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Results for “Integrative taxonomy”

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PubMed2000

Surveying hospital network structure in New York State: how are they structured?

We determine the most common network structures in New York state. The taxonomy employed uses three structural dimensions: integration, complexity, and risk-sharing between organizations. Based on a survey conducted in 1996, the most common type of network (26.4 percent) had medium levels of integration, medium or high levels of complexity, and some risk-sharing. Also common were networks with low levels of integration, low levels of complexity, and no risk-sharing (22.1 percent).

Data Collection↗

PubMed2005

E-MSD: an integrated data resource for bioinformatics.

The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the worldwide Protein Data Bank (wwPDB) and to work towards the integration of various bioinformatics data resources. One of the major obstacles to the improved integration of structural databases such as MSD and sequence databases like UniProt is the absence of up to date and well-maintained mapping between corresponding entries. We have worked closely with the UniProt group at the EBI to clean up the taxonomy and sequence cross-reference information in the MSD and UniProt databases. This information is vital for the reliable integration of the sequence family databases such as Pfam and Interpro with the structure-oriented databases of SCOP and CATH. This information has been made available to the eFamily group (http://www.efamily.org.uk/) and now forms the basis of the regular interchange of information between the member databases (MSD, UniProt, Pfam, Interpro, SCOP and CATH). This exchange of annotation information has enriched the structural information in the MSD database with annotation from wider sequence-oriented resources. This work was carried out under the 'Structure Integration with Function, Taxonomy and Sequences (SIFTS)' initiative (http://www.ebi.ac.uk/msd-srv/docs/sifts) in the MSD group.

Amino Acid Sequence↗

PubMedDate not supplied

[The problem of individuality in taxonomy].

The ideas of wholeness of superorganism units consist of three constituents: 1) emergeness of properties of the whole; 2) structureness; 3) separability of the whole. Emergeness is a character of both integrated and complex units. Integrated units in strict sense are those that consist of functionally different parts. Species but not super-specific taxa are integrated units. The ideas of unity are based on formula "unity is an aggregation of shape and matter". In taxonomy the idea of archaetype can be used as a shape. Superspecific taxa but not species are recognized as unitary units in taxonomy. Unitary but not integrated units can be considered as individuals.

Animal Population Groups↗

PubMed2006

Virtual Ribosome--a comprehensive DNA translation tool with support for integration of sequence feature annotation.

Virtual Ribosome is a DNA translation tool with two areas of focus. (i) Providing a strong translation tool in its own right, with an integrated ORF finder, full support for the IUPAC degenerate DNA alphabet and all translation tables defined by the NCBI taxonomy group, including the use of alternative start codons. (ii) Integration of sequences feature annotation--in particular, native support for working with files containing intron/exon structure annotation. The software is available for both download and online use at http://www.cbs.dtu.dk/services/VirtualRibosome/.

Animals↗

PubMed2025

Hybridization as driving force for cryptic species diversity in the Caribbean coral genus Madracis.

Species boundaries in scleractinian corals remain highly elusive due to conflicting patterns between morphological and molecular phylogenies, often caused by morphological plasticity, occurrence of cryptic species, incomplete lineage sorting or introgressive hybridization. Here, we use an integrated systematics approach, which combines reduced representation genome sequencing (nextRAD), micro-morphometric characterization, SEM analyses and compilation of life history traits, to infer phylogenetic relationships among closely related species in the Caribbean coral genus Madracis. In total, we analyzed 235 Madracis specimens from Curaçao and Bermuda collected from 10-90 m depth. Sequence- and SNP-based analyses for 115 samples generated unprecedented species resolution in Madracis, greatly supporting the morphology-based taxonomy of the current, accepted Caribbean species M. senaria, M. decactis, M. formosa, M. carmabi and M. mirabilis (M. auretenra). The exception was M. pharensis, in which we found evidence for three separate lineages, and for which we found signatures of admixture and introgression. These three M. pharensis lineages showed distinct depth distributions (thus classified as shallow, deep and very deep) and were partially distinguishable on the basis of fine microstructural elements of the collumella, septa and coenosteum. Further taxonomic comparisons are needed to formalize these putative cryptic species. Overall, our integrated systematics approach further resolves species relationships in the Caribbean genus Madracis, supports the morphological descriptions for most of the recognized species, but also reveals the existence of cryptic diversity in groups marked by high admixture, thus suggesting hybridization as a driving force in coral species diversity.

Animals↗

PubMed2026

RePo index: a multidimensional framework to quantify genetic resilience in data-limited amphibian faunas.

This study explores the resilience of Chilean amphibians to environmental disturbances through an integrative approach that combines ecological, demographic, bibliometric, and molecular information. A total of 58 species distributed across 14 genera and 9 families were evaluated via the resilience potential (RePo) index, which incorporates eleven criteria grouped into five dimensions: distribution, population trends, emerging diseases, evolutionary history, and genetic records. The results revealed high ecological vulnerability: 83% of the species were classified as non resilient (45% with no resilience and 38% with low resilience), and none reached the high-resilience category. At the family level, Telmatobiidae presented the lowest resilience values, whereas Leptodactylidae presented the highest. At the genus level, Insuetophrynus was identified as the most vulnerable taxon, with no molecular records and an extremely restricted distribution. In contrast, species such as Rhinella spinulosa and Pleurodema thaul presented moderate resilience, suggesting greater adaptive potential and relevance for functional studies. From a bibliometric perspective, a bias toward classical research topics (distribution, physiology, and taxonomy) was detected, with limited representation of integrative approaches such as genetic conservation or climate change. The conceptual modularity in the literature was low (Q = 0.1328), indicating weak thematic differentiation and little integration of omics tools. Most species lack transcriptomic and genomic data, severely limiting the assessment of their adaptive mechanisms. In this context, the RePo index has emerged as an integrative tool useful for operationalizing concepts such as evolutionarily significant units (ESUs) and management units (MUs), which are essential for evidence-based conservation. Finally, this study highlights the need to incorporate high-throughput sequencing (HTS) technologies and to participate in international initiatives, such as the Amphibian Genomics Consortium, as a strategic path forward for advancing adaptive conservation of Chilean amphibians.

Animals↗

PubMed1996

Predictive validity of Marlatt's relapse taxonomy versus a more general relapse code.

Marlatt's system for classifying relapses involves integrating information about the context of a relapse into a judgment about the most critical aspects of the situation. Constraints in this taxonomy, however, may limit its validity. On a sample of 300 subjects drawn from six treatment facilities, we compared the predictive validity of Marlatt's taxonomy with that of a coding scheme with fewer constraints. Marlatt's taxonomy does not significantly predict drinking outcome, nor does it predict time to relapse. There is weak evidence, however, that under some circumstances Marlatt's taxonomy can predict the type of relapse subsequently observed. The alternative coding system also does not seem useful for predicting drinking outcome, although a possible association was found between internal attribution and time to return to heavy drinking. The alternative system does seem to be able to detect repetitive aspects of subsequent relapse situations; lack of social interactions, family setting, anxiety and depression were most likely to repeat. It may be useful to consider these relapse attributes in treatment planning. The minimal predictive validity for both the Marlatt and the alternative relapse code may be due to weaknesses in the relatively unstructured interview used to gather the data, or to failure to assess the most critical dimensions relating to subsequent relapse.

Adult↗

PubMed1986

The description and interpretation of aphasic language disorder.

The nature of aphasic impairment is reviewed from four viewpoints: (1) the construction of behavioural classifications that predict the locus of brain damage; (2) the initial assessment of a range of psycholinguistic functions sufficiently wide to detect the main outlines of deficit and preservation; (3) the elucidation of change in functional status, including both spontaneous and therapy-aided recovery; (4) the relationship between models of normal linguistic performance and the structure of pathological disorder. Arguments are provided against studies of aphasia based upon clinical (or other) taxonomies; arguments are given for the closer integration of analyses of normal and aphasic language.

Aphasia↗

PubMed2004

Challenges and rewards of research in marine natural products chemistry in Brazil.

Brazil is blessed with a great biodiversity, which constitutes one of the most important sources of biologically active compounds, even if it has been largely underexplored. As is the case of the Amazon and Atlantic rainforests, the Brazilian marine fauna remains practically unexplored in the search for new biologically active natural products. Considering that marine organisms have been shown to be one of the most promising sources of new bioactive compounds for the treatment of different human diseases, the 8000 km of the Brazilian coastline represents a great potential for finding new pharmacologically active secondary metabolites. This review presents the status of marine natural products chemistry in Brazil, including results reported by different research groups with emphasis on the isolation, structure elucidation, and evaluation of biological activities of natural products isolated from sponges, ascidians, octocorals, and Opistobranch mollusks. A brief overview of the first Brazilian program on the isolation of marine bacteria and fungi, directed toward the production of biologically active compounds, is also discussed. The current multidisciplinary collaborative program under development at the Universidade de São Paulo proposes to establish a new paradigm toward the management of the Brazilian marine biodiversity, integrating research on the species diversity, ecology, taxonomy, and biogeography of marine invertebrates and microorganisms. This program also includes a broad screening program of Brazilian marine bioresources, to search for active compounds that may be of interest for the development of new drug leads.

Animals↗

PubMed1993

[Quality assurance by developing strategical and professional nursing care goals].

Quality assurance by developing strategical and professional nursing care goals. The purpose of this study was to develop strategical and professional nursing care goals. The theoretical base for the study was the 'VIPS-model' This model includes four concepts: well-being, integrity, prevention and safety, from which a taxonomy is generated. In order to measure the quality of nursing care the DySSSy-model was used. Four standards, based on the previously mentioned concepts were developed and evaluated at two surgical wards. The ward nurses were asked through a questionnaire how they valued the strategical and professional nursing care goals. The conclusion from the study is (1) that the taxonomy can be useful for structuring strategical and professional nursing care goals (2) that three of the developed standards are useful at surgical wards, and (3) that the questionnaire can be used as an instrument for defining how nurses value the chosen nursing care goals.

Humans↗

PubMed2005

A framework for integrating NANDA, NIC, and NOC terminology in electronic patient records.

PURPOSE: To describe the methods used in design of a framework that (a) encompasses nursing knowledge, (b) functions as a cognitive map for clinicians, and (c) increases the efficiency of using the North American Nursing Diagnosis Association (NANDA), Nursing Intervention Classification (NIC), and Nursing Outcome Classification (NOC) terminologies together in the electronic patient record. METHODS: The taxonomies of the NANDA, NIC, and NOC terminologies were integrated to form a preliminary structure of domains and classes. New concepts and collocations of concepts were constructed using Walker and Avant's (1983, 1988) method for concept synthesis. The framework was validated using an expert group and clinical testing. RESULTS: A framework organized as a taxonomy with eight domains (Physiological, Functional, Psychocognitive, Safety, Existential, Lifestyle, Family, and Environment) and 29 classes. CONCLUSIONS: The framework has the potential to enhance the quality of nursing documentation, contribute to nursing research and education, and reduce job stress.

Attitude to Health↗

PubMed1994

A taxonomy of shared care for chronic disease.

BACKGROUND: Shared care is promoted as a way of integrating primary and secondary services and achieving one of the targets set for the NHS in the 1990s. We aimed to compose a taxonomy of shared care schemes for chronic disease in order to inform the development of develop shared care. METHODS: A two-phase postal questionnaire survey of Scotland and North West Thames Region, England. In the first phase we identified the number of shared care schemes for chronic disease, which were followed up in the second phase. RESULTS: Shared care schemes were classified into six groups, or models, according to their method of data transfer. These are: (I) community clinics, where the specialist undertakes a clinic in general practice; (II) basic, where communication comprises the regular exchange of letters or standardized record sheets; (III) liaison, where the hospital team and general practitioner (GP) meet to discuss and agree the management of patients under shared care; (IV) shared care record cards, where the exchange of information is made through a booklet or 'cooperation card', commonly carried by the patient; (V) computer-assisted shared care, where a circuit of information is established between GP and hospital specialist based on data collected at each patient visit and mediated through computer-generated summaries; (VI) electronic mail, where hospital specialist and GP both have access to the same data on patients shared between them. CONCLUSION: Despite substantial variation in the operation of shared care, schemes can be broadly classified and constructed in six different ways. In establishing this taxonomy, a choice is offered to health care workers wishing to develop shared care.

Chronic Disease↗

PubMed2026

"Updates on diagnostic and prognostic molecular biomarkers of CNS tumors".

The diagnosis and classification of central nervous system (CNS) tumors has undergone a paradigm shift over the past decade, evolving from a purely histology-based approach to an integrated framework that incorporates molecular and epigenetic features. This review summarizes recent updates in key genomic and epigenomic biomarkers across major CNS tumor categories, with a focus on their diagnostic, prognostic, and therapeutic implications. DNA methylation profiling has emerged as a valuable tool for tumor classification, subgrouping, and grading, complementing traditional histopathologic assessment. Across diffuse gliomas, newly characterized molecular alterations have refined grading criteria and clarified the boundaries between tumor types, including important caveats about the use of individual molecular features as sole diagnostic criteria. In ependymomas, medulloblastomas, atypical teratoid/rhabdoid tumors, meningiomas, pineal tumors, and embryonal tumors, methylation profiling now defines biologically and clinically meaningful subgroups that inform risk stratification and treatment selection. The emerging recognition of mismatch repair-deficient gliomas and fusion-driven tumor entities further underscores the expanding complexity of CNS tumor taxonomy. As molecular technologies continue to advance, the integration of genomic, epigenomic, histopathologic, and clinical data will be essential to improving diagnostic precision, guiding therapy, and ultimately enhancing patient outcomes.

Embryonal↗

PubMed2003

PANDORA: keyword-based analysis of protein sets by integration of annotation sources.

Recent advances in high-throughput methods and the application of computational tools for automatic classification of proteins have made it possible to carry out large-scale proteomic analyses. Biological analysis and interpretation of sets of proteins is a time-consuming undertaking carried out manually by experts. We have developed PANDORA (Protein ANnotation Diagram ORiented Analysis), a web-based tool that provides an automatic representation of the biological knowledge associated with any set of proteins. PANDORA uses a unique approach of keyword-based graphical analysis that focuses on detecting subsets of proteins that share unique biological properties and the intersections of such sets. PANDORA currently supports SwissProt keywords, NCBI Taxonomy, InterPro entries and the hierarchical classification terms from ENZYME, SCOP and GO databases. The integrated study of several annotation sources simultaneously allows a representation of biological relations of structure, function, cellular location, taxonomy, domains and motifs. PANDORA is also integrated into the ProtoNet system, thus allowing testing thousands of automatically generated clusters. We illustrate how PANDORA enhances the biological understanding of large, non-uniform sets of proteins originating from experimental and computational sources, without the need for prior biological knowledge on individual proteins.

Computational Biology↗

PubMed2004

The Unified Medical Language System (UMLS): integrating biomedical terminology.

The Unified Medical Language System (http://umlsks.nlm.nih.gov) is a repository of biomedical vocabularies developed by the US National Library of Medicine. The UMLS integrates over 2 million names for some 900,000 concepts from more than 60 families of biomedical vocabularies, as well as 12 million relations among these concepts. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank. In addition to data, the UMLS includes tools for customizing the Metathesaurus (MetamorphoSys), for generating lexical variants of concept names (lvg) and for extracting UMLS concepts from text (MetaMap). The UMLS knowledge sources are updated quarterly. All vocabularies are available at no fee for research purposes within an institution, but UMLS users are required to sign a license agreement. The UMLS knowledge sources are distributed on CD-ROM and by FTP.

Animals↗

PubMed2026

Advances in the diagnosis and classification of B-ALL: comparative insights from updated guidelines.

Accurate molecular classification is essential for diagnosis, risk stratification, and treatment selection in B-cell lymphoblastic leukemia (B-ALL). In this study, we performed a comprehensive, real-world reclassification of 1015 consecutively diagnosed B-ALL patients using the fifth edition of the World Health Organization Classification of Haematolymphoid Tumours (WHO-HAEM5) and the International Consensus Classification (ICC). An integrative genomic strategy that combined whole transcriptome sequencing, fusion detection, mutational analysis, and cytogenetics enabled reclassification according to both the WHO-HAEM5 and ICC frameworks, thereby substantially reducing the proportion of unclassifiable B-ALL from 41.9% (2016 WHO revision [WHO-HAEM4R]) to 15.9% (WHO-HAEM5) and 11.9% (ICC). Distinct clinical and prognostic features were identified across newly defined subtypes. Multivariable analysis confirmed that this genomic classification is a robust, independent predictor of survival after adjusting for age, minimal residual disease status, and transplant intervention. Specifically, HLF-rearranged and MEF2D-rearranged B-ALL conferred a persistently poor prognosis across all age groups despite allogeneic hematopoietic stem cell transplantation, highlighting an urgent need for novel therapeutic strategies. Gene expression profiling resolved cryptic subtypes, including ETV6::RUNX1-like, ZNF384-rearranged-like, and BCR::ABL1-like B-ALL, and uncovered diagnostic ambiguity in patients with concurrent lesions. In addition, we report emerging high-risk groups, including IDH1/2- and ZEB2 Q1072-mutated B-ALL, that may warrant recognition as distinct molecular entities. Our findings demonstrate the clinical use of integrative transcriptomic profiling in refining B-ALL taxonomy in guiding risk-adapted therapies and informing future revisions of diagnostic standards. This study supports the incorporation of high-throughput molecular diagnostics into routine leukemia classification and precision treatment planning.

Humans↗

PubMed1989

Primary fibromyalgia is greater than tender points: toward a multiaxial taxonomy.

Primary fibromyalgia remains a controversial and puzzling condition. The diagnosis is based on subjective symptoms, exclusionary criteria and the presence of tender points. Much of the discussion of primary fibromyalgia centers on physical or psychological bases for the etiology, exacerbation and maintenance of the symptoms. An alternative to the current dichotomous way of conceptualizing primary fibromyalgia is presented based on a multiaxial perspective that integrates physical, psychosocial and behavioral factors creating an empirically derived taxonomy. The utility of this approach is illustrated from research with groups of patients with chronic pain. The implications of the multiaxial taxometric approach for understanding primary fibromyalgia and its treatment are described.

Fibromyalgia↗

PubMed2006

The structure of maladaptive personality traits in childhood: a step toward an integrative developmental perspective for DSM-V.

The present study describes the construction of a taxonomy of trait-related symptoms in childhood, the Dimensional Personality Symptom Item Pool (DIPSI), and examines the replicability of the taxonomy's higher order structure across maternal ratings of referred (N = 205) and nonreferred (N = 242) children and self-ratings of adolescents (N = 453). The DIPSI's 4 higher order factors--that is, Emotional Instability, Disagreeableness, Introversion, and Compulsivity--showed clear correspondence with the dimensions of personality pathology found in adulthood (Dimensional Assessment of Personality Pathology-Basic Questionnaire; W. J. Livesley, 1990; Schedule for Nonadaptive and Adaptive Personality; L. A. Clark, 1993). These 4 factors can be further organized into 2 superfactors, representing Internalizing and Externalizing Traits, demonstrating empirical and conceptual relationships with psychopathology models in childhood and adulthood. The implications for the assessment and conceptualization of early trait pathology are discussed in the context of an integrative developmental perspective on the construction of the Diagnostic and Statistical Manual of Mental Disorders-Fifth Edition.

Adjustment Disorders↗