the priority to addressed and current information. Sixty one per cent of them spend 60 min. weekly in retrieving the necessary SMI, and 40 per cent--over 240 min weekly, processing the relevant literature found.

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PubMed2000

Knowledge representation and indexing using the unified medical language system.

Ontologies and semantic frameworks can be used to improve the accuracy and expressiveness of natural language processing for the purpose of extracting meaning from technical documents. This is especially true when a rich ontology such as the Unified Medical Language System (UMLS) is available. This paper reports on some tools being developed to make this possible and on some experience with a user interface based on ontologies and semantic networks that allows for interactive knowledge exploration.

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PubMed1989

The outcome index. A method of quality assurance in the special care area.

A method of quality assurance for a surgical intensive care unit is described. A system outcome score is devised, incorporating only easily obtained objective components that reflect the likelihood of death. Through the use of a derived outcome index, the actual mortality rate is compared with the predicted mortality rate as a method of monitoring the quality of care provided. Subroutines exist to identify errors in data entry, to detect malicious interference in patient care, to add nonscoring components for the purposes of clinical studies, and to facilitate retrieval of a concise summary of the major events during the stay of every patient admitted to the intensive care unit.

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PubMed1996

An evaluation of statistical approaches to MEDLINE indexing.

Whether or not high accuracy classification methods can be scaled to large applications is crucial for the ultimate usefulness of such methods in text categorization. This paper applies two statistical learning algorithms, the Linear Least Squares Fit (LLSF) mapping and a Nearest Neighbor classifier named ExpNet, to a large collection of MEDLINE documents. With the use of suitable dimensionality reduction techniques and efficient algorithms, both LLSF and ExpNet successfully scaled to this very large problem with a result significantly outperforming word-matching and other automatic learning methods applied to the same corpus.

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PubMed1996

A concept-based retrieval system for thoracic radiology.

Current digital information systems in radiology are insufficient to accommodate the retrieval needs of academicians. Significant efforts are required in retrieving clinical cases for teaching and research. We describe a prototype system that supports intelligent case retrieval based on a combined specification of patient demographics, radiologic findings, and pathologic diagnoses. The documents for these cases can be distributed among multiple heterogeneous data bases. The system features automatic indexing of radiology and pathology reports, a comprehensive lexicon for thoracic radiology, an interface to a hospital information system, radiology information system, and picture archiving and communication systems, and a graphical user interface for query formulation and results visualization. The prototype system was developed within the domain of thoracic radiology involving patients with lung cancer.

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PubMed1999

Evaluation of the Information Sources Map.

As part of preliminary studies for the development of a digital library, we have studied the possibility of using the UMLS Information Sources Map (ISM) database to provide the means to connect and map different terminologies, as well as to facilitate access to available information sources. The main issues discussed are the indexing of and connection to relevant online sources. We found the features of the ISM to be consistent with the need to support automated source selection and retrieval. However, attention should be paid to three aspects of the information: granularity, completeness, and accuracy. We found the ISM to be potentially useful; however, significant modifications will be required if the ISM is to be able to support automated source selection and retrieval.

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PubMed1992

Natural language processing and semantical representation of medical texts.

For medical records, the challenge for the present decade is Natural Language Processing (NLP) of texts, and the construction of an adequate Knowledge Representation. This article describes the components of an NLP system, which is currently being developed in the Geneva Hospital, and within the European Community's AIM programme. They are: a Natural Language Analyser, a Conceptual Graphs Builder, a Data Base Storage component, a Query Processor, a Natural Language Generator and, in addition, a Translator, a Diagnosis Encoding System and a Literature Indexing System. Taking advantage of a closed domain of knowledge, defined around a medical specialty, a method called proximity processing has been developed. In this situation no parser of the initial text is needed, and the system is based on semantical information of near words in sentences. The benefits are: easy implementation, portability between languages, robustness towards badly-formed sentences, and a sound representation using conceptual graphs.

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PubMed1990

Cost and volume trends in health care facility construction.

In 1987, the Health Care Financing Administration proposed adding capital cost reimbursement to the prospective payment system. A data base was developed from which an index was calculated to adjust for geographic variation in construction cost. Findings from the data base, along with a description of trends in health care facility construction from 1970 through 1986, are presented. Spending (in constant 1986 dollars) and volume of health care facility construction declined from 1970 to 1986. Construction cost per square foot increased until 1983, followed by a decline to pre-1980 levels after the 1983 implementation of the prospective payment system.

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PubMed2006

Mapping the literature of maternal-child/gynecologic nursing.

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 maternal-child/gynecologic nursing and the indexing services that access the cited journals. METHODS: Three source journals were selected and subjected to a citation analysis of articles from 1996 to 1998. RESULTS: Journals were the most frequently cited format (74.1%), followed by books (19.7%), miscellaneous (4.2%), and government documents (1.9%). Bradford's Law of Scattering was applied to the results, ranking cited journal references in descending order. One-third of the citations were found in a core of 14 journal titles; one-third were dispersed among a middle zone of 100 titles; and the remaining third were scattered in a larger zone of 1,194 titles. Indexing coverage for the core titles was most comprehensive in PubMed/MEDLINE, followed by Science Citation Index and CINAHL. CONCLUSION: The core of journals cited in this nursing specialty revealed a large number of medical titles, thus, the biomedical databases provide the best access. The interdisciplinary nature of maternal-child/ gynecologic nursing topics dictates that social sciences databases are an important adjunct. The study results will assist librarians in collection development, provide end users with guidelines for selecting databases, and influence database producers to consider extending coverage to identified titles.

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