An element may have heterogeneous semantic interpretations in different ontologies. Therefore, understanding the real local meanings of elements is very useful for ontology operations such as querying and reasoning, w...
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An element may have heterogeneous semantic interpretations in different ontologies. Therefore, understanding the real local meanings of elements is very useful for ontology operations such as querying and reasoning, which are the foundations for many applications including semantic searching, ontology matching, and linked data analysis. However, since different ontologies have different preferences to describe their elements, obtaining the semantic context of an element is an open problem. A semantic subgraph was proposed to capture the real meanings of ontology elements. To extract the semantic subgraphs, a hybrid ontology graph is used to represent the semantic relations between elements. An extracting algorithm based on an electrical circuit model is then used with new conductivity calculation rules to improve the quality of the semantic subgraphs. The evaluation results show that the semantic subgraphs properly capture the local meanings of elements. Ontology matching based on semantic subgraphs also demonstrates that the semantic subgraph is a promising technique for ontology applications.
There exists growing evidence that circRNAs are concerned with many complex diseases physiological processes and pathogenesis and may serve as critical therapeutic targets. Identifying disease-associated circRNAs thro...
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There exists growing evidence that circRNAs are concerned with many complex diseases physiological processes and pathogenesis and may serve as critical therapeutic targets. Identifying disease-associated circRNAs through biological experiments is time-consuming, and designing an intelligent, precise calculation model is essential. Recently, many models based on graph technology have been proposed to predict circRNA-disease association. However, most existing methods only capture the neighborhood topology of the association network and ignore the complex semantic information. Therefore, we propose a Dual-view Edge and Topology Hybrid Attention model for predicting CircRNA-Disease Associations (DETHACDA), effectively capturing the neighborhood topology and various semantics of circRNA and disease nodes in a heterogeneous network. The 5-fold cross-validation experiments on circRNADisease indicate that the proposed DETHACDA achieves the area under receiver operating characteristic curve of 0.9882, better than four state-of-the-art calculation methods.
Problem: Biomedical literature and databases contain important clues for the identification of potential disease biomarkers. However, searching these enormous knowledge reservoirs and integrating findings across heter...
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Problem: Biomedical literature and databases contain important clues for the identification of potential disease biomarkers. However, searching these enormous knowledge reservoirs and integrating findings across heterogeneous sources is costly and difficult. Here we demonstrate how semantically integrated knowledge, extracted from biomedical literature and structured databases, can be used to automatically identify potential migraine biomarkers. Method: We used a knowledge graph containing more than 3.5 million biomedical concepts and 68.4 million relationships. Biochemical compound concepts were filtered and ranked by their potential as biomarkers based on their connections to a subgraph of migraine-related concepts. The ranked results were evaluated against the results of a systematic literature review that was performed manually by migraine researchers. Weight points were assigned to these reference compounds to indicate their relative importance. Results: Ranked results automatically generated by the knowledge graph were highly consistent with results from the manual literature review. Out of 222 reference compounds, 163 (73%) ranked in the top 2000, with 547 out of the 644 (85%) weight points assigned to the reference compounds. For reference compounds that were not in the top of the list, an extensive error analysis has been performed. When evaluating the overall performance, we obtained a ROC-AUC of 0.974. Discussion: semantic knowledge graphs composed of information integrated from multiple and varying sources can assist researchers in identifying potential disease biomarkers. (C) 2017 The Author(s). Published by Elsevier Inc.
Dear editor,Most existing ontology matching methods utilize literal information to discover alignments [1, 2]. However, some literal information in ontologies may be opaque and some ontologies may not have sufficient ...
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Dear editor,Most existing ontology matching methods utilize literal information to discover alignments [1, 2]. However, some literal information in ontologies may be opaque and some ontologies may not have sufficient literal information. These ontologies are named weak informative ontologies(WIOs)and it is challenging for existing methods to match WIOs.
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