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PubMedDate not supplied

From cognition to the system: developing a multilevel taxonomy of patient safety in general practice.

The paper describes the process of developing a taxonomy of patient safety in general practice. The methodologies employed included fieldwork, task analysis and confidential reporting of patient-safety events in five West Midlands practices. Reported events were traced back to their root causes and contributing factors. The resulting taxonomy is based on a theoretical model of human cognition, includes multiple levels of classification to reflect the chain of causation and considers affective and physiological influences on performance. Events are classified at three levels. At level one, the information-processing model of cognition is used to classify errors. At level two, immediate causes are identified, internal and external to the individual. At level three, more remote causal factors are classified as either 'work organization' or 'technical' with subcategories. The properties of the taxonomy (validity, reliability, comprehensiveness) as well as its usability and acceptability remain to be tested with potential users.

Classification↗

PubMed2005

The logical basis of phylogenetic taxonomy.

Phylogenetic taxonomy, like modern Linnean taxonomy, was modeled on a phylogenetic tree rather than a cladogram and, like its predecessor, perpetuates the use of morphology as a means of recognizing clades. Both practices have generated confusion in graphical representation, operational terminology, and definitional rationale in phylogenetic taxonomy, the history of which is traced. The following points are made: (1) cladograms, rather than trees or hybrid cladogram-trees, provide the framework for the simplest graphical depiction of phylogenetic definitions; (2) a complete notational scheme for phylogenetic definitions is presented that distinguishes symbolic notation from shorthand and longhand versions; (3) phylogenetic definitions are composed of three components (paradigm, specifier, qualifier) arranged in two fundamental patterns-node and stem; (4) apomorphies do not constitute a fundamental definitional pattern but rather serve to qualify a stem-based definition (as do time and geographic range); (5) formulation of phylogenetic definitions involves three heuristic criteria (stability, simplicity, prior use); (6) reasoned definitional revision is encouraged and better defined (textual substitution, first-and second-order revision); and (7) a database, TaxonSearch, allows rapid recall of taxonomic and definitional information.

Classification↗

PubMed2003

NEWT, a new taxonomy portal.

NEWT is a new taxonomy portal to the SWISS-PROT protein sequence knowledgebase. It contains taxonomy data, which is updated daily, for the complete set of species represented in SWISS-PROT, as well as those stored at the NCBI. Users can navigate through the taxonomy tree and access corresponding SWISS-PROT protein entries. In addition, a manually curated selection of external links allows access to specific information on selected species. NEWT is available at http://www.ebi.ac.uk/newt/.

Classification↗

PubMedDate not supplied

A nurse-staffing taxonomy for decision making in long-term care nursing facilities.

A nurse-staffing taxonomy is proposed to facilitate informed staffing decisions in long-term care nursing facilities and to set forth construct components for empirically related research. Recommendations from an expert workgroup were synthesized with current staffing research to define a staffing taxonomy. Refinements were made, incorporating on-site nursing home quality assessments and concepts founded on psychometric theory and Donabedian's model. A quality monitoring protocol, based on the staffing taxonomy, was used to assess quality improvement systems. Results from 48 US nursing facilities indicate that most long-term care facilities struggle with staffing allocation and the integration of staffing into a quality monitoring process.

Attitude of Health Personnel↗

PubMed1996

Research to support holistic nursing taxonomies.

A philosophy of holism and the development of nursing taxonomies may appear to have goals that are inconsistent. Taxonomies are typically hierarchic in structure, and their content often consists of atomic level elements rather than holistic concepts. The article explores the development of taxonomies and how they can be enriched by a holistic perspective.

Holistic Nursing↗

PubMed2002

Individual, practice, and system causes of errors in nursing: a taxonomy.

Practice errors by nurses can cause harm to patients, families, practitioners, systems, and the profession. Because the nursing errors reported to the State Boards of Nursing are typically serious, analyzing their data has great potential for developing new strategies to reduce dangerous errors. With the guiding rationale being identification of categories central to the nurse's role and function in healthcare delivery errors, 21 case studies of nursing errors from 9 State Boards of Nursing files were analyzed to develop a taxonomy of nursing errors. Eight categories of nursing errors representing a broad range of possible errors and contributive or causative factors were identified: lack of attentiveness; lack of agency/fiduciary concern; inappropriate judgment; lack of intervention on the patient's behalf; medication errors; lack of prevention; missed or mistaken MD/healthcare provider's orders; and documentation errors. Causes for the error, at the system and practice responsibility levels, were identified in each case. The categories, an assessment of causes of errors, and an examination of the remediation actions taken were the first steps in devising a taxonomy of nursing error, designed with prevention in mind. The authors discuss their work and present the taxonomy.

Aged↗

PubMed2004

Exploring prokaryotic taxonomy.

Techniques drawn from exploratory data analysis, using tools found in the S-Plus statistical software package, have been used to inspect and maintain the Bergey's Taxonomic Outline and to move towards an automated and community-based means of working on the outline. These techniques can be used to classify sequences from unnamed and uncultured organisms, to visualize errors in the taxonomy or in the curation of the sequences, to suggest emendations to the taxonomy or to the classification of extant species and to complement the visualization of phylogenies based on treeing methods. A dataset of more than 9200 aligned small-subunit rRNA sequences was analysed in the context of the current taxonomic outline. The use of the algorithm in exploring and modifying the taxonomy is illustrated with an example drawn from the family Comamonadaceae.

Bacteria↗

PubMed1999

Susceptibility to affect: a comparison of three personality taxonomies.

This study had three major goals: to clarify the relationships between Eysenck's, Gray's, and Cloninger's personality taxonomies, to show that traits from these taxonomies predict differential sensitivities to emotional states, and to explore the relationship between sensitivity to an emotional state and how much that state is actually experienced. A factor analysis of traits from Eysenck's, Gray's, and Cloninger's personality taxonomies resulted in three factors that were named reward sensitivity, impulsivity-thrill seeking, and punishment sensitivity. These factors predicted a global measure of affect, emotional reactions to a laboratory mood induction, and self-reported affect in daily life. Generally, reward sensitivity predicted positive, but not negative emotions, whereas punishment sensitivity predicted negative, but not positive emotions. Impulsivity-thrill seeking predicted few emotions in either context. Coherence among the relationships found across methodological contexts suggests that the traits that predict emotion susceptibilities in the laboratory similarly predict emotional experience in ongoing daily life.

Adult↗

PubMed2005

Multi-dimensional phenotyping: towards a new taxonomy for airway disease.

All the real knowledge which we possess, depends on methods by which we distinguish the similar from the dissimilar. The greater the number of natural distinctions this method comprehends the clearer becomes our idea of things. The more numerous the objects which employ our attention the more difficult it becomes to form such a method and the more necessary. Classification is a fundamental part of medicine. Diseases are often categorized according to pre-20th century descriptions and concepts of disease based on symptoms, signs and functional abnormalities rather than on underlying pathogenesis. Where the aetiology of disease has been revealed (for example in the infectious diseases) a more precise classification has become possible, but in the chronic inflammatory diseases, and in the inflammatory airway diseases in particular, where pathogenesis has been stubbornly difficult to elucidate, we still use broad descriptive terms such as asthma and chronic obstructive pulmonary disease, which defy precise definition because they encompass a wide spectrum of presentations and physiological and cellular abnormalities. It is our contention that these broad-brush terms have outlived their usefulness and that we should be looking to create a new taxonomy of airway disease-a taxonomy that more closely reflects the spectrum of phenotypes that are encompassed within the term airway inflammatory diseases, and that gives full recognition to late 20th and 21st century insights into the disordered physiology and cell biology that characterizes these conditions in the expectation that these will map more closely to both aetiology and response to treatment. Development of this taxonomy will require a much more complete and sophisticated correlation of the many variables that make up a condition than has been usual to employ in an approach that encompasses multi-dimensional phenotyping and uses complex statistical tools such as cluster analysis.

Animals↗

PubMed2007

Stability of an empirical psychosocial taxonomy across type of diabetes and treatment.

AIMS: The aims of the study were (i) to examine whether an empirical psychosocial taxonomy, based on key diabetes-related variables, is independent of type of diabetes and treatment, and (ii) to further establish the external validation of the taxonomy. METHODS: In a cross-sectional study, 82 patients with Type 1 and 86 patients with Type 2 diabetes mellitus were assigned to one of three psychosocial patient profiles based on their Multidimensional Diabetes Questionnaire (MDQ) scores. General psychological and diabetes-specific measures were obtained through self-report and HbA(1c) was measured. RESULTS: Equal proportions of Type 1 and Type 2 patients, and of patients using insulin and oral medication/diet only were classified within each of the three psychosocial profiles. External validation confirmed the validity and distinctiveness of the patients' profiles. The patient profiles were independent of demographic variables, body mass index, duration of diabetes, complexity of treatment, number of complications, social desirability, and major stress levels. CONCLUSIONS: The Psychosocial Taxonomy for Patients with Diabetes provides a new way to categorize individuals who may have more in common than just their type of diabetes and/or its treatment and can help target interventions to individual patients' needs.

Adult↗

PubMed1995

Self-with-other representations and a taxonomy of motives: two approaches to studying persons.

This article discusses two approaches to studying persons. Part 1 describes data gathering procedures that lead to an integrated visual display of particular self-representations of an individual in various spheres of life. "Self-with-other representation" is introduced as a central unit of analysis in this research. This concept is integrated into a method that is exemplified in this article by a description of how life can be injected into static trait characterization of a person. In the context of a case study, it is shown that the method provides information about how traits are organized in terms of self-with-other working models and the conditions under which a particular working model is likely to prevail. Part 2 presents a new taxonomy of motives. This taxonomy is a product of having dipped into the area of operant conditioning and reformulating behavioral consequences into motivational causes. This intrusion into reinforcement theory has resulted in a two-dimensional classification system (referred to as PACK) that accounts for motives to keep or acquire positive experiences, and to cure or prevent negative experiences. After the taxonomy is described, it is used to organize motivational concepts in the area of goal-directed behaviors, and it is applied to purpose statements of individuals in different age groups.

Adult↗

PubMed2006

Integrating software into PRA: a software-related failure mode taxonomy.

Probabilistic risk assessment is a methodology to assess the probability of failure or success of a mission. Results provided by the risk assessment methodology are used to make decisions concerning choice of upgrades, scheduling of maintenance, decision to launch, etc. However, current PRA neglects the contribution of software to the risk of failure of the mission. Our research has developed a methodology to account for the impact of software to system failure. This article focuses on an element of the approach: a comprehensive taxonomy of software-related failure modes. Application of the taxonomy is discussed in this article. A validation of the taxonomy and conclusions drawn from this validation effort are described. Future research is also summarized.

Journal Article↗

PubMed1995

Validation and coding of the NIC taxonomy structure. Iowa Intervention Project. Nursing Interventions Classification.

Processes for validation and coding of the taxonomy for the Nursing Interventions Classification (NIC) are described. A sample of nurses expert in theory development rated the NIC taxonomy using five criteria. Following identification of a stable structure, the taxonomy was coded with each intervention receiving a unique number. A coded and valid taxonomic structure facilitates use of the classification in computerization and makes possible the collection of comparable data. A coded classification can also be used in reimbursement systems.

Cluster Analysis↗

PubMedDate not supplied

Axes: focus of taxonomy II.

A number of persistent issues in the nursing diagnosis community have challenged the ability of one nursing diagnosis taxonomy to account for nursing's practice. The North American Nursing Diagnosis Association (NANDA) Taxonomy Committee, charged with the preparation of one taxonomy for all, has struggled with some of these issues and has initiated development of axes. The issues, figuratively speaking, become the axes. The axes are intended to describe the dimensions of the human condition. This article, third in a series of four, describes the process and development of the proposed axes.

Age Factors↗

PubMed1996

A taxonomy for lay risk perceptions of dentistry.

OBJECTIVE: This paper aims to develop and organize a set of variables that can be used to: (1) test the widely held but unproven assumption that lay risk perceptions can adversely affect dental care, (2) investigate the possible influence of lay risk perceptions on dental care and (3) permit the evaluation of risk communication strategies in dentistry. METHODS: We reviewed the literature regarding risk perception and risk communication in health care and technology. We then selected a set of variables that could be measured in a study of the general public and organized these in a taxonomy to suggest likely relationships among the variables. RESULTS: The central relationship of the proposed taxonomy is between a lay person's perception of dental risk and a set of measurable outcomes that could affect that person's dental care. The taxonomy lists three possible influences on the lay person's risk perception: attributes of the individual, attributes of the dental procedure or technology perceived as risky, and attributes of the dental practice. CONCLUSIONS: Systematic testing of the proposed variables should demonstrate whether lay risk perceptions substantially influence dental care, and if so, which factors most strongly influence risk perceptions. A model of lay risk perceptions of dentistry then could be developed and strategies could be devised to minimize the detriment, if any, to dental care from risk perception.

Attitude to Health↗

PubMed2002

Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches.

The practice of classifying organisms into hierarchical groups originated with Aristotle and was codified into nearly immutable biological law by Linnaeus. The heart of taxonomy is the biological species, which forms the foundation for higher levels of classification. Whereas species have long been established among sexual eukaryotes, achieving a meaningful species concept for prokaryotes has been an onerous task and has proven exceedingly difficult for describing viruses and bacteriophages. Moreover, the assembly of viral "species" into higher-order taxonomic groupings has been even more tenuous, since these groupings were based initially on limited numbers of morphological features and more recently on overall genomic similarities. The wealth of nucleotide sequence information that catalyzed a revolution in the taxonomy of free-living organisms necessitates a reevaluation of the concept of viral species, genera, families, and higher levels of classification. Just as microbiologists discarded dubious morphological traits in favor of more accurate molecular yardsticks of evolutionary change, virologists can gain new insight into viral evolution through the rigorous analyses afforded by the molecular phylogenetics of viral genes. For bacteriophages, such dissections of genomic sequences reveal fundamental flaws in the Linnaean paradigm that necessitate a new view of viral evolution, classification, and taxonomy.

Bacteriophages↗

PubMed2002

The dilemma of phage taxonomy illustrated by comparative genomics of Sfi21-like Siphoviridae in lactic acid bacteria.

The complete genome sequences of two dairy phages, Streptococcus thermophilus phage 7201 and Lactobacillus casei phage A2, are reported. Comparative genomics reveals that both phages are members of the recently proposed Sfi21-like genus of Siphoviridae, a widely distributed phage type in low-GC-content gram-positive bacteria. Graded relatedness, the hallmark of evolving biological systems, was observed when different Sfi21-like phages were compared. Across the structural module, the graded relatedness was represented by a high level of DNA sequence similarity or protein sequence similarity, or a shared gene map in the absence of sequence relatedness. This varying range of relatedness was found within Sfi21-like phages from a single species as demonstrated by the different prophages harbored by Lactococcus lactis strain IL1403. A systematic dot plot analysis with 11 complete L. lactis phage genome sequences revealed a clear separation of all temperate phages from two classes of virulent phages. The temperate lactococcal phages share DNA sequence homology in a patchwise fashion over the nonstructural gene cluster. With respect to structural genes, four DNA homology groups could be defined within temperate L. lactis phages. Closely related structural modules for all four DNA homology groups were detected in phages from Streptococcus or Listeria, suggesting that they represent distinct evolutionary lineages that have not uniquely evolved in L. lactis. It seems reasonable to base phage taxonomy on data from comparative genomics. However, the peculiar modular nature of phage evolution creates ambiguities in the definition of phage taxa by comparative genomics. For example, depending on the module on which the classification is based, temperate lactococcal phages can be classified as a single phage species, as four distinct phage species, or as two if not three different phage genera. We propose to base phage taxonomy on comparative genomics of a single structural gene module (head or tail genes). This partially phylogeny-based taxonomical system still mirrors some aspects of the current International Committee on Taxonomy in Virology classification system. In this system the currently sequenced lactococcal phages would be grouped into five genera: c2-, sk1, Sfi11-, r1t-, and Sfi21-like phages.

Base Sequence↗

PubMedDate not supplied

Phase II evaluation of clinical coding schemes: completeness, taxonomy, mapping, definitions, and clarity. CPRI Work Group on Codes and Structures.

OBJECTIVE: To compare three potential sources of controlled clinical terminology (READ codes version 3.1, SNOMED International, and Unified Medical Language System (UMLS) version 1.6) relative to attributes of completeness, clinical taxonomy, administrative mapping, term definitions and clarity (duplicate coding rate). METHODS: The authors assembled 1929 source concept records from a variety of clinical information taken from four medical centers across the United States. The source data included medical as well as ample nursing terminology. The source records were coded in each scheme by an investigator and checked by the coding scheme owner. The codings were then scored by an independent panel of clinicians for acceptability. Codes were checked for definitions provided with the scheme. Codes for a random sample of source records were analyzed by an investigator for "parent" and "child" codes within the scheme. Parent and child pairs were scored by an independent panel of medical informatics specialists for clinical acceptability. Administrative and billing code mapping from the published scheme were reviewed for all coded records and analyzed by independent reviewers for accuracy. The investigator for each scheme exhaustively searched a sample of coded records for duplications. RESULTS: SNOMED was judged to be significantly more complete in coding the source material than the other schemes (SNOMED* 70%; READ 57%; UMLS 50%; *p < .00001). SNOMED also had a richer clinical taxonomy judged by the number of acceptable first-degree relatives per coded concept (SNOMED* 4.56, UMLS 3.17; READ 2.14, *p < .005). Only the UMLS provided any definitions; these were found for 49% of records which had a coding assignment. READ and UMLS had better administrative mappings (composite score: READ* 40.6%; UMLS* 36.1%; SNOMED 20.7%, *p < .00001), and SNOMED had substantially more duplications of coding assignments (duplication rate: READ 0%; UMLS 4.2%; SNOMED* 13.9%, *p < .004) associated with a loss of clarity. CONCLUSION: No major terminology source can lay claim to being the ideal resource for a computer-based patient record. However, based upon this analysis of releases for April 1995, SNOMED International is considerably more complete, has a compositional nature and a richer taxonomy. Is suffers from less clarity, resulting from a lack of syntax and evolutionary changes in its coding scheme. READ has greater clarity and better mapping to administrative schemes (ICD-10 and OPCS-4), is rapidly changing and is less complete. UMLS is a rich lexical resource, with mappings to many source vocabularies. It provides definitions for many of its terms. However, due to the varying granularities and purposes of its source schemes, it has limitations for representation of clinical concepts within a computer-based patient record.

Abstracting and Indexing↗