Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies

Journal of Extracellular Vesicles
Sai Lakshmi SubramanianAleksandar Milosavljevic

Abstract

The large diversity and volume of extracellular RNA (exRNA) data that will form the basis of the exRNA Atlas generated by the Extracellular RNA Communication Consortium pose a substantial data integration challenge. We here present the strategy that is being implemented by the exRNA Data Management and Resource Repository, which employs metadata, biomedical ontologies and Linked Data technologies, such as Resource Description Framework to integrate a diverse set of exRNA profiles into an exRNA Atlas and enable integrative exRNA analysis. We focus on the following three specific data integration tasks: (a) selection of samples from a virtual biorepository for exRNA profiling and for inclusion in the exRNA Atlas; (b) retrieval of a data slice from the exRNA Atlas for integrative analysis and (c) interpretation of exRNA analysis results in the context of pathways and networks. As exRNA profiling gains wide adoption in the research community, we anticipate that the strategies discussed here will increasingly be required to enable data reuse and to facilitate integrative analysis of exRNA data.

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Citations

Nov 19, 2015·Nucleic Acids Research·Chunlei WuAndrew I Su
Nov 5, 2016·Journal of Alzheimer's Disease : JAD·Theresa A LusardiJulie A Saugstad
Aug 10, 2016·Scientific Reports·Zhiyun WeiAnna M Krichevsky
Sep 30, 2017·Bioinformatics·Karolina Elzbieta Kaczor-UrbanowiczDavid T W Wong
Mar 22, 2018·Molecular Cancer·Ruihao ZhouGuofu Huang
Jul 17, 2018·Nature Biotechnology·Maria D GiraldezMuneesh Tewari
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Mar 14, 2020·Scientific Reports·Jiang LiKelan G Tantisira
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Jul 19, 2017·Journal of Extracellular Vesicles·Julie A SaugstadFred H Hochberg
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Jun 15, 2019·Journal of Biomedical Semantics·Lucy Lu WangJohn H Gennari
May 19, 2019·Scientific Reports·Jacob L BarberMark A Sarzynski
Aug 20, 2020·Reviews in the Neurosciences·Barbora KonečnáGabriela Repiská
Jan 14, 2021·Scientific Reports·George I MiasJin He
Mar 30, 2019·Journal of Biomedical Informatics·Alina Trifan, José Luís Oliveira

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Methods Mentioned

BETA
RNA-seq
chemical treatments

Software Mentioned

Sequence Ontology ( SO )
BioGPS
exRNA Atlas
Ontobee
Uber Anatomy Ontology ( UBERON ) Ontology ( CL
Open Biological and Biomedical Ontology ( OBO ) Foundry
exRNA Workbench
iOS
REST
Cytoscape

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