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Biomedical subjects

A T McCray

Publications and source records attributed to A T McCray.

At least 19 recordsLinked to original sources
PubMed2006

On exemplary scientific conduct regarding submission of manuscripts to biomedical informatics journals.

As the Editors of leading international biomedical informatics journals, the authors report on a recent pattern of improper manuscript submissions to journals in our field. As a guide for future authors, we describe ethical and pragmatic issues related to submitting work for peer-reviewed journal publication. We propose a coordinated approach to the problem that our respective journals will follow. This Editorial is being jointly published in the following journals represented by the authors: Computer Methods and Programs in Biomedicine, International Journal of Medical Informatics, Journal of Biomedical Informatics, Journal of the American Medical Informatics Association, and Methods of Information in Medicine.

Biomedical Research↗
PubMed2006

Triangulation applied to Jan H. van Bemmel.

OBJECTIVE: To describe the person of Jan H. van Bemmel from different points of view. METHOD: Triangulation. RESULTS AND CONCLUSIONS: Jan H. van Bemmel successfully contributed to research and education in medical informatics. He inspired a lot of people in The Netherlands and internationally.

Biomedical Research↗
PubMed2005

Biomedical ontologies.

Explore the source record for details and available documents.

Cell Physiological Phenomena↗
PubMed2003

From phenotype to genotype: issues in navigating the available information resources.

OBJECTIVES: As part of an investigation of connecting health professionals and the lay public to both disease and genomic information, we assessed the availability and nature of the data from the Human Genome Project relating to human genetic diseases. METHODS: We focused on a set of single gene diseases selected from main topics in MEDLINEplus, the NLM's principal resource focused on consumers. We used publicly available websites to investigate specific questions about the genes and gene products associated with the diseases. We also investigated questions of knowledge and data representation for the information resources and navigational issues. RESULTS: Many online resources are available but they are complex and technical. The major challenges encountered when navigating from phenotype to genotype were (1) complexity of the data, (2) dynamic nature of the data, (3) diversity of foci and number of information resources, and (4) lack of use of standard data and knowledge representation methods. CONCLUSIONS: Three major informatics issues arise from the navigational challenges. First, the official gene names are insufficient for navigation of these web resources. Second, navigational inconsistencies arise from difficulties in determining the number and function of alternate forms of the gene or gene product and maintaining currency with this information. Third, synonymy and polysemy cause much confusion. These are severe obstacles to computational navigation from phenotype to genotype, especially for individuals who are novices in the underlying science. Tools and standards to facilitate this navigation are sorely needed.

Databases, Genetic↗
PubMed2001

Aggregating UMLS semantic types for reducing conceptual complexity.

The conceptual complexity of a domain can make it difficult for users of information systems to comprehend and interact with the knowledge embedded in those systems. The Unified Medical Language System (UMLS) currently integrates over 730,000 biomedical concepts from more than fifty biomedical vocabularies. The UMLS semantic network reduces the complexity of this construct by grouping concepts according to the semantic types that have been assigned to them. For certain purposes, however, an even smaller and coarser-grained set of semantic type groupings may be desirable. In this paper, we discuss our approach to creating such a set. We present six basic principles, and then apply those principles in aggregating the existing 134 semantic types into a set of 15 groupings. We present some of the difficulties we encountered and the consequences of the decisions we have made. We discuss some possible uses of the semantic groups, and we conclude with implications for future work.

Semantics↗
PubMed2001

Evaluating UMLS strings for natural language processing.

The National Library of Medicine's Unified Medical Language System (UMLS) is a rich source of knowledge in the biomedical domain. The UMLS is used for research and development in a range of different applications, including natural language processing (NLP). In this paper we investigate the nature of the strings found in the UMLS Metathesaurus and evaluate them for their usefulness in NLP. We begin by identifying a number of properties that might allow us to predict the likelihood of a given string being found or not found in a corpus. We use a statistical model to test these predictors against our corpus, which is derived from the MEDLINE database. For one set of properties the model correctly predicted 77% of the strings that do not belong to the corpus, and 85% of the strings that do belong to the corpus. For another set of properties the model correctly predicted 96% of the strings that do not belong to the corpus and 29% of the strings that do belong to the corpus.

MEDLINE↗
PubMed2000

Better access to information about clinical trials.

Access to information about clinical trials is important to researchers, health care professionals, and patients. Many have argued for the establishment of clinical trials registries, citing their substantial benefits. Although some registries do exist, it has been difficult to create comprehensive, easily accessible systems. This paper briefly reviews existing registries, discusses the challenges in building registries, and reviews some of their benefits. The paper concludes with a description of a new, extensive Web-based registry called ClinicalTrials.gov (http://clinicaltrials. gov/), which was developed at the National Institutes of Health (NIH) by the National Library of Medicine as a result of recent legislation calling for a comprehensive, publicly accessible registry of clinical trials. The first version of the system became available in late February 2000 and contains information about approximately 5000 trials. The first release contains primarily NIH-sponsored trials, and new trials are regularly added to the system. Subsequent versions will contain information about trials sponsored by other federal agencies and by the private sector. The system was developed in accordance with basic informatics principles, including adherence to standards, usability considerations, and iterative testing and evaluation.

Clinical Trials as Topic↗
PubMed2000

Digital library research and application.

The last decade has seen an exponential rise in the amount and the nature of information that is available on the Internet. Internet and World Wide Web technology have raised many technical as well as social and economic issues. The paper begins with a description of the recent digital library research initiative funded by the U.S. federal government. Digital library research addresses a host of informatics issues relevant to the current Internet-based environment. The paper continues with a discussion of some problems in information access, including a discussion of the potential of the Unified Medical Language System for navigating among multiple biomedical information systems. Next, some issues in creating Web-accessible resources for health care consumers are addressed, with a focus on recent work at the National Library of Medicine, including a description of the MEDLINEplus system. The paper ends with a brief discussion of some implications of digital library research for the health informatics community.

Internet↗
PubMed2000

Usability issues in developing a Web-based consumer health site.

ClinicalTrials.gov is a Web-based system intended for a diverse audience, including patients, family members and other members of the public. Throughout the system design and development process, our decisions have been driven by usability concerns. We first describe the overall design of the site, including the home page, which provides a site overview and rapid access to the information contained within it. Next we discuss the data presentation format which has been standardized in spite of data coming to us from many different sources. We provide a detailed description of the search and browse features that are intended to simplify the complexities of medical terminology and support information discovery. We conclude with a review of our evaluation activities and future plans.

Clinical Trials as Topic↗
PubMed1999

Terminology issues in user access to Web-based medical information.

We conducted a study of user queries to the National Library of Medicine Web site over a three month period. Our purpose was to study the nature and scope of these queries in order to understand how to improve users' access to the information they are seeking on our site. The results show that the queries are primarily medical in content (94%), with only a small percentage (5.5%) relating to library services, and with a very small percentage (.5%) not being medically relevant at all. We characterize the data set, and conclude with a discussion of our plans to develop a UMLS-based terminology server to assist NLM Web users.

Databases as Topic↗
PubMed1998

From French vocabulary to the Unified Medical Language System: a preliminary study.

The Unified Medical Language System (UMLS) is an extensive source of biomedical knowledge developed and maintained by the U.S. National Library of Medicine (NLM). The UMLS began to include biomedical terms in other languages a few years ago. However, providing foreign terms for existing concepts is only the first step for the UMLS to become international. The current limits of the use of the UMLS in French are analyzed (partial translation, unique source of the translated concepts, improper character set, and absence of lexical resources for lexical matching tools). Some suggestions are given for French to be better integrated into the UMLS, especially for adapting the lexical resources to French. Once completed, our present work is expected to give the UMLS the capability to be effectively queried in French.

France↗
PubMed1998

The nature of lexical knowledge.

This paper considers the nature of lexical knowledge and its role in language and information processing. The lexicon is the central component of language and plays a pivotal role in current linguistic theory [3, 4] and, increasingly, in natural language processing systems [5-7]. The lexicon embodies information about the lexical items of the language and serves as the foundation for morphologic, syntactic, and semantic processing. The differences as well as commonalities among dictionaries, thesauri, and lexicons are discussed, and distinctions between words, lexical items, and terms are drawn. Next, the scope and content of the SPECIALIST lexicon are presented, followed by a discussion of certain writing conventions that can be troublesome for text processing applications. One approach to handling orthographic and other lexical variation is discussed in a section that reports on the design and implementation of the SPECIALIST lexical programs. The paper concludes with a discussion of controlled terminologies for the medical domain. Throughout the discussion, examples are drawn from the SPECIALIST lexicon and from the other UMLS knowledge sources [8, 9].

Humans↗
PubMed1998

Discovering the modifiers in a terminology data set.

We recently conducted a study of a subset of the data collected in the NLM/AHCPR Large Scale Vocabulary Test (LSVT). We studied those 11,387 terms in the LSVT data that were narrower in meaning than the UMLS concepts mapped to. We hypothesized that when one term is narrower in meaning than another, the first and second terms are likely to differ primarily by modification. We compared three lexical processing methods of increasing sophistication and measured the ability of each of these methods to correctly identify the modifiers in the data set. The results indicate that when using the most powerful of the methods, 63% of the term pairs were found to differ only by premodification, by postmodification or by both, 31% share some lexical material, and the remaining 6% have no lexical items in common. The implications of the study are discussed.

Methods↗
PubMed1997

Conducting the NLM/AHCPR Large Scale Vocabulary Test: a distributed Internet-based experiment.

The Large Scale Vocabulary Test, sponsored by the National Library of Medicine (NLM) and the Agency for Health Care Policy and Research (AHCPR), was conducted to determine the extent to which a combination of existing health-related terminologies cover vocabulary needed in health care information systems. The test was conducted over the Internet using a sophisticated World Wide Web interface with over 60 participants and over 40,000 terms submitted. This paper discusses the issues encountered in the design and execution of the experiment, including the design of the interface and the issues of recruitment, training, and guidance of remote participants over the Internet. Test data are currently undergoing expert review. Upon completion of the expert review, the results of the test will be fully reported.

Computer Communication Networks↗
PubMed1996

The UMLS Knowledge Source Server: a versatile Internet-based research tool.

The National Library of Medicine's Unified Medical Language System (UMLS) project regularly distributes a set of Knowledge Sources to the research community. In 1995 the UMLS data were made available for the first time through the Internet-based UMLS Knowledge Source Server. The server can be accessed through three different client interfaces. The World Wide Web interface allows users to browse and explore the data and to see how those data are organized in the UMLS. The command-line interface is best suited for batch processing, and the application programming interface allows developers at remote sites to embed calls in their application programs to the Knowledge Source Server.

Computer Communication Networks↗
PubMed1995

ASN.1: defining a grammar for the UMLS knowledge sources.

The unified Medical Language System (UMLS) project provides resources on an experimental basis to the research community. In 1995 the four UMLS Knowledge Sources have been provided in an additional data format, Abstract Syntax Notation One (ASN.1). The benefits of ASN.1 are that it provides a standard, formal grammar for complex data and allows exchange of that data in a way which is independent of the particular software and hardware environment in which the data are created and stored. The paper begins with an introduction to the ASN.1 standard itself. It continues with a discussion of the ASN.1 implementation of the UMLS Knowledge Sources and some of the consequences for the newly released UMLS Knowledge Source Server. It concludes with a discussion of some of the benefits of using ASN.1 encoded data.

Computer Communication Networks↗
PubMed1995

The UMLS Knowledge Source server.

The UMLS Knowledge Source server is an evolving tool for accessing information stored in the UMLS Knowledge Sources. The system architecture is based on the client-server paradigm wherein remote site users send their requests to a centrally managed server at the U.S. National Library of Medicine. The client programs can run on platforms supporting the TCP/IP communication protocol. Access to the system is provided through a command-line interface and through an Application Programming Interface.

Computer Communication Networks↗