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PubMed2025

Persistent gaps and errors in reference databases impede ecologically meaningful taxonomy assignments in 18S rRNA studies: a case study of terrestrial and marine nematodes.

In metabarcoding studies, Linnaean taxonomy assignments of Operational Taxonomic Units (OTUs) or Amplicon Sequence Variants (ASVs) underpin many downstream bioinformatics analyses and ecological interpretations of environmental DNA (eDNA) datasets. However, public molecular databases (i.e., SILVA, EUKARYOME, BOLD) for most microbial metazoan phyla (nematodes, tardigrades, kinorhynchs, etc.) are sparsely populated, negatively impacting our ability to assign ecologically meaningful taxonomy to these understudied groups. Additionally, the choice of bioinformatics parameters and computational algorithms can further impact the accuracy of eDNA taxonomy assignments. Here, we use two in-silico datasets to show that taxonomy assignments using the 18S rRNA gene can be dramatically improved by curating Linnaean taxonomy strings associated with each reference sequence and closing phylogenetic gaps by improving taxon sampling. Using free-living nematodes as a case study, we applied two commonly used taxonomy assignment algorithms (BLAST+ and the QIIME2 Naïve Bayes classifier) across six iterations of the SILVA 138 reference database to evaluate the precision and accuracy of taxonomy assignments. The BLAST+ top hit with a 90% sequence similarity cutoff often returned the highest percentage of correctly assigned taxonomy at the genus level, and the QIIME2 Naïve Bayes classifier performed similarly well when paired with a reference database containing corrected taxonomy strings. Our results highlight the urgent need for phylogenetically-informed expansions of public reference databases (encompassing both genomes and common gene markers), focused on poorly sampled lineages which are now robustly recovered via eDNA metabarcoding approaches. Additional taxonomy curation efforts should be applied to popular reference databases such as SILVA, and taxon sampling could be rapidly improved by more frequent incorporation of newly published GenBank sequences linked to genus and/or species level identifications.

18S rRNA metabarcoding↗

PubMed2004

A cognitive taxonomy of medical errors.

OBJECTIVE: Propose a cognitive taxonomy of medical errors at the level of individuals and their interactions with technology. DESIGN: Use cognitive theories of human error and human action to develop the theoretical foundations of the taxonomy, develop the structure of the taxonomy, populate the taxonomy with examples of medical error cases, identify cognitive mechanisms for each category of medical error under the taxonomy, and apply the taxonomy to practical problems. MEASUREMENTS: Four criteria were used to evaluate the cognitive taxonomy. The taxonomy should be able (1) to categorize major types of errors at the individual level along cognitive dimensions, (2) to associate each type of error with a specific underlying cognitive mechanism, (3) to describe how and explain why a specific error occurs, and (4) to generate intervention strategies for each type of error. RESULTS: The proposed cognitive taxonomy largely satisfies the four criteria at a theoretical and conceptual level. CONCLUSION: Theoretically, the proposed cognitive taxonomy provides a method to systematically categorize medical errors at the individual level along cognitive dimensions, leads to a better understanding of the underlying cognitive mechanisms of medical errors, and provides a framework that can guide future studies on medical errors. Practically, it provides guidelines for the development of cognitive interventions to decrease medical errors and foundation for the development of medical error reporting system that not only categorizes errors but also identifies problems and helps to generate solutions. To validate this model empirically, we will next be performing systematic experimental studies.

Cognition↗

PubMed2004

Reexamining organizational configurations: an update, validation, and expansion of the taxonomy of health networks and systems.

OBJECTIVES: To (a) assess how the original cluster categories of hospital-led health networks and systems have changed over time; (b) identify any new patterns of cluster configurations; and (c) demonstrate how additional data can be used to refine and enhance the taxonomy measures. DATA SOURCES; 1994 and 1998 American Hospital Association (AHA) Annual Survey of Hospitals. STUDY DESIGN: As in the original taxonomy, separate cluster solutions are identified for health networks and health systems by applying three strategic/structural dimensions (differentiation, integration, and centralization) to three components of the health service/product continuum (hospital services, physician arrangements, and provider-based insurance activities). DATA EXTRACTION METHODS: Factor, cluster, and discriminant analyses are used to analyze the 1998 data. Descriptive and comparative methods are used to analyze the updated 1998 taxonomy relative to the original 1994 version. PRINCIPAL FINDINGS: The 1998 cluster categories are similar to the original taxonomy, however, they reveal some new organizational configurations. For the health networks, centralization of product/service lines is occurring more selectively than in the past. For the health systems, participation has grown in and dispersed across a more diverse set of decentralized organizational forms. For both networks and systems, the definition of centralization has changed over time. CONCLUSIONS: In its updated form, the taxonomy continues to provide policymakers and practitioners with a descriptive and contextual framework against which to assess organizational programs and policies. There is a need to continue to revisit the taxonomy from time to time because of the persistent evolution of the U.S. health care industry and the consequent shifting of organizational configurations in this arena. There is also value in continuing to move the taxonomy in the direction of refinement/expansion as new opportunities become available.

American Hospital Association↗

PubMedDate not supplied

Development of definitions for taxonomy II.

In the process of placing diagnoses into Taxonomy I, certain inconsistencies became apparent. Inadequate definition of both diagnoses and human response patterns, lack of defining characteristics, and inconsistency in the levels of abstraction within the taxonomic hierarchy made the task of assigning a diagnosis to a taxonomic pattern difficult. Ambiguity in the definitions of the nine patterns resulted in ambiguity in the basic foundation, which affected the entire structure. The Taxonomy Committee, before evaluating the current structure, had to make the following decisions regarding the current human response patterns: (1) Should the nine human response patterns be retained for further taxonomic work? and (2) If they are retained, what should be the first step in examining Taxonomy I-Revised? This second article in a series of four will familiarize the readers with the process and decisions by which Taxonomy II of the North American Nursing Diagnosis Association (NANDA) is evolving through the work of the Taxonomy Committee. This article also will identify the specific problems encountered in the development of Taxonomy I and Taxonomy I-Revised, and describe the steps establishing the validity of the process of formation of the nine human response patterns.

Classification↗

PubMed1987

Development of a taxonomy of therapist difficulties: initial report.

While psychotherapists discuss amongst themselves and in supervision the struggles they experience face-to-face with their patients, empirical study of therapists' experience of psychotherapy has been scant and there has been little investigation of therapists' difficulties. We require tools for such investigation and in this initial report we describe the development of a taxonomy of situations that psychotherapists experience as difficult and indicate lines of research to which the taxonomy might be applied. We also suggest that our procedure might serve as a model of collective self-study for other groups of practitioner-researchers. Using accounts of our own difficulties as therapists, we constructed a consensual set of experimental categories that could be applied to describe them. These were designated as Therapist (T)-Incompetent, T-Damaging, T-Puzzled, T-Threatened, T-Out of Rapport, T's Personal Issues, Painful Reality/T's Ethical Dilemma (a combined category), T-Stuck, and T-Thwarted. We then employed a fresh set of 30 accounts, which were also drawn from our own experience but had not contributed to the development of the taxonomy, to study the taxonomy's reliability. Each of us rated the presence and predominance of the categories for each of the 30 accounts. Both presence and predominance of all nine categories in the taxonomy could be reliably identified, with about three raters required to ensure good reliability for all categories; alphas (for our group of seven raters) were in the range 0.88-0.95 for presence-absence and 0.83-0.94 for predominance. We conclude that the taxonomy is a serviceable tool for further investigation. We also show that we are discriminable from one another as therapists in terms of the kinds of difficulty we reported, differences amongst us conforming to what we know of one another's therapeutic practice. We note implications for the diagnostic use of the taxonomy in training and supervision.

Clinical Competence↗

PubMed1996

Polyphasic taxonomy, a consensus approach to bacterial systematics.

Over the last 25 years, a much broader range of taxonomic studies of bacteria has gradually replaced the former reliance upon morphological, physiological, and biochemical characterization. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them in a consensus type of classification, framed in a general phylogeny derived from 16S rRNA sequence analysis. In some cases, the consensus classification is a compromise containing a minimum of contradictions. It is thought that the more parameters that will become available in the future, the more polyphasic classification will gain stability. In this review, the practice of polyphasic taxonomy is discussed for four groups of bacteria chosen for their relevance, complexity, or both: the genera Xanthomonas and Campylobacter, the lactic acid bacteria, and the family Comamonadaceae. An evaluation of our present insights, the conclusions derived from it, and the perspectives of polyphasic taxonomy are discussed, emphasizing the keystone role of the species. Taxonomists did not succeed in standardizing species delimitation by using percent DNA hybridization values. Together with the absence of another "gold standard" for species definition, this has an enormous repercussion on bacterial taxonomy. This problem is faced in polyphasic taxonomy, which does not depend on a theory, a hypothesis, or a set of rules, presenting a pragmatic approach to a consensus type of taxonomy, integrating all available data maximally. In the future, polyphasic taxonomy will have to cope with (i) enormous amounts of data, (ii) large numbers of strains, and (iii) data fusion (data aggregation), which will demand efficient and centralized data storage. In the future, taxonomic studies will require collaborative efforts by specialized laboratories even more than now is the case. Whether these future developments will guarantee a more stable consensus classification remains an open question.

Amino Acid Sequence↗

PubMed2000

A taxonomy of generic clinical questions: classification study.

OBJECTIVE: To develop a taxonomy of doctors' questions about patient care that could be used to help answer such questions. DESIGN: Use of 295 questions asked by Oregon primary care doctors to modify previously developed taxonomy of 1101 clinical questions asked by Iowa family doctors. SETTING: Primary care practices in Iowa and Oregon. PARTICIPANTS: Random samples of 103 Iowa family doctors and 49 Oregon primary care doctors. MAIN OUTCOME MEASURES: Consensus among seven investigators on a meaningful taxonomy of generic questions; interrater reliability among 11 individuals who used the taxonomy to classify a random sample of 100 questions: 50 from Iowa and 50 from Oregon. RESULTS: The revised taxonomy, which comprised 64 generic question types, was used to classify 1396 clinical questions. The three commonest generic types were "What is the drug of choice for condition x?" (150 questions, 11%); "What is the cause of symptom x?" (115 questions, 8%); and "What test is indicated in situation x?" (112 questions, 8%). The mean interrater reliability among 11 coders was moderate (kappa=0.53, agreement 55%). CONCLUSIONS: Clinical questions in primary care can be categorised into a limited number of generic types. A moderate degree of interrater reliability was achieved with the taxonomy developed in this study. The taxonomy may enhance our understanding of doctors' information needs and improve our ability to meet those needs.

Classification↗

PubMedDate not supplied

[Classical and non-classical taxonomy: where does the boundary pass?].

Rise of non-classical science during XX century had certain influence upon development of biological taxonomy. Scientific pluralism (especially normative naturalism of Laudan), contrary to positivist and early post-positivist treatments, made taxonomy acknowledged scientific discipline of its own right. The present state of some schools of taxonomy makes it possible to consider them as a part of non-classical science and constituting the non-classical taxonomy. The latter is characterized by the following most important features. Ontological substantiation of both classificatory approaches and particular classifications is requested which invalidates such formal approaches as nominalistic and phenetic (numerical) schools. This substantiation takes a form of content-wise background preferably causal models which include certain axioms and presumptions about taxonomic diversity being studied, together with its causes, and thus define initial conditions of classificatory procedures. From this viewoint, phylogenetic classificatory approach is the most developed part of non-classical taxonomy. The entire taxonomic diversity is structured into several aspects of different levels of generality, each being outlined by a particular consideration aspect. The latter makes personal knowledge constituting an irremovable part of any scientific statement about taxonomic diversity, thus opposition of "objectively" and "subjectively" elaborated classifications becomes vague. Interrelation of various species concepts corresponding to its different consideration aspects is described by uncertainty relation principle. Classificatory algorithms are to be compatible with the conditions of a background model to ensure particular classifications obtained by their means are interpretable within the same model: this is provided by the correspondence principle. Classification is considered as a taxonomic hypothesis, i.e. a conjectural judgement about structure of particular fragment of taxonomic diversity considered within given consideration aspect; wich is to be forwarded and tested according to certain rules. Recognition of different aspects of taxonomic diversity makes it "legal" to elaborate several classifications of equal status, each reflecting a particular aspect of a fixed fragment of that diversity. This viewpoint makes classical ideas of the "ultimate" Natural (whatever might be its definition) or the best reference systems futile. In general, any pretension of an approach to be "the best" in reflecting taxonomic divesrity is contr-productive. Instead, elaboration of particular spectra of complementary classifications becomes the main task of non-classical taxonomy which describes in sum the entire taxonomic diversity. So, not opposition but correct mutual interpretation of such classifications and uniting them into the comprehensive picture of taxonomic diversity become focal points of non-classical taxonomy.

Biodiversity↗

PubMed1996

The reliability of Marlatt's taxonomy for classifying relapses.

Marlatt's focus on the relapse situation has had a major impact upon research and clinical practice in treating addictions. One component of his work was the development of a taxonomy for classifying precipitants of relapse. This taxonomy has been incorporated into the nomenclature of clinicians and clinical researchers as part of an explanatory framework for understanding relapses. Despite the taxonomy's influence it has never been examined for the reliability of its use across research studies. The present study compared the reliability of independent classifications of 149 relapse episodes by trained raters at three research laboratories. Despite considerable across-laboratory training, reliability was found to be inconsistent for research purposes. It is concluded that comparability of results based on Marlatt's relapse taxonomy across independent studies must be subject to question, and assumptions necessary for the aggregation of a knowledge base are not supported. Recommendations are offered for improving the reliability of the taxonomy and the methods used to collect taxonomy data. More generally, questions regarding the value of the specific relapse categories, as well as the overall taxonomy, are raised.

Adult↗

PubMed2001

Using measures of agreement to develop a taxonomy of passivity in dementia.

A comprehensive taxonomy categorizing passive behaviors in people with dementia was developed and revised through the use of expert raters. The taxonomy was first derived from the synthesis of 15 empirical studies that addressed this phenomenon, then was rated by an expert panel of six nurse-scientists with expertise in dementia and neuroscience research. This article describes the application of two measures of agreement, multiple rater kappa and proportion of agreement for multiple raters, calculated using Stata and SPSS, to evaluate and revise the taxonomy. The method proved useful for estimating the content validity of the taxonomy and provided evidence of stronger agreement among raters for the revised and final forms of the taxonomy. Nurse researchers will find this methodology to be an efficient, practical approach to applying measures of agreement for a variety of purposes, including taxonomy development.

Dementia↗

PubMed2001

Development of the Functional Assessment Taxonomy.

The development of the Functional Assessment Taxonomy is described and the taxonomy is presented. The taxonomy provides a method to classify and organize constructs that are used to assess the functional abilities of people with medical impairments to determine work disability. The taxonomy has 131 constructs that are organized into 33 conceptual factors that are nested in 5 domains. Each construct is defined and is categorized in terms of the work disability model and the unit of analysis that is commonly used to measure the construct. The use of the taxonomy in the Disability Methodology Redesign Project is described. Other possible uses for the taxonomy are presented.

Classification↗

PubMed2006

DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success.

DNA barcoding and DNA taxonomy have recently been proposed as solutions to the crisis of taxonomy and received significant attention from scientific journals, grant agencies, natural history museums, and mainstream media. Here, we test two key claims of molecular taxonomy using 1333 mitochondrial COI sequences for 449 species of Diptera. We investigate whether sequences can be used for species identification ("DNA barcoding") and find a relatively low success rate (< 70%) based on tree-based and newly proposed species identification criteria. Misidentifications are due to wide overlap between intra- and interspecific genetic variability, which causes 6.5% of all query sequences to have allospecific or a mixture of allo- and conspecific (3.6%) best-matching barcodes. Even when two COI sequences are identical, there is a 6% chance that they belong to different species. We also find that 21% of all species lack unique barcodes when consensus sequences of all conspecific sequences are used. Lastly, we test whether DNA sequences yield an unambiguous species-level taxonomy when sequence profiles are assembled based on pairwise distance thresholds. We find many sequence triplets for which two of the three pairwise distances remain below the threshold, whereas the third exceeds it; i.e., it is impossible to consistently delimit species based on pairwise distances. Furthermore, for species profiles based on a 3% threshold, only 47% of all profiles are consistent with currently accepted species limits, 20% contain more than one species, and 33% only some sequences from one species; i.e., adopting such a DNA taxonomy would require the redescription of a large proportion of the known species, thus worsening the taxonomic impediment. We conclude with an outlook on the prospects of obtaining complete barcode databases and the future use of DNA sequences in a modern integrative taxonomy.

Animals↗

PubMed2005

The JCAHO patient safety event taxonomy: a standardized terminology and classification schema for near misses and adverse events.

BACKGROUND: The current US national discussions on patient safety are not based on a common language. This hinders systematic application of data obtained from incident reports, and learning from near misses and adverse events. OBJECTIVE: To develop a common terminology and classification schema (taxonomy) for collecting and organizing patient safety data. METHODS: The project comprised a systematic literature review; evaluation of existing patient safety terminologies and classifications, and identification of those that should be included in the core set of a standardized taxonomy; assessment of the taxonomy's face and content validity; the gathering of input from patient safety stakeholders in multiple disciplines; and a preliminary study of the taxonomy's comparative reliability. RESULTS: Elements (terms) and structures (data fields) from existing classification schemes and reporting systems could be grouped into five complementary root nodes or primary classifications: impact, type, domain, cause, and prevention and mitigation. The root nodes were then divided into 21 subclassifications which in turn are subdivided into more than 200 coded categories and an indefinite number of uncoded text fields to capture narrative information. An earlier version of the taxonomy (n = 111 coded categories) demonstrated acceptable comparability with the categorized data requirements of the ICU safety reporting system. CONCLUSIONS: The results suggest that the Joint Commission on Accreditation of Healthcare Organizations (JCAHO) Patient Safety Event Taxonomy could facilitate a common approach for patient safety information systems. Having access to standardized data would make it easier to file patient safety event reports and to conduct root cause analyses in a consistent fashion.

Causality↗

PubMed2000

A taxonomy of passive behaviors in people with Alzheimer's disease.

PURPOSE: To construct a taxonomy of passive behaviors for understanding people with Alzheimer's disease. Passive behaviors are those associated with decreased motor movements, decreasing interactions with the environment, and feelings of apathy and listlessness. Little is known about behaviors associated with passivity, and these behaviors have not been categorized. ORGANIZING CONSTRUCT: Taxonomy construction. Passive behaviors in people with Alzheimer's disease were conceptualized as disturbing behaviors, patterns of personality change, and negative symptoms. METHODS: The taxonomy was developed using critical reviews of 15 empirical studies published 1985 through 1998. Procedures included listing behaviors; clustering behaviors into inductively derived groupings; conducting an expert panel-review, making revisions, and conducting a second review; establishing global and category-by-category reliability using Cohen's Kappa. FINDINGS: The nonhierarchic, natural taxonomy indicated five categories of behaviors associated with passivity in Alzheimer's disease: diminutions of cognition, psychomotor activity, emotions, interactions with people, and interactions with the environment. Analysis indicated substantial agreement beyond chance and showed statistically significant agreement among the six nurse-expert rates. Areas of synchrony between the taxonomy and the Need-Driven Dementia Compromised Behavior Model were identified. CONCLUSIONS: This taxonomy of passive behaviors in patients with Alzheimer's disease showed empirical rigor and compatibility with a middle-range theory and can be viewed as a sensitizing analytic scheme to guide future practice, research, and theory development.

Affect↗

PubMedDate not supplied

Taxonomy of the genus Leishmania: present and future trends and their implications.

The application of different taxonomic methods (Cladistic, Evolutionary Taxonomy and Numerical Taxonomy) to the taxonomy of the Genus Leishmania are reviewed. The major groupings of the most recent classifications obtained using the cladistical approach agree with the major divisions of previous classifications which used traditional taxonomy (Evolutionary Taxonomy). The advantage of the cladistical approach is that it produces cladograms whose branches indicate more accurately levels of relationships between the different taxa. Numerical Taxonomy is useful for identification but not as good as the cladistical approach for classification. The ancient division of this monophyletic genus into two major evolutionary lines supports the use of the subgeneric names Leishmania and Viannia.

Animals↗

PubMed1981

The perceptual domain: a taxonomy for allied health educators.

A taxonomy of the perceptual domain was proposed over a decade ago. It is hierarchical, as are the taxonomies in the cognitive, affective, and psychomotor domains. Perception involves extraction of information from presenting stimuli, and there is progression of information extraction as the hierarchy is ascended. Perceptual performance at the higher levels of the taxonomy assumes perceptual abilities at the lower levels. A modified version of the perceptual taxonomy applicable to allied health education is presented. Methods concerning application of the taxonomy are suggested. Use of the taxonomy of the perceptual domain would help allied health educators plan instruction and evaluate teaching.

Allied Health Personnel↗

PubMed1994

Toward unification of taxonomy databases in a distributed computer environment.

All the taxonomy databases constructed with the DNA databases of the international DNA data banks are powerful electronic dictionaries which aid in biological research by computer. The taxonomy databases are, however not consistently unified with a relational format. If we can achieve consistent unification of the taxonomy databases, it will be useful in comparing many research results, and investigating future research directions from existent research results. In particular, it will be useful in comparing relationships between phylogenetic trees inferred from molecular data and those constructed from morphological data. The goal of the present study is to unify the existent taxonomy databases and eliminate inconsistencies (errors) that are present in them. Inconsistencies occur particularly in the restructuring of the existent taxonomy databases, since classification rules for constructing the taxonomy have rapidly changed with biological advancements. A repair system is needed to remove inconsistencies in each data bank and mismatches among data banks. This paper describes a new methodology for removing both inconsistencies and mismatches from the databases on a distributed computer environment. The methodology is implemented in a relational database management system, SYBASE.

Animals↗

PubMed2005

BrainMap taxonomy of experimental design: description and evaluation.

Coordinate-based, voxel-wise meta-analysis is an exciting recent addition to the human functional brain mapping literature. In view of the critical importance of selection criteria for any valid meta-analysis, a taxonomy of experimental design should be an important tool for aiding in the design of rigorous meta-analyses. The coding scheme of experimental designs developed for and implemented within the BrainMap database provides a candidate taxonomy. In this study, the BrainMap experimental-design taxonomy is described and evaluated by comparing taxonomy fields to data-filtering choices made by subject-matter experts carrying out meta-analyses of the functional imaging literature. Fifteen publications reporting a total of 46 voxel-wise meta-analyses were included in this assessment. Collectively these 46 meta-analyses pooled data from 351 publications, selected for experimental similarity within each meta-analysis. Filter implementations within BrainMap were graded by ease-of-use (A-C) and by stage-of-use (1-3). Quality filters and content filters were tabulated separately. Quality filters required for data entry into BrainMap were classed as mandatory (five filters), being above the use grading system. All authors spontaneously adopted the five mandatory filters in constructing their meta-analysis, indicating excellent agreement on data quality among authors and between authors and the BrainMap development team. Two non-mandatory quality filters (group size and imaging modality) were applied by all authors; both were Stage 1, Grade A filters. Field-of-view filters were the least-accessible quality filters (Stage 3, Grade C); two field-of-view filters were applied by six and four authors, respectively. Authors made a total of 115 content-filter choices. Of these, 78 (68%) were Stage 1, Grade A filters; 16 (14%) were Stage 2, Grade A; and 21 (18%) were Stage 2, Grade C. No author-applied filter was absent from the taxonomy.

Brain Mapping↗