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ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets

High-throughput sequencing has become ubiquitous in biomedical sciences. As new technologies emerge and sequencing costs decline, the diversity and volume of available data increases exponentially, and successfully navigating the data becomes more challenging. Though datasets are often hosted by pub...

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Autores principales: Lavender, Christopher A., Shapiro, Andrew J., Day, Frank S., Fargo, David C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7001987/
https://www.ncbi.nlm.nih.gov/pubmed/31978042
http://dx.doi.org/10.1371/journal.pcbi.1007571
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author Lavender, Christopher A.
Shapiro, Andrew J.
Day, Frank S.
Fargo, David C.
author_facet Lavender, Christopher A.
Shapiro, Andrew J.
Day, Frank S.
Fargo, David C.
author_sort Lavender, Christopher A.
collection PubMed
description High-throughput sequencing has become ubiquitous in biomedical sciences. As new technologies emerge and sequencing costs decline, the diversity and volume of available data increases exponentially, and successfully navigating the data becomes more challenging. Though datasets are often hosted by public repositories, scientists must rely on inconsistent annotation to identify and interpret meaningful data. Moreover, the experimental heterogeneity and wide-ranging quality of high-throughput biological data means that even data with desired cell lines, tissue types, or molecular targets may not be readily interpretable or integrated. We have developed ORSO (Online Resource for Social Omics) as an easy-to-use web application to connect life scientists with genomics data. In ORSO, users interact within a data-driven social network, where they can favorite datasets and follow other users. In addition to more than 30,000 datasets hosted from major biomedical consortia, users may contribute their own data to ORSO, facilitating its discovery by other users. Leveraging user interactions, ORSO provides a novel recommendation system to automatically connect users with hosted data. In addition to social interactions, the recommendation system considers primary read coverage information and annotated metadata. Similarities used by the recommendation system are presented by ORSO in a graph display, allowing exploration of dataset associations. The topology of the network graph reflects established biology, with samples from related systems grouped together. We tested the recommendation system using an RNA-seq time course dataset from differentiation of embryonic stem cells to cardiomyocytes. The ORSO recommendation system correctly predicted early data point sources as embryonic stem cells and late data point sources as heart and muscle samples, resulting in recommendation of related datasets. By connecting scientists with relevant data, ORSO provides a critical new service that facilitates wide-ranging research interests.
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spelling pubmed-70019872020-02-18 ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets Lavender, Christopher A. Shapiro, Andrew J. Day, Frank S. Fargo, David C. PLoS Comput Biol Research Article High-throughput sequencing has become ubiquitous in biomedical sciences. As new technologies emerge and sequencing costs decline, the diversity and volume of available data increases exponentially, and successfully navigating the data becomes more challenging. Though datasets are often hosted by public repositories, scientists must rely on inconsistent annotation to identify and interpret meaningful data. Moreover, the experimental heterogeneity and wide-ranging quality of high-throughput biological data means that even data with desired cell lines, tissue types, or molecular targets may not be readily interpretable or integrated. We have developed ORSO (Online Resource for Social Omics) as an easy-to-use web application to connect life scientists with genomics data. In ORSO, users interact within a data-driven social network, where they can favorite datasets and follow other users. In addition to more than 30,000 datasets hosted from major biomedical consortia, users may contribute their own data to ORSO, facilitating its discovery by other users. Leveraging user interactions, ORSO provides a novel recommendation system to automatically connect users with hosted data. In addition to social interactions, the recommendation system considers primary read coverage information and annotated metadata. Similarities used by the recommendation system are presented by ORSO in a graph display, allowing exploration of dataset associations. The topology of the network graph reflects established biology, with samples from related systems grouped together. We tested the recommendation system using an RNA-seq time course dataset from differentiation of embryonic stem cells to cardiomyocytes. The ORSO recommendation system correctly predicted early data point sources as embryonic stem cells and late data point sources as heart and muscle samples, resulting in recommendation of related datasets. By connecting scientists with relevant data, ORSO provides a critical new service that facilitates wide-ranging research interests. Public Library of Science 2020-01-24 /pmc/articles/PMC7001987/ /pubmed/31978042 http://dx.doi.org/10.1371/journal.pcbi.1007571 Text en https://creativecommons.org/publicdomain/zero/1.0/ This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 (https://creativecommons.org/publicdomain/zero/1.0/) public domain dedication.
spellingShingle Research Article
Lavender, Christopher A.
Shapiro, Andrew J.
Day, Frank S.
Fargo, David C.
ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets
title ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets
title_full ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets
title_fullStr ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets
title_full_unstemmed ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets
title_short ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets
title_sort orso (online resource for social omics): a data-driven social network connecting scientists to genomics datasets
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7001987/
https://www.ncbi.nlm.nih.gov/pubmed/31978042
http://dx.doi.org/10.1371/journal.pcbi.1007571
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