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PubMed1983

Segregation index: an orsametric for measuring discrimination against minorities.

Orsametrics, the science of data and measurement appropriate to decision-making models, was proposed by H. M. Wagner in 1971. This paper proposes an orsametric measuring the distance between the current distribution of minorities in the organization and the worst distribution that minorities could have, given a specified proportion of minorities present in the organization. Measurement of this distance via the absolute value norm leads to a constrained model in which a convex, absolute-value functional must be maximized. This is accomplished by means of an algorithm designed to take advantage of the special structural properties of the model. An example is provided to demonstrate how the segregation index can be used to track discrimination levels within an organization through time. (Orsametrics: public sector applications-quantification of discriminatory hiring promotion practices; mathematical modelling-nonlinear, maximizing a convex function subject to linear constraints.

Abstracting and Indexing↗

PubMed1991

A comparison of the currency of secondary information sources in the biomedical literature. I. Weekly current awareness services.

Three biomedical current awareness products which are distributed on floppy disc, were studied over a period of 3 months. They were monitored for the speed with which primary journal issues were indexed, and for the coverage of the journals which were selected for study. Data on issues of 72 monthly journals (38 North American and 34 European) and nine weekly titles (four from North America and five from Europe) were recorded. The time to elapse between publication date and arrival of hard copy in the British libraries and appearance in secondary sources varied enormously. The findings suggest that monthly journal issues appear in the secondary sources on average 6-7 weeks after publication date and weekly journals appear after approximately 4 weeks. Indexing of North American monthly journals is 1 week ahead of European titles in the two products from the US, but the European service indexed European publications sooner. One product, Current Contents on Diskette, contained all issues included in the 3-month period covered by the study, but Reference Update omitted 9.1% of the issues and Medical Science Weekly 1.6%, including leading biomedical journals.

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PubMed2002

HealthCyberMap: a semantic visual browser of medical Internet resources based on clinical codes and the human body metaphor.

OBJECTIVES: HealthCyberMap (HCM-http://healthcybermap.semanticweb.org) is a web-based service for healthcare professionals and librarians, patients and the public in general that aims at mapping parts of the health information resources in cyberspace in novel ways to improve their retrieval and navigation. METHODS AND SERVICE DESCRIPTION: HCM adopts a clinical metadata framework built upon a clinical coding ontology for the semantic indexing, classification and browsing of Internet health information resources. A resource metadata base holds information about selected resources. HCM then uses GIS (Geographic Information Systems) spatialization methods to generate interactive navigational cybermaps from the metadata base. These visual cybermaps are based on familiar medical metaphors. CONCLUSIONS: HCM cybermaps can be considered as semantically spatialized, ontology-based browsing views of the underlying resource metadata base. Using a clinical coding scheme as a metric for spatialization ('semantic distance') is unique to HCM and is very much suited for the semantic categorization and navigation of Internet health information resources. Clinical codes ensure reliable and unambiguous topical indexing of these resources. HCM also introduces a useful form of cyberspatial analysis for the detection of topical coverage gaps in the resource metadata base using choropleth (shaded) maps of human body systems.

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PubMed2004

Doublet method for very fast autocoding.

BACKGROUND: Autocoding (or automatic concept indexing) occurs when a software program extracts terms contained within text and maps them to a standard list of concepts contained in a nomenclature. The purpose of autocoding is to provide a way of organizing large documents by the concepts represented in the text. Because textual data accumulates rapidly in biomedical institutions, the computational methods used to autocode text must be very fast. The purpose of this paper is to describe the doublet method, a new algorithm for very fast autocoding. METHODS: An autocoder was written that transforms plain-text into intercalated word doublets (e.g. "The ciliary body produces aqueous humor" becomes "The ciliary, ciliary body, body produces, produces aqueous, aqueous humor"). Each doublet is checked against an index of doublets extracted from a standard nomenclature. Matching doublets are assigned a numeric code specific for each doublet found in the nomenclature. Text doublets that do not match the index of doublets extracted from the nomenclature are not part of valid nomenclature terms. Runs of matching doublets from text are concatenated and matched against nomenclature terms (also represented as runs of doublets). RESULTS: The doublet autocoder was compared for speed and performance against a previously published phrase autocoder. Both autocoders are Perl scripts, and both autocoders used an identical text (a 170+ Megabyte collection of abstracts collected through a PubMed search) and the same nomenclature (neocl.xml, containing over 102,271 unique names of neoplasms). In side-by-side comparison on the same computer, the doublet method autocoder was 8.4 times faster than the phrase autocoder (211 seconds versus 1,776 seconds). The doublet method codes 0.8 Megabytes of text per second on a desktop computer with a 1.6 GHz processor. In addition, the doublet autocoder successfully matched terms that were missed by the phrase autocoder, while the phrase autocoder found no terms that were missed by the doublet autocoder. CONCLUSIONS: The doublet method of autocoding is a novel algorithm for rapid text autocoding. The method will work with any nomenclature and will parse any ascii plain-text. An implementation of the algorithm in Perl is provided with this article. The algorithm, the Perl implementation, the neoplasm nomenclature, and Perl itself, are all open source materials.

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PubMed2004

MeSH and specialized terminologies: coverage in the field of molecular biology.

There is real need among researchers for data in molecular biology, due to the explosive development in this field. Information extraction techniques have been developed in this specific domain, to extract structured information from the literature. The National Library of Medicine provides access to 12 million MEDLINE citations, accessible via PubMed. Information retrieval techniques which are used to select documents that are relevant according to user request. As other domains in medicine, biomolecular scientific literature is indexed by MeSH terms. Automatic identification of protein and gene names in scientific articles is an important step in the indexing process, since proteins and genes are often associated with multiple names, and authors alternate between these synonyms. In this article we assess the contribution of specialized terminologies in the field of molecular biology compared to MeSH.

Abstracting and Indexing↗

PubMed1988

The comprehensiveness of computer-assisted searches of the medical literature.

Bibliographic searches using MEDLINE, the National Library of Medicine computerized database, can usually be done in less time and with greater specificity than searches using Index Medicus. To use a computer-assisted bibliographic retrieval system to full advantage, it is necessary to understand the indexing system. The study reported here compares both the number and the relevance of references retrieved using various search terms for two clinical questions. Based on the outcomes of these searches, recommendations are made for clinicians who plan to use MEDLINE services.

Abstracting and Indexing↗

PubMedDate not supplied

PathMaster: content-based cell image retrieval using automated feature extraction.

OBJECTIVE: Currently, when cytopathology images are archived, they are typically stored with a limited text-based description of their content. Such a description inherently fails to quantify the properties of an image and refers to an extremely small fraction of its information content. This paper describes a method for automatically indexing images of individual cells and their associated diagnoses by computationally derived cell descriptors. This methodology may serve to better index data contained in digital image databases, thereby enabling cytologists and pathologists to cross-reference cells of unknown etiology or nature. DESIGN: The indexing method, implemented in a program called PathMaster, uses a series of computer-based feature extraction routines. Descriptors of individual cell characteristics generated by these routines are employed as indexes of cell morphology, texture, color, and spatial orientation. MEASUREMENTS: The indexing fidelity of the program was tested after populating its database with images of 152 lymphocytes/lymphoma cells captured from lymph node touch preparations stained with hematoxylin and eosin. Images of "unknown" lymphoid cells, previously unprocessed, were then submitted for feature extraction and diagnostic cross-referencing analysis. RESULTS: PathMaster listed the correct diagnosis as its first differential in 94 percent of recognition trials. In the remaining 6 percent of trials, PathMaster listed the correct diagnosis within the first three "differentials." CONCLUSION: PathMaster is a pilot cell image indexing program/search engine that creates an indexed reference of images. Use of such a reference may provide assistance in the diagnostic/prognostic process by furnishing a prioritized list of possible identifications for a cell of uncertain etiology.

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PubMed2005

Regional journals in medicine and public health: a look to the future upon the indexing of the Revista Chilena de Infectología.

Revista Chilena de Infectología has recently been accepted for index listing in the Index Medicus via the MEDLINE data base. This breakthrough prompts reflection on the nature of regionally focused subspecialty journals and what such a listing means for better dissemination of scientific and medical discoveries reported in such journals. There is a conscientious global effort at present to better represent regional journals in indexing systems and to make access easier for persons in less wealthy nations to medical and public health information via the internet. These trends are reviewed and discussed in the context of Chile's national medical and public health literature.

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PubMed2006

Mapping the literature of emergency nursing.

PURPOSE: Emergency nursing covers a broad spectrum of health care from trauma surgery support to preventive health care. The purpose of this study is to identify the core literature of emergency nursing and to determine which databases provide the most thorough indexing access to the literature cited in emergency nursing journals. This study is part of the Medical Library Association's Nursing and Allied Health Resources Section's project to map the nursing literature. METHODS: Four key emergency nursing journals were selected and subjected to citation analysis based on Bradford's Law of Scattering. RESULTS: A group of 12 journals made up 33.3% of the 7,119 citations, another 33.3% of the citations appeared in 92 journals, with the remaining 33.3% scattered across 822 journals. Three of the core 12 journals were emergency medicine titles, and 2 were emergency nursing titles from the selected source journals. Government publications constituted 7.5% of the literature cited. CONCLUSIONS: PubMed/MEDLINE provided the best overall indexing coverage for the journals, followed by CINAHL. However, CINAHL provided the most complete coverage for the source journals and the majority of the nursing and emergency medical technology publications and should be consulted by librarians and nurses seeking emergency nursing literature.

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PubMed1996

Modeling principles for QMR medical findings.

Structured representation of medical information is essential for ensuring the accuracy and reliability of computerized decision support applications. Such systems require input that is error-free and clinically pertinent. This paper reviews existing medical models, particularly those exploited for natural language understanding, and highlights modeling features important to future indexing of medical texts with controlled vocabularies. A hybrid representation derived from existing frame-based and conceptual-graph-based systems is proposed to represent relevant medical terms as used by experts.

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PubMed2005

Influence of strategic direction for NHS Scotland knowledge services on indexing policy for the NHS Scotland e-library.

OBJECTIVES: Indexing policy for the NHS Scotland e-Library needs to maximize future inter-operability with other significant health- and social-care-related resources. The strategic drive towards integration and partnership working means that the indexing system has to be widely acceptable to the full range of disciplines within the integrated health-care family. METHODS: Indexes identified by various means and then shortlisted using predefined criteria. RESULTS: Three subject indexes have been chosen--Medical Subject Headings (MeSH), CareData and the Government Category List (GCL), plus mapping between natural language and MeSH terms. This decision was a reasonable compromise between the strategy-driven aim of seamless access for all 'partners in care', and practical constraints of time/manpower. Other authority files (e.g. geographical area, language) are also standards based, and customised to reflect the information needs of an increasingly integrated health-care system. CONCLUSIONS: No single index could provide the scope required to meet the widening range of NHS information need. The influence of high-level strategic aims and objectives have extended their reach to influence indexing policy for the e-Library. Our indexing policy will continue to evolve and contribute to a knowledge management infrastructure capable of supporting current and future NHS Scotland information needs and strategy. Layperson terminology was identified as a gap; additional measures to address this gap are highlighted.

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PubMed1983

Problems in the diagnosis of intermittent explosive disorder.

The authors studied the accuracy with which intermittent explosive disorder was diagnosed in a university hospital setting. An index of diagnostic features abstracted from the description of intermittent explosive disorder in DSM-III was used for chart review. Diagnosis of the disorder was made in 20 out of 830 admissions (2.4%). In 14 cases (1.7%) it was a primary one; in another five (.6%) it was secondary; and in one case (.1%) it was tertiary. The authors discuss the varied rigorousness of the diagnosis and the importance of using an index of diagnostic features to enhance diagnostic accuracy.

Adolescent↗

PubMed2003

Metadata element set in a quality-controlled subject gateway: a step to a health semantic Web.

BACKGROUND: Quality-controlled subject gateways are Internet services which apply a selected set of targeted measures to support systematic resource discovery. Considerable manual effort is used to process a selection of resources which meet quality criteria and to display a extensive description and indexing of these resources with standards-based metadata. OBJECTIVE: Several metadata element sets are proposed to describe, index and quality health resources to be included in a French quality-controlled health gateway called CISMeF. The main objectives were to enhance Internet health document retrieval and navigation, and to allow interoperability with other Internet services. RESULTS: The Dublin Core metadata element set is used to describe and index all Internet health resources included in CISMeF. For teaching resources, some elements from IEEE1484 Learning Object Metadata are also used. For evidenced-base medicine resources, specific metadata are employed which assess the health content quality. The HIDDEL metadata set is used to enhance transparency, trust and quality of health information on the Internet. CONCLUSION: Comprehensive metadata element sets can be extremely useful to describe, index and assess health resources on the Internet in a quality-controlled subject gateway. Machine-readable metadata creates an Semantic Web which is more efficient for end-users as compared to the current Web.

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PubMed2006

Mapping the general literature of American 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 by general or "popular" US nursing journals and the indexing services that cover the cited journals. METHODS: Three journals were selected for analysis: American Journal of Nursing, Nursing 96-98, and RN. The source journals were subjected to a citation analysis of articles from 1996 to 1998, followed by an analysis of database access to the most frequently cited journal titles. RESULTS: Cited formats included journals (63.7%), books (26.6%), government documents (3.0%), Internet (0.5%), and miscellaneous (6.2%). Cited references were relatively current; most (86.6%) were published in the current decade. One-third of the citations were found in a core of 24 journal titles; one-third were dispersed among a middle zone of 94 titles; and the remaining third were scattered in a larger zone of 694 titles. Indexing coverage for the core titles was most comprehensive in PubMed/MEDLINE, followed by CINAHL and Science Citation Index. CONCLUSIONS: Results support the popular (not scholarly) nature of these titles. While not a good source for original research, they fulfill a key role of disseminating nursing knowledge with their relevantly current citations to a broad variety of sources.

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PubMed1986

[Codus: a coding system for ultrasonic examinations].

A semeiologic and anatomic code for ultrasound imaging data has been in use for 3 years. A simple index, it allows coding under specific headings of almost all ultrasound record sheets and can be modified as a function of the requirement of different departments. It is also perfectly well adapted for inclusion in a data-processing system.

Abstracting and Indexing↗

PubMed2005

Automatic assignment of biomedical categories: toward a generic approach.

MOTIVATION: We report on the development of a generic text categorization system designed to automatically assign biomedical categories to any input text. Unlike usual automatic text categorization systems, which rely on data-intensive models extracted from large sets of training data, our categorizer is largely data-independent. METHODS: In order to evaluate the robustness of our approach we test the system on two different biomedical terminologies: the Medical Subject Headings (MeSH) and the Gene Ontology (GO). Our lightweight categorizer, based on two ranking modules, combines a pattern matcher and a vector space retrieval engine, and uses both stems and linguistically-motivated indexing units. RESULTS AND CONCLUSION: Results show the effectiveness of phrase indexing for both GO and MeSH categorization, but we observe the categorization power of the tool depends on the controlled vocabulary: precision at high ranks ranges from above 90% for MeSH to <20% for GO, establishing a new baseline for categorizers based on retrieval methods.

Abstracting and Indexing↗

PubMed2003

SIRW: A web server for the Simple Indexing and Retrieval System that combines sequence motif searches with keyword searches.

SIRW (http://sirw.embl.de/) is a World Wide Web interface to the Simple Indexing and Retrieval System (SIR) that is capable of parsing and indexing various flat file databases. In addition it provides a framework for doing sequence analysis (e.g. motif pattern searches) for selected biological sequences through keyword search. SIRW is an ideal tool for the bioinformatics community for searching as well as analyzing biological sequences of interest.

Abstracting and Indexing↗

PubMed1986

Usage of "principal" and "primary" designations in disease and operations indexes.

The medical record practitioner must maintain proficiency in all areas related to coding and indexing of disease and operation information. This article presents evidence that there is confusion concerning the basic terminology used to designate such information. It appears that many practitioners have lost sight of the purpose in making the distinctions "primary" and "principal".

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