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PubMed1998

On the way to a Web based hospital information system: concepts for the use of a medical data dictionary to present context sensitive information in an intranet environment.

Many authors have promoted the www-paradigm to build modern hospital information systems. However currently web-based applications are better suited to information "browsing" than to build complex data entry features. This prompted us to start with our first web based developments inside the Giessen University Hospital Information System in the field of pure presentation of stored knowledge and information. This article describes the concepts which will be used in Giessen to convert available information sources to the www paradigm and to implement context-sensitive knowledge presentation mechanisms inside the clinical information system. The approach is based upon a web-based medical data dictionary server. The data dictionary is used to map terms of interest, chosen from the clinical user during work with a HIS-application, to a semantic network of relationships. The dictionary server will follow those semantic links in order to find and display the webpages, which are linked to the subject.

Dictionaries as Topic↗
PubMed2005

Interchanging lexical information for a multilingual dictionary.

OBJECTIVE: To facilitate the interchange of lexical information for multiple languages in the medical domain. To pave the way for the emergence of a generally available truly multilingual electronic dictionary in the medical domain. METHODS: An interchange format has to be neutral relative to the target languages. It has to be consistent with current needs of lexicon authors, present and future. An active interaction between six potential authors aimed to determine a common denominator striking the right balance between richness of content and ease of use for lexicon providers. RESULTS: A simple list of relevant attributes has been established and published. The format has the potential for collecting relevant parts of a future multilingual dictionary. An XML version is available. CONCLUSION: This effort makes feasible the exchange of lexical information between research groups. Interchange files are made available in a public repository. This procedure opens the door to a true multilingual dictionary, in the awareness that the exchange of lexical information is (only) a necessary first step, before structuring the corresponding entries in different languages.

Dictionaries, Medical as Topic↗
PubMed2005

Multilingual biomedical dictionary.

We present a unique technique to create a multilingual biomedical dictionary, based on a methodology called Morpho-Semantic indexing. Our approach closes a gap caused by the absence of free available multilingual medical dictionaries and the lack of accuracy of non-medical electronic translation tools. We first explain the underlying technology followed by a description of the dictionary interface, which makes use of a multilingual subword thesaurus and of statistical information from a domain-specific, multilingual corpus.

Abstracting and Indexing↗
PubMed2006

Extraction of gene-disease relations from Medline using domain dictionaries and machine learning.

We describe a system that extracts disease-gene relations from Medline. We constructed a dictionary for disease and gene names from six public databases and extracted relation candidates by dictionary matching. Since dictionary matching produces a large number of false positives, we developed a method of machine learning-based named entity recognition (NER) to filter out false recognitions of disease/gene names. We found that the performance of relation extraction is heavily dependent upon the performance of NER filtering and that the filtering improves the precision of relation extraction by 26.7% at the cost of a small reduction in recall.

Animals↗
PubMed2005

HLA dictionary 2004: summary of HLA-A, -B, -C, -DRB1/3/4/5, -DQB1 alleles and their association with serologically defined HLA-A, -B, -C, -DR, and -DQ antigens.

This report presents serologic equivalents of human leukocyte antigen (HLA)-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, and -DQB1 alleles. The dictionary is an update of the one published in 2001. The data summarize equivalents obtained by the World Health Organization (WHO) Nomenclature Committee for Factors of the HLA System, the International Cell Exchange (UCLA), the National Marrow Donor Program, recent publications, and individual laboratories. This latest update of the dictionary is enhanced by the inclusion of results from studies performed during the 13th International Histocompatibility Workshop and from neural network analyses. A summary of the data as recommended serologic equivalents is presented as expert assigned types. The tables include remarks for alleles, which are or may be expressed as antigens with serologic reaction patterns that differ from the well-established HLA specificities. The equivalents provided will be useful in guiding searches for unrelated hematopoietic stem cell donors in which patients and/or potential donors are typed by either serology or DNA-based methods. The serological-DNA equivalent dictionary will also aid in typing and matching procedures for organ transplant programs whose waiting lists of potential donors and recipients are comprised of mixtures of serologic and DNA-based typings. The tables with HLA equivalents and a questionnaire for submission of serologic reaction patterns for poorly identified allelic products will be made available through the World Marrow Donor Association Web page (www.worldmarrow.org).

Alleles↗
PubMed2001

Blind source separation by sparse decomposition in a signal dictionary.

The blind source separation problem is to extract the underlying source signals from a set of linear mixtures, where the mixing matrix is unknown. This situation is common in acoustics, radio, medical signal and image processing, hyperspectral imaging, and other areas. We suggest a two-stage separation process: a priori selection of a possibly overcomplete signal dictionary (for instance, a wavelet frame or a learned dictionary) in which the sources are assumed to be sparsely representable, followed by unmixing the sources by exploiting the their sparse representability. We consider the general case of more sources than mixtures, but also derive a more efficient algorithm in the case of a nonovercomplete dictionary and an equal numbers of sources and mixtures. Experiments with artificial signals and musical sounds demonstrate significantly better separation than other known techniques.

Journal Article↗
PubMed2003

Readers' opinions of romantic poetry are consistent with emotional measures based on the Dictionary of Affect in Language.

A principal components analysis of 68 volunteers' subjective ratings of 20 excerpts of Romantic poetry and of Dictionary of Affect scores for the same excerpts produced four components representing Pleasantness, Activation, Romanticism, and Nature. Dictionary measures and subjective ratings of the same constructs loaded on the same factor. Results are interpreted as providing construct validity for the Dictionary of Affect.

Affect↗
PubMed1997

Integration of a knowledge-based system and a clinical documentation system via a data dictionary.

This paper describes the design and realisation of a knowledge-based system and a clinical documentation system linked via a data dictionary. The software was developed as a shell with object oriented methods and C++ for IBM-compatible PC's and WINDOWS 3.1/95. The data dictionary covers terminology and document objects with relations to external classifications. It controls the terminology in the documentation program with form-based entry of clinical documents and in the knowledge-based system with scores and rules. The software was applied to the clinical field of acute abdominal pain by implementing a data dictionary with 580 terminology objects, 501 document objects, and 2136 links; a documentation module with 8 clinical documents and a knowledge-based system with 10 scores and 7 sets of rules.

Abdominal Pain↗
PubMed1999

Combining dictionary techniques with extensible markup language (XML)--requirements to a new approach towards flexible and standardized documentation.

In oncology various international and national standards exist for the documentation of different aspects of a disease. Since elements of these standards are repeated in different contexts, a common data dictionary could support consistent representation in any context. For the construction of such a dictionary existing documents have to be worked up in a complex procedure, that considers aspects of hierarchical decomposition of documents and of domain control as well as aspects of user presentation and models of the underlying model of patient data. In contrast to other thesauri, text chunks like definitions or explanations are very important and have to be preserved, since oncologic documentation often means coding and classification on an aggregate level and the safe use of coding systems is an important precondition for comparability of data. This paper discusses the potentials of the use of XML in combination with a dictionary for the promotion and development of standard conformable applications for tumor documentation.

Documentation↗
PubMed2006

[Some problems existing in current Chinese-English dictionaries of TCM nouns].

The paper discusses some problems existing in the current Chinese-English dictionaries of TCM nouns, points out their negative effects, hoping that people will attach great importance to the problems. Meanwhile the author puts forth the urgency of compiling high quality Chinese-English TCM dictionaries, and the role of such dictionaries in the standardization of English translation of TCM nouns.

Medicine, Chinese Traditional↗
PubMed1995

Integration of a data dictionary and a clinical database in an expert system for acute abdominal pain.

Despite promising results, computer-aided diagnosis in acute abdominal pain is rarely used in the clinic. We therefore developed an expert system for acute abdominal pain to be used in clinical routine. The system is based on a new approach integrating a data dictionary, a clinical database and the knowledge base. A data dictionary editor has been developed (C++, WINDOWS, IBM-compatible PC) and a data dictionary for acute abdominal pain has been built up. The clinical database has been linked to a documentation program providing three modes of data entry. The documentation program has been evaluated extensively by clinicians. The integrated approach clearly separates clinical data from knowledge, but guarantees high consistency of data.

Abdominal Pain↗
PubMedDate not supplied

[Spanish version of the epidemiologic dictionary of J. M. Last].

We comment briefly on the original edition of Last's dictionary of epidemiology and we make a detailed criticism of the translated version of the dictionary. We show several general problems of the spanish version and specifically discuss four epidemiology concepts (power, verosimility, child mortality and odds ratio) in which the definitions of the translated version are particularly confusing.

Dictionaries as Topic↗
PubMedDate not supplied

Medical dictionaries for patient encoding systems: a methodology.

Medical language is highly compositional and makes extensive use of common roots, especially Latino-Greek roots. Besides words devoted to common sense, medical language presents some typical characteristics, especially on morphological and semantic aspects of word formation. Morphological decomposition and identification precedes semantic analysis. It is only when these two prerequisites are fulfilled that an attempt to grasp the meaning of a whole expression is made possible. The main aim of the proposed approach is that of coping with 'the lack of coverage of the medical lexical knowledge', in order to help physicians find the correct international classification for diseases (ICD) codes for a written diagnosis. The proposed methodology allows the development of a powerful dynamic dictionary dedicated to natural language processing in the field of diagnoses and narrative procedures. It describes the design of an analyser that can profit from a dictionary. The methods used have proved to be efficient for various classifications, s well as for multiple languages, as the system presently supports French, German, English and Dutch for ICD-9 and ICD-10 classifications.

Classification↗
PubMed2002

Dictionary-driven protein annotation.

Computational methods seeking to automatically determine the properties (functional, structural, physicochemical, etc.) of a protein directly from the sequence have long been the focus of numerous research groups. With the advent of advanced sequencing methods and systems, the number of amino acid sequences that are being deposited in the public databases has been increasing steadily. This has in turn generated a renewed demand for automated approaches that can annotate individual sequences and complete genomes quickly, exhaustively and objectively. In this paper, we present one such approach that is centered around and exploits the Bio-Dictionary, a collection of amino acid patterns that completely covers the natural sequence space and can capture functional and structural signals that have been reused during evolution, within and across protein families. Our annotation approach also makes use of a weighted, position-specific scoring scheme that is unaffected by the over-representation of well-conserved proteins and protein fragments in the databases used. For a given query sequence, the method permits one to determine, in a single pass, the following: local and global similarities between the query and any protein already present in a public database; the likeness of the query to all available archaeal/ bacterial/eukaryotic/viral sequences in the database as a function of amino acid position within the query; the character of secondary structure of the query as a function of amino acid position within the query; the cytoplasmic, transmembrane or extracellular behavior of the query; the nature and position of binding domains, active sites, post-translationally modified sites, signal peptides, etc. In terms of performance, the proposed method is exhaustive, objective and allows for the rapid annotation of individual sequences and full genomes. Annotation examples are presented and discussed in Results, including individual queries and complete genomes that were released publicly after we built the Bio-Dictionary that is used in our experiments. Finally, we have computed the annotations of more than 70 complete genomes and made them available on the World Wide Web at http://cbcsrv.watson.ibm.com/Annotations/.

Algorithms↗
PubMed2000

The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues.

A consensus approach has been developed for identifying distant structural homologues. This is based on the CATH Dictionary of Homologous Superfamilies (DHS), a database of validated multiple structural alignments annotated with consensus functional information for evolutionary protein superfamilies (URL: http://www. biochem.ucl.ac.uk/bsm/dhs). Multiple structural alignments have been generated for 362 well-populated superfamilies in the CATH structural domain database and annotated with secondary structure, physicochemical properties, functional sequence patterns and protein-ligand interaction data. Consensus functional information for each superfamily includes descriptions and keywords extracted from SWISS-PROT and the ENZYME database. The Dictionary provides a powerful resource to validate, examine and visualize key structural and functional features of each homologous superfamily. The value of the DHS, for assessing functional variability and identifying distant evolutionary relationships, is illustrated using the pyridoxal-5'-phosphate (PLP) binding aspartate aminotransferase superfamily. The DHS also provides a tool for examining sequence-structure relationships for proteins within each fold group.

Amino Acid Sequence↗
PubMed2004

A simple and practical dictionary-based approach for identification of proteins in Medline abstracts.

OBJECTIVE: The aim of this study was to develop a practical and efficient protein identification system for biomedical corpora. DESIGN: The developed system, called ProtScan, utilizes a carefully constructed dictionary of mammalian proteins in conjunction with a specialized tokenization algorithm to identify and tag protein name occurrences in biomedical texts and also takes advantage of Medline "Name-of-Substance" (NOS) annotation. The dictionaries for ProtScan were constructed in a semi-automatic way from various public-domain sequence databases followed by an intensive expert curation step. MEASUREMENTS: The recall and precision of the system have been determined using 1000 randomly selected and hand-tagged Medline abstracts. RESULTS: The developed system is capable of identifying protein occurrences in Medline abstracts with a 98% precision and 88% recall. It was also found to be capable of processing approximately 300 abstracts per second. Without utilization of NOS annotation, precision and recall were found to be 98.5% and 84%, respectively. CONCLUSION: The developed system appears to be well suited for protein-based Medline indexing and can help to improve biomedical information retrieval. Further approaches to ProtScan's recall improvement also are discussed.

Abstracting and Indexing↗
PubMedDate not supplied

Dictionary-based medical image I/O.

A general-purpose image I/O library is presented, whose properties derive from externally defined data dictionaries. The library has primarily been developed for image I/O in a medical image processing environment. It hence addresses all issues found in this field such as a variety of pixel types, architecture independence, automatic type conversion, and an unlimited number of image parameters. The data access routines in the library automatically convert the data types when needed. By redefining the data dictionaries, the I/O library can be tuned for other application areas. Explicit support for image compression is provided. The library is written in C++, and is available for interested parties.

Data Collection↗
PubMed2004

[Chemistry dictionary of Pierre-Joseph Macquer].

In 1976, Pierre-Joseph Macquer publishes the first edition of his Chemistry dictionary, the first concerning this science. A second edition with many additions has been printed in 1778, bearing in mind the new concepts borned with the chemistry evolution. All chemists are unanimous to salute this monumental and precious work. These different aspects are presented in this Note, near the examination of the exemplary of this dictionary annotated by Jean Hermann, alsatian doctor and naturalist contemporary of Macquer.

Chemistry↗