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Results for “Integrative taxonomy”

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PubMed1991

Membrane fatty acids as phenotypic markers in the polyphasic taxonomy of methylotrophs within the Proteobacteria.

A polyphasic approach to bacterial taxonomy attempts to integrate phylogenetic relationships with phenotypic marker analysis. This study describes the application of membrane fatty acids as a phenotypic marker for methylotrophs. Detailed phospholipid, ester-linked fatty acid (PLFA) profiles are reported for 17 methylotrophic eubacterial strains. These profiles included verification of double bond positions and geometries, both critical features for this analysis. Multivariate cluster analysis was used to indicate groupings of these strains along with literature values of both methylotrophs and non-methylotrophs based on the PLFA phenotype. Like many phenotypic characteristics, PLFA profiles were influenced by environmental conditions. The instabilities displayed, however, were predictable from physiological studies including increased trans/cis and cyclopropyl/cis ratios. Cluster analysis of PLFA profiles generated by separate investigators with different culture conditions indicated reproducibility by strain and species. The PLFA phenotype relationships compare favourably with phylogenetic associations based on 16S rRNA data for methylotrophs and will continue to be a valuable phenotypic marker for Proteobacteria taxonomy.

Cell Membrane↗

PubMed2026

Painting new pathways: Castilleja enters the genomic era.

Castilleja (Orobanchaceae), commonly known as Indian paintbrush, is a genus of approximately 200 hemiparasitic species found primarily across the Americas. Long studied for its taxonomic complexity, vibrant floral displays, and ecological interactions with host plants, Castilleja has recently emerged as a versatile research system spanning parasitic biology, specialized metabolism, conservation genetics, and pharmacology. The availability of whole-genome sequencing is transforming the field, revealing expanded gene families involved in host recognition, enabling genomic species delimitation of cryptic taxa, and providing frameworks for mapping biosynthetic pathways of bioactive compounds, including iridoid glycosides and phenylethanoid glycosides. This review synthesizes advances across these disciplines and highlights how genomics serves as an integrative force connecting taxonomy, ecology, phytochemistry, and parasitic biology in this genus.

Castilleja↗

PubMed2002

SeqHound: biological sequence and structure database as a platform for bioinformatics research.

BACKGROUND: SeqHound has been developed as an integrated biological sequence, taxonomy, annotation and 3-D structure database system. It provides a high-performance server platform for bioinformatics research in a locally-hosted environment. RESULTS: SeqHound is based on the National Center for Biotechnology Information data model and programming tools. It offers daily updated contents of all Entrez sequence databases in addition to 3-D structural data and information about sequence redundancies, sequence neighbours, taxonomy, complete genomes, functional annotation including Gene Ontology terms and literature links to PubMed. SeqHound is accessible via a web server through a Perl, C or C++ remote API or an optimized local API. It provides functionality necessary to retrieve specialized subsets of sequences, structures and structural domains. Sequences may be retrieved in FASTA, GenBank, ASN.1 and XML formats. Structures are available in ASN.1, XML and PDB formats. Emphasis has been placed on complete genomes, taxonomy, domain and functional annotation as well as 3-D structural functionality in the API, while fielded text indexing functionality remains under development. SeqHound also offers a streamlined WWW interface for simple web-user queries. CONCLUSIONS: The system has proven useful in several published bioinformatics projects such as the BIND database and offers a cost-effective infrastructure for research. SeqHound will continue to develop and be provided as a service of the Blueprint Initiative at the Samuel Lunenfeld Research Institute. The source code and examples are available under the terms of the GNU public license at the Sourceforge site http://sourceforge.net/projects/slritools/ in the SLRI Toolkit.

Amino Acid Sequence↗

PubMed2026

Genetic and metabolite diversity of Sundaland Heptapleurum (Araliaceae) insight into evolutionary and specialized metabolite.

BACKGROUND: The genus Heptapleurum Gaertn (previously treated as Schefflera J.R.Forst. & G.Forst.) within the Araliaceae family is recognized for its significant medicinal value and complex taxonomy. However, an integrated understanding of its evolutionary and metabolite diversity remains unexplored, especially in the Sundaland region (i.e., Java and Sumatra). Here, we integrate genomics and metabolomics to unravel the evolutionary relationships and metabolite diversity of 10 Heptapleurum species from Sundaland. RESULTS: We assembled 10 new complete plastid genomes (plastomes) and 45S nuclear ribosomal DNA (nrDNA) sequences, identifying significant variation and potential key molecular markers. Metabolomics identified 152 metabolites, mainly phenolics and terpenoids. Metabolite profiles of H. rhynchocarpum and H. capituliferum were more correlated with phylogeny than with geography; these two species were separate from the main Heptapleurum clade. Four species, H. farinosum, H. longifolium, H. rigidum, and H. fastigiatum, have almost identical plastomes and 45S nrDNA structures, suggesting they may represent closely related species with different phenotypes, as evidenced by distinctive metabolite compositions. CONCLUSIONS: Crucially, there is an incongruence between the genetic and chemical phylogenies, underscoring that while chemotaxonomy reflects functional diversity, genetic data remains the definitive standard for evolutionary inference, with the potential for reclassifying H. rhynchocarpum and H. capituliferum. This study provides a foundation for future taxonomic revisions, conservation, and drug discovery of Heptapleurum.

Phylogeny↗

PubMed2004

Integration of Web-based and PC-based clinical research databases.

UNLABELLED: We have created a Web-based repository or data library of information about measurement instruments used in studies of multi-factorial geriatric health conditions (the Geriatrics Research Instrument Library - GRIL) based upon existing features of two separate clinical study data management systems. GRIL allows browsing, searching, and selecting measurement instruments based upon criteria such as keywords and areas of applicability. Measurement instruments selected can be printed and/or included in an automatically generated standalone microcomputer database application, which can be downloaded by investigators for use in data collection and data management. METHODS: Integration of database applications requires the creation of a common semantic model, and mapping from each system to this model. Various database schema conflicts at the table and attribute level must be identified and resolved prior to integration. Using a conflict taxonomy and a mapping schema facilitates this process. RESULTS: Critical conflicts at the table level that required resolution included name and relationship differences. CONCLUSIONS: A major benefit of integration efforts is the sharing of features and cross-fertilization of applications created for similar purposes in different operating environments. Integration of applications mandates some degree of metadata model unification.

Aged↗

PubMed2003

It's time to rework the blueprints: building a science for clinical psychology.

The aims in this article are to connect the conceptual structure of clinical psychological science to what the author believes to be the omnipresent principles of evolution, use the evolutionary model to create a deductively derived clinical theory and taxonomy, link the theory and taxonomy to comprehensive and integrated approaches to assessment, and outline a framework for an integrative synergistic model of psychotherapy. These foundations also provide a framework for a systematic approach to the subject realms of personology and psychopathology. Exploring nature's deep principles, the model revives the personologic concept christened by Henry Murray some 65 years ago; it also parallels the interface between human social functioning and evolutionary biology proposed by Edward Wilson in his concept of sociobiology.

Biological Evolution↗

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↗

PubMed1978

[The experience in dental education of Cayetano Heredia University of Peru].

This article describes the educational experience gained in the dentistry program of Cayetano Heredia University in Peru. The programs for professional and auxiliary personnel training were drawn up after analyzing the health needs of the population and the services required to meet them, which resulted in the elaboration of an original methodology and taxonomy. Learning is an integral experience, one that takes place in the dental clinic, the hospital, and the community. The curriculum includes the following components: units for the intensive learning of clinical functions, fewer preclinical activities, clinical training with the ongoing assistance of auxiliary staff, extended interaction with marginal urban communities, rural internships, and hospital externships. A summary account is given of the gains made, the difficulties encountered, and plans for devising in-service teaching approaches that more effectively meet the needs of the community.

Community Dentistry↗

PubMed2005

Broadly predicting specific gene functions with expression similarity and taxonomy similarity.

Previous studies on computational gene functional prediction have not fully exploited the taxonomy structure of Gene Ontology (GO). They just select a few classes from GO into a set, and conduct classwise learning of these classes. The pre-selection of learning classes, often done according to the annotation sizes, limits the prediction breadth and depth. This way of pre-selecting learning classes ignores the taxonomy relations among classes, and so wastes the valuable functional knowledge encoded in the DAG structure of GO. This paper proposes GESTS, a novel gene functional prediction approach based on both gene expression similarity and GO taxonomy similarity, which circumvents the problem of arbitrary learning class pre-selection. GESTS is a semi-supervised approach that reasonably and efficiently incorporates the ontology-formed gene functional knowledge into automated functional analyses of local gene clustering. By integrating both expression similarity and taxonomy similarity into the learning process, GESTS achieves better prediction breadth, depth, and precision than previous studies on the fibroblast serum response dataset and the yeast expression dataset.

Computational Biology↗

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↗

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↗

PubMed2005

Use of endogenous retroviral sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy.

BACKGROUND: Endogenous retroviral sequences (ERVs) are integral parts of most eukaryotic genomes and vastly outnumber exogenous retroviruses (XRVs). ERVs with a relatively complete structure were retrieved from the genetic archives of humans and chickens, diametrically opposite representatives of vertebrate retroviruses (over 3300 proviruses), and analyzed, using a bioinformatic program, RetroTector, developed by us. This rich source of proviral information, accumulated in a local database, and a collection of XRV sequences from the literature, allowed the reconstruction of a Pol based phylogenetic tree, more extensive than previously possible. The aim was to find traits useful for classification and evolutionary studies of retroviruses. Some of these traits have been used by others, but they are here tested in a wider context than before. RESULTS: In the ERV collection we found sequences similar to the XRV-based genera: alpha-, beta-, gamma-, epsilon- and spumaretroviruses. However, the occurrence of intermediates between them indicated an evolutionary continuum and suggested that taxonomic changes eventually will be necessary. No delta or lentivirus representatives were found among ERVs. Classification based on Pol similarity is congruent with a number of structural traits. Acquisition of dUTPase occurred three times in retroviral evolution. Loss of one or two NC zinc fingers appears to have occurred several times during evolution. Nucleotide biases have been described earlier for lenti-, delta- and betaretroviruses and were here confirmed in a larger context. CONCLUSION: Pol similarities and other structural traits contribute to a better understanding of retroviral phylogeny. "Global" genomic properties useful in phylogenies are i.) translational strategy, ii.) number of Gag NC zinc finger motifs, iii.) presence of Pro N-terminal dUTPase (dUTPasePro), iv.) presence of Pro C-terminal G-patch and v.) presence of a GPY/F motif in the Pol integrase (IN) C-terminal domain. "Local" retroviral genomic properties useful for delineation of lower level taxa are i.) host species range, ii.) nucleotide compositional bias and iii.) LTR lengths.

Endogenous Retroviruses↗

PubMed2000

Evidence of a disposition toward fearfulness and vulnerability to posttraumatic stress in dysfunctional pain patients.

Few investigations have addressed whether patient subgroups derived using the Multiaxial Assessment of Pain (MAP) [Turk, D. C., & Rudy, T. E. (1987). Towards a comprehensive assessment of chronic pain patients. Behaviour Research and Therapy, 25, 237-249; Turk, D. C., & Rudy, T. E. (1988). Toward an empirically derived taxonomy of chronic pain patients: integration of psychological assessment data. Journal of Consulting and Clinical Psychology, 56, 233-238.] differ with regard to fear and avoidance. It has, however, been reported that dysfunctional patients exhibit more pain-specific fear and avoidance than patients classified as interpersonally distressed or minimizers/adaptive copers [Asmundson, G. J. G., Norton, G. R., & Allerdings, M. D. (1997). Fear and avoidance in dysfunctional chronic back pain patients. Pain, 69, 231-236.]. We attempted to extend these findings by examining two fear constructs that are receiving increased attention in the chronic pain literature-anxiety sensitivity and PTSD. The sample comprised 115 patients with chronic pain. Of these, 14 (12.2%) were classified as dysfunctional, 21 (18.3%) as interpersonally distressed and 47 (40.8%) as minimizers/adaptive copers. Between-group differences were observed on the fear of cognitive and emotional dyscontrol dimension of anxiety sensitivity, total and symptom cluster scores on the PTSD measure, and depression. No differences were observed for the fear of somatic sensations dimension of anxiety sensitivity or agoraphobia, social phobia, and blood/injury fears. Dysfunctional patients generally exhibited elevated scores relative to one or both of the other MAP subgroups on fear of cognitive and emotional dyscontrol, depressed affect, PTSD symptom total score and PTSD symptom cluster scores. As well, a substantial proportion of dysfunctional and interpersonally distressed patients were classified as having PTSD (71.4 and 42.9%, respectively) when compared to minimizers/adaptive copers (21.3%). These results suggest that MAP subgroups differ with regard to their propensity to be(come) fearful and in their likelihood of having PTSD. Theoretical and clinical implications are discussed.

Adaptation, Psychological↗

PubMed2002

Thysanoptera biodiversity in the Neotropics.

It is suggested that descriptive taxonomy of thrips must be integrated into biological studies if we are to understand patterns of evolutionary and ecological diversity. Collecting and describing new taxa is easy, but understanding their position in ecosystems and how they have contributed to the origin and maintenance of biological diversity is more important yet more difficult. Many authors fail to appreciate that individual thrips species are commonly highly polymorphic, both within and between sexes, with the result that 20% of species names and 30% of generic names are currently placed into synonymy. The biological significance of such polymorphism has been little studied, but the presence of large and small males in a species is presumed to indicate some form of male/male competition for resources; this is particularly common in fungus feeding species. Amongst phytophagous species, the recognition of the host plants on which thrips actually breed is a prerequisite to understanding patterns of diversity, some thrips lineages being associated with particular groups of plants whereas others exploit a diverse range of plants. Attempts to understand the diversity of thrips, including the application of cladistic methods, are severely limited by the lack of studies on the biology of individual species, although thrips exhibit a wide range of interesting biological phenomena, including various levels of sociality, gall-induction, specific pollination associations, virus transmission, and ectoparasitism.

Animals↗

PubMed1984

[L.I.C.E.T.-D 100: a new approach to the diagnosis of depression].

L.I.C.E.T.-D 100 or List of Integrated Criteria for Evaluation and Taxonomy in Depression is a diagnostic instrument permitting to record all information required to make a diagnosis following different classification systems, and to compute the diagnosis for each system, either by hand or automatically using a simple computer program. The present article presents the principles and purposes of the method and provides the technical information required for using the instrument.

Depressive Disorder↗

PubMed2003

Foundation for the integration of biologically based therapy in the management of prostate cancer.

The cure of advanced prostate cancer (PCa) will be achieved through the clinical application of biological observations. To achieve this, a new classification of human PCa is needed. Unlike in previous classifications of PCa which were based on anatomic determinates of outcome, we propose to integrate emerging PCa biology into this taxonomy. Three biologically based categories were identified (amphotropic, clonal expansion, and heterotopic), and each has unique features that influence therapy selection. It is unlikely that any single agent or modality will successfully control PCa. It is hoped that the classification and trial designs we propose will facilitate the application of integrated treatment and prevention strategies.

Algorithms↗

PubMed2003

Organizing the animal hierarchy into a Linnean Taxonomy in SNOMED CT.

SNOMED Clinical Terms (SNOMED CT) was created from a merger of SNOMED Reference Terminology (SNOMED RT)and CTV3 the Read Codes. The animal hierarchy in SNOMED RT was organized by common names, such as "Dog" and "Cat". It was later decided to convert common names to Linnean Taxonomy in SNOMED CT, such as Canis familiaris and Felis Sylvestris,in accordance with the Integrated Taxonomic Information System (ITIS) and the Smithsonian mammalian taxonomy.

Animals↗

PubMed2005

An empirical taxonomy of social-psychological risk indicators in youth suicide .

The current study integrates descriptive (though primarily social-psychological) statements about youth suicide into a coherent, empirically supported taxonomy. Drawing from relevant literature, a set of 107 items characterizing these contributions about youth suicide was created. Seventy-two participants sorted these statements according to their "face-value" by following two separate procedures. Analyses of these two data sets using multi-dimensional scaling resulted in a common "map" depicting inter-item (dis)similarities. Non-arbitrary rotation of this map revealed three bipolar and orthogonal dimensions labelled as under- and overengagement, rejection-turmoil, and self- to death-identification. It is suggested this dimensional analysis could provide a viable frame for examining and interpreting descriptions about suicide risk and may serve to extend theoretical accounts.

Adolescent↗