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Results for “Terminology as Topic”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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PubMed1987

A critical discussion of DSM-III dysthymic disorder.

The authors review the history of the concept of dysthymia and the literature on the epidemiology, course, and treatment of chronic depression. They present a critical discussion of DSM-III and DSM-III-R criteria for dysthymic disorder. On the basis of this review, they suggest that future revisions of the nomenclature include further subcategorization of chronic depressive disorders and that the term "dysthymic disorder" be reserved for chronic depressive disorders with an insidious onset at an early age. The relationships between dysthymic disorders and personality disorders and the response of subcategories of chronic depression to different treatment modalities need to be researched.

Adult↗
PubMed1998

What's in a name?

Explore the source record for details and available documents.

Dental Research↗
PubMed2006

Discovering semantic features in the literature: a foundation for building functional associations.

BACKGROUND: Experimental techniques such as DNA microarray, serial analysis of gene expression (SAGE) and mass spectrometry proteomics, among others, are generating large amounts of data related to genes and proteins at different levels. As in any other experimental approach, it is necessary to analyze these data in the context of previously known information about the biological entities under study. The literature is a particularly valuable source of information for experiment validation and interpretation. Therefore, the development of automated text mining tools to assist in such interpretation is one of the main challenges in current bioinformatics research. RESULTS: We present a method to create literature profiles for large sets of genes or proteins based on common semantic features extracted from a corpus of relevant documents. These profiles can be used to establish pair-wise similarities among genes, utilized in gene/protein classification or can be even combined with experimental measurements. Semantic features can be used by researchers to facilitate the understanding of the commonalities indicated by experimental results. Our approach is based on non-negative matrix factorization (NMF), a machine-learning algorithm for data analysis, capable of identifying local patterns that characterize a subset of the data. The literature is thus used to establish putative relationships among subsets of genes or proteins and to provide coherent justification for this clustering into subsets. We demonstrate the utility of the method by applying it to two independent and vastly different sets of genes. CONCLUSION: The presented method can create literature profiles from documents relevant to sets of genes. The representation of genes as additive linear combinations of semantic features allows for the exploration of functional associations as well as for clustering, suggesting a valuable methodology for the validation and interpretation of high-throughput experimental data.

Abstracting and Indexing↗
PubMed2006

An environment for relation mining over richly annotated corpora: the case of GENIA.

BACKGROUND: The biomedical domain is witnessing a rapid growth of the amount of published scientific results, which makes it increasingly difficult to filter the core information. There is a real need for support tools that 'digest' the published results and extract the most important information. RESULTS: We describe and evaluate an environment supporting the extraction of domain-specific relations, such as protein-protein interactions, from a richly-annotated corpus. We use full, deep-linguistic parsing and manually created, versatile patterns, expressing a large set of syntactic alternations, plus semantic ontology information. CONCLUSION: The experiments show that our approach described is capable of delivering high-precision results, while maintaining sufficient levels of recall. The high level of abstraction of the rules used by the system, which are considerably more powerful and versatile than finite-state approaches, allows speedy interactive development and validation.

Abstracting and Indexing↗
PubMed2006

A critical review of PASBio's argument structures for biomedical verbs.

BACKGROUND: Propositional representations of biomedical knowledge are a critical component of most aspects of semantic mining in biomedicine. However, the proper set of propositions has yet to be determined. Recently, the PASBio project proposed a set of propositions and argument structures for biomedical verbs. This initial set of representations presents an opportunity for evaluating the suitability of predicate-argument structures as a scheme for representing verbal semantics in the biomedical domain. Here, we quantitatively evaluate several dimensions of the initial PASBio propositional structure repository. RESULTS: We propose a number of metrics and heuristics related to arity, role labelling, argument realization, and corpus coverage for evaluating large-scale predicate-argument structure proposals. We evaluate the metrics and heuristics by applying them to PASBio 1.0. CONCLUSION: PASBio demonstrates the suitability of predicate-argument structures for representing aspects of the semantics of biomedical verbs. Metrics related to theta-criterion violations and to the distribution of arguments are able to detect flaws in semantic representations, given a set of predicate-argument structures and a relatively small corpus annotated with them.

Abstracting and Indexing↗
PubMed2005

The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data.

We have developed an ontology to provide standardized nomenclature for anatomical terms in the postnatal mouse. The Adult Mouse Anatomical Dictionary is structured as a directed acyclic graph, and is organized hierarchically both spatially and functionally. The ontology will be used to annotate and integrate different types of data pertinent to anatomy, such as gene expression patterns and phenotype information, which will contribute to an integrated description of biological phenomena in the mouse.

Animals↗
PubMed2004

Reported use of data monitoring committees in the main published reports of randomized controlled trials: a cross-sectional study.

BACKGROUND: We describe a review of published main reports of randomized controlled trials (RCTs), in order to measure the frequency of reported use of data monitoring committees (DMCs) and factors associated with reported DMC use. METHODS: Twenty-four higher impact general and specialist medical journals were handsearched for main reports of RCTs in order to provide a cross-sectional sample of trials published in the year 2000. Additionally, the same general medical journals were handsearched for 1990 to allow a comparison across time. RESULTS: Of 662 RCTs published in 2000, 120 (18%) explicitly reported using a DMC, while 107 (16%) reported planned interim analyses. Overall, about a quarter (24%) reported at least one of these. A higher proportion of trials reported using a DMC in 2000 than 1 990 (70/282, 25% versus 21/204, 10%) in the general medical journals. Logistic regression models suggested the more important variables associated with increased reported DMC use were: later year of publication, publication in general medical journal, survival-based endpoint, multicentre trial, increasing number of patients recruited, at least one arm involving a placebo, at least one arm involving a drug, factorial design and USA involvement in the trial. CONCLUSIONS: In 2000, about a quarter of main RCT reports mention use of a DMC. Actual use of DMCs is likely to be somewhat greater. Reporting use of a DMC was more likely for larger and longer trials among other factors. We believe the factors affecting reported use affect actual use. It is recommended that when a DMC oversees a trial, brief details should be explicitly included in the main trial paper. Standard nomenclature for DMCs is recommended.

Clinical Trials Data Monitoring Committees↗
PubMedDate not supplied

Mapping abbreviations to full forms in biomedical articles.

OBJECTIVE: To develop methods that automatically map abbreviations to their full forms in biomedical articles. METHODS: The authors developed two methods of mapping defined and undefined abbreviations (defined abbreviations are paired with their full forms in the articles, whereas undefined ones are not). For defined abbreviations, they developed a set of pattern-matching rules to map an abbreviation to its full form and implemented the rules into a software program, AbbRE (for "abbreviation recognition and extraction"). Using the opinions of domain experts as a reference standard, they evaluated the recall and precision of AbbRE for defined abbreviations in ten biomedical articles randomly selected from the ten most frequently cited medical and biological journals. They also measured the percentage of undefined abbreviations in the same set of articles, and they investigated whether they could map undefined abbreviations to any of four public abbreviation databases (GenBank LocusLink, SWISSPROT, LRABR of the UMLS Specialist Lexicon, and BioABACUS). RESULTS: AbbRE had an average 0.70 recall and 0.95 precision for the defined abbreviations. The authors found that an average of 25 percent of abbreviations were defined in biomedical articles and that of a randomly selected subset of undefined abbreviations, 68 percent could be mapped to any of four abbreviation databases. They also found that many abbreviations are ambiguous (i.e., they map to more than one full form in abbreviation databases). CONCLUSION: AbbRE is efficient for mapping defined abbreviations. To couple AbbRE with abbreviation databases for the mapping of undefined abbreviations, not only exhaustive abbreviation databases but also a method to resolve the ambiguity of abbreviations in the databases are needed.

Abbreviations as Topic↗
PubMed2004

Structured representation of the pharmacodynamics section of the summary of product characteristics for antibiotics: application for automated extraction and visualization of their antimicrobial activity spectra.

OBJECTIVE: The aim of this study was to construct automatically a knowledge base concerning the pharmacodynamic properties of antibiotics and a visualization tool. DESIGN: The authors studied the various guidelines used to write the pharmacodynamics section of the Summary of Product Characteristics (SPC) for antibiotics and constructed a conceptual model of the information. Particular words, syntagms, and punctuation elements were marked in the SPC texts, and automatic extraction was then used to build a knowledge base. This base was used to create dynamic HTML tables displaying the activity spectra of the antibiotics. MEASUREMENTS: The authors analyzed the performances of automatic extraction (recall and precision). RESULTS: The conceptual pharmacodynamics model dealt with antibiotics, pathogens, susceptibility tests, and the prevalence of resistance. Automatic extraction had a recall rate of 97.9% and a precision of 96.2%. The tool displaying antibiotic spectra and resistance prevalences used color codes to identify differences in susceptibility. CONCLUSION: This tool can provide an overview of the prevalence of resistance as expressed in SPC in primary care settings. Its potential impact should be evaluated.

Anti-Bacterial Agents↗
PubMed2002

Medically unexplained physical symptoms in medical practice: a psychiatric perspective.

Clusters of medically unexplained physical symptoms have been referred to in the literature by many different labels, including somatization, symptom-based conditions, and functional somatic syndromes, among many others. The traditional medical perspective has been to classify and study these symptoms and functional syndromes separately. In psychiatry, current taxonomies (Diagnostic and Statistical Manual of Mental Disorder, 4th edition, and The International Statistical Classification of Diseases and Related Health Problems, 10th revision) classify these syndromes together under the rubric of somatoform disorders. In this article we approach medically unexplained physical symptoms from a psychiatric perspective and discuss the common features that unite multiple unexplained symptoms or functional somatic syndromes as a class. Included in this article is a discussion of nosological issues, clinical assessment, how these syndromes are viewed within the various medical specialties, and clinical management and treatment.

Diagnosis, Differential↗