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  1. 23201
    “…Applied to small cell lung cancer (SCLC), the workflow identifies four subtypes based on global gene expression patterns and ontologies. Three correspond to known subtypes (SCLC-A, SCLC-N, and SCLC-Y), while the fourth is a previously undescribed ASCL1+ neuroendocrine variant (NEv2, or SCLC-A2). …”
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    Systems-level network modeling of Small Cell Lung Cancer subtypes identifies master regulators and destabilizers
  2. 23202
    “…Successful implementation of life science cyberinfrastructure is improving data standards, ontologies, analytic workflows, and integrated database platforms for both model and non‐model plant species. …”
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    Cyberinfrastructure and resources to enable an integrative approach to studying forest trees
  3. 23203
    “…Ontologically distinct populations of macrophages differentially contribute to organ fibrosis through unknown mechanisms. …”
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    A spatially restricted fibrotic niche in pulmonary fibrosis is sustained by M-CSF/M-CSFR signalling in monocyte-derived alveolar macrophages
  4. 23204
    “…Gene expression profiles for several thousand genes are formalized in both wild-type and experimentally-manipulated conditions, using formal anatomical ontologies. These data can be explored through three complementary types of browsers, each offering a different view-point. …”
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    ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates
  5. 23205
    “…Other notable enhancements to BovineMine include the incorporation of genomes and gene annotation datasets for non-bovine ruminant species (goat and sheep), support for multiple assemblies per organism in the Regions Search tool, integration of additional ontologies and development of many new template queries. …”
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    Bovine Genome Database: new annotation tools for a new reference genome
  6. 23206
    “…Transcriptomic and functional enrichment analyses revealed genes and ontologies implicated in glyoxylic acid-mediated ripening, including AOX, TCA cycle, fatty acid metabolism, amino acid metabolism, organic acid metabolism, and ethylene-responsive pathways. …”
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    Glyoxylic acid overcomes 1-MCP-induced blockage of fruit ripening in Pyrus communis L. var. ‘D’Anjou’
  7. 23207
    “…Directed mutants were created in a set of 10 genes of different genetic ontologies and their role was determined in ex vivo models. …”
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    Identification of conditionally essential genes for Streptococcus suis infection in pigs
  8. 23208
    por Pietrasik, Marcin, Reformat, Marek
    Publicado 2020
    “…One area which seems to receive less attention is that of inducing a class taxonomy from such graphs. Ontologies, which provide the axiomatic foundation on which knowledge graphs are built, are often governed by a set of class subsumption axioms. …”
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    A Simple Method for Inducing Class Taxonomies in Knowledge Graphs
  9. 23209
    “…Transcriptomic analysis of genes belonging to five ontological groups has been conducted. Six genes showed increased expression after IVM (ARHGEF2, MAP1B, CXCL12, FN1, DAB2, and SOX9), while the majority of genes decreased expression after IVM. …”
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    Cortical Granule Distribution and Expression Pattern of Genes Regulating Cellular Component Size, Morphogenesis, and Potential to Differentiation are Related to Oocyte Developmental Competence and Maturational Capacity In Vivo and In Vitro
  10. 23210
    “…Approximately 100 unique host proteins were identified as a result of these analyses. Ontological assessments reveal enriched Molecular Functions and Biological Processes relevant to alphaviral infection. …”
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    Comparative analyses of alphaviral RNA:Protein complexes reveals conserved host-pathogen interactions
  11. 23211
    “…The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes. Ontologies can be designed to aid in comparing and reconciling metabolic reconstructions that differ in how they represent various metabolic pathways. …”
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    The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes
  12. 23212
    “…Key features are the representation of experimental errors, the normalization of measurement units, annotation of information to biological ontologies, calculation of pharmacokinetic parameters from concentration-time profiles, a workflow for collaborative data curation, strong validation rules on the data, computational access via a REST API as well as human access via a web interface. …”
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    PK-DB: pharmacokinetics database for individualized and stratified computational modeling
  13. 23213
    “…Dataset topics were represented with 10 215 distinct terms from 12 ontologies, for a total of 54 316 topic annotations (mean topics/dataset = 5.2). …”
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    Curation of over 10 000 transcriptomic studies to enable data reuse
  14. 23214
    “…WGCNA identified 5 co-methylated gene-modules associated to HPS markers, mainly related to nervous and neuroendocrine system, apoptotic processes, gut bacterial translocation, angiogenesis and vascular remodeling ontologies. To conclude, HPS is associated with nervous/neuroendocrine system and vascular remodeling related liver epigenetic changes.…”
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    Liver epigenome changes in patients with hepatopulmonary syndrome: A pilot study
  15. 23215
    “…This semantic model consists of classes and relations from a number of existing ontologies, including Workflow4ever, PROV, EDAM, and BPMN. …”
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    Towards FAIR protocols and workflows: the OpenPREDICT use case
  16. 23216
    “…The results reinforce the importance of an ontological approach in communication of CM roles and actions and provides learnings for integrated care roles across countries and contexts.…”
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    Vagueness and Ambiguity in Communication of Case Management: A Content Analysis in the Australian National Disability Insurance Scheme
  17. 23217
    “…Furthermore, the regulatory (PPP1R18, and PPP1R12A) and catalytic (PPP1CA) subunits of phosphatase PP1 were identified among the top novel CIP2A interactors. Evaluation of the ontologies associated with the proteins in this interactome revealed that they were linked with RNA metabolic processing and splicing, protein traffic, cytoskeleton regulation and ubiquitin-mediated protein degradation processes. …”
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    Protein interactome of the Cancerous Inhibitor of protein phosphatase 2A (CIP2A) in Th17 cells
  18. 23218
    “…The concept of a class is one of the core elements used to define the ontologies which sustain most of the existing KGs. Moreover, classes are an excellent tool to refer to an abstract idea which groups many individuals (or instances) in the context of a given KG, which is handy to use when producing summaries of its content. …”
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    Approaches to measure class importance in Knowledge Graphs
  19. 23219
    “…In the resulting platform, heterogeneous data are validated using predefined ontologies and stored in a relational database, to ensure data quality and ease of access. …”
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    ReMeDy: a platform for integrating and sharing published stem cell research data with a focus on iPSC trials
  20. 23220
    “…It insists on imposing its recipes on political, epistemological, and ontological peripheries created and maintained through coloniality. …”
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    From Modern Planetary Health to Decolonial Promotion of One Health of Peripheries
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