The effect of contraceptive knowledge source upon knowledge accuracy and contraceptive behavior.
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Ontology acquisition from on-line knowledge sources.
Electronic knowledge representation is becoming more and more pervasive both in the form of formal ontologies and less formal reference vocabularies, such as UMLS. The developers of clinical knowledge bases need to reuse these resources. Such reuse requires a new generation of tools for ontology development and management. Medical experts with little or no computer science experience need tools that will enable them to develop knowledge bases and provide capabilities for directly importing knowledge not only from formal knowledge bases but also from reference terminologies. The portions of knowledge bases that are imported from disparate resources then need to be merged or aligned to one another in order to link corresponding terms, to remove redundancies, to resolve logical conflicts. We discuss the requirements for ontology-management tools that will enable interoperability of disparate knowledge sources. Our group is developing a suite of tools for knowledge-base management based on the Protégé-2000 environment for ontology development and knowledge acquisition. We describe one such tool in detail here: an application for incorporating information from remote knowledge sources such as UMLS into a Protégé knowledge base.
Artificial Intelligence↗
Semantic visualization of oncology knowledge sources.
Visualization of knowledge sources can have a substantial impact on the use of such sources at the point of care. This is because barriers to use at the point of care include hours required to master the electronic interfaces to those sources, and minutes required to master the electronic interfaces to those sources, and minutes required to accomplish any one retrieval. For a system to be used regularly at the point of care, therefore, it must be intuitive and fast. This paper presents a three dimensional interface to oncology knowledge sources that aims to meet this challenge.
Databases, Factual↗
Profiling Canadian nurses' preferred knowledge sources for clinical practice.
Several researchers have examined nurses' knowledge sources within the context of research utilization, but conclusions are equivocal. Common problems include a lack of replication, conflicting results, poor generalizability of results, and unclear implications for practice. The objectives of this study were to: (a) describe sources of knowledge and their frequency of use among staff nurses across 7 surgical units, (b) compare knowledge-source patterns across the units, (c) determine whether knowledge-source preferences correlate to research utilization scores, and (d) profile staff nurses' knowledge-source patterns over time. A total of 230 nurses in 5 adult and 2 pediatric surgical units from 4 hospitals in the Canadian provinces of Alberta and Ontario completed a self-administered survey. The results were compared to the findings of previous studies. Nurses' knowledge-source preferences were consistent across the 7 units despite differences in education and in research utilization scores. Across all units, nurses preferred to use knowledge gained through personal experience and interactions with co-workers and with individual patients rather than journal articles or textbooks. These findings are consistent with the longitudinal comparison in the 2 earlier studies. In contrast to the knowledge privileged by nurse clinicians, researchers tend to place greater value on research-based knowledge than on experience-based knowledge. To increase research utilization in the practice setting, researchers and others need first to understand the reasons behind clinicians' valuing of experiential and social knowledge sources and then to consider research dissemination and implementation strategies that are more closely aligned with clinician preferences.
Attitude of Health Personnel↗
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↗
Extracting medical knowledge for a coded problem list vocabulary from the UMLS Knowledge Sources.
INTRODUCTION: The Unified Medical Language System (UMLS) Knowledge Sources embody a rich source of medical knowledge. We sought to extract a portion of this knowledge by incorporating information about relationships between UMLS concepts into an existing problem list vocabulary. METHODS: We matched terms from the coded problem list of The Medical Record (TMR), a computer-based patient record system, with those found in the UMLS Metathesaurus. Those UMLS concepts that participate in 'parent' relationships with the matched TMR concepts were translated back into TMR codes and the relationship information was retained for integration into the coded problem list of TMR. RESULTS: Of the coded problems currently in use in TMR, 67% (1627/2436) could be matched by normalized string matches to the UMLS Knowledge Sources. Of these matched TMR concepts, 91% (1488/1627) participated in at least one UMLS-identified parent relationship but only 28% of the matched concepts (454/1627) participated in parent relationships that already matched to a TMR code. As a result, although 67% of TMR codes were matched to UMLS concepts, only 19% of our original problem list (454/2436) could be augmented by relationship information contained in UMLS without improving the rate of matches or adding additional UMLS concepts as coded problems in TMR. CONCLUSION: This study illustrates the rapid decline in overall rates of matching that result from a multiplicative effect of successive matches of terms to concepts, concepts to relationships and concepts back to entry terms. This effect will hamper any effort to extract relationship knowledge from the UMLS for incorporation into an entry vocabulary that is not already one of the source vocabularies of the UMLS Metathesaurus.
Humans↗
Integrating genomic knowledge sources through an anatomy ontology.
Modern genomic research has access to a plethora of knowledge sources. Often, it is imperative that researchers combine and integrate knowledge from multiple perspectives. Although some technology exists for connecting data and knowledge bases, these methods are only just beginning to be successfully applied to research in modem cell biology. In this paper, we argue that one way to integrate multiple knowledge sources is through anatomy--both generic cellular anatomy, as well as anatomic knowledge about the tissues and organs that may be studied via microarray gene expression experiments. We present two examples where we have combined a large ontology of human anatomy (the FMA) with other genomic knowledge sources: the gene ontology (GO) and the mouse genomic databases (MGD) of the Jackson Labs. These two initial examples of knowledge integration provide a proof of concept that anatomy can act as a hub through which we can usefully combine a variety of genomic knowledge and data.
Anatomy↗
Assessing and enhancing the value of the UMLS Knowledge Sources.
The goal of the UMLS Project is to give practitioners and researchers easy access to machine-readable information from diverse sources. Assessment of the first experimental versions of the UMLS Knowledge Sources is essential to measuring progress toward that goal and to identifying needed enhancements. As of July 30, 1991, copies of the first edition of the UMLS Knowledge Sources had been distributed to 143 individuals and institutions; 66 had provided initial feedback information. The information received indicates that the UMLS Knowledge Sources will undergo broad testing in the patient care, medical education, library service, and product development environments. Preliminary data support the hypothesis that expanded coverage of routine clinical concepts is needed. Key enhancements planned for 1992 and beyond include expanded coverage of ICD-9-CM and CPT.
National Library of Medicine (U.S.)↗
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↗
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↗
The UMLS knowledge source server: an object model for delivering UMLS data.
The Unified Medical Language System (UMLS), a project of the National Library of Medicine (NLM), regularly distributes a set of knowledge sources to the research community. These data are made available over the Internet through the UMLS Knowledge Source Server (UMLSKS). The new version of the UMLSKS is a complete redesign of the original system using Java and the Extensible Markup Language (XML) technologies to implement a fast, reliable, flexible, and extensible UMLS data retrieval system that includes an Application Programmer's Interface (API) and an Object Model of each of the Knowledge Sources: the UMLS Metathesaurus, the Semantic Network, and the SPECIALIST Lexicon. In this paper we present the design of the new system, outline each of the system design goals, the UMLS Object Model, and statistics showing the usage of the new UMLSKS and associated data. We conclude with implications for future work.
Information Storage and Retrieval↗
Coach: applying UMLS knowledge sources in an expert searcher environment.
With the development of the Unified Medical Language System (UMLS) Knowledge Sources, the National Library of Medicine (NLM) has produced a resource of great potential for improving the searching of MEDLINE. The Coach expert searcher system, an inhouse research project at NLM, is designed to help users of the GRATEFUL MED front-end software improve MEDLINE search and retrieval capabilities. This paper describes the Coach program, the knowledge sources it uses, and some of the ways it applies elements of the UMLS Metathesaurus to facilitate access to the biomedical literature.
Grateful Med↗
Evaluation of the Unified Medical Language System as a medical knowledge source.
OBJECTIVE: The authors evaluated the use of the Unified Medical Language System (UMLS) as a medical knowledge source for the representation of medical procedures in the MAOUSSC system. DESIGN: MAOUSSC, a multiaxial coding system, was used for the representation of 1500 procedures from 15 clinical specialties, using UMLS concepts (augmented by full sources for three new vocabularies being added to the UMLS) and relationships whenever possible. Evaluation criteria for the UMLS included (1) completeness of representation of concepts and of inter-concept relationships, (2) consistency in the categorization of both concepts and inter-concept relationships, and (3) usability, including adaptability of the UMLS to a foreign language (French), its suitability to a geographic region with different medical practices than the USA, and issues relative to the annual update changes in the test vocabularies. RESULTS: During the MAOUSSC trial, the number of missing concepts or relationships identified in the augmented UMLS sources was deemed to be inconsequential relative to overall project goals. "Missing" UMLS inter-concept relationships were identified, although they were small in number. Some inconsistencies in the UMLS were noted, especially in the area of hierarchic relationships. CONCLUSION: After UMLS was used for five years as a knowledge source for representing 1500 complex medical procedures in MAOUSSC, its value is considered significant. Future editions of the UMLS are expected to improve representation of inter-concept relationships and global consistency.
Language↗
Sublexical Orthographic-Phonological Relations Early in the Acquisition of Reading: The Knowledge Sources Account
Tests are made of an aspect of the "knowledge sources" theoretical account of acquisition of reading in which, contrary to the developmental bypass hypothesis, it is postulated that sublexical relations between orthographic and phonological components are formed very early in learning by spontaneous induction from stored print word experience. Experiments 1 and 2, conducted with 5- and 6-year-old children, indicated as predicted that positional frequency of orthographic components in experienced print words influenced reading responses to unfamiliar pseudoword items. In Experiment 3 positional frequency of an orthographic component was manipulated in a training-transfer paradigm. Transfer to pseudoword reading was as predicted. The results could not be given alternative explanations by the developmental bypass hypothesis nor by accounts which predict exclusive use of onset and rime units at this early reading level.
Journal Article↗
Interactive query workstation: a demonstration of the practical use of UMLS knowledge sources.
The Interactive Query Workstation (IQW) has been developed to provide clinicians with a uniform program interface for retrieving medical-related information from various computer-based information resources. These resources can vary in content (bibliographic databases, drug information, general medical text databases), function (article retrieval, differential diagnosis, drug interaction detection, or drug dosage and administration information), and media formats (local hard disk, CD-ROM, local area network, or distant telecommunication link). IQW allows modular addition of new resources as well as extension of previously installed resources. The National Library of Medicine's three Unified Medical Language System (UMLS) Knowledge Sources, the Metathesaurus (Meta), the Semantic Network, and the Information Sources Map (ISM) have been incorporated into many aspects of IQW. Meta provides information about medical terminology and aids IQW in isolating the basic concepts from a clinician's question. The Semantic Network provides information about the categorization of concepts and possible relations between concepts. It also assists IQW in determining which queries are appropriate for a set of concepts contained in the clinician's question. The ISM provides information about the content available from a computer-based resources and aids IQW in selecting an appropriate resource from which to collect information. The computer-based resource selection is performed without user intervention. This interactive demonstration shows an environment which increases the accessibility of medical information to clinicians by utilizing the three UMLS Knowledge Sources.
Information Storage and Retrieval↗
Aligning knowledge sources in the UMLS: methods, quantitative results, and applications.
The UMLS Semantic Network and Metathesaurus are two complementary knowledge sources. While many studies compare relationships across the two structures, their alignment has never been attempted. We applied two methods based on lexical and conceptual similarity to aligning the Semantic Network with the UMLS Metathesaurus. Approximately two thirds of the semantic types could be aligned by lexical similarity. Conceptual similarity suggested mappings in all but ten cases. Potential applications enabled by the alignment are discussed, namely auditing the consistency between the Semantic Network and the Metathesaurus and extending the Semantic Network downwards. The relative contribution and limitations of the two methods used for the alignment are also discussed.
Semantics↗
A Web Services architecture for UMLS Knowledge Sources.
A web service is a collection of industry standards to enable reusability of services and interoperability of heterogeneous applications. The UMLS Knowledge Source (UMLSKS) Server provides remote access to the UMLSKS and related resources. We propose a Web Services Architecture that encapsulates UMLSKS-API and makes it available in distributed and heterogeneous environments. This is the first step towards intelligent and automatic UMLS services discovery and invocation by computer systems in distributed environments such as web.
Internet↗
The rubber meets the road: integrating the Unified Medical Language System Knowledge Source Server into the computer-based patient record.
Ongoing improvements in the content of the Unified Medical Language System, coupled with the recent release of the Internet-based Knowledge Source Server (KSS), have prompted us to develop an interface between the KSS and our computer-based patient record. We confronted many challenges while developing a robust interface to an Internet-based server, and in integrating the process of codification into the workflow of clinicians. An initial evaluation of the interface in the clinical environment suggests that acceptable performance is attainable. The benefits of using an Internet-accessible tool in a clinical information system appear to justify the effort required.
Humans↗