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PubMed2003

Consistency across the hierarchies of the UMLS Semantic Network and Metathesaurus.

OBJECTIVE: To develop and test a method for automatically detecting inconsistencies between the parent-child is-a relationships in the Metathesaurus and the ancestor-descendant relationships in the Semantic Network of the Unified Medical Language System (UMLS). METHODS: We exploited the fact that each Metathesaurus concept is assigned one or more semantic types from the UMLS Semantic Network and that the semantic types are arranged in a hierarchy. We compared the semantic types of each pair of parent and child concepts to determine if the types "explained" the Metathesaurus is-a relationships. We considered cases where the semantic type of the parent was neither the same as, nor an ancestor of, the semantic type of the child to be "unexplained." We applied this method to the January 2002 release of the UMLS and examined the unexplained cases we discovered to determine their causes. RESULTS: We found that 17022 (24.3%) of the parent-child is-a relationships in the UMLS Metathesaurus could not be explained based on the semantic types of the concepts. Causes for these discrepancies included cases where the parent or child was missing a semantic type, cases where the semantic type of the child was too general or the semantic type of the parent was too specific, cases where the parent-child relationship was incorrect, and cases where an ancestor-descendant relationship should be added to the UMLS Semantic network. In many cases, the specific cause of the discrepancy cannot be resolved without authoritative judgment by the UMLS developers. CONCLUSIONS: Our method successfully detects inconsistencies between the hierarchies of the UMLS Metathesaurus and Semantic Network. We believe that our method should be added to the set of tools that the UMLS developers use to maintain and audit the UMLS knowledge sources.

Abstracting and Indexing↗

PubMed1994

A comparison of four schemes for codification of problem lists.

We set out to evaluate the completeness of four major coding schemes in representation of the patient problem list: the Unified Medical Language System (UMLS, 4th edition), the Systematized Nomenclature of Medicine (SNOMED International), the Read coding system (version 2), and the International Classification of Diseases (9th Clinical Modification)(ICD-9-CM). We gathered 400 problems from patient records at primary care sites in Omaha and Seattle. Matching these against the best description found in each of the coding schemes, we asked five medical faculty reviewers to rate the matches on a five-point Likert scale assessing their satisfaction with the results. For the four schemes, we computed the following rates of dissatisfaction, satisfaction, and average scores: [table: see text] From this analysis, we conclude that UMLS and SNOMED performed substantially better in capturing the clinical content of the problem lists than READ or ICD-9-CM. No scheme could be considered comprehensive. Depending on the goal of systems developers, UMLS and SNOMED may offer different, and complementary, advantages.

Disease↗

PubMed1995

Knowledge acquisition from the UMLS sources: application to the description of surgical procedures.

The re-usability of lexicons and knowledge in medicine is a crucial challenge. The Unified Medical Language System (UMLS) project has attempted to provide a repository of concepts, semantically categorized for biomedical domain. This paper describes some results about the relevance of UMLS structures for specific purposes. We have focused on the description of surgical procedures. Discussion concerns synonymy of terms, granularity of concepts, and ontology. A preliminary work on the exploitation of interconcept links by a computerized application reveals a heterogeneous implementation of those relationships. However, the UMLS provides a powerful knowledge base for developers.

General Surgery↗

PubMed2001

An object-oriented model for representing semantic locality in the UMLS.

Several information models have been developed for the Unified Medical Language System (UMLS). While some models are term-oriented, a knowledge-oriented model is needed for representing semantic locality, i.e. the various semantic links among concepts. We propose an object-oriented model in which the semantic features of the UMLS are made available through four major classes for representing Metathesaurus concepts, semantic types, inter-concept relationships and Semantic Network relationships. Additional semantic methods for reducing the complexity of the hierarchical relationships represented in the UMLS are proposed. Implementation details are presented, as well as examples of use. The interest of this approach is discussed.

Artificial Intelligence↗

PubMed2004

Towards the development of a conceptual distance metric for the UMLS.

The objective of this work is to investigate the feasibility of conceptual similarity metrics in the framework of the Unified Medical Language System (UMLS). We have investigated an approach based on the minimum number of parent links between concepts, and evaluated its performance relative to human expert estimates on three sets of concepts for three terminologies within the UMLS (i.e., MeSH, ICD9CM, and SNOMED). The resulting quantitative metric enables computer-based applications that use decision thresholds and approximate matching criteria. The proposed conceptual matching supports problem solving and inferencing (using high-level, generic concepts) based on readily available data (typically represented as low-level, specific concepts). Through the identification of semantically similar concepts, conceptual matching also enables reasoning in the absence of exact, or even approximate, lexical matching. Finally, conceptual matching is relevant for terminology development and maintenance, machine learning research, decision support system development, and data mining research in biomedical informatics and other fields.

Algorithms↗

PubMed2002

The lexical properties of the gene ontology.

The Gene Ontology (GO) is a construct developed for the purpose of annotating molecular information about genes and their products. The ontology is a shared resource developed by the GO Consortium, a group of scientists who work on a variety of model organisms. In this paper we investigate the nature of the strings found in the Gene Ontology and evaluate them for their usefulness in natural language processing (NLP). We extend previous work that identified a set of properties that reliably identifies natural language phrases in the Unified Medical Language System (UMLS). The results indicate that a large percentage (79%) of GO terms are potentially useful for NLP applications. Some 35% of the GO terms were found in a corpus derived from the MEDLINE bibliographic database, and 27% of the terms were found in the current edition of the UMLS.

Genes↗

PubMed2003

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↗

PubMed2005

Identifying consumer-friendly display (CFD) names for health concepts.

We have developed a systematic methodology using corpus-based text analysis followed by human review to assign "consumer-friendly display (CFD) names" to medical concepts from the National Library of Medicine (NLM) Unified Medical Language System (UMLS) Metathesaurus. Using NLM MedlinePlus queries as a corpus of consumer expressions and a collaborative Web-based tool to facilitate review, we analyzed 425 frequently occurring concepts. As a preliminary test of our method, we evaluated 34 ana-lyzed concepts and their CFD names, using a questionnaire modeled on standard reading assessments. The initial results that consumers (n=10) are more likely to understand and recognize CFD names than alternate labels suggest that the approach is useful in the development of consumer health vocabularies for displaying understandable health information.

Community Participation↗

PubMed1998

An international dermatological image atlas on the WWW: practical use for undergraduate and continuing medical education, patient education and epidemiological research.

We describe the development of an image database DOIA (Dermatological OnlIne Atlas) and present several spin-off projects using images of the atlas, e.g. student education using the atlas including results of an questionnaire evaluating computer-literacy, prerequisites and interests of students for using computers and the World-Wide-Web (WWW), a patient information system and an experiment to collect epidemiological data from patients with dermatological diseases via WWW. The database, available on the WWW at http:@www.derma.med.uni-erlangen.de, contains about 3,000 clinical images covering more than 540 dermatological diagnoses. It is designed for worldwide use; international submissions are encouraged. One aim of the project is to compile an international reference for dermatological images, containing images of high educational quality and also covering conditions on different skin types and rare diagnoses which are not commonly illustrated in ordinary textbooks. All images were originally mapped to the Erlanger Diagnosis Code, which is a proprietary modified ICD-9 key, later also to the UMLS (Unified Medical Language System). In addition, images are described with keys for the location, physical attributes of the location and clinical and histopathological features of the lesion. In order to facilitate the integration of the atlas into other web-based medical resources and to allow easy access to additional information, the Erlanger Diagnosis Code was mapped to the CUIs (unique concept identifiers) of the UMLS Metathesaurus. One purpose of the UMLS is to allow conversion of terms from one controlled medical vocabulary to another, thus, mapping of our diagnosis code to the UMLS CUIs allows simultaneous search for a given diagnosis in a number of other databases and also access to our image database from other databases. Mapping was successful for 619 out of 1383 dermatological diagnosis terms. For images with these diagnoses we are able to provide a hyperlink to other databases available on the Internet, such as MEDLINE, PDQ and OMIM, with automatic retrieval using the preferred vocabulary of the respective database. By grouping all diagnoses into sets with similar morphologies we further integrated a differential diagnosis mode. In order to educate patients via the Internet, a separate patient information system has been developed, using images of the electronic atlas. As an experiment to explore the feasibility of the Internet to gather epidemiological data from patients, users are asked to complete an electronic questionnaire covering signs for atopy. We conclude that an online image atlas has multiple educational, clinical and research applications.

Computer-Assisted Instruction↗

PubMed1999

Exploring the UMLS: a rough sets based theoretical framework.

The Unified Medical Language System (UMLS) [1] has a unique and leading position in the evolution of thesauri and metathesauri. Features that set it apart are: its composition from more than fifty component health care vocabularies; the sophisticated UMLS ontology linking the Metathesaurus with structures such as the Semantic Network and the SPECIALIST lexicon; and the high level of social collaboration invested in its construction and growth. It is our thesis that in order to successfully harness such a complex vocabulary for text retrieval we need sophisticated methods derived from a deeper understanding of the UMLS system. Thus we propose a theoretical framework based on the theory of rough sets, that supports the systematic and exploratory investigation of the UMLS Metathesaurus for text retrieval. Our goal is to make it more feasible for individuals such as patients and health care professionals to access relevant information at the point of need.

Humans↗

PubMed1992

Evaluation of a Meta-1-based automatic indexing method for medical documents.

This paper describes MetaIndex, an automatic indexing program that creates symbolic representations of documents for the purpose of document retrieval. MetaIndex uses a simple transition network parser to recognize a language that is derived from the set of main concepts in the Unified Medical Language System Metathesaurus (Meta-1). MetaIndex uses a hierarchy of medical concepts, also derived from Meta-1, to represent the content of documents. The goal of this approach is to improve document retrieval performance by better representation of documents. An evaluation method is described, and the performance of MetaIndex on the task of indexing the Slice of Life medical image collection is reported.

Abstracting and Indexing↗

PubMed2003

Exploring medical expressions used by consumers and the media: an emerging view of consumer health vocabularies.

Healthcare consumers often have difficulty expressing and understanding medical concepts. The goal of this study is to identify and characterize medical expressions or "terms" (linguistic forms and associated concepts) used by consumers and health mediators. In particular, these terms were characterized according to the degree to which they mapped to professional medical vocabularies. Lay participants identified approximately 100,000 term tokens from online discussion forum postings and print media articles. Of the over 81,000 extracted term tokens reviewed, more than 75% were mapped as synonyms or quasi-synonyms to the Unified Medical Language System (UMLS) Metathesaurus. While 80% conceptual overlap was found between closely mapped lay (consumer and mediator) and technical (professional) medical terms, about half of these overlapping concepts contained lay forms different from technical forms. This study raises questions about the nature of consumer health vocabularies that we believe have theoretical and practical implications for bridging the medical vocabulary gap between consumers and professionals.

Delivery of Health Care↗

PubMed2004

Ontology development for unified traditional Chinese medical language system.

Traditional Chinese medicine (TCM) as a complete knowledge system researches into human health conditions via a different approach compared to orthodox medicine. We are developing a unified traditional Chinese medical language system (UTCMLS) through an ontology approach that will support TCM language knowledge storage, concept-based information retrieval and information integration. UTCMLS is a huge knowledge project, which is a broad collaboration of 16 distributed groups, most of them with no prior experience of formal ontology development. Therefore, the cooperative and comprehensive ontology engineering is crucial. We use Protégé 2000 for ontology development of concepts and relationships that represent the domain and that will permit storage of TCM knowledge. This paper focuses on the methodology, design and development of ontology for UTCMLS.

Humans↗

PubMed2005

Generating models of surgical procedures using UMLS concepts and multiple sequence alignment.

Surgical procedures can be viewed as a process composed of a sequence of steps performed on, by, or with the patient's anatomy. This sequence is typically the pattern followed by surgeons when generating surgical report narratives for documenting surgical procedures. This paper describes a methodology for semi-automatically deriving a model of conducted surgeries, utilizing a sequence of derived Unified Medical Language System (UMLS) concepts for representing surgical procedures. A multiple sequence alignment was computed from a collection of such sequences and was used for generating the model. These models have the potential of being useful in a variety of informatics applications such as information retrieval and automatic document generation.

Abstracting and Indexing↗

PubMedDate not supplied

Knowledge-based approaches to the maintenance of a large controlled medical terminology.

OBJECTIVE: Develop a knowledge-based representation for a controlled terminology of clinical information to facilitate creation, maintenance, and use of the terminology. DESIGN: The Medical Entities Dictionary (MED) is a semantic network, based on the Unified Medical Language System (UMLS), with a directed acyclic graph to represent multiple hierarchies. Terms from four hospital systems (laboratory, electrocardiography, medical records coding, and pharmacy) were added as nodes in the network. Additional knowledge about terms, added as semantic links, was used to assist in integration, harmonization, and automated classification of disparate terminologies. RESULTS: The MED contains 32,767 terms and is in active clinical use. Automated classification was successfully applied to terms for laboratory specimens, laboratory tests, and medications. One benefit of the approach has been the automated inclusion of medications into multiple pharmacologic and allergenic classes that were not present in the pharmacy system. Another benefit has been the reduction of maintenance efforts by 90%. CONCLUSION: The MED is a hybrid of terminology and knowledge. It provides domain coverage, synonymy, consistency of views, explicit relationships, and multiple classification while preventing redundancy, ambiguity (homonymy) and misclassification.

Computer Simulation↗

PubMed1992

Enhancing the Metathesaurus with clinically relevant concepts: anatomic representations.

To create a comprehensive taxonomy for medical concepts it is necessary to identify gaps and reconcile differences that exist between clinical, bibliographic, and other source vocabularies. As part of the Unified Medical Language System project, we have proposed enhancements to the Metathesaurus by the inclusion of terms from two source vocabularies with different unique perspectives or views. This process has disclosed a number of issues that arise as complexity increases. These issues must be resolved if the resultant Metathesaurus is to support the variety of uses for which it is intended.

Abstracting and Indexing↗

PubMed2000

Knowledge engineering the UMLS.

In order to transform a major portion of the Unified Medical Language System (UMLS) into a formally sound description logics system we have developed a four-step knowledge engineering approach. We report on experiments with a Loom knowledge base which consists of 164,000 concepts and 76,000 relations covering human anatomy and pathology. We discuss the fully automatized as well as interactive semiautomatic steps. The latter ones focus on the manual work necessary to render the formal target representation structures complete and adequate.

Artificial Intelligence↗

PubMedDate not supplied

Representing the UMLS as an object-oriented database: modeling issues and advantages.

OBJECTIVE: The Unified Medical Language System (UMLS) combines many well-established authoritative medical informatics terminologies in one knowledge representation system. Such a resource is very valuable to the health care community and industry. However, the UMLS is very large and complex and poses serious comprehension problems for users and maintenance personnel. The authors present a representation to support the user's comprehension and navigation of the UMLS. DESIGN: An object-oriented database (OODB) representation is used to represent the two major components of the UMLS-the Metathesaurus and the Semantic Network-as a unified system. The semantic types of the Semantic Network are modeled as semantic type classes. Intersection classes are defined to model concepts of multiple semantic types, which are removed from the semantic type classes. RESULTS: The authors provide examples of how the intersection classes help expose omissions of concepts, highlight errors of semantic type classification, and uncover ambiguities of concepts in the UMLS. The resulting UMLS OODB schema is deeper and more refined than the Semantic Network, since intersection classes are introduced. The Metathesaurus is classified into more mutually exclusive, uniform sets of concepts. The schema improves the user's comprehension and navigation of the Metathesaurus. CONCLUSIONS: The UMLS OODB schema supports the user's comprehension and navigation of the Metathesaurus. It also helps expose and resolve modeling problems in the UMLS.

Databases as Topic↗