Dataset Information

BY-COVID Knowledge Graph: A comprehensive network integrating various data resources of BY-COVID project

ABSTRACT: The BY-COVID Knowledge Graph integrates biological and chemical data from BY-COVID project partner sites. These data are further enriched with information such as biological processes, assays, drug candidates, drug indications, mechanism of action and side effects to form a dynamic and comprehensive network. This is achieved by using the UniProt, ChEMBL and OpenTargets API. The KG is compliant with FAIR annotations allowing seamless transformation and integration to/with other formats and infrastructures. Please check the github for more details: https://github.com/Fraunhofer-ITMP/BY-COVID-KG.

SUBMITTER: Reagon Karki

PROVIDER: MODEL2209020001 | BioModels | 2022-10-17

REPOSITORIES: BioModels

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			Action	DRS
	MODEL2209020001?filename=bycovidgraph_2ndSep.csv	Csv
	MODEL2209020001?filename=bycovidgraph_2ndSep.graphml	Other
	MODEL2209020001?filename=bycovidgraph_2ndSep.pkl	Other
	MODEL2209020001?filename=bycovidgraph_2ndSep.sif	Other

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Project description:Saliva, a biofluid enriched in biological omic constituents, has emerged as a promising source for exosomal biomarkers due to its easy accessibility. Despite the understanding of the coronavirus disease-19 (COVID-19), the role of Salivary Extracellular Vesicles (sEVs) in COVID-19 remains poorly understood. Exploring the proteomic cargo of sEVs could prove valuable for diagnostic and prognostic purposes in assessing COVID-19. The proteomic cargo of sEVs from COVID-19 (+) subjects and their healthy close contacts (HCC) was explored. Nine COVID-19 positive (+) patients and eleven in-house close contact patients identified by real-time quantitative polymerase chain reaction (RT-qPCR) of nasopharyngeal swabs were included. In-house close contacts were defined as individuals with a negative RT-qPCR result sharing a residence with a confirmed COVID-19 case. sEVs were isolated by ultracentrifugation from unstimulated saliva samples, and subsequently characterized through nanoparticle tracking, transmission electron microscopy, and western-blot analyses. The proteomic cargo of sEVs was processed by LC-MS/MS. sEVs were morphologically compatible with EVs, with the presence of Syntenin-1 and CD81 EVs markers. The sEVs proteome showed 1,417 proteins: 1,288 in COVID-19 (+) cases and 1,382 in HCC. 35 proteins were found exclusively and 89 were more abundant in sEVs from COVID-19 (+) subjects. “Coronavirus disease response”, “complement and coagulation cascades”, and “PMN extracellular trap formation” were the most enriched KEGG pathways in COVID-19 (+) cases. The most represented biological processes were “Hemoglobin and haptoglobin binding” and “oxygen carrier activity”, and the best-denoted molecular functions were “regulated exocytosis and secretion” and “leucocyte and PMN mediated immunity”. We suggest that sEVs proteomic cargo in COVID-19 is related to immune response processes, oxygen transport, and antioxidant mechanisms. In contrast, in HCC, sEVs signature profiles are mainly associated with epithelial homeostasis.

Dataset Information

BY-COVID Knowledge Graph: A comprehensive network integrating various data resources of BY-COVID project

Dataset's files

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