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At least 19 recordsLinked to original sources
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↗
PubMed1992

Symptoms of impairment, disability and handicap in low back pain: a taxonomy.

The functional consequences on everyday living which result from chronic low back pain commonly require services which are difficult to access. This deficiency in meeting the needs of these patients is partially explained by inadequacies in clinical assessment. Medical evaluation may be exhaustive, but frequently the assessment of physical and psycho-social dysfunction at the personal and family level is inadequate. In low back pain, as with most chronic ailments, there is no agreed-upon taxonomy of the functional consequences of the disorder upon which to establish a comprehensive clinical appraisal. In this paper a taxonomy is presented for the impairments, disabilities and handicaps which result from chronic low back pain. The taxonomy has been based on data from a survey of 74 individuals with low back pain and is structured generally according to the International Classification of Impairments, Disabilities and Handicaps (WHO 1980). The taxonomy is proposed as a conceptual framework and vocabulary for both clinical practice and research. The taxonomy is not a measurement instrument nor does it indicate the frequency of occurrence of disabilities. A classification is basic to the advancement of scientific understanding, and usage of a standard vocabulary such as this plays an important role in establishing a responsive health service capable of meeting the needs of the population with chronic low back pain.

Activities of Daily Living↗
PubMed2026

Programmatic access to ICTV virus taxonomy through a public ontology API.

BACKGROUND: The International Committee on Taxonomy of Viruses (ICTV) is responsible for developing and maintaining a universal virus taxonomy. As the reference framework for organising the viral world, it is essential for virology and related fields. Despite its widespread use in research and public health, programmatic access to ICTV taxonomy has remained limited, posing challenges for integration, versioning, and interoperability across databases and bioinformatics resources requiring up-to-date virus taxonomy. FINDINGS: To address this, we developed a public and sustainable solution leveraging ontology-based APIs. All available ICTV Master Species List (MSL) releases, from MSL1 to MSL41, were transformed into a unified, semantically structured ontology comprising more than 195,000 current and historical entities and deployed through the Ontology Lookup Service (OLS). The ontology is automatically rebuilt and republished whenever a new MSL release becomes available. Complementary ICTV-NCBI mappings and helper libraries support integration into downstream systems. CONCLUSIONS: Together, these resources enable, for the first time, public programmatic retrieval of current and historical ICTV taxon names, taxonomic relationships, metadata, and persistent identifiers through stable endpoints, including resolution of former taxonomic terms to their current accepted taxon or taxa and retrieval of taxon histories across releases. More broadly, this work illustrates a general strategy for transforming structured biological datasets into semantically enriched graph resources exposed through scalable public APIs. These developments enhance interoperability, reduce manual curation, and support FAIR-aligned taxonomic data management in virology and pandemic preparedness.

API↗
PubMed2026

Programmatic access to ICTV virus taxonomy through a public ontology API.

The International Committee on Taxonomy of Viruses (ICTV) is responsible for developing and maintaining a universal virus taxonomy. As the reference framework for organising the viral world, it is essential for virology and related fields. Despite its widespread use in research and public health, programmatic access to ICTV taxonomy has remained limited, posing challenges for integration, versioning, and interoperability across databases and bioinformatics resources requiring up-to-date virus taxonomy. To address this, we developed a public and sustainable solution leveraging ontology-based APIs. Successive ICTV Master Species List (MSL) releases were transformed into a structured ontology and deployed as a unified representation through the Ontology Lookup Service (OLS). The framework also provides ICTV-NCBI mappings and helper libraries for integration into downstream systems. This enables, for the first time, public programmatic retrieval of current and historical virological taxon names, taxonomic relationships, metadata, and persistent identifiers through stable endpoints. More broadly, this work illustrates a general strategy for transforming structured biological datasets into semantically enriched graph resources exposed through scalable public APIs. These developments enhance interoperability, reduce manual curation, and support FAIR-aligned taxonomic data management in virology and pandemic preparedness.

API↗
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↗
PubMed1976

A taxonomy for behavioral objectives in a dental school.

This paper describes a taxonomy proposed for use by dental school faculties as an aid in specifying their course objectives in behavioral terms. This taxonomy, developed and tried at the Harvard School of Dental Medicine, is simpler than taxonomies previously proposed because it reduces the number of categories. In addition, the categories themselves are designed to communicate to and be interpreted by dental educators. The six categories are (1) knowledge of facts, concepts, and principles; (2) comprehension; (3) perceptual ability; (4) diagnosis and treatment planning skills; (5) motor skills; and (6) interactive skills. Each category is briefly defined and illustrated with two samples from operative dentistry.

Behavior↗
PubMed1992

Specific infectivity and host resistance have predicated potyviral and pathotype nomenclature but relate less to taxonomy.

The names of potyviruses and viral-strains have represented the occurrence of predominant pathotypes on predominant crop genotypes. Thus virus nomenclature, but not viral taxonomy, has been decisively influenced by plant-genotype susceptibility and indirectly by host genetic resistance. REsistance to infection (i.e., host range) continues to serve a practical role in differentiating recognized viruses. Plant genes that confer disease tolerance or viral resistance remain a principal means of viral pathotype differentiation, as well as a principal control measure against major viral pathogens. Degrees of genetic diversity among isolates of recognized viruses should not be underestimated, and any system of viral taxonomy should be prepared for flexibility at the species level.

Immunity, Innate↗
PubMed1992

The recombinative nature of potyviruses: implications for setting up true phylogenetic taxonomy.

Sequence comparisons reveal that positive-strand RNA viruses not only evolve by divergence from common ancestors but also by interviral recombination. A considerable number of these viruses, exemplified by the family Potyviridae, can in fact, be regarded as successful products of a number of recombination events. It is concluded that the recombinative character of RNA viruses will hamper any attempt to set up a true phylogenetic taxonomy. It is advisable, therefore, to avoid the introduction of any taxon higher-than-family in virus taxonomy.

Picornaviridae↗
PubMed1977

[Taxonomy and assessment of psychological investigation methods in psychotropic drug trials (author's transl)].

Psychological tests are bound with specific goals. Four goal aspects are differentiated: status vs. processdiagnostics, normoriented vs. criterionoriented diagnostic, testing vs. inventarization, measurement of true scores vs. decision oriented diagnostic. Every diagnostic procedure is characterized by a specific personality theory and theory of measurement (classical vs. probabilistic test model). The diagnostic procedures traditionally used for evaluating drugs prefer status diagnostic, normoriented diagnostic, testing and measurement of true scores. Similar one-sidedness in personality theory and theory of measurement restrict validity and usefulness of psychological tests. In clinical practice we find a theoretically and empirically unjustified restriction in the selection of measurement devices on ratings and questionnaires. If we suppose multidimensionality of drug induced changes, we must apply a multimethod approach in outcome studies and use beside ratings and questionnaires behavior observations, objective tests, psychophysiological and neurophysiological measures. We propose a descriptive taxonomy of methods for planning multimethod outcome and process studies. From this taxonomy the methods of measurement for effects and side effects of drugs may be derived. The necessity of the multimethod approach is confirmed by empirical research. With this concept, the following neglected research questions become more obvious: concordance and discordance, synchrony and desynchrony of methods of measurement. We conclude with recommendations for clinical practice and research of outcome and process effects in drug therapy.

Clinical Trials as Topic↗
PubMed2026

A novel transformer model of protein domains for viral taxonomy classification.

MOTIVATION: Viruses with carefully curated taxonomic assignments (such as those in the ICTV taxonomy) still represent only a small fraction of viruses identified through sequencing data from virome or microbiome projects. It is therefore critical to develop methods that can assign viruses at multiple taxonomic ranks, so that a virus deemed novel at a given rank may still be placed into a higher-level taxon. Sequence-similarity-based approaches can classify viruses that share substantial genomic similarity with known viruses (e.g. those belonging to the same species or genus); however, their performance drops significantly when applied to more divergent viruses. Recent deep learning models, such as ViTax, which utilize DNA language models, aim to address these limitations, but their performance also degrades when applied to novel viruses lacking genus-level similarity to known references. Proteins are more conserved than genomic sequences, and the multiple proteins encoded by a virus can be leveraged to reveal evolutionary relationships among viruses. RESULTS: We propose a new tool, D2T (Domain-to-Taxonomy), that leverages recent advances in protein language models to improve viral taxonomic assignment. D2T represents a virus as a sequence of protein domain tokens and learns a transformer-based model for taxonomic classification. Experiments on multiple closed-set and open-set datasets show that D2T excels at assigning higher-level taxonomic labels (family and above). Furthermore, by combining D2T with Kraken2, which performs well at the genus level, the hybrid method (K+D2T) achieves accurate viral taxonomic classification across multiple taxonomic ranks. AVAILABILITY AND IMPLEMENTATION: D2T is available as a GitHub repository at https://github.com/mgtools/D2T.

Viruses↗
PubMed1976

The clinical significance of classifications of cirrhosis. A comparison between conventional criteria and numerical taxonomy.

Classification of patients with cirrhosis serves the clinical purpose of selecting patients for adequate therapy. A material of 441 patients from a randomized clinical trial of prednisone treatment were classified according to different criteria, and the effect of this therapy was assessed by comparing the survival curves of controls and treated patients in the groups. Six classifications based on single criteria were studied, viz. females vs. males, alcoholics vs. non-alcoholics, compensated vs. decompensated cases, active vs. inactive cases, manifest vs. latent cases, and non-primary biliary vs. primary biliary cirrhosis. The latter group was too small for further analysis. Furthermore, the material was classified by numerical taxonomy, based on 56 clinical symptoms and signs and histological and serological changes. The taxonomical classification showed interdependence with all the clinical classifications, except that of primary biliary cirrhosis. Three clinical classifications, viz. those based on sex, alcoholism, and compensation, and one taxonomic class showed a significant therapeutic relevance. Combination of these criteria revealed that female patients with compensated non-alcoholic cirrhosis, previously demonstrated to benefit from prednisone treatment, showed a markedly greater prednisone effect if they belonged to the taxonomic group than if they did not. According to clinical, histologic, and laboratory data, the latter group was characterized as less severe cases than the former one. Whereas this discrepancy between clinical severity and therapeutic effect cannot be fully explained, the data do suggest that clinical criteria may not be ideal for selection of patients with cirrhosis for steroid therapy, and that numerical taxonomy may provide clues for more clinically significant classifications.

Alcoholism↗
PubMedDate not supplied

[Numerical taxonomy of the genus Desulfovibrio by group analysis].

The Desulfovibrio genus has a particular interest because it includes the microorganisms connected with the corrosion produced microbiologically. The taxonomy of the genus shows disadvantages due to its metabolical and physiological characteristics. In this paper, 14 strains of the Desulfovibrio type were studied from the metabolical point of view. Numeric taxonomy was carried out according to the Group Analysis method, using and comparing the change possibilities of the method. The Consensus Method was also applied. The results obtained indicate a low metabolic activity of the strains with regard to the number of compounds which can be used as energy source. The taxonomic method showed a better structure with more clear divisions, corresponding to Simple Matching coefficient (which coincides with other symmetric coefficients and with the distance coefficient) with average bond (UPGMA). It is estimated that the present classification will vary in time with new strains with different metabolic characteristics. The two groups of bacteria correspond to those with more and less degrading ability.

Algorithms↗
PubMed2026

Stage-Independent Real-Time Subtype Classification and Comprehensive Biopsy Profiling of Urothelial Carcinomas by the Lund Taxonomy System.

Bladder cancer is a heterogeneous malignancy with diverse clinical outcomes, and conventional pathological assessment alone is insufficient to capture its underlying biology. Gene expression profiling can stratify tumors into molecular subtypes with prognostic and predictive potential, but the reliability of transcriptomic classification and its clinical utility remains to be established. The translational/observational UROSCANSEQ study (ISRCTN15459149) prospectively evaluates RNA-based Lund Taxonomy (LundTax) molecular subtype classification in a clinical setting. Among 784 consecutive biopsies collected between 2018 and 2022, RNA sequencing was successful for 90% of all biopsies, encompassing 662 bladder cancer patients with a stage distribution of 48% Ta, 27% T1, 24% ≥T2, and 1% CIS. We demonstrate that the LundTax subtype classification algorithm, applied to individual samples, accurately identifies cancer cell phenotypes with characteristic gene and protein expression patterns in a manner robust to RNA quality, data preprocessing strategies, and batch effects, supporting its clinical feasibility across both non-muscle-invasive and muscle-invasive disease. We further extend the LundTax framework by incorporating single-sample molecular risk scores reflecting tumor grade, proliferation, and progression risk, as well as tumor microenvironment signatures. Both risk scores and overall immune and stromal content in biopsies were significantly associated with an increased risk of clinical progression in noninvasive disease. In a separate analysis of the relative cellular composition of the tumor microenvironment, however, only the fraction of natural killer cells remained significant. Together, the expanded LundTax system provides a comprehensive molecular portrait of individual tumor biopsies. By explicitly separating cancer cell-intrinsic phenotypes, prognostic indexes, and microenvironmental signals, the framework minimizes biological confounding and establishes a strong foundation for future studies evaluating clinical outcomes and treatment responses.

Humans↗
PubMed1975

The skin primates. XLIV. Numerical taxonomy of primate skin.

Data on 84 characteristics of the skin of 36 species of primates were extracted from a series of articles describing the histological and histochemical properties of the skin of primates. The data were subjected to a cluster analysis. The results were in reasonably good agreement with orthodox primate taxonomies although some exceptions were apparent. The species clustered into four main groups approximately comparable to Prosimii, Cercopithecoidea, pithecoidea, and Hominoidea are commensurate with standard taxonomic practice. Within the Ceboidea, however, the Atelinae and Alouattinae tend to group with the Hominoidea, Aotus and Saimiri show variable placements, and Callimico groups with the Callithricidae.

Animals↗
PubMed1992

A viewpoint on the taxonomy of potyviruses infecting sugarcane, maize, and sorghum.

The value of taxonomy lies in its ability to communicate concepts and relationships. Our present concepts of the poaceous potyviruses, based on their biology, serology, and biochemistry, identify four viruses that can be distinguished by each characteristic. Identifying these as four distinct viruses has important implications for disciplines such as epidemiology, plant breeding, and diagnostics.

Edible Grain↗
PubMed1975

The fine structure of Herpetosiphon, and a note on the taxonomy of the genus.

The fine structure of the Gram-negative filamentous gliding bacterium, Herpetosiphon is described. The outer membrane of the cell envelope could not be resolved as a separate structure, probably because it is fused with the underlying dense (peptidoglycan) layer. There was an additional wall layer outside this membrane-peptidoglycan complex, but a sheath in the classical sense, as postulated in the definition of the genus, was lacking. On the cell surface a loose network of fibrils could be seen. Inside the cells 3 types of intracytoplasmic membranes were discernible: a) true mesosomes near cross walls; b) a system of coarser membranes which was not connected with the septa and formed networks or tubular complexes; c) degenerated septa within bulbs. The bulbs are swollen sections of filaments, occurred mainly in ageing cultures, and are probably a degeneration phenomenon. The filaments contained necridia, i.e. dead and empty cells, across which breaks may occur so that empty cell wall cylinders remain attached to the ends of the daughter filaments, falsely suggesting the presence of a sheath. The taxonomy of Herpetosiphon is discussed in detail: The organism has been described before as Flexibacter giganteus. It is proposed to abandon the species H. aurantiacus in favor of H. giganteus, but to retain the genus Herpetosiphon. An improved definition of the genus is given.

Cell Wall↗
PubMed1979

Discussion of the relationships between Schistosoma and their intermediate hosts, assessment of the degree of host-parasite compatibility and evaluation of schistosome taxonomy.

Studies of the spectrum of the intermediate hosts of schistosomes and the relationships between parasites and intermediate host snails have been carried out with each researcher using different methods. A comparison between compatibility studies has therefore been impossible. The following three basic problems in these kind of studies are discussed in this paper: (1) the standardization of experimental materials such as schistosomes, intermediate and final hosts, (2) the methods involved in the experiments, and (3) the sort of data which must be collected. Standardized methods and materials are described in this paper. The relationships between the genus Schistosoma and the intermediate host snails belonging to the two genera Biomphalaria and Bulinus, and the mechanisms behind the process resulting in various degrees of compatibility between the two involved organisms are reviewed and discussed. Why certain combinations of schistosomes and snails result in the production of cercariae and others do not is still unknown, but there is now some indication of a camouflage behaviour during the intramolluscan stages, e.g., the larvae in the snails cover themselves with snail material and are not recognized as foreign objects. The same mechanism has already been found in the schistosomules in the final host. Much of the confusion in the discussion of the relationships between schistosomes and intermediate hosts is the result of a lack of an objective way to describe and assess the compatibility between the two. Based on a series of experiments with S. haematobium, S. intercalatum, S. bovis, S. mansoni, and several species of possible intermediate hosts, the following index for estimating the degree of compatibility is proposed: the total cercarial production from 100 exposed snails (TCP/100 exposed snails). Seven classes have been suggested: the first one (Class 0) with a TCP/100 exposed snails of zero, is called 'refractory'; the next one (Class I) called 'not very compatible' has a TCP /100 exposed snails between 1 and 10,000; the last group (Class IV) called 'extremely compatible' produced more than 500,001 per 100 exposed snails during the entire lifespan. The ability to use a spectrum of intermediate hosts and the compatibility in the taxonomy of schistosomes is discussed. The results for the different species of schistosomes indicated that each species consists of strains with 'hybrid populations' in between.

Animals↗