SEARCH · PubMed Health

Results for “Vocabulary, Controlled”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9Linked to original sources

PubMed2006

Unified medical language system coverage of emergency-medicine chief complaints.

BACKGROUND: Emergency department (ED) chief-complaint (CC) data increasingly are important for clinical-care and secondary uses such as syndromic surveillance. There is no widely used ED CC vocabulary, but experts have suggested evaluation of existing health-care vocabularies for ED CC. OBJECTIVES: To evaluate the ED CC coverage in existing biomedical vocabularies from the Unified Medical Language System (UMLS). METHODS: The study sample included all CC entries for all visits to three EDs over one year. The authors used a special-purpose text processor to clean CC entries, which then were mapped to UMLS concepts. The UMLS match rates then were calculated and analyzed for matching concepts and nonmatching entries. RESULTS: A total of 203,509 ED visits was included. After cleaning with the text processor, 82% of the CCs matched a UMLS concept. The authors identified 5,617 unique UMLS concepts in the ED CC data, but many were used for only one or two visits. One thousand one hundred thirty-six CC concepts were used more than ten times and covered 99% of all the ED visits. The largest biomedical vocabulary in the UMLS is the Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT), which included concepts for 79% of all ED CC entries. However, some common CCs were not found in SNOMED CT. CONCLUSIONS: The authors found that ED CC concepts are well covered by the UMLS and that the best source of vocabulary coverage is from SNOMED CT. There are some gaps in UMLS and SNOMED CT coverage of ED CCs. Future work on vocabulary control for ED CCs should build upon existing vocabularies.

Data Collection↗

PubMed2001

Vocabulary development in Italian children: a longitudinal evaluation of quantitative and qualitative aspects.

In this study vocabulary development of a sample of 42 Italian children was evaluated through monthly administration of the Italian version of the CDI. Data collection started at 1;0-1;1 for 32 children and at 1;3-1;4 for the remaining subjects and continued until children's vocabulary reached 200 words. At fixed stages of vocabulary size (50, 100 and 200 words), individual differences in percentile scores and vocabulary composition were examined. Individual growth curves were analysed in order to verify the presence of a vocabulary spurt and the type of lexical items which contributed most to rapid acceleration in vocabulary growth. Stylistic differences in vocabulary composition were examined regarding the 'referential-expressive' distinction, controlling vocabulary size. Data have shown that general trends in vocabulary development are quite similar to those obtained for other languages using CDI adaptations. Moreover, all children in this sample eventually exhibited a vocabulary spurt, even if some can be defined as 'late spurters'. The type of lexical items which are learned during the spurt depend on both infant vocabulary size and referential score. About 28% of infants in this sample were defined 'referential' when their vocabulary size was about 50 words, but the stylistic differences disappeared at the 100- and 200-word stages. Composition of vocabulary did not differ in relation to precocity in reaching different stages of vocabulary development. The only exception was that infants who reached the 50-word stage first also had a vocabulary with a lower proportion of function words.

Child Language↗

PubMed2004

Comparative genomic analysis as a tool for biological discovery.

The recent completion of the human genome sequence has enabled the identification of a large fraction of our gene catalogue and their physical chromosomal position. However, current efforts lag at defining the cis-regulatory sequences that control the spatial and temporal patterns of each gene's expression. This task remains difficult due to our lack of knowledge of the vocabulary controlling gene regulation and the vast genomic search space, with greater than 95% of our genome being noncoding. Recent comparative genomic-based strategies are beginning to aid in the identification of functional sequences based on their high levels of evolutionary conservation. This has proven successful for comparisons between closely related species such as human-primate or human-mouse, but also holds true for distant evolutionary comparisons, such as human-fish or human-bird. In this review we provide support for the utility of cross-species sequence comparisons by illustrating several applications of this strategy, including the identification of new genes and functional non-coding sequences. We also discuss emerging concepts as this field matures, such as how to properly select which species for comparison, which may differ significantly between independent studies.

Animals↗

PubMed1996

Integrating DXplain into a clinical information system using the World Wide Web.

The World Wide Web(WWW) offers a cross-platform environment and standard protocols that enable integration of various applications available on the Internet. The authors use the Web to facilitate interaction between their Web-based Clinical Information System and a decision-support system-DXplain, at the Massachusetts General Hospital-using local architecture and Common Gateway Interface programs. The current application translates patients laboratory test results into DXplain's terms to generate diagnostic hypotheses. Two different access methods are utilized for this model; Hypertext Transfer Protocol (HTTP) and TCP/IP function calls. While clinical aspects cannot be evaluated as yet, the model demonstrates the potential of Web-based applications for interaction and integration and how local architecture, with a controlled vocabulary server, can further facilitate such integration. This model serves to demonstrate some of the limitations of the current WWW technology and identifies issues such as control over Web resources and their utilization and liability issues as possible obstacles for further integration.

Computer Communication Networks↗

PubMed1993

A survey of electronic drug information resources and identification of problems associated with the differing vocabularies used to key them.

Drug information resources are increasingly becoming electronically available. They differ in scope, granularity, and purpose. These considerations have shaped the selection of dissimilar drug name keys, complicating access. An abbreviated and simplified historical context of the development of official controlled vocabularies and their relationships is followed by a review of the kinds of information available in several electronic drug information resources. The key vocabularies used are discussed with examples. Problems using the differing terms of the resource vocabularies are identified.

Abstracting and Indexing↗

PubMed1992

A comparison of retrieval effectiveness for three methods of indexing medical literature.

Conventional approaches to indexing medical literature include the human assignment of terms from a controlled vocabulary, such as MeSH, or the computer assignment of all words in the title and abstract as indexing terms. Human indexing suffers from inconsistency, while word-based indexing suffers from the multiple meanings of words. SAPHIRE is a computer program designed to provide indexing using controlled terms that are assigned by computer, based on their occurrence in the title and abstract. In this first evaluation of SAPHIRE, the authors compared the retrieval performance of the three indexing approaches--human-based MEDLINE with text words; machine-based SAPHIRE with text words; and text words only--for searches by measuring recall and precision for each search using a test collection of 200 abstracts. The abstracts were judged by human reviewers for relevance as applied to 12 literature queries. The results suggest that text word indexing is more effective than indexing with MeSH terms. SAPHIRE's indexing performance was slightly inferior but the program has other advantageous features.

Abstracting and Indexing↗

PubMed2001

Decision support for infectious diseases--a working prototype.

This paper presents a decision support system for nosocomial infections and its integration in the large HIS of the University Hospital of Giessen. The system comprises five different engines and a data dictionary. It is designed to detect hospital acquired infections even in a situation where only a restricted amount of clinical data is available (the data is split up in different information systems). Furthermore the model prevents time consuming manual data entry. The five engines split the main task into: (1) a preselection, which sorts out patients who definitely do not have a nosocomial infection; (2) a rule based reasoning process which detects patients likely to have such an infection; (3) an alarm process which is responsible for the presentation of the alert; (4) an explanation process to follow up the reasoning; and (5) statistic tools to answer specific hygienic questions. A data dictionary supplies the controlled vocabulary, which is required to understand data structures used in the different clinical subsystems and may those with each other.

Artificial Intelligence↗

PubMed2004

Cytologic diagnosis: expression of probability by clinical pathologists.

BACKGROUND: Clinical pathologists use descriptive terms or modifiers to express the probability or likelihood of a cytologic diagnosis. Words are imprecise in meaning, however, and may be used and interpreted differently by pathologists and clinicians. OBJECTIVES: The goals of this study were to 1) assess the frequency of use of 18 modifiers, 2) determine the probability of a positive diagnosis implied by the modifiers, 3) identify preferred modifiers for different levels of probability, 4) ascertain the importance of factors that affect expression of diagnostic certainty, and 5) evaluate differences based on gender, employment, and experience. METHODS: We surveyed 202 clinical pathologists who were board-certified by the American College of Veterinary Pathologists (Clinical Pathology). Surveys were distributed in October 2001 and returned by e-mail, fax, or surface mail over a 2-month period. Results were analyzed by parametric and nonparametric tests. RESULTS: Survey response rate was 47.5% (n = 96) and primarily included clinical pathologists at veterinary schools (n = 58) and diagnostic laboratories (n = 31). Eleven of 18 terms were used "often" or "sometimes" by >/= 50% of respondents. Broad variability was found in the probability assigned to each term, especially those with median values of 75 to 90%. Preferred modifiers for 7 numerical probabilities ranging from 0 to 100% included 68 unique terms; however, a set of 10 terms was used by >/= 50% of respondents. Cellularity and quality of the sample, experience of the pathologist, and implications of the diagnosis were the most important factors affecting the expression of probability. CONCLUSION: Because of wide discrepancy in the implied likelihood of a diagnosis using words, defined terminology and controlled vocabulary may be useful in improving communication and the quality of data in cytology reporting.

Adult↗

PubMed2005

Electronic laboratory reporting for the infectious diseases physician and clinical microbiologist.

BACKGROUND: One important benefit of electronic health information is the improved interface between infectious diseases practice and public health. Electronic communicable disease reporting (CDR), given its legal mandate and clear public health importance, is a significant early step in the sifting and pooling of health data for purposes beyond patient care and billing. Over the next 5-10 years, almost all CDR will move to the internet. METHODS: This paper reviews the components of electronic laboratory reporting (ELR), including sifting through data in a laboratory information management system for reportable results, controlled "vocabularies" (e.g., LOINC, Logical Observation Identifiers Names and Codes [Regenstrief Institute], and SNOMED, Systematized Nomenclature of Medicine [College of American Pathologists]), the "syntax" of an electronic message (e.g., health level 7 [HL7]), the implications of the Health Insurance Portability and Accountability Act for ELR, and the obstacles to and potential benefits of ELR. RESULTS: There are several ways that infectious diseases physicians, infection control professionals, and microbiology laboratorians will participate in electronic CDR, including web-based case reporting and ELR, the direct, automated messaging of communicable disease reports from clinical lab information management systems to the appropriate public health jurisdiction's information system. CONCLUSIONS: ELR has the potential to make a large impact on the timeliness and the completeness of communicable disease reporting, but it does not replace the clinician's responsibility to submit a case report with important demographic and epidemiologic information.

Clinical Laboratory Information Systems↗

PubMed1992

The Meta-1.2 engine: a refined strategy for linking biomedical vocabularies.

This paper presents a preliminary description of the database schema and associated procedures that are the foundation for the "engine" that will produce Meta-1.2. Meta-1.2 is the next incarnation of the Metathesaurus, which is one of the principal components of the National Library of Medicine's Unified Medical Language System (UMLS). We use the word "engine" as a generic term that includes a database and the programs that operate on it. While this design builds heavily upon previous work, it incorporates some major changes in philosophy. A major hypothesis is that the simple representation described here is suitable for any controlled vocabulary in the biomedical domain. Indeed, this hypothesis is central to a strategy for producing future versions of the Metathesaurus and for supporting collaboration with people who wish to contribute additional terms and relationships to the Metathesaurus. Another change involves the representation of classes and relationships. The revised database schema includes an explicit representation of the source or "authority" for relationships, which is analogous to the way that the sources of terms have been represented since the first version of the Metathesaurus. A sequence of steps utilizing the new representations to produce the Metathesaurus is presented.

Databases, Factual↗

PubMed2005

Searching the MEDLINE literature database through PubMed: a short guide.

The Medline database from the National Library of Medicine (NLM) contains more than 12 million bibliographic citations from over 4,600 international biomedical journals. One of the interfaces for searching Medline is PubMed, provided by the NLM for free access via the Internet (www.pubmed.gov). Also searchable with the PubMed interface are non-Medline citations, i.e. articles supplied by publishers to the NLM. Direct access to an electronic full text version is also possible if the article is available from a publisher or institution participating in Linkout (www.ncbi.nlm.nih.gov/entrez/linkout/). Some publishers provide free access to their journals. Other journals require an online license and are fee based. The following example demonstrates some of the most important search functions in PubMed. We will start out with a fast and simple approach without the use of specific searching techniques and then continue with a more sophisticated search that requires the knowledge of Medline search functions. This example will show how the application of Medline search tools and how the use of the controlled vocabulary of 'Medical Subject Headings' (MeSH) will influence the results in comparison with the fast and simple approach. Let's try to find the best evidence to answer the following question: Is a 30-year-old man with typical acid reflux symptoms for many years (gastroesophageal reflux disease, GERD) more likely to develop esophageal cancer than people without reflux symptoms? This question can be split into several components: -a patient with reflux symptoms (GERD), -esophageal cancer: etiology, risk, -study design for etiology studies: cohort studies, case-control studies.

Database Management Systems↗

PubMed2002

The completeness of existing lexicons for representing radiology report information.

Although most medical lexicons contain up to 80% of clinical terms used in an ambulatory patient medical records archive, preliminary research suggests that they may be far less complete for radiology terms. We therefore compared the likelihood that several existing medical lexicons would contain terms found in a radiology report to the likelihood they would contain terms found in an ambulatory care medical record. We used three samples of imaging terms to assess the completeness of existing lexicons for medical imaging: (1) a random sample of imaging terms from the Unified Medical Language System Large Scale Vocabulary Test (UMLS-LSVT; n = 218), (2) terms actually used in the first 80 clinical knee magnetic resonance imaging reports generated by the routine clinical use of a structured reporting system (eDictation, Marlton, NJ; n = 76), and (3) terms listed in a glossary of thoracic imaging prepared by the Fleischner Society (n = 173). Using the UMLS Web-based Knowledge Source Server (http://umlsks.nlm.nih. gov/), we measured the rate at which terms in each of the above three sources were found in the UMLS and two of its major constituent terminologies: ICD-9-CM and SNOMED International. ICD-9-CM contained matches for 3%, 8%, and 11% of terms from the Fleischner Society Glossary, eDictation, and NLM-LSVT, respectively. SNOMED International contained matches for 32%, 46%, and 36% of terms from the Fleischner Society Glossary, eDictation, and NLM-LSVT, respectively. The UMLS contained matches for 36%, 50%, and 45% of terms from the Fleischner Society Glossary, eDictation, and NLM-LSVT, respectively. The assessed vocabularies were least likely to contain a term from the Fleischner Society Glossary and most likely to contain a term from the eDictation lexicon. The UMLS was the most complete, and ICD-9 was the least complete of the three systems evaluated. No lexicon achieved greater than 50% completeness for any test set of imaging terms. Our results show that no single lexicon is sufficiently complete to allow comprehensive indexing, search, and retrieval of radiology report information. These results confirm the few results available from the medical literature indicating that existing controlled vocabularies are insufficiently complete to represent the contents of radiology reports. A subjective analysis of these results may identify particular imaging sub-areas for which new terms should be developed.

Humans↗

PubMed1997

SAM: speech-aware applications in medicine to support structured data entry.

In the last two years, improvement in speech recognition technology has directed the medical community's interest to porting and using such innovations in clinical systems. The acceptance of speech recognition systems in clinical domains increases with recognition speed, large medical vocabulary, high accuracy, continuous speech recognition, and speaker independence. Although some commercial speech engines approach these requirements, the greatest benefit can be achieved in adapting a speech recognizer to a specific medical application. The goals of our work are first, to develop a speech-aware core component which is able to establish connections to speech recognition engines of different vendors. This is realized in SAM. Second, with applications based on SAM we want to support the physician in his/her routine clinical care activities. Within the STAMP project (STAndardized Multimedia report generator in Pathology), we extend SAM by combining a structured data entry approach with speech recognition technology. Another speech-aware application in the field of Diabetes care is connected to a terminology server. The server delivers a controlled vocabulary which can be used for speech recognition.

Cell Biology↗

PubMed2002

The sentinel role of poisons centers in the protection of children's environmental health.

Growing concern exists about the threats posed by environmental pollutants and physical agents on children's health. A number offactors, including globalization, increased industrialization, and trade of chemicals and poverty have an impact on the quality of the environment and on children's health. Acute toxic exposures lead to poisoning, and chronic low-level exposures may cause functional and organ damage during periods of special vulnerability. The need to protect children's environmental health is urgent, in view of the magnitude of the problem and the fact that "children are not little adults." The effects suffered during special developmental periods-"windows of vulnerability"-can be permanent and irreversible. The main global environmental problems affecting children's health are lack of access to safe drinking water and sanitation and exposure to indoor air pollution. Furthermore, environmentally related accidents, injuries, and poisonings have a major impact on children and adolescent's morbidity and mortality. A number of examples that illustrate the complexity of assessing and dealing with children's environmental health issues are presented. A Task Force on the Protection of Children's Environmental Health that aims to prevent disease and disability in children associated with chemical and physical threats was set up in 1999 by the World Health Organization. The priorities for action include the consideration of accidents, injuries, and poisonings (accidental, intentional, and occupational), and children in the workplace (e.g., scavenging children, children in cottage industries). Poisons Centers and related toxicology centers are in a strategic position to play a "sentinel" role in the protection of children's environmental health. They record acute and chronic toxic exposures in children in a harmonized manner, using controlled vocabularies and definitions. This will allow collecting a large, highly valuable database on the main toxicological problems affecting children, including those of environmental origin. The analysis of observations entered in such a database will help assess the burden of disease and collect the evidence for planning prevention and promoting regulatory measures. Centers are called to play a proactive role in raising awareness about children's environmental health and contribute to research, information dissemination, training, and other activities required for the protection of children's health and development.

Child↗

PubMed2003

Development and evaluation of an automated annotation pipeline and cDNA annotation system.

Manual curation has long been held to be the "gold standard" for functional annotation of DNA sequence. Our experience with the annotation of more than 20,000 full-length cDNA sequences revealed problems with this approach, including inaccurate and inconsistent assignment of gene names, as well as many good assignments that were difficult to reproduce using only computational methods. For the FANTOM2 annotation of more than 60,000 cDNA clones, we developed a number of methods and tools to circumvent some of these problems, including an automated annotation pipeline that provides high-quality preliminary annotation for each sequence by introducing an "uninformative filter" that eliminates uninformative annotations, controlled vocabularies to accurately reflect both the functional assignments and the evidence supporting them, and a highly refined, Web-based manual annotation tool that allows users to view a wide array of sequence analyses and to assign gene names and putative functions using a consistent nomenclature. The ultimate utility of our approach is reflected in the low rate of reassignment of automated assignments by manual curation. Based on these results, we propose a new standard for large-scale annotation, in which the initial automated annotations are manually investigated and then computational methods are iteratively modified and improved based on the results of manual curation.

Animals↗

PubMed2004

Annotation of post-translational modifications in the Swiss-Prot knowledge base.

High-throughput proteomic studies produce a wealth of new information regarding post-translational modifications (PTMs). The Swiss-Prot knowledge base is faced with the challenge of including this information in a consistent and structured way, in order to facilitate easy retrieval and promote understanding by biologist expert users as well as computer programs. We are therefore standardizing the annotation of PTM features represented in Swiss-Prot. Indeed, a controlled vocabulary has been associated with every described PTM. In this paper, we present the major update of the feature annotation, and, by showing a few examples, explain how the annotation is implemented and what it means. Mod-Prot, a future companion database of Swiss-Prot, devoted to the biological aspects of PTMs (i.e., general description of the process, identity of the modification enzyme(s), taxonomic range, mass modification) is briefly described. Finally we encourage once again the scientific community (i.e., both individual researchers and database maintainers) to interact with us, so that we can continuously enhance the quality and swiftness of our services.

Computational Biology↗

PubMed2006

Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA.

The theme of the third annual Spring workshop of the HUPO-PSI was "proteomics and beyond" and its underlying goal was to reach beyond the boundaries of the proteomics community to interact with groups working on the similar issues of developing interchange standards and minimal reporting requirements. Significant developments in many of the HUPO-PSI XML interchange formats, minimal reporting requirements and accompanying controlled vocabularies were reported, with many of these now feeding into the broader efforts of the Functional Genomics Experiment (FuGE) data model and Functional Genomics Ontology (FuGO) ontologies.

Animals↗

PubMedDate not supplied

Design and realization of an on-line database for multidimensional microscopic images of biological specimens.

The BioImage database is a new scientific database for multidimensional microscopic images of biological specimens, which is available through the World Wide Web (WWW). The development of this database has followed an iterative approach, in which requirements and functionality have been revised and extended. The complexity and innovative use of the data meant that technical and biological expertise has been crucial in the initial design of the data model. A controlled vocabulary was introduced to ensure data consistency. Pointers are used to reference information stored in other databases. The data model was built using InfoModeler as a database design tool. The database management system is the Informix Dynamic Server with Universal Data Option. This object-relational system allows the handling of complex data using features such as collection types, inheritance, and user-defined data types. Informix datablades are used to provide additional functionality: the Web Integration Option enables WWW access to the database; the Video Foundation Blade provides functionality for video handling.

Animals↗