“…The purpose of this study is to investigate whether such ELN protocols can be used to create semantic documentation of the provenance of research data by the use of ontologies and linked data methodologies. METHODS: Based on an ELN protocol of a biomedical wet-lab experiment, a retrospective provenance model of the raised research data describing the details of the experiment in a machine-interpretable way is manually engineered. …”
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“…Regardless of age, sex‐associated changes of the whole bone transcriptomes were primarily associated not only with bone but also vascular and connective tissue ontologies. A pattern‐based approach used to screen the entire Gene Expression Omnibus (GEO) database against those that were sex‐specific in bone identified two coordinately regulated gene sets: one related to high phosphate–induced aortic calcification and one induced by mechanical stimulation in bone. …”
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“…MATERIALS AND METHODS: The National COVID Cohort Collaborative (N3C) table of laboratory measurement data—over 3.1 billion patient records and over 19 000 unique measurement concepts in the Observational Medical Outcomes Partnership (OMOP) common-data-model format from 55 data partners. We grouped ontologically similar OMOP concepts together for 52 variables relevant to COVID-19 research, and developed a unit-harmonization pipeline comprised of (1) selecting a canonical unit for each measurement variable, (2) arriving at a formula for conversion, (3) obtaining clinical review of each formula, (4) applying the formula to convert data values in each unit into the target canonical unit, and (5) removing any harmonized value that fell outside of accepted value ranges for the variable. …”
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“…By analyzing the differentially expressed genes and gene ontologies, Lmx1b expression was found to be upregulated in the osteolysis group compared to that in the control group. …”
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“…In the present investigation, we developed a comparative parcellation reasoning system (ComPaRe), which is a formal ontological system in human and non-human primate brains based on the cortical cytoarchitectonic mapping used for both species as detailed by Brodmann. …”
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“…The study has opted for a relativist ontological position and social constructionist epistemological position to understand different realities in the same context and how customers experience internet banking in a fearful environment. …”
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“…Furthermore, the behavior of these factors at the genetic level, considering both ontological and network perspectives was explored, enabling the gain of a deeper understanding of PTSD by capturing their interconnectivity and biological roles. …”
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“…Results  Four DQ dimensions were defined and represented as disjunct ontological categories. Based on these top dimensions, 9 DQ concepts, 10 DQ indicators, and 25 DQ parameters were developed and applied to different data sets. …”
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“…Moreover, we account for ontological relationships between labels in the model evaluation to accommodate for differences in annotation granularity across datasets. …”
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“…The evolutionary approach is supported by the use of predefined metadata, adherence to standard ontological mappings, and the ability for the user to adjust these classifications using an electronic notebook. …”
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“…To overcome the limitations of studies based on morphological comparison, we explored a comprehensive quantitative method for defining the constrained stage using expressed sequence tag (EST) data, gene ontologies (GO), and available genomes of various animals. …”
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“…Enrichment evaluation upon both gene ontologies and transcription factors, verifies the inflammation-specific character of the selections and the rationalization of the burn-induced inflammatory response. …”
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“…We could functionally classify 776 (35%) sequences using the Gene Ontologies (GO) and established pathway associations to 696 (31%) sequences in Kyoto Encyclopedia of Genes and Genomes (KEGG). …”
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“…Utilizing identification-centered proteomics techniques (fluorescence two-dimensional differential gel electrophoresis, robotic tryptic digestion and mass spectrometry) coupled with Protein ANalysis THrough Evolutionary Relationships (PANTHER) ontological classifications, we determined that in amniotic fluids with Q-profile the differentially expressed proteins are primarily involved in non-inflammatory biological processes such as protein metabolism, signal transduction and transport. …”
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“…Using microarray-based gene expression profiling in striatum, we found 618 (false discovery rate < 1%) morphine-responsive transcripts. Through ontologic classification, we linked particular sets of genes to biologic functions, including metabolism, transmission of nerve impulse, and cell-cell signaling. …”
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“…The temporal relationships between ontologies that are associated with various biologic, metabolic, and regulatory pathways were identified and related to developmental processes associated with skeletogenesis, vasculogenesis, and neurogenesis. …”
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“…Approximately 85 differentially and constantly expressed proteins (> two-fold change, P < 0.05) were identified, including 52 up-regulated and 33 down-regulated. Gene ontological methods were employed to identify the biological processes that were over-represented in this carcinogenic stage. …”
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“…A Scratchpad allows users to organise data around user-defined or imported ontologies, including biological classifications. Automated semantic annotation and indexing is applied to all content, allowing users to navigate intuitively and curate diverse biological data, including content drawn from third party resources. …”
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“…For example, words matching to existing biological ontologies are highlighted and database identifiers are linked to their database of origin. …”
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“…The 135 k Brassica Exon Array was validated by quantifying transcriptome differences between leaf and root tissue from a reference Brassica rapa line (R-o-18), and categorisation by Gene Ontologies (GO) based on gene orthology with Arabidopsis thaliana. …”
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