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PubMed2004

Semantic distance norms computed from an electronic dictionary (WordNet).

WordNet, an electronic dictionary (or lexical database), is a valuable resource for computational and cognitive scientists. Recent work on the computing of semantic distances among nodes (synsets) in WordNet has made it possible to build a large database of semantic distances for use in selecting word pairs for psychological research. The database now contains nearly 50,000 pairs of words that have values for semantic distance, associative strength, and similarity based on co-occurrence. Semantic distance was found to correlate weakly with these other measures but to correlate more strongly with another measure of semantic relatedness, featural similarity. Hierarchical clustering analysis suggested that the knowledge structure underlying semantic distance is similar in gross form to that underlying featural similarity. In experiments in which semantic similarity ratings were used, human participants were able to discriminate semantic distance. Thus, semantic distance as derived from WordNet appears distinct from other measures of word pair relatedness and is psychologically functional. This database may be downloaded from www.psychonomic.org/archive/.

Cognitive Science↗
PubMed2003

Use of Dictionary of Occupational Titles (DOT) on formwork carpentry--a comparison between the United States and Hong Kong.

OBJECTIVES: This study aimed at investigating the utilization and applicability of the Dictionary of Occupational Titles (DOT) as a methodology to study the job profile (nature and physical demand) of formwork carpentry in the local situation. STUDY DESIGN: Thirty male formwork carpenters were recruited by convenient sampling to participate in a two-hour interview, with reference to the DOT Physical Demand Questionnaire (DOTPDQ) and the WestTool Sort Questionnaire. The information obtained was further consolidated by comparing the results from the interview to three construction sites and training guidelines from the formwork carpentry training centers. The triangulation of the data formulated a job profile of formwork carpenters. RESULTS: The results from the DOTPDQ revealed that workers' work demands were standing, walking, pushing, pulling, reaching, climbing, balancing, stooping, crouching, lifting, carrying, handling and near acuity. This produced an agreement of 84.6% with the original DOT. A discrepancy was found in the demands of kneeling, fingering, far acuity and depth perception. CONCLUSIONS: The discrepancy between the data from the United States and local appeared to be minimal. It was thus inferred that the DOT-based job profile was largely valid for describing formwork carpentry in Hong Kong. In-depth analysis should be conducted to further substantiate the validity of utilizing the DOT system for other job types and their physical demands.

Adult↗
PubMedDate not supplied

Nephrology in the Lancisi Medical Dictionary (1672-1720).

Giovanni Maria Lancisi (1654-1720) shows a particular interest in urological and nephrological diseases, especially evident in a course of lectures held at Studium Urbis in 1696-97, which reflected his vast knowledge and familiarity with various important texts devoted to urology and nephrology. This interest is further documented in commentaries on articles on nephrological diseases in his Repertorium medicum (a sort of medical dictionary written between 1672 and his death). Lancisi's quoting medical authorities clarifies the clinical answers he gave in some of his unpublished Consulti concerning nephrological pathologies.

Dictionaries, Medical as Topic↗
PubMed1990

[Blood bank dictionary, definition of the concept and blood unit status for blood recipients--an electronic data processing system].

The definition of terms using the blood bank data dictionary results in a number of advantages in practice. Previously vague terms could be clearly defined when they are broken down into their constituent parts. The relationships within a blood bank can be more precisely documented by working with standard terms. The descriptions within the specification are thereby unambiguous and in this way a precise program specification can be achieved. Standardized terms facilitate the functional comparison of programs from different authors or different software sources. The use of defined terms within wards and the blood bank area results in more transparency even before the introduction of data processing.

Blood Banks↗
PubMed1995

The architecture of a distributed medical dictionary.

Exploiting high-speed computer networks to provide a national medical information infrastructure is a goal for medical informatics. The Distributed Medical Dictionary under development at Baylor College of Medicine is a model for an architecture that supports collaborative development of a distributed online medical terminology knowledge-base. A prototype is described that illustrates the concept. Issues that must be addressed by such a system include high availability, acceptable response time, support for local idiom, and control of vocabulary.

Artificial Intelligence↗
PubMed1998

Dictionary of recurrent domains in protein structures.

The rapid growth in the number of experimentally determined three-dimensional protein structures has sharpened the need for comprehensive and up-to-date surveys of known structures. Classic work on protein structure classification has made it clear that a structural survey is best carried out at the level of domains, i.e., substructures that recur in evolution as functional units in different protein contexts. We present a method for automated domain identification from protein structure atomic coordinates based on quantitative measures of compactness and, as the new element, recurrence. Compactness criteria are used to recursively divide a protein into a series of successively smaller and smaller substructures. Recurrence criteria are used to select an optimal size level of these substructures, so that many of the chosen substructures are common to different proteins at a high level of statistical significance. The joint application of these criteria automatically yields consistent domain definitions between remote homologs, a result difficult to achieve using compactness criteria alone. The method is applied to a representative set of 1,137 sequence-unique protein families covering 6,500 known structures. Clustering of the resulting set of domains (substructures) yields 594 distinct fold classes (types of substructures). The Dali Domain Dictionary (http://www.embl-ebi.ac.uk/dali/) not only provides a global structural classification, but also a comprehensive description of families of protein sequences grouped around representative proteins of known structure. The classification will be continuously updated and can serve as a basis for improving our understanding of protein evolution and function and for evolving optimal strategies to complete the map of all natural protein structures.

Amino Acid Sequence↗
PubMed2006

Measurement qualities of a self-report and therapist-scored functional capacity instrument based on the Dictionary of Occupational Titles.

Studies provide convincing arguments to support the development of functional capacity instruments based on the Dictionary of Occupational Titles (DOT). The purpose of this study is to investigate the item-level measurement qualities of a newly developed DOT-based functional capacity instrument for clients undergoing rehabilitation treatment for back pain. Client and therapist ratings were collected on 124 clients from 27 rehabilitation sites using the newly developed Occupational Rehabilitation Data Base (ORDB) functional capacity instrument. Rasch analysis was used to investigate: (1) unidimensionality, (2) hierarchical item difficulty continuum, (3) rater severity, and 4) person-item match. Overall, the functional capacity scale of the ORDB showed good measurement qualities. All items, except the Handling item fit the Rasch measurement model. Because of high fit statistics and loading on factors independent from the remainder of the items, the "handling" item was removed, from further analyses. Separate client-rated and therapist-rated instruments retained good item-level psychometrics. While client and therapist items showed similar item-difficulty hierarchical structures, clients had a tendency to be more severe in their rating and the correlation between client and therapist ratings was relatively low, 0.32. These findings suggest that Handling items should not be included as a DOT measure for clients with back pain. While the above psychometric study supports using client or therapist ratings as independent instruments, the lack of concordance between these ratings requires further investigation.

Adult↗
PubMed2000

Expanding DIOGENE with a clinical information system based on a new hospital-wide clinical findings dictionary.

The DIOGENE hospital information system has been expanded with a centralized and integrated patient clinical database recording structured patient data. The objective is to provide a standardized framework for the building of future clinical databases and for the integration of existing heterogeneous ones. The combined 'across time view' and 'across departments view' generated from the integrated clinical data will enable an evolutionary view of the patient state, both across time and across medical specialties. For this purpose and to permit the communication and exchange of data, a new controlled vocabulary for representing clinical data has been created. The construction of this vocabulary is based on the international ICD classification, already being used in DIOGENE for encoding patient diagnosis and procedures. A new extension of the ICD is proposed for medical information that goes beyond diagnosis and procedures encoding. The building of a common clinical findings dictionary, recording the definition of clinical entities, is based on this newly developed clinical vocabulary. This process is incremental, manual and substantial.

Decision Support Systems, Clinical↗
PubMedDate not supplied

Fast generation of an alkane-series dictionary ordered by side-chain complexity.

Selecting the main chain of an alkane as the path that yields the least complex side chains without the maximum-length constraint leads to an efficient generating algorithm representable as nested binary trees. The largest side chain required to specify an N-carbon alkane becomes (N-1)/3. This allows 3.8 million C1-C22 alkanes to be coded for name translation in dictionary order, using an alphabet of 33 C1-C6 alkyl groups also ranked by complexity. The generating process produces reversible isomer codes already in canonical order, making the computation rate in isomers per second inverse linear with N and much faster than reported rates for other structure generators.

Journal Article↗
PubMedDate not supplied

Evaluation of similarity measures for searching the dictionary of natural products database.

Similarity searches using combinations of seven different similarity coefficients and six different representations have been carried out on the Dictionary of Natural Products database. The objective was to discover if any special methods of searching apply to this database, which is very different in nature from the many synthetic databases that have been the subject of previous studies of similarity searching. Search effectiveness was assessed by a recall analysis of the search outputs from sets of pharmacologically active target structures. The different target sets produce exceptional but contradictory results for the Russell-Rao and Forbes coefficients, which have been shown to be due to a dependence on molecular size; these are the coefficients of choice in the case of large and small structures, respectively. Rankings from these results have been combined using a data fusion scheme and some small gains in performance were normally obtained by using substructural fingerprints and molecular holograms in combination with the Squared Euclidean or Tanimoto coefficients.

Biological Products↗
PubMed1999

The HLA dictionary 1999: a 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 90 HLA-A, 190 HLA-B and 145 HLA-DRB1 alleles. The equivalents cover over 70% of the presently identified HLA-A, -B and -DRB1 alleles. The dictionary is an update of the one published in 1997 and now also includes equivalents for HLA-C, DRB3, DRB4, DRB5 and DQB1 alleles. The data summarize information obtained by the WHO HLA Nomenclature Committee, the International Cell Exchange (UCLA), the National Marrow Donor Program (NMDP) and by individual laboratories. In addition, a listing is provided of alleles which are expressed as antigens with serologic reaction patterns that differ from the well-established HLA specificities and that often lack official WHO nomenclature. The provided equivalents will be useful in guiding searches for unrelated donors in which patients and/or potential donors are typed by either serology or DNA-based methods. These equivalents will also serve typing and matching procedures for organ transplant programs where HLA typings from donors and from recipients on waiting lists represent mixtures of serologic and molecular typings. Some guidelines are provided for the use of appropriate WHO HLA nomenclature for serological typings and for generic and allele specific typings obtained with molecular methods. The tables with HLA equivalents and the questionnaire for submission of serology on poorly identified alleles will also be available at the WMDA web page: www:bmdw.org/wmda.

Alleles↗
PubMed2001

The HLA Dictionary 2001: a 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 the serologic equivalents of 123 HLA-A, 272 HLA-B and 155 HLA-DRB1 alleles. The equivalents cover over 64% of the presently identified HLA-A, -B and -DRB1 alleles. The dictionary is an update of the one published in 1999 and also includes equivalents for HLA-C, DRB3, DRB4, DRB5 and DQB1 alleles. The data summarize information obtained by the WHO Nomenclature Committee for Factors of the HLA System, the International Cell Exchange (UCLA), the National Marrow Donor Program (NMDP) and individual laboratories. In addition, a listing is provided of alleles which are 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. These equivalents will also serve typing and matching procedures for organ transplant programs where HLA typings from donors and from recipients on waiting lists represent mixtures of serologic and molecular typings. The tables with HLA equivalents and a questionnaire for submission of serologic reaction patterns for poorly identified allelic products will also be available on the WMDA web page: http://www.worldmarrow.org.

HLA Antigens↗
PubMed2001

The HLA Dictionary 2001: a summary of HLA-A, -B, -C, -DRB1/3/4/5 and -DQB1 alleles and their association with serologically defined HLA-A, -B, -C, -DR and -DQ antigens.

This report presents the serological equivalents of 123 HLA-A, 272 HLA-B and 155 HLA-DRB1 alleles. The equivalents cover over 64% of the presently identified HLA-A, -B and -DRB1 alleles. The dictionary is an update of the one published in 1999 (<1>Schreuder et al., 1999, Tissue Antigens, 54, 409) and also includes equivalents for HLA-C, DRB3, DRB4, DRB5 and DQB1 alleles. The data summarize information obtained by the WHO Nomenclature Committee for Factors of the HLA System, the International Cell Exchange (UCLA), the National Marrow Donor Program (NMDP) and individual laboratories. In addition, a listing is provided of alleles that are expressed as antigens with serological 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. These equivalents will also serve typing and matching procedures for organ transplant programmes where HLA typings from donors and from recipients on waiting lists represent mixtures of serological and molecular typings. The tables with HLA equivalents and a questionnaire for submission of serological reaction patterns for poorly identified allelic products will also be available on the WMDA web page: www.worldmarrow.org

Alleles↗
PubMed2001

A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3.

The Dali Domain Dictionary (http://www.ebi.ac.uk/dali/domain) is a numerical taxonomy of all known structures in the Protein Data Bank (PDB). The taxonomy is derived fully automatically from measurements of structural, functional and sequence similarities. Here, we report the extension of the classification to match the traditional four hierarchical levels corresponding to: (i) supersecondary structural motifs (attractors in fold space), (ii) the topology of globular domains (fold types), (iii) remote homologues (functional families) and (iv) homologues with sequence identity above 25% (sequence families). The computational definitions of attractors and functional families are new. In September 2000, the Dali classification contained 10 531 PDB entries comprising 17 101 chains, which were partitioned into five attractor regions, 1375 fold types, 2582 functional families and 3724 domain sequence families. Sequence families were further associated with 99 582 unique homologous sequences in the HSSP database, which increases the number of effectively known structures several-fold. The resulting database contains the description of protein domain architecture, the definition of structural neighbours around each known structure, the definition of structurally conserved cores and a comprehensive library of explicit multiple alignments of distantly related protein families.

Amino Acid Motifs↗
PubMed1992

Construction of a dictionary of sequence motifs that characterize groups of related proteins.

An automatic procedure is proposed to identify, from the protein sequence database, conserved amino acid patterns (or sequence motifs) that are exclusive to a group of functionally related proteins. This procedure is applied to the PIR database and a dictionary of sequence motifs that relate to specific superfamilies constructed. The motifs have a practical relevance in identifying the membership of specific superfamilies without the need to perform sequence database searches in 20% of newly determined sequences. The sequence motifs identified represent functionally important sites on protein molecules. When multiple blocks exist in a single motif they are often close together in the 3-D structure. Furthermore, occasionally these motif blocks were found to be split by introns when the correlation with exon structures was examined.

Amino Acid Sequence↗
PubMed2005

Chemical effects in biological systems--data dictionary (CEBS-DD): a compendium of terms for the capture and integration of biological study design description, conventional phenotypes, and 'omics data.

A critical component in the design of the Chemical Effects in Biological Systems (CEBS) Knowledgebase is a strategy to capture toxicogenomics study protocols and the toxicity endpoint data (clinical pathology and histopathology). A Study is generally an experiment carried out during a period of time for the purpose of obtaining data, and the Study Design Description captures the methods, timing, and organization of the Study. The CEBS Data Dictionary (CEBS-DD) has been designed to define and organize terms in an attempt to standardize nomenclature needed to describe a toxicogenomics Study in a structured yet intuitive format and provide a flexible means to describe a Study as conceptualized by the investigator. The CEBS-DD will organize and annotate information from a variety of sources, thereby facilitating the capture and display of toxicogenomics data in biological context in CEBS, i.e., associating molecular events detected in highly-parallel data with the toxicology/pathology phenotype as observed in the individual Study Subjects and linked to the experimental treatments. The CEBS-DD has been developed with a focus on acute toxicity studies, but with a design that will permit it to be extended to other areas of toxicology and biology with the addition of domain-specific terms. To illustrate the utility of the CEBS-DD, we present an example of integrating data from two proteomics and transcriptomics studies of the response to acute acetaminophen toxicity (A. N. Heinloth et al., 2004, Toxicol. Sci. 80, 193-202).

Acetaminophen↗
PubMed1999

Validity of the dictionary of occupational titles residual functional capacity battery.

BACKGROUND DATA: The Dictionary of Occupational Titles (DOT) is a U.S. government publication that defines each job in the United States according to 20 job factors. Fishbain et al. (Spine 1994;19:872-80) developed a DOT residual functional capacity (RFC) battery whose predictive validity for employment/unemployment had not been tested previously. OBJECTIVES: The purposes of this study were as follows: (a) to determine whether results of a DOT-RFC battery performed at completion of pain facility treatment predicted employment status at 30 months' follow-up and (b) to determine whether the DOT-RFC battery predicted employment capacity as determined by the DOT employment levels of the chronic pain patients' (CPPs) jobs. STUDY DESIGN: This is a prospective low back pain CPP pain facility treatment study using employment status and the DOT occupational levels as outcome measures. METHODS: One hundred eighty-five consecutive CPPs who fitted the selection criteria completed a DOT-RFC battery at the completion of pain facility treatment and were contacted at 1, 3, 6, 12, 18, 24, and 30 months for determination of their employment status and DOT employment level. Eight DOT job factors plus pain and worker compensation status were found to be significantly different between employed and unemployed CPPs and between those employed in different DOT employment levels. For the 10 variables, stepwise discriminant analysis was used to select final predictor variables. Sensitivity and specificity were calculated along with pain level cutpoints that separated the groups. RESULTS: The eight DOT job factors found to be statistically significant between groups were the following: stooping, climbing, balancing, crouching, feeling shapes, handling left and right, lifting, carrying, and pain and worker compensation status. In the discriminant analysis, these variables could discriminate between the employed and unemployed categories, with a sensitivity and specificity of approximately 75%. The pain level cutpoint between employed and unemployed was 5.4 on a 10-point scale. CONCLUSIONS: We cannot as yet predict DOT-RFC employment levels. However, if a CPP can pass the above eight DOT job factors and has a pain level less than the 5.4 cutpoint, that CPP will have a 75% chance of being employed at 30 months after treatment at the pain facility. Therefore, some DOT-RFC battery job factors demonstrate a predictive validity in the "real work world."

Discriminant Analysis↗
PubMed1994

Measuring residual functional capacity in chronic low back pain patients based on the Dictionary of Occupational Titles.

STUDY DESIGN: This study designed and tested a functional battery based on the Dictionary of Occupational Titles (DOT). OBJECTIVES: Such a battery can be used to measure residual functional capacity (RFC) in chronic pain patients (CPP) and results can be matched against the demand minimum functional capacities (DMFC) of DOT jobs. SUMMARY OF BACKGROUND DATA: Physicians have difficulty translating medical impairment into functional limitation and thereby establishing the RFC of CPPs. METHODS: The DOT, a USA government publication, provides information about physical demands of every USA job according to 36 factors and subfactors. The authors defined and developed a functional battery based on these factors/subfactors. This battery was tested on 67 consecutive CPPs to determine the percentage of CPPs able to pass specific job factors and the full battery and return to some DOT job, and evaluated the effects of pain on battery performance. The data were factor analyzed. RESULTS: The battery determined if CPPs could perform DOT job factors and had the necessary RFC to be placed in a DOT job. The vast majority of CPPs could not pass the full battery and the presence of pain and original job classification predicted whether a CPP could perform a job factor. Factor analyses grouped the factors into four independent categories supporting the design of the battery. CONCLUSION: The battery can assess whether CPPs are able to return to work.

Adult↗