“…By mostly reusing terms from existing ontologies (e.g., TCMDPO for traditional Chinese medicines, NCBITaxon for taxonomy, ChEBI for chemical elements, and OAE for adverse events) and making semantic axioms linking different entities, we developed the Ontology of Chinese Medicine for Rheumatism (OCMR) that includes over 3000 class terms. …”
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“…Zebrafish and mouse anatomical ontologies with their controlled vocabulary (CV) and defined hierarchy are used with the ontoCAT R package to aggregate data for comparison and visualization. …”
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“…METHODS AND RESULTS: In this study, we created a computational resource to facilitate genetic studies of cardiac physiology by integrating literature curation with attention to an improved and expanded ontological representation of heart processes in the Gene Ontology. …”
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“…In this review, we summarize recent work characterizing cell types in the human central nervous and immune systems using single-cell and single-nuclei RNA sequencing, and discuss the implications that these discoveries are having on the representation of cell types in the reference Cell Ontology (CL). We propose a method, based on random forest machine learning, for identifying sets of necessary and sufficient marker genes, which can be used to assemble consistent and reproducible cell type definitions for incorporation into the CL. …”
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“…The network, enriched with molecular function ontology, was analyzed using Network Based Inference (NBI). …”
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“…MOTIVATION: Modern problems of concept annotation associate an object of interest (gene, individual, text document) with a set of interrelated textual descriptors (functions, diseases, topics), often organized in concept hierarchies or ontologies. Most ontology can be seen as directed acyclic graphs (DAGs), where nodes represent concepts and edges represent relational ties between these concepts. …”
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“…MOTIVATION: The ever-increasing number of biomedical datasets provides tremendous opportunities for re-use but current data repositories provide limited means of exploration apart from text-based search. Ontological metadata annotations provide context by semantically relating datasets. …”
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“…Our method borrows information from the Cell Ontology to establish if batch adjustment leads to a better agreement between observed pairwise similarity and similarity of cell types inferred from the ontology. …”
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“…Secondly, the normalized features and other context information are stored using an ontology-based model (OBM). Thirdly, an improved method of self-adaptive correlation analysis is designed to select the most effective EEG features. …”
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“…Measuring the semantic similarity between Gene Ontology (GO) terms is an essential step in functional bioinformatics research. …”
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“…To identify learner’s mental states, the ontology operates on the basis of the theoretical and data-driven knowledge of emotions. …”
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“…In this paper, we propose an integrated model, PmiRGO, to infer the gene ontology (GO) functions of miRNAs by integrating multiple data sources, including the expression profiles of miRNAs, miRNA-target interactions, and protein-protein interactions (PPI). …”
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“…Linking each identified entity mention in text to an ontology/dictionary concept is an essential task to make sense of the identified entities. …”
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“…We trained our model on two biomedical ontologies—the Human Phenotype Ontology (HPO) and Systematized Nomenclature of Medicine - Clinical Terms (SNOMED-CT). …”
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“…The evaluations with ontology auditing tools confirmed that PACO is structurally and logically consistent and satisfies the majority of the best practice rules of ontology authoring. …”
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“…In this study, we used gene ontology (GO) terms and biological pathways to study an extended version of PPI (protein–protein functional associations) and subsequently identify some essential GO terms and pathways that can indicate the difference between two proteins with and without functional associations. …”
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“…To obtain a coherent RDF graph the chosen ontology must be consistently applied. However, addition of new diverse data causes the ontology to evolve, which could lead to accumulation of unintended erroneous composites. …”
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