“…AnGeLi searches for significant enrichments among multiple qualitative and quantitative information sources, including gene and phenotype ontologies, genetic and protein interactions, numerous features of genes, transcripts, translation, and proteins such as copy numbers, chromosomal positions, genetic diversity, RNA polymerase II and ribosome occupancy, localization, conservation, half-lives, domains, and molecular weight among others, as well as diverse sets of genes that are co-regulated or lead to the same phenotypes when mutated. …”
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“…Among shared polymorphisms, we also find highly differentiated SNPs, in which the derived allele is higher in frequency in the wild (Fst*(wild>lab)), enriched for similar neurogenetic ontologies, indicative of relaxed selection on more active wild alleles in the lab. …”
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“…Although not observed in a second ADHD‐cohort, we identified a similar enrichment among genes duplicated by eight de novo CNVs present in eight individuals with Hyperactivity and/or Short attention span (“Hyperactivity/SAS”, the ontologically‐derived phenotypic components of ADHD). …”
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“…The Gleason system does not allow the identification of low aggressive carcinomas by some precise criteria. The ontological dichotomy implies the application of an objective, quantitative approach for the evaluation of tumor aggressiveness as an alternative. …”
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“…In this regard, and in order to design an appropriate Information System, important aspects on which the culture collection community should focus include: the interoperability of data sets with the ontologies to be used; setting best practice in data management, and the definition of an appropriate data standard.…”
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“…In BEL relationships (called BEL statements), the entities are normalized to defined namespaces mainly derived from public repositories, such as sequence databases, MeSH or publicly available ontologies. In the BEL nanopubs, the BEL statements are associated with citation information and supportive evidence such as a text excerpt. …”
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“…METHODS: Reviews of existing ontologies and interviews with cancer researchers were used to inform iterative development of a cancer phenotype information model. …”
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“…RESULTS: We identified a six-metagene signature (138 genes) containing metagenes enriched in different gene ontologies. The gene clusters were named as follows: Immunity, Tumor suppressors/proliferation, Interferon, Signal transduction, Hormone/survival and Matrix clusters. …”
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“…Although enhancement of NTC emerges in different cancer types from different genomic profiles, we identified a subset of 90 common genes that are related to elevated NTC in all studied tumors. Our ontological analysis shows that these genes are associated with enhanced cell division, DNA replication, stress response, and other cellular functions and processes typically upregulated in cancer. …”
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“…We performed a systematic analysis of the FDA AERS database using MySQL by standardizing the database using structured terminologies and ontologies. We compared adverse event profiles of atypical versus typical antipsychotic medications among adult (18-65), pediatric (age < 18), and geriatric (> 65) populations. …”
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“…Data classification can be established and implemented via ontological analysis and formal logic but we claim that a context-based selection of data should be integrated in the data distribution application. …”
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“…Both of these compartments can be dynamically or ontologically regulated, with metabolic and immunological stimuli altering lipid body content and granule numbers responding to contextual signals from tissue. …”
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“…About 60% of these unigenes returned GO blastX hits for Biological Process, Molecular Function and Cellular Component ontologies. We identified 512 KEGG unique KOs distributed among 275 pathways, elucidating the majority of metabolism roles related to high protein metabolism, growth and immunity. …”
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“…Among these genes, ontological analysis suggested significant implication of phosphatidylinositol 3-kinase signaling, and analysis focused on this pathway demonstrated marked upregulation of angiopoietin 1 and insulin-like growth factor 1. …”
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“…Preparing and tracking data provenance, using common data elements and biomedical ontologies are important for standardizing the data description, making the interpretation and reuse of data easier. …”
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“…Our method involves developing data-model-specific i2b2 ontologies and mapping these to query non-standard table structure. …”
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“…Given that actual dietary intake and reported memories of perceptions of intake are not in the same ontological category, epidemiologists committed the logical fallacy of “Misplaced Concreteness.” …”
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“…The enrichment test for the P restriction treatment showed 123 enriched gene ontologies (GO) for IAC Imperador, while DOR 364 enriched only 24. …”
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“…Many automatic scoring methods yield metrics that are difficult to relate to the theories behind manual scoring methods, and most require manually-curated linguistic ontologies or large corpus infrastructure. In this paper, we propose a novel automatic scoring method based on Wikipedia, Backlink-VSM, which is easily adaptable to any of the 61 languages with more than 100k Wikipedia entries, can account for cultural differences in semantic relatedness, and covers a wide range of item categories. …”
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“…HCC-associated circRNA expression profiles GSE94508 and GSE97332 were downloaded from the Gene Expression Omnibus database (GEO), and 87 differentially expressed circRNAs (DECs) between HCC tissues and paired non-cancer tissues were identified, including 76 up-regulated and 11 down-regulated circRNAs. Gene ontolog (GO) and pathway analyses of the host genes of these DECs suggested that these host genes were enriched in cell adhesion, cytosol, and protein binding, and were associated with tight junction and Wnt signaling pathways. …”
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