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PubMedDate not supplied

A UMLS-based knowledge acquisition tool for rule-based clinical decision support system development.

Decision support systems in the medical field have to be easily modified by medical experts themselves. The authors have designed a knowledge acquisition tool to facilitate the creation and maintenance of a knowledge base by the domain expert and its sharing and reuse by other institutions. The Unified Medical Language System (UMLS) contains the domain entities and constitutes the relations repository from which the expert builds, through a specific browser, the explicit domain ontology. The expert is then guided in creating the knowledge base according to the pre-established domain ontology and condition-action rule templates that are well adapted to several clinical decision-making processes. Corresponding medical logic modules are eventually generated. The application of this knowledge acquisition tool to the construction of a decision support system in blood transfusion demonstrates the value of such a pragmatic methodology for the design of rule-based clinical systems that rely on the highly progressive knowledge embedded in hospital information systems.

Artificial Intelligence↗

PubMed1998

Evaluating lexical variant generation to improve information retrieval.

Techniques for managing lexical variation constitute an integral part of information retrieval systems. We report on a series of experiments aimed at evaluating LVG, a lexical variant management tool which addresses the particular problems involved in matching health related vocabularies to concepts in the Unified Medical Language System (UMLS) Metathesaurus. Experiments conducted on data from the Large Scale Vocabulary Test indicate the effectiveness of this approach to managing biomedical information.

Evaluation Studies as Topic↗

PubMedDate not supplied

Lessons learned from a pilot implementation of the UMLS information sources map.

OBJECTIVE: To explore the software design issues involved in implementing an operational information sources map (ISM) knowledge base (KB) and system of navigational tools that can help medical users access network-based information sources relevant to a biomedical question. DESIGN: A pilot biomedical ISM KB and associated client-server software (ISM/Explorer) have been developed to help students, clinicians, researchers, and staff access network-based information sources, as part of the National Library of Medicine's (NLM) multi-institutional Unified Medical Language System (UMLS) project. The system allows the user to specify and constrain a search for a biomedical question of interest. The system then returns a list of sources matching the search. At this point the user may request 1) further information about a source, 2) that the list of sources be regrouped by different criteria to allow the user to get a better overall appreciation of the set of retrieved sources as a whole, or 3) automatic connection to a source. RESULTS: The pilot system operates in client-server mode and currently contains coded information for 121 sources. It is in routine use from approximately 40 workstations at the Yale School of Medicine. The lessons that have been learned are that: 1) it is important to make access to different versions of a source as seamless as possible, 2) achieving seamless, cross-platform access to heterogeneous sources is difficult, 3) significant differences exist between coding the subject content of an electronic information resource versus that of an article or a book, 4) customizing the ISM to multiple institutions entails significant complexities, and 5) there are many design trade-offs between specifying searches and viewing sets of retrieved sources that must be taken into consideration. CONCLUSION: An ISM KB and navigational tools have been constructed. In the process, much has been learned about the complexities of development and evaluation in this new environment, which are different from those for Gopher, wide area information servers (WAIS), World-Wide-Web (WWW), and MOSAIC resources.

Abstracting and Indexing↗

PubMed2002

The cohesive metaschema: a higher-level abstraction of the UMLS Semantic Network.

The Unified Medical Language System (UMLS) joins together a group of established medical terminologies in a unified knowledge representation framework. Two major resources of the UMLS are its Metathesaurus, containing a large number of concepts, and the Semantic Network (SN), containing semantic types and forming an abstraction of the Metathesaurus. However, the SN itself is large and complex and may still be difficult to view and comprehend. Our structural partitioning technique partitions the SN into structurally uniform sets of semantic types based on the distribution of the relationships within the SN. An enhancement of the structural partition results in cohesive, singly rooted sets of semantic types. Each such set is named after its root which represents the common nature of the group. These sets of semantic types are represented by higher-level components called metasemantic types. A network, called a metaschema, which consists of the meta-semantic types connected by hierarchical and semantic relationships is obtained and provides an abstract view supporting orientation to the SN. The metaschema is utilized to audit the UMLS classifications. We present a set of graphical views of the SN based on the metaschema to help in user orientation to the SN. A study compares the cohesive metaschema to metaschemas derived semantically by UMLS experts.

Algorithms↗

PubMed1994

Medical data and knowledge management by integrated medical workstations: summary and recommendations.

The health care professional workstation will function as an interface between the user and the patient data as well as an interface pertinent medical knowledge. Appropriate knowledge focus will require the workstation to recognize the concepts and structure of patient data, and understand the scope and access methods of knowledge sources. Issues are organized around five major themes: (i) structure, (ii) reliability and validation, (iii) views, (iv) location, and (v) ethical and legal. Conventional database representations can effectively address data structure and format variations that will inevitably persist in local data stores. The reliability of data and the validation of knowledge are critical issues that may determine the ultimate utility of clinical workstations. Alternative views of patient information and knowledge sources represent the true power of an intelligent data portal, represented by a well-designed clinical workstation. Both data and knowledge are optimally represented in decentralized information networks, although the confidentiality and ownership of this information must be respected. Evolutionary progress toward consistent representations of knowledge and patient data will be facilitated by the establishment of self-documentation standards for the developers of data encoding systems and knowledge sources, perhaps extended from the preliminary model afforded by the Unified Medical Language System (UMLS).

Computer Security↗

PubMed1997

MedWeaver: integrating decision support, literature searching, and Web exploration using the UMLS Metathesaurus.

Integrating functions from disparate and widely-distributed information systems has been an interest of the medical informatics community for some time. Barriers to progress have included the lack of network-accessible information sources, inadequate methods for inter-system messaging, and lack of vocabulary translation services. With the advent of the World Wide Web (WWW) and the evolution of the National Library of Medicine's Unified Medical Language System (UMLS), it is now possible to develop applications that integrate functions from diverse, distributed systems. In this paper we describe one such system, MedWeaver, a WWW application that integrates functions from a decision support application (DXplain), a literature searching system (WebMedline), and a clinical Web searching system (CliniWeb) using the UMLS Metathesaurus for vocabulary translation. This system demonstrates how application developers can design systems around anticipated clinical information needs and then draw together the needed content and functionality from diverse sources.

Computer Communication Networks↗

PubMed1993

UMLS knowledge for biomedical language processing.

This paper describes efforts to provide access to the free text in biomedical databases. The focus of the effort is the development of SPECIALIST, an experimental natural language processing system for the biomedical domain. The system includes a broad coverage parser supported by a large lexicon, modules that provide access to the extensive Unified Medical Language System (UMLS) Knowledge Sources, and a retrieval module that permits experiments in information retrieval. The UMLS Metathesaurus and Semantic Network provide a rich source of biomedical concepts and their interrelationships. Investigations have been conducted to determine the type of information required to effect a map between the language of queries and the language of relevant documents. Mappings are never straightforward and often involve multiple inferences.

Humans↗

PubMed2002

Semantic annotation for concept-based cross-language medical information retrieval.

We present a framework for concept-based cross-language information retrieval in the medical domain, which is under development in the MUCHMORE project. Our approach is based on using the Unified Medical Language System (UMLS) as the primary source of semantic data. Documents and queries are annotated with multiple layers of linguistic information. Linguistic processing includes part-of-speech tagging, morphological analysis, phrase recognition and the identification of medical terms and semantic relations between them. The paper describes experiments in monolingual and cross-language document retrieval, performed on a corpus of medical abstracts. Results show that linguistic processing, especially lemmatization and compound analysis for German, is a crucial step in achieving a good baseline performance. On the other hand, they show that semantic information, specifically the combined use of concepts and relations, increases the performance in monolingual and cross-language retrieval.

Humans↗

PubMed2004

A comparative study on concept representation between the UMLS and the clinical terms in Korean medical records.

The Unified Medical Language System (UMLS) is a rich source of knowledge in the biomedical domain. In this paper, we evaluated the coverage of UMLS as compared with Korean medical terms and identified differences in concept representation between two vocabulary sets. We measured the concept coverage by mapping clinical terms extracted from the discharge records of Seoul National University Hospital (SNUH) and the UMLS "Sign or Symptom" and "Disease or Syndrome" concepts. Thirty-five percent of the complaints in the SNUH were conceptually matched with the UMLS "Sign or Symptom" concept. Fifty-eight percent were found to be matched with the UMLS "Disease or Syndrome" concept rather than the "Sign or Symptom" concept. The remaining seven percent were not found in the UMLS concepts mapped above or those terms that used to special circumstances of a tertiary hospital in Korea. We then analyzed some of different expression patterns used by the two vocabulary sets and addressed issues to be taken into consideration.

Humans↗

PubMed2005

The comparative study on concept representation between the UMLS and the clinical terms in Korean medical records.

OBJECTIVE: 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 across wide range of different applications. In this paper, we evaluated the coverage of UMLS as compared with medical terms extracted from Korean medical records and identified differences in concept representation between two terminology sets. DESIGN AND MEASUREMENT: We measured the concept coverage of the UMLS. For this study, we mapped the clinical terms extracted from the discharge records of Seoul National University Hospital (SNUH) to the UMLS. RESULTS: Thirty-five percent of the entry terms used in chief complaint of SNUH were conceptually matched with the UMLS 'Sign or Symptom' concepts. Fifty-eight percent of the terms were found to be matched with the UMLS 'Disease or Syndrome' concept rather than the 'Sign or Symptom' concept. The remaining 7% were not found in the UMLS concepts. We then analyzed some of different expression patterns used by the two term sets and addressed issues to be taken into consideration. CONCLUSION: We found out that the UMLS was comparable with Korean medical records, since most of concepts of Korean medical records were covered with the UMLS concepts.

Humans↗

PubMed1991

From patient reports to bibliographic retrieval: a Meta-1 front-end.

A software front-end has been programmed to help construct Medline query expressions from selected text in clinical records. The user "clicks" to choose pertinent words or phrases from the text with a pointing device and the words are translated into Medical Subject Headings (MeSH). The National Library of Medicine's Unified Medical Language System Meta-1 Thesaurus is used to look up the words selected by the user. The software traces through chains of synonyms to assemble a small set of MeSH indexing terms. The user then makes the final selection from among the MeSH terms and combines chosen terms using logical connectives to form a Medline query which is passed on to Grateful Med. This approach provides the clinical user with a natural starting point, the text of a patient report with no need to know the MeSH terminology. The software handles the translation that otherwise would necessitate looking up terms in MeSH guidebooks, as well as handling the added drudgery of checking out different synonyms. Preliminary evaluation of this approach with clinical trainees indicated that they find the front-end a straightforward way to search for literature relevant to a clinical case. Having a tool for immediate translation from clinical terminology to indexing terminology seems to be an important factor. Apparently minor issues in interface design, such as keeping the clinical report displayed simultaneously along with the search under construction, and keeping both visible during the search itself seem to help orient the user.

Grateful Med↗

PubMed1998

Towards interoperability of information sources within a hospital Intranet.

Information is usually available in heterogeneous data format and various legacy sources. Interoperability appears to be a major approach for applications to access information. The project ARIANE is devoted to provide end-users with an easy to use and natural access to information databases. In this frame we defined actors able to operate the mediation between end-users and information servers: a "broker" which selects appropriate resources and "mediators" which access data suppliers. We have implemented a web-oriented stand-alone prototype accessing three types of information sources: a bibliographical server, a SQL database server and a hypertext server. Both broker and mediators exploit the Unified Medical Language System knowledge sources, especially the Information Sources Map which allows a way to identify information servers.

Computer Communication Networks↗

PubMed1998

Conceptual integration of information databases into an Intranet.

Large information systems handle massive volume of data stored in heterogeneous sources of information. Each server has its own model of concepts representation with regard to its aims. One of the main problems encountered by end-users when accessing different servers is to match their own viewpoint on biomedical concepts with their various representations that are made in the database servers. The aim of the project ARIANE is to provide end-users with easy-to-use and natural means to access and query heterogeneous information databases. The objectives of this research work consist in building a conceptual interface by means of the Internet technology inside an enterprise Intranet, and to propose a method to realize it. Moreover, this method provides designers of web sites with a powerful tool to manage them on the basis of an ontology of the biomedical domain. This method is based on the knowledge sources provided by the Unified Medical Language System project of the U.S. National Library of Medicine and exploits intensively the conceptual graphs theory.

Computer Communication Networks↗

PubMedDate not supplied

Standard Generalized Markup Language for self-defining structured reports.

Structured reporting is the process of using standardized data elements and predetermined data-entry formats to record observations. The Standard Generalized Markup Language (SGML; International Standards Organization (ISO) 8879:1986)--an open, internationally accepted standard for document interchange was used to encode medical observations acquired in an Internet-based structured reporting system. The resulting report is self-documenting: it includes a definition of its allowable data fields and values encoded as a report-specific SGML document type definition (DTD). The data-entry forms, DTD, and report document instances are based on report specifications written in a simple, SGML-based language designed for that purpose. Reporting concepts can be linked with those of external vocabularies such as the Unified Medical Language System (UMLS) Metathesaurus. The use of open standards such as SGML is an important step in the creation of open, universally comprehensible structured reports.

Information Storage and Retrieval↗

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↗

PubMedDate not supplied

A system that facilitates the orientation within procedure nomenclatures through a semantic approach.

The representation of medical concepts should provide the flexibility required to support several purposes. We have implemented a model in which medical terms are represented in a standard format based on a semantic description of the terms. We have focused on the description of procedures. Underlying this project is the assumption that information about medical procedures is crucial in the healthcare system. A prototype has been developed for urology. Because of the large number of terms in the Unified Medical Language System (UMLS) and the abundance of links between them, we have experimented in the use of the UMLS as the foundation for our concept base. We assess the usefulness of this approach and discuss its improvements.

Algorithms↗

PubMed2001

Meeting medical terminology needs--the Ontology-Enhanced Medical Concept Mapper.

This paper describes the development and testing of the Medical Concept Mapper, a tool designed to facilitate access to online medical information sources by providing users with appropriate medical search terms for their personal queries. Our system is valuable for patients whose knowledge of medical vocabularies is inadequate to find the desired information, and for medical experts who search for information outside their field of expertise. The Medical Concept Mapper maps synonyms and semantically related concepts to a user's query. The system is unique because it integrates our natural language processing tool, i.e., the Arizona (AZ) Noun Phraser, with human-created ontologies, the Unified Medical Language System (UMLS) and WordNet, and our computer generated Concept Space, into one system. Our unique contribution results from combining the UMLS Semantic Net with Concept Space in our deep semantic parsing (DSP) algorithm. This algorithm establishes a medical query context based on the UMLS Semantic Net, which allows Concept Space terms to be filtered so as to isolate related terms relevant to the query. We performed two user studies in which Medical Concept Mapper terms were compared against human experts' terms. We conclude that the AZ Noun Phraser is well suited to extract medical phrases from user queries, that WordNet is not well suited to provide strictly medical synonyms, that the UMLS Metathesaurus is well suited to provide medical synonyms, and that Concept Space is well suited to provide related medical terms, especially when these terms are limited by our DSP algorithm.

Algorithms↗

PubMed1992

The findings--diagnosis continuum: implications for image descriptions and clinical databases.

As part of the Unified Medical Language System (UMLS) project, we have been exploring the use of semantic net representation to build a medical ontology that can adapt to the needs and perspective of differing kinds of users with varying purposes. A principal objective is to facilitate indexing and retrieval of objects in a variety of target databases, using their own source vocabularies, while maintaining the representation of concepts to which these source vocabularies refer in a single consistent form, so that retrievals that span resource types can be accommodated. In addition, a particular area of deficiency of the existing UMLS Metathesaurus is that of clinical findings, a part of the problem being the multiple alternative views and granularity levels at which clinical findings are described in different target databases. The problem is particularly obvious when one examines the way in which image findings are described, which may be at a purely perceptual level, or at varying levels of aggregation into higher level observations or interpretations. We have developed a recursive model for representing observations and interpretations in a semantic net along a continuum of degree of aggregation, that appears to lend itself well to adaptation to varying perspectives.

Diagnosis, Computer-Assisted↗