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PubMed1978

Automatic indexing of pathology data.

A procedure for automated indexing of pathology diagnostic reports at the National Institutes of Health is described. Diagnostic statements in medical English are encoded by computer into the Systematized Nomenclature of Pathology (SNOP). SNOP is a structured indexing language constructed by pathologists for manual indexing. It is of interest that effective automatic encoding can be based upon an existing vocabulary and code designed for manual methods. Morphosyntactic analysis, a simple syntax analysis, matching of dictionary entries consisting of several words, and synonym substitutions are techniques utilized.

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PubMed1991

Citation analysis of selected clinical pharmacology journals.

Perceptions of pharmacy and medical journal quality vary widely. One objective measure of the quality of a scientific journal is the impact factor that can be defined as "a measure of the frequency with which the 'average article' in a journal has been cited in a particular year." The purpose of this study was to evaluate the clinical pharmacology journals available through the Science Citation Index and determine those that have the greatest impact. From these data, it appears that the premier primary literature journal in clinical pharmacology is Clinical Pharmacology and Therapeutics while the premier review journal has been Clinical Pharmacokinetics. Possible explanations for impact factor fluctuations over time are also discussed.

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PubMed1998

Medicare program; hospice wage index--HCFA. Notice.

This notice announces the annual update to the hospice wage index as required by 42 CFR 418,306(c). This update is effective October 1, 1998. The wage index is used to reflect local differences in wage levels. The hospice wage index methodology and values are based on recommendations of a negotiated rulemaking advisory committee and were originally published in the Federal Register on August 8, 1997. This update is the second year of a 3-year transition period. The second transition year begins October 1, 1998 and ends September 30, 1999.

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PubMed1990

Automatic updating of the EMBL database via EMBNet.

The paper describes a procedure for updating the EMBL (European Molecular Biology Laboratory, Heidelberg) database of nucleic acid sequences and its indexes used by the University of Wisconsin Genetics Computer Group (GCG) software package, using updated entries for this database distributed via EMBNet. At present the procedure is being run on a MRC Clinical Research Centre's (CRC) SUN 4/280 server using SUNOS version 4.0.1 operating system.

Abstracting and Indexing↗
PubMedDate not supplied

Performances of 27 MEDLINE systems tested by searches with clinical questions.

OBJECTIVE: To compare the performances of online and compact-disc (CD-ROM) versions of the National Library of Medicine's (NLM) MEDLINE database. DESIGN: Analytic survey. INTERVENTION: Clinical questions were drawn from 18 searches originally conducted spontaneously by clinicians from wards and clinics who had used Grateful Med Version 4.0. Clinicians' search strategies were translated to meet the specific requirements of 13 online and 14 CD-ROM MEDLINE systems. A senior librarian and vendors' representatives constructed independent searches from the clinicians' questions. The librarian and clinician searches were run through each system, in command mode for the librarian and menu mode for clinicians, when available. Vendor searches were run through the vendors' own systems only. MAIN MEASUREMENTS: Numbers of relevant and irrelevant citations retrieved, cost (for online systems only), and time. RESULTS: Systems varied substantially for all searches, and for librarian and clinician searches separately, with respect to the numbers of relevant and irrelevant citations retrieved (p < 0.001 for both) and the cost per relevant citation (p = 0.012), but not with respect to the time per search. Based on combined rankings for the highest number of relevant and the lowest number of irrelevant citations retrieved, the SilverPlatter CD-ROM MEDLINE clinical journal subset performed best for librarian searches, while the PaperChase online system worked best for clinician searches. For cost per relevant citation retrieved, Dialog's Knowledge Index performed best for both librarian and clinician searches. CONCLUSIONS: There were substantial differences in the performances of competing MEDLINE systems, and performance was affected by search strategy, which was conceived by a librarian or by clinicians.

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PubMed2004

Identifying respiratory findings in emergency department reports for biosurveillance using MetaMap.

Clinical conditions described in patients' dictated reports are necessary for automated detection of patients with respiratory illnesses such as inhalational anthrax and pneumonia. We applied MetaMap to emergency department reports to extract a set of 71 clinical conditions relevant to detection of a lower respiratory outbreak. We indexed UMLS terms in emergency department reports with MetaMap, filtered the indexed output with a specialized lexicon of UMLS terms for the domain, and mapped the clinical conditions of interest to concepts in the lexicon. We compared MetaMap's ability to accurately identify the conditions against a physician's manual annotations and evaluated incorrectly indexed features to determine what additional processing is necessary. MetaMap identified the clinical conditions with a recall of 0.72 and a precision of 0.56. Necessary processing beyond MetaMap's indexing includes finding validation, temporal discrimination, anatomic location discrimination, finding-disease discrimination, and contextual inference. Successful identification of clinical conditions in an emergency department report with MetaMap requires processing techniques specific to the clinical question of interest.

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PubMed1995

Information retrieval in medicine: the SAPHIRE experience.

Information retrieval systems are proliferating in biomedical settings, but many problems in indexing, retrieval, and evaluation of systems continue to exist. The SAPHIRE Project was undertaken to seek solutions to these problems. This paper summarizes the evaluation studies that have been done with SAPHIRE, highlighting the lessons learned and laying out the challenges ahead to all medical information retrieval efforts.

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PubMed2002

Applicability of the adult comorbidity evaluation - 27 and the Charlson indexes to assess comorbidity by notes extraction in a cohort of United Kingdom patients with head and neck cancer: a retrospective study.

The term comorbidity stands for disease processes that co-exist and are not related to the index disease being studied. Comorbidity in cancer has been shown to be a major determinant in treatment selection and survival. Patients with head and neck cancer can have significant comorbidity owing to the high incidence of tobacco and alcohol abuse. No studies to date have addressed this problem in head and neck cancer patients in the United Kingdom. The applicability of the adult comorbidity evaluation - 27 index (ACE-27) and the Charlson index (CI) to assess the comorbidity burden by retrospective notes review is studied here. Retrospective data collection and completion of a comorbidity index in a United Kingdom setting is feasible. We conclude that the pre-assessment visit is a useful time to record comorbidity and as a significant amount of information required for grading relates to historical items, this is best done using a self-administered patient questionnaire.

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PubMed1995

An overview of statistical methods for the classification and retrieval of patient events.

Statistical methods that can support text retrieval are becoming an increasing focus of medical informatics activities. We overview our adaptation of existing knowledge sources to create pseudo-documents for concept based latent semantic indexing. Experience demonstrated this tack of limited practical value, since retrieval performance was invariably unsatisfactory. We discovered this was due in part to the introduction of a vocabulary gap between the queries and the cases we sought to retrieve. In part to address this problem, and to avail our large body of humanly coded text as a knowledge source, we developed a least squares fit alternative for the computer assisted indexing and retrieval of biomedical texts. This technique demonstrates equivalent or superior retrieval performance when compared to all other textual retrieval techniques. It does not depend upon elaborate knowledge bases, lexicons, or thesauri. It is a promising technique for classifying and retrieving the large volumes of clinical text.

Abstracting and Indexing↗
PubMed1983

Using unbound subheadings to increase recall in MEDLINE.

Indexers use subheadings more often than their equivalent main headings. Of a selected group of subheadings, one third had twice as many postings as the equivalent exploded main heading. Searching the subheading as an unbound heading, detached from any main heading descriptors, can be an efficient way of increasing search retrieval.

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PubMed1996

Identifying a core set of medical informatics serials: an analysis using the MEDLINE database.

A study was undertaken to test the hypothesis that a core set of medical informatics serials could be identified by using standard bibliometric techniques. All journal articles indexed by the National Library of Medicine between 1990 and 1994 were included. Articles were identified by using the "MEDICAL INFORMATICS" Medical Subject Heading (MeSH) term. Each serial title containing articles was then ranked according to (1) the total number of medical informatics journal articles indexed and (2) the percentage of medical informatics journal articles indexed. Twenty-eight serials had more than 100 articles indexed under the "MEDICAL INFORMATICS" MeSH term. Thirty serials had more than 40% of their articles indexed under the "MEDICAL INFORMATICS" MESH term. A "core" set of fourteen serials had 100 or more medical informatics articles indexed, including more than 70% of all articles they published. The methodology described provides librarians with another tool to use in the difficult task of journal selection. The set of "core" serials identified provides librarians with a ranked list of serials, based on which a medical informatics collection can be developed.

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PubMed2004

JPEG2000 and dissemination of cultural heritage over the Internet.

By applying the latest technologies in image compression for managing the storage of massive image data within cultural heritage databases and by exploiting the universality of the Internet we are now able not only to effectively digitize, record and preserve, but also to promote the dissemination of cultural heritage. In this work we present an application of the latest image compression standard JPEG2000 in managing and browsing image databases, focusing on the image transmission aspect rather than database management and indexing. We combine the technologies of JPEG2000 image compression with client-server socket connections and client browser plug-in, as to provide with an all-in-one package for remote browsing of JPEG2000 compressed image databases, suitable for the effective dissemination of cultural heritage.

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PubMed2006

Font adaptive word indexing of modern printed documents.

We propose an approach for the word-level indexing of modern printed documents which are difficult to recognize using current OCR engines. By means of word-level indexing, it is possible to retrieve the position of words in a document, enabling queries involving proximity of terms. Web search engines implement this kind of indexing, allowing users to retrieve Web pages on the basis of their textual content. Nowadays, digital libraries hold collections of digitized documents that can be retrieved either by browsing the document images or relying on appropriate metadata assembled by domain experts. Word indexing tools would therefore increase the access to these collections. The proposed system is designed to index homogeneous document collections by automatically adapting to different languages and font styles without relying on OCR engines for character recognition. The approach is based on three main ideas: the use of Self Organizing Maps (SOM) to perform unsupervised character clustering, the definition of one suitable vector-based word representation whose size depends on the word aspect-ratio, and the run-time alignment of the query word with indexed words to deal with broken and touching characters. The most appropriate applications are for processing modern printed documents (17th to 19th centuries) where current OCR engines are less accurate. Our experimental analysis addresses six data sets containing documents ranging from books of the 17th century to contemporary journals.

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PubMed1981

A computerized on-line key word indexing system for drug information retrieval.

The Idaho Drug Information Service has been in operation since 1972. During this time, five different files and manual methods of filing have evolved. As a result of confusion over indexing terms, information became lost within the filing systems, and the files fell into disuse. A reorganization of the files was undertaken in an attempt to develop a filing system that would be functional and efficient. Methods of manual filing are briefly reviewed. A computerized on-line key word indexing system for information storage and retrieval was initiated. The development and operation of the Drug Information Retrieval Terminal System (DIRTS) is described completely. At this time, DIRTS is fully operational. The system has eliminated the previous problems encountered with the manual filing systems, and user response has been good.

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PubMed2003

A literature-based method for assessing the functional coherence of a gene group.

MOTIVATION: Many experimental and algorithmic approaches in biology generate groups of genes that need to be examined for related functional properties. For example, gene expression profiles are frequently organized into clusters of genes that may share functional properties. We evaluate a method, neighbor divergence per gene (NDPG), that uses scientific literature to assess whether a group of genes are functionally related. The method requires only a corpus of documents and an index connecting the documents to genes. RESULTS: We evaluate NDPG on 2796 functional groups generated by the Gene Ontology consortium in four organisms: mouse, fly, worm and yeast. NDPG finds functional coherence in 96, 92, 82 and 45% of the groups (at 99.9% specificity) in yeast, mouse, fly and worm respectively.

Abstracting and Indexing↗
PubMed2000

CISMeF: a structured health resource guide.

In 1999, the Internet has become a major source of health information. The objective of CISMeF is to catalogue and index the main French-speaking health resources. In September 1999, the number of indexed resources totaled over 7,100 with a mean of 75 new sites per week. CISMeF uses two standard tools for organizing information: the Medline bibliographic database MeSH thesaurus and the Dublin Core metadata format. Resources included in CISMeF are described by the following: title, author or creator, subject and keywords, description, publisher, date, resource type, format, identifier, and language. To index resources, CISMeF uses five levels of hierarchy: "meta-term", category, keyword, subheading, and resource type. CISMeF contains a thematic index, including medical specialities and an alphabetic index. CISMeF respects the Net Scoring, criteria to assess the quality of health information on the Internet. The CISMeF project offers a valuable tool for the French-speaking health community: 2,500 computer users visit the Web site each working day.

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PubMed1993

An information sources map for Occupational and Environmental Medicine: guidance to network-based information through domain-specific indexing.

This paper describes a prototype information sources map (ISM), an on-line information source finder, for Occupational and Environmental Medicine (OEM). The OEM ISM was built as part of the Unified Medical Language System (UMLS) project of the National Library of Medicine. It allows a user to identify sources of on-line information appropriate to a specific OEM question, and connect to the sources. In the OEM ISM we explore a domain-specific method of indexing information source contents, and also a domain-specific user interface. The indexing represents a domain expert's opinion of the specificity of an information source in helping to answer specific types of domain questions. For each information source, an index field represents whether a source might provide useful information in an occupational, industrial, or environmental category. Additional fields represent the degree of specificity of a source in individual question types in each category. The paper discusses the development, design, and implementation of the prototype OEM ISM.

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PubMed1987

A vocabulary for medical informatics.

The terminology in medical informatics is evolving rapidly. The organizers of MEDINFO and SCAMC have used different sets of keywords to index their documents. Recognizing the limitations of this approach, members of those organizations joined with the National Library of Medicine in the creation of a better terminology for medical informatics. A hierarchical structure was placed on the terms to produce a thesaurus typical of the sort often used in the indexing and retrieving of documents. The building of this thesaurus began with an automatic merging of the thesaurus used by the Association of Computing Machinery and the Information Sciences component of the "Medical Subject Headings." This product was pruned by eliminating terms not related to those in the MEDINFO keyword list or not in the medical informatics literature. Further refinement of the thesaurus resulted from extensive discussions among the authors of this paper. The first major application of this terminology has been to the indexing of the articles in "MEDINFO-86 Proceedings." Major components of this medical informatics thesaurus also have been incorporated into the "Medical Subject Headings." This paper describes the process of preparing the thesaurus and presents an evaluation of its coverage of the "MEDINFO-86 Proceedings."

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