Opportunities and challenges in sharing and reusing genomic interval data

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Published in:	Frontiers in genetics Vol. 14; p. 1155809
Main Authors:	Xue, Bingjie, Khoroshevskyi, Oleksandr, Gomez, R Ariel, Sheffield, Nathan C
Format:	Journal Article
Language:	English
Published:	Switzerland Frontiers Media S.A 20-03-2023
Subjects:	data integration data sharing and reuse epigenome analysis Genetics genomic intervals genomic regions epigenome analysis genomic regions data integration data sharing and reuse genomic intervals
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Author	Khoroshevskyi, Oleksandr Xue, Bingjie Gomez, R Ariel Sheffield, Nathan C
AuthorAffiliation	5 Department of Public Health Sciences , School of Medicine , University of Virginia , Charlottesville , VA , United States 3 Child Health Research Center , School of Medicine , University of Virginia , Charlottesville , VA , United States 4 School of Data Science , University of Virginia , Charlottesville , VA , United States 1 Center for Public Health Genomics , School of Medicine , University of Virginia , Charlottesville , VA , United States 2 Department of Biomedical Engineering , School of Medicine , University of Virginia , Charlottesville , VA , United States 6 Department of Biochemistry and Molecular Genetics , School of Medicine , University of Virginia , Charlottesville , VA , United States
AuthorAffiliation_xml	– name: 5 Department of Public Health Sciences , School of Medicine , University of Virginia , Charlottesville , VA , United States – name: 1 Center for Public Health Genomics , School of Medicine , University of Virginia , Charlottesville , VA , United States – name: 6 Department of Biochemistry and Molecular Genetics , School of Medicine , University of Virginia , Charlottesville , VA , United States – name: 3 Child Health Research Center , School of Medicine , University of Virginia , Charlottesville , VA , United States – name: 4 School of Data Science , University of Virginia , Charlottesville , VA , United States – name: 2 Department of Biomedical Engineering , School of Medicine , University of Virginia , Charlottesville , VA , United States
Author_xml	– sequence: 1 givenname: Bingjie surname: Xue fullname: Xue, Bingjie organization: Department of Biomedical Engineering, School of Medicine, University of Virginia, Charlottesville, VA, United States – sequence: 2 givenname: Oleksandr surname: Khoroshevskyi fullname: Khoroshevskyi, Oleksandr organization: Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA, United States – sequence: 3 givenname: R Ariel surname: Gomez fullname: Gomez, R Ariel organization: Child Health Research Center, School of Medicine, University of Virginia, Charlottesville, VA, United States – sequence: 4 givenname: Nathan C surname: Sheffield fullname: Sheffield, Nathan C organization: Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, United States
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Cites_doi	10.1093/nar/gkw211 10.12688/f1000research.18676.1 10.1093/bioinformatics/btv612 10.1101/gr.229102 10.1093/bioinformatics/btab524 10.1093/nar/gky1094 10.1093/nargab/lqab036 10.1093/nar/gkv1226 10.3390/genes3040651 10.1038/nature14248 10.1186/s12859-016-1274-4 10.1093/bioinformatics/btad069 10.1093/nargab/lqab123 10.1093/nar/gkac199 10.1093/database/baac036 10.1093/bioinformatics/btm254 10.1016/j.cell.2016.11.007 10.1038/nature11247 10.1093/nar/gks1193 10.3324/haematol.2013.094243 10.1016/j.patter.2021.100322
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Copyright	Copyright © 2023 Xue, Khoroshevskyi, Gomez and Sheffield. 2023 Xue, Khoroshevskyi, Gomez and Sheffield
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Keywords	epigenome analysis genomic regions data integration data sharing and reuse genomic intervals
Language	English
License	This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
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Notes	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Jingyuan Hu, Dana–Farber Cancer Institute, United States Edited by: Ayush Raman, Broad Institute, United States Reviewed by: Changxin Wan, Duke University, United States This article was submitted to ELSI in Science and Genetics, a section of the journal Frontiers in Genetics
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References	Leipzig (B12) 2021; 2 Zheng (B20) 2018; 47 Khoroshevskyi (B8) 2023; 39 Stolarczyk (B17) 2021; 3 Garcia (B6) 2022; 2022 Kent (B7) 2002; 12 Kuksa (B10) 2022; 4 Kundaje (B11) 2015; 518 Albrecht (B1) 2016; 44 Davis (B4) 2007; 23 (B5) 2012; 489 Martens (B13) 2013; 98 Sheffield (B15) 2016; 32 Stunnenberg (B18) 2016; 167 Kitts (B9) 2015; 44 Qin (B14) 2016; 17 Choudhary (B3) 2019; 8 Zou (B21) 2022; 50 Sheffield (B16) 2012; 3 Barrett (B2) 2013; 41 Yates (B19) 2021; 38
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large-scale functional genomics knowledge publication-title: NAR Genomics Bioinforma. doi: 10.1093/nargab/lqab123 contributor: fullname: Kuksa – volume: 50 start-page: W175 year: 2022 ident: B21 article-title: ChIP-atlas 2021 update: A data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and bisulfite-seq data publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkac199 contributor: fullname: Zou – volume: 2022 start-page: baac036 year: 2022 ident: B6 article-title: GeMI: Interactive interface for transformer-based genomic metadata integration publication-title: Database doi: 10.1093/database/baac036 contributor: fullname: Garcia – volume: 23 start-page: 1846 year: 2007 ident: B4 article-title: GEOquery: A bridge between the gene expression omnibus (GEO) and BioConductor publication-title: Bioinformatics doi: 10.1093/bioinformatics/btm254 contributor: fullname: Davis – volume: 167 start-page: 1145 year: 2016 ident: B18 article-title: The international human epigenome consortium: A blueprint for scientific collaboration and discovery publication-title: Cell doi: 10.1016/j.cell.2016.11.007 contributor: fullname: Stunnenberg – volume: 489 start-page: 57 year: 2012 ident: B5 article-title: An integrated encyclopedia of DNA elements in the human genome publication-title: Nature doi: 10.1038/nature11247 – volume: 41 start-page: D991 year: 2013 ident: B2 article-title: NCBI GEO: Archive for functional genomics data sets–update publication-title: Nucleic Acids Res. doi: 10.1093/nar/gks1193 contributor: fullname: Barrett – volume: 98 start-page: 1487 year: 2013 ident: B13 article-title: Blueprint: Mapping human blood cell epigenomes publication-title: Haematologica doi: 10.3324/haematol.2013.094243 contributor: fullname: Martens – volume: 2 start-page: 100322 year: 2021 ident: B12 article-title: The role of metadata in reproducible computational research publication-title: Patterns doi: 10.1016/j.patter.2021.100322 contributor: 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Title	Opportunities and challenges in sharing and reusing genomic interval data
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