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PubMed1995

Comparing clinical vocabularies using coding system fidelity.

Much effort has been directed toward the development of an ideal multipurpose controlled medical vocabulary for use in human and veterinary medicine. SNOMED International is one effort that has resulted in a larger and more complex nomenclature system. Although it was able to code more concepts, SNOMED International failed to statistically improve vocabulary fidelity when compared with the 30+ year old SNVDO vocabulary. We found that SNOMED has a lower intercoder consistency than SNVDO and that a greater number of codes were necessary to represent an individual concept. Our study shows a significant Coder-Vocabulary interaction which suggests that more emphasis should be placed on coding guidelines and coder training. Clinician data entry and coding may be necessary for maximum vocabulary fidelity.

Abstracting and Indexing↗
PubMed2001

Psychiatric, psychosocial, and cognitive functioning of female adolescents with ADHD.

OBJECTIVE: To characterize the psychiatric, psychosocial, and cognitive functioning of female adolescents with attention-deficit/hyperactivity disorder (ADHD) in comparison with female controls and males with ADHD. Female controls were also compared with male controls to verify gender differences in a nonclinical sample. METHOD: One hundred seven adolescents from Southern Ontario aged 13 to 16 were included: 24 females with ADHD, 35 males with ADHD, 28 control females, and 20 control males. All were assessed with semistructured interviews, questionnaires, and tests of achievement and intellectual functioning. RESULTS: After controlling for parental education and estimated Full Scale IQ, females with ADHD were more impaired than control females in depression, anxiety, distress, teacher relationships, stress, attributional styles, and locus of control and on all cognitive and achievement measures. Females with ADHD were more impaired than males with ADHD in self-reported anxiety, distress, depression, locus of control, and vocabulary scores. These group differences were confirmed by higher ratings by parents and teachers in symptoms of psychopathology. Males with ADHD were more impaired in processing speed. Some gender differences (locus of control and vocabulary scores) were eliminated when controlling for ADHD severity. The absence of any differences between male and female controls indicates gender differences were specific to the clinical groups. CONCLUSION: Females with ADHD are at high risk for more psychological impairment than both males with ADHD and control females. The identified psychosocial problems point to areas for intervention.

Achievement↗
PubMedDate not supplied

Read Code quality assurance: from simple syntax to semantic stability.

As controlled clinical vocabularies assume an increasing role in modern clinical information systems, so the issue of their quality demands greater attention. In order to meet the resulting stringent criteria for completeness and correctness, a quality assurance system comprising a database of more than 500 rules is being developed and applied to the Read Thesaurus. The authors discuss the requirement to apply quality assurance processes to their dynamic editing database in order to ensure the quality of exported products. Sources of errors include human, hardware, and software factors as well as new rules and transactions. The overall quality strategy includes prevention, detection, and correction of errors. The quality assurance process encompasses simple data specification, internal consistency, inspection procedures and, eventually, field testing. The quality assurance system is driven by a small number of tables and UNIX scripts, with "business rules" declared explicitly as Structured Query Language (SQL) statements. Concurrent authorship, client-server technology, and an initial failure to implement robust transaction control have all provided valuable lessons. The feedback loop for error management needs to be short.

Clinical Medicine↗
PubMedDate not supplied

Evaluating the coverage of controlled health data terminologies: report on the results of the NLM/AHCPR large scale vocabulary test.

OBJECTIVE: To determine the extent to which a combination of existing machine-readable health terminologies cover the concepts and terms needed for a comprehensive controlled vocabulary for health information systems by carrying out a distributed national experiment using the Internet and the UMLS Knowledge Sources, lexical programs, and server. METHODS: Using a specially designed Web-based interface to the UMLS Knowledge Source Server, participants searched the more than 30 vocabularies in the 1996 UMLS Metathesaurus and three planned additions to determine if concepts for which they desired controlled terminology were present or absent. For each term submitted, the interface presented a candidate exact match or a set of potential approximate matches from which the participant selected the most closely related concept. The interface captured a profile of the terms submitted by the participant and for each term searched, information about the concept (if any) selected by the participant. The term information was loaded into a database at NLM for review and analysis and was also available to be downloaded by the participant. A team of subject experts reviewed records to identify matches missed by participants and to correct any obvious errors in relationships. The editors of SNOMED International and the Read Codes were given a random sample of reviewed terms for which exact meaning matches were not found to identify exact matches that were missed or any valid combinations of concepts that were synonymous to input terms. The 1997 UMLS Metathesaurus was used in the semantic type and vocabulary source analysis because it included most of the three planned additions. RESULTS: Sixty-three participants submitted a total of 41,127 terms, which represented 32,679 normalized strings. More than 80% of the terms submitted were wanted for parts of the patient record related to the patient's condition. Following review, 58% of all submitted terms had exact meaning matches in the controlled vocabularies in the test, 41% had related concepts, and 1% were not found. Of the 28% of the terms which were narrower in meaning than a concept in the controlled vocabularies, 86% shared lexical items with the broader concept, but had additional modification. The percentage of exact meanings matches varied by specialty from 45% to 71%. Twenty-nine different vocabularies contained meanings for some of the 23,837 terms (a maximum of 12,707 discrete concepts) with exact meaning matches. Based on preliminary data and analysis, individual vocabularies contained < 1% to 63% of the terms and < 1% to 54% of the concepts. Only SNOMED International and the Read Codes had more than 60% of the terms and more than 50% of the concepts. CONCLUSIONS: The combination of existing controlled vocabularies included in the test represents the meanings of the majority of the terminology needed to record patient conditions, providing substantially more exact matches than any individual vocabulary in the set. From a technical and organizational perspective, the test was successful and should serve as a useful model, both for distributed input to the enhancement of controlled vocabularies and for other kinds of collaborative informatics research.

Evaluation Studies as Topic↗
PubMed2003

Data representation in healthcare: a design for a freely-available openly-developed international reference terminology for healthcare.

The importance of data representation in healthcare has been of concern for centuries. In the last fifty years there has been an increasing awareness of the need for formal representations of terminological systems. We propose that terminological system development should be consensus driven and the product of iterative open refinement in order to practically serve the needs of the healthcare community. The system of development and maintenance of such a system must involve recruitment of the best and the brightest in the medical community to take responsibility for insuring the accuracy and completeness of such an effort. We suggest a method for algorithmically building a starting point for such a reference terminology. Further we suggest a distributed authoring environment that would allow domain experts to contribute regardless of their location or language. Open intellectual contribution is the necessary ingredient for a consensus based international health reference terminology.

Algorithms↗
PubMed2006

Quality assurance of medical ontologies.

OBJECTIVE: To review the literature concerning the quality assurance of medical ontologies. METHODS: scholar.google.com was searched using the search strings (+ontology +"quality assurance") and (+ontology +"evaluation/evaluating"). Relevant publications were selected by manual review. Other work already familiar to the author, or suggested by other researchers contacted by the author, were included. The papers were analysed for common themes. RESULTS: Four broad properties of an ontology were identified that may be quality-assured: philosophical validity, compliance with meta-ontological commitments, 'content correctness', and fitness for purpose. Each published methodology addressed only a subset of these properties. 'Content' may be divided into domain knowledge content, and metadata describing either the provenance of domain knowledge content, or relationships between it and lexical information (e.g. for display and retrieval). 'Correctness' (whether of domain knowledge content or metadata) may also be further subdivided into truth, completeness, parsimony and internal consistency. CONCLUSIONS: Understanding of how to assure the quality of ontologies, or evaluate their fitness for specific purposes, is improving but remains poor. A combination of methodologies is required, but tools to support a comprehensive quality assurance programme remain lacking. Perfect quality of an ontology is not provable and may not be desirable: an ontology compliant with all current philosophical theories, following necessary ontological commitments, and with entirely 'correct' content, may be too complex to be directly usable or useful. The extent to which an ontology's fitness for purpose is predicted or influenced by its other properties remains to be determined. Field studies of ontologies in use, including interrater effects, are required.

Medical Informatics↗
PubMed2004

GOChase: correcting errors from Gene Ontology-based annotations for gene products.

SUMMARY: The Gene Ontology (GO) is a controlled biological vocabulary that provides three structured networks of terms to describe biological processes, cellular components and molecular functions. Many databases of gene products are annotated using the GO vocabularies. We found that some GO-updating operations are not easily traceable by the current biological databases and GO browsers. Consequently, numerous annotation errors arise and are propagated throughout biological databases and GO-based high-level analyses. GOChase is a set of web-based utilities to detect and correct the errors in GO-based annotations.

Database Management Systems↗
PubMed1994

Data storage and knowledge representation for clinical workstations.

The representation of patient information for use in clinical workstations is a complex problem. Ideally, it should be addressed in a way that allows multiple uses of the data, including simple manual review, sharing and pooling across institutions, and as input to knowledge-based decision support systems. To a great extent, this means coding information with controlled medical vocabularies, but it does not mean that all information must be codable before workstations are feasible. This paper defines some of the choices, both current and future, that are available to address the needs of controlled medical vocabularies for representing data and knowledge in clinical workstations and explores some of the implications of those choices.

Computer Communication Networks↗
PubMed1996

Cognitive evaluation of the user interface and vocabulary of an outpatient information system.

This paper describes an innovative approach to the evaluation of the user interface and vocabulary of a medical information system. The use of video recording for collecting usability data is detailed. The technique employed involves the collection of data consisting of transcripts of physicians as they "think aloud" while interacting with the system, along with a video record of the complete user-computer interaction. Using methods of analysis from cognitive science, the study was able to distinguish the source of physician problems in using the system's interface and in interacting with its controlled medical vocabulary. Analysis of the protocols indicated that all subjects encountered several generic problems, the most common ones indicative of a need for greater consistency in the interface design. Based on this evaluation, parts of the user interface have been re-implemented in an ongoing process of iterative system development.

Ambulatory Care Facilities↗
PubMed2001

A metadata vocabulary for self- and third-party labeling of health web-sites: Health Information Disclosure, Description and Evaluation Language (HIDDEL).

We describe HIDDEL (Health Information Disclosure, Description and Evaluation Language), formerly known as medPICS (platform for Internet content selection in medicine), a metadata vocabulary designed to enhance transparency, trust and quality of health information on the web. The vocabulary may be used (1) by webmasters to self-describe their contents and policies; (2) by infomediaries (e.g. Healthfinder, NHS Direct/NeLH), e.g. third party evaluators, rating or portal services, to annotate other websites; (3) and by users, to describe their preferences. As an XML application it conforms to the W3C's RDF Specification. The metadata vocabulary is primarily intended to enable descriptions of whole health websites or health information providers. The vocabulary is designed to provide a computer-readable electronic "label" of a health website, telling users who is behind the website, how the website is sponsored, what the con-tent, aim and target audience is, how the information was compiled, what risks the service bears, or what people say about the resource. Client-software can "read" this label automatically, compare it to the user s own set of preferences and needs, and alert and advise users.

Information Services↗
PubMed1999

A large-scale evaluation of terminology integration characteristics.

OBJECTIVE: To describe terminology integration characteristics of local specialty specific and general vocabularies in order to facilitate the appropriate inclusion and mapping of these terms into a large-scale terminology. METHODS: We compared the sensitivity, specificity, positive predictive value, and positive likelihood ratios for Automated Term Composition to correctly map 9050 local specialty specific (dermatology) terms and 4994 local general terms to UMLS using Metaphrase. Results were systematically combined among exact matches, semantic type filtered matches, and non-filtered matches. For the general set, an analysis of semantic type filtering was performed. RESULTS: Dermatology exact matches defined a sensitivity of 51% (57% for general terms) and a specificity of 86% (92% general terms). Including semantic type filtered matches increased sensitivity (75% dermatology; 88% general); as did inclusion of non-filtered matches (98% and 99%). These inclusions correspondingly decreased specificity (filtered: 82% and 74%; non-filtered: 52% and 32%). Positive predictive values for exact matches (93.0% dermatology, 97.6% general) were improved by small but significant (p < 0.001) margins by including filtered matches (95.1% dermatology, 98.4% general) but decreased with non-filtered matches (89.2% dermatology, 87.8% general). Adding additional semantic types to the filtering algorithm failed to improve the positive predictive value or the positive likelihood ratio of term mapping, in spite of a 2.3% improvement in sensitivity. CONCLUSIONS: Automated methods for mapping local "colloquial" terminologies to large-scale controlled health vocabulary systems are practical (ppv 95% dermatology, 98% general). Semantic type filtering improves specificity without sacrificing sensitivity and yields high positive predictive values in every set analyzed.

Algorithms↗
PubMedDate not supplied

Quality assurance in anatomic pathology: automated SNOMED coding.

This case study details the set-up and implementation of the PathNet autocoder (Cerner Corporation) in a busy anatomic pathology laboratory. After initial start-up, procedures were developed to improve the system's performance. Four classes of software coding errors were identified, and an index was developed to measure the number of cases between errors (CBE). Through modifications in the program, the CBE increased sharply by the end of the six-month study period. During the last three months of the study, the efficiency of case retrieval was tested by comparing manual and electronic methods on the same reference cases. This demonstrated significant time saving and removed the variability of manual coding. The technique employed in this study may assist other institutions seeking to implement such a coding system within their respective environments.

Clinical Laboratory Information Systems↗
PubMed2006

Quality control for terms and definitions in ontologies and taxonomies.

BACKGROUND: Ontologies and taxonomies are among the most important computational resources for molecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO), the most prominent taxonomic resource in these fields, is marked by flaws of certain characteristic types, which flow from a failure to address basic ontological principles. As yet, no methods have been proposed which would allow ontology curators to pinpoint flawed terms or definitions in ontologies in a systematic way. RESULTS: We present computational methods that automatically identify terms and definitions which are defined in a circular or unintelligible way. We further demonstrate the potential of these methods by applying them to isolate a subset of 6001 problematic GO terms. By automatically aligning GO with other ontologies and taxonomies we were able to propose alternative synonyms and definitions for some of these problematic terms. This allows us to demonstrate that these other resources do not contain definitions superior to those supplied by GO. CONCLUSION: Our methods provide reliable indications of the quality of terms and definitions in ontologies and taxonomies. Further, they are well suited to assist ontology curators in drawing their attention to those terms that are ill-defined. We have further shown the limitations of ontology mapping and alignment in assisting ontology curators in rectifying problems, thus pointing to the need for manual curation.

Artificial Intelligence↗
PubMed1999

Multimedia explorer: image database, image proxy-server and search-engine.

Multimedia plays a major role in medicine. Databases containing images, movies or other types of multimedia objects are increasing in number, especially on the WWW. However, no good retrieval mechanism or search engine currently exists to efficiently track down such multimedia sources in the vast of information provided by the WWW. Secondly, the tools for searching databases are usually not adapted to the properties of images. HTML pages do not allow complex searches. Therefore establishing a more comfortable retrieval involves the use of a higher programming level like JAVA. With this platform independent language it is possible to create extensions to commonly used web browsers. These applets offer a graphical user interface for high level navigation. We implemented a database using JAVA objects as the primary storage container which are then stored by a JAVA controlled ORACLE8 database. Navigation depends on a structured vocabulary enhanced by a semantic network. With this approach multimedia objects can be encapsulated within a logical module for quick data retrieval.

Computer Graphics↗
PubMed2001

Culling a clinical terminology: a systematic approach to identifying problematic content.

The College of American Pathologists and the National Health Service (NHS) in the United Kingdom are merging their respective clinical terminologies, SNOMED RT and Clinical Terms Version 3, into a new terminology, SNOMED CT. This requires mapping concept descriptions between the two existing terminologies. During the mapping process, many descriptions were identified as being potentially problematic. They require further review by the SNOMED editorial process before either (1) being incorporated into SNOMED CT, or (2) retired from active use. This article presents data on the concept descriptions that were identified as needing further review during the early phases of SNOMED CT development. Based on this work, we describe fourteen types of problematic terminology content. Identifying problematic terminology content can be approached in a systematic manner.

Clinical Medicine↗
PubMed1995

Coding medical concepts: a controlled experiment with a computerised coding tool.

In clinical routine there is a growing need to encode medical concepts with available standard coding systems. The coding process can be time consuming and may significantly add to daily paperwork, particularly regarding patients with multiple diagnoses and in busy clinical environments with a high turnover of patients. We have developed a generic computerised encoding tool--the PADS encoder--to ensure rapid, correct and complete coding of diagnoses in daily routine. The tool is integrated into an electronic patient record system (PADS, Patient Archiving & Documentation System) and takes full advantage of the user friendly Macintosh interface. The tool was tested in a controlled experiment by 18 clinicians who encoded a total of 666 medical concepts in each protocol (study protocol vs. control). The following positive findings were significantly associated with the use of the computerised coding tool: the number of correctly encoded medical concepts was higher (99.55% vs. 86.1%), coding errors were lower (0% vs. 10.81%), more modifier codes were encoded correctly (increase by up to 43%), less coding errors were made (decrease by up to 43%), the overall rate of correctly encoded and complete main and modifier codes was increased by 31.27% (97.29% vs. 66.02%), coding time was reduced by 50%. This paper presents data to suggest that a computerised coding tool can produce more complete data of higher quality and can save time compared with the traditional approach to encode medical concepts.

Computer Communication Networks↗
PubMed2003

Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO).

MOTIVATION: A critical element of the computational infrastructure required for functional genomics is a shared language for communicating biological data and knowledge. The Gene Ontology (GO; http://www.geneontology.org) provides a taxonomy of concepts and their attributes for annotating gene products. As GO increases in size, its ongoing construction and maintenance becomes more challenging. In this paper, we assess the applicability of a Knowledge Base Management System (KBMS), Protégé-2000, to the maintenance and development of GO. RESULTS: We transferred GO to Protégé-2000 in order to evaluate its suitability for GO. The graphical user interface supported browsing and editing of GO. Tools for consistency checking identified minor inconsistencies in GO and opportunities to reduce redundancy in its representation. The Protégé Axiom Language proved useful for checking ontological consistency. The PROMPT tool allowed us to track changes to GO. Using Protégé-2000, we tested our ability to make changes and extensions to GO to refine the semantics of attributes and classify more concepts. AVAILABILITY: Gene Ontology in Protégé-2000 and the associated code are located at http://smi.stanford.edu/projects/helix/gokbms/. Protégé-2000 is available from http://protege.stanford.edu.

Artificial Intelligence↗