Difference between revisions of "Journal:Principles of metadata organization at the ENCODE data coordination center"

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==Introduction==
==Introduction==
The goal of the Encyclopedia of DNA Elements (ENCODE) project is to annotate functional regions in the human and mouse genomes. Functional regions include those that code protein-coding or non-coding RNA gene products as well as regions that could have a regulatory role.<ref name="EPCAnInt12">{{cite journal |title=An integrated encyclopedia of DNA elements in the human genome |journal=Nature |author=ENCODE Project Consortium |volume=489 |issue=7414 |pages=57-74 |year=2012 |doi=10.1038/nature11247 |pmid=22955616 |pmc=PMC3439153}}</ref><ref name="YueAComp14">{{cite journal |title=A comparative encyclopedia of DNA elements in the mouse genome |journal=Nature |author=Yue, F.; Cheng, Y.; Breschi, A. et al. |volume=515 |issue=7527 |pages=355-64 |year=2014 |doi=10.1038/nature13992 |pmid=25409824 |pmc=PMC4266106}}</ref> To this end, the project has surveyed the landscape of the human genome using over 35 high-throughput experimental methods in  more than 250 different cell and tissue types, resulting in over 4000 experiments.<ref name="EPCAnInt12" /><ref name="ECPIdentif07">{{cite journal |title=Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project |journal=Nature |author=ENCODE Project Consortium et al. |volume=447 |issue=7146 |pages=799–816 |year=2007 |doi=10.1038/nature05874 |pmid=17571346 |pmc=PMC2212820}}</ref> These datasets are submitted to a Data Coordinating Center (DCC), whose role is to describe, organize and provide access to these diverse datasets.<ref name="SloanENCODE16">{{cite journal |title=ENCODE data at the ENCODE portal |journal=Nucleic Acids Research |author=Sloan, C.A.; Chan, E.T.; Davidson, J.M. et al. |volume=44 |issue=D1 |pages=D726-32 |year=2016 |doi=10.1093/nar/gkv1160 |pmid=26527727 |pmc=PMC4702836}}</ref>
The goal of the Encyclopedia of DNA Elements (ENCODE) project is to annotate functional regions in the human and mouse genomes. Functional regions include those that code protein-coding or non-coding RNA gene products as well as regions that could have a regulatory role.<ref name="EPCAnInt12">{{cite journal |title=An integrated encyclopedia of DNA elements in the human genome |journal=Nature |author=ENCODE Project Consortium |volume=489 |issue=7414 |pages=57-74 |year=2012 |doi=10.1038/nature11247 |pmid=22955616 |pmc=PMC3439153}}</ref><ref name="YueAComp14">{{cite journal |title=A comparative encyclopedia of DNA elements in the mouse genome |journal=Nature |author=Yue, F.; Cheng, Y.; Breschi, A. et al. |volume=515 |issue=7527 |pages=355-64 |year=2014 |doi=10.1038/nature13992 |pmid=25409824 |pmc=PMC4266106}}</ref> To this end, the project has surveyed the landscape of the human genome using over 35 high-throughput experimental methods in  more than 250 different cell and tissue types, resulting in over 4000 experiments.<ref name="EPCAnInt12" /><ref name="ECPIdentif07">{{cite journal |title=Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project |journal=Nature |author=ENCODE Project Consortium et al. |volume=447 |issue=7146 |pages=799–816 |year=2007 |doi=10.1038/nature05874 |pmid=17571346 |pmc=PMC2212820}}</ref> These datasets are submitted to a Data Coordinating Center (DCC), whose role is to describe, organize and provide access to these diverse datasets.<ref name="SloanENCODE16">{{cite journal |title=ENCODE data at the ENCODE portal |journal=Nucleic Acids Research |author=Sloan, C.A.; Chan, E.T.; Davidson, J.M. et al. |volume=44 |issue=D1 |pages=D726-32 |year=2016 |doi=10.1093/nar/gkv1160 |pmid=26527727 |pmc=PMC4702836}}</ref>
A description of these datasets, collectively known as metadata, encompasses, but is not limited to, the identification of the experimental method used to generate the data, the sex and age of the donor from whom a skin biopsy was taken, and the software used to align the sequencing reads to a reference genome. Defining and organizing the set of metadata that is relevant, informative and applicable to diverse experimental techniques is challenging. These challenges are not unique to the ENCODE DCC. Several major experimental consortia similar in scale to the ENCODE project exist, as well as public database projects that collect and distribute high-throughput genomic data. Analogous to the ENCODE project, the modENCODE project was begun in 2007 to identify functional elements in the model organisms ''Caenorhabditis elegans'' and ''Drosophila melanogaster''. The modENCODE DCC faced similar challenges in trying to integrate diverse data types using a variety of experimental techniques.<ref name="WashingtonTheModENC11">{{cite journal |title=The modENCODE Data Coordination Center: Lessons in harvesting comprehensive experimental details |journal=Database |author=Washington, N.L.; Stinson, E.O.; Perry, M.D. et al. |volume=2011 |pages=bar023 |year=2011 |doi=10.1093/database/bar023 |pmid=21856757 |pmc=PMC3170170}}</ref> Other consortia, such as the Roadmap Epigenomics Mapping Centers, also have been tasked with defining the metadata.<ref name="BernsteinTheNIH10">{{cite journal |title=The NIH Roadmap Epigenomics Mapping Consortium |journal=Nature Biotechnology |author=Bernstein, B.E.; Stamatoyannopoulos, J.A.; Costello, J.F. et al. |volume=28 |issue=10 |pages=1045-8 |year=2010 |doi=10.1038/nbt1010-1045 |pmid=20944595 |pmc=PMC3607281}}</ref> In addition, databases such as ArrayExpress at the EBI, GEO and SRA at the NCBI, Data Dryad (http://datadryad.org/) and FigShare (http://figshare.com/) serve as data repositories, accepting diverse data types from large consortia as well as from individual research laboratories.<ref name="KolesnikovArrray15">{{cite journal |title=ArrayExpress update -- Simplifying data submissions |journal=Nucleic Acids Research |author=Kolesnikov, N.; Hastings, E.; Keays, M. et al. |volume=43 |issue=D1 |pages=D1113-6 |year=2015 |doi=10.1093/nar/gku1057 |pmid=25361974 |pmc=PMC4383899}}</ref><ref name="BarrettNCBI13">{{cite journal |title=NCBI GEO: Archive for functional genomics data sets -- Update |journal=Nucleic Acids Research |author=Barrett, T.; Wilhite, S.E.; Ledoux, P. et al. |volume=41 |issue=D1 |pages=D991-5 |year=2013 |doi=10.1093/nar/gks1193 |pmid=23193258 |pmc=PMC3531084}}</ref><ref name="NCBIDatabase15">{{cite journal |title=Database resources of the National Center for Biotechnology Information |journal=Nucleic Acids Research |author=NCBI Resource Coordinators |volume=43 |issue=D1 |pages=D6–17 |year=2015 |doi=10.1093/nar/gku1130 |pmid=25398906 |pmc=PMC4383943}}</ref>


==References==
==References==

Revision as of 20:38, 6 September 2016

Full article title Principles of metadata organization at the ENCODE data coordination center
Journal Database
Author(s) Hong, Eurie L.; Sloan, Cricket A.; Chan, Esther T.; Davidson, Jean M.; Malladi, Venkat S.; Strattan, J. Seth; Hitz, Benjamin C.;
Gabdank, Idan; Narayanan, Aditi K.; Ho, Marcus; Lee, Brian T.; Rowe, Laurence D.; Dreszer, Timothy R.; Roe, Greg R.;
Podduturi, Nikhil R.; Tanaka, Forrest; Hilton, Jason A.; Cherry, J. Michael
Author affiliation(s) Stanford University, University of California - Santa Cruz
Primary contact Email: cherry at stanford dot edu
Year published 2016
Page(s) baw001
DOI 10.1093/database/baw001
ISSN 1758-0463
Distribution license Creative Commons Attribution 4.0 International
Website http://database.oxfordjournals.org/content/2016/baw001
Download http://database.oxfordjournals.org/content/2016/baw001.full.pdf+html (PDF)
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Abstract

The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center (DCC) is responsible for organizing, describing and providing access to the diverse data generated by the ENCODE project. The description of these data, known as metadata, includes the biological sample used as input, the protocols and assays performed on these samples, the data files generated from the results and the computational methods used to analyze the data. Here, we outline the principles and philosophy used to define the ENCODE metadata in order to create a metadata standard that can be applied to diverse assays and multiple genomic projects. In addition, we present how the data are validated and used by the ENCODE DCC in creating the ENCODE Portal (https://www.encodeproject.org/).

Database URL: www.encodeproject.org

Introduction

The goal of the Encyclopedia of DNA Elements (ENCODE) project is to annotate functional regions in the human and mouse genomes. Functional regions include those that code protein-coding or non-coding RNA gene products as well as regions that could have a regulatory role.[1][2] To this end, the project has surveyed the landscape of the human genome using over 35 high-throughput experimental methods in  more than 250 different cell and tissue types, resulting in over 4000 experiments.[1][3] These datasets are submitted to a Data Coordinating Center (DCC), whose role is to describe, organize and provide access to these diverse datasets.[4]

A description of these datasets, collectively known as metadata, encompasses, but is not limited to, the identification of the experimental method used to generate the data, the sex and age of the donor from whom a skin biopsy was taken, and the software used to align the sequencing reads to a reference genome. Defining and organizing the set of metadata that is relevant, informative and applicable to diverse experimental techniques is challenging. These challenges are not unique to the ENCODE DCC. Several major experimental consortia similar in scale to the ENCODE project exist, as well as public database projects that collect and distribute high-throughput genomic data. Analogous to the ENCODE project, the modENCODE project was begun in 2007 to identify functional elements in the model organisms Caenorhabditis elegans and Drosophila melanogaster. The modENCODE DCC faced similar challenges in trying to integrate diverse data types using a variety of experimental techniques.[5] Other consortia, such as the Roadmap Epigenomics Mapping Centers, also have been tasked with defining the metadata.[6] In addition, databases such as ArrayExpress at the EBI, GEO and SRA at the NCBI, Data Dryad (http://datadryad.org/) and FigShare (http://figshare.com/) serve as data repositories, accepting diverse data types from large consortia as well as from individual research laboratories.[7][8][9]

References

  1. ↑ 1.0 1.1 ENCODE Project Consortium (2012). "An integrated encyclopedia of DNA elements in the human genome". Nature 489 (7414): 57-74. doi:10.1038/nature11247. PMC PMC3439153. PMID 22955616. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439153. 
  2. ↑ Yue, F.; Cheng, Y.; Breschi, A. et al. (2014). "A comparative encyclopedia of DNA elements in the mouse genome". Nature 515 (7527): 355-64. doi:10.1038/nature13992. PMC PMC4266106. PMID 25409824. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266106. 
  3. ↑ ENCODE Project Consortium et al. (2007). "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project". Nature 447 (7146): 799–816. doi:10.1038/nature05874. PMC PMC2212820. PMID 17571346. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2212820. 
  4. ↑ Sloan, C.A.; Chan, E.T.; Davidson, J.M. et al. (2016). "ENCODE data at the ENCODE portal". Nucleic Acids Research 44 (D1): D726-32. doi:10.1093/nar/gkv1160. PMC PMC4702836. PMID 26527727. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702836. 
  5. ↑ Washington, N.L.; Stinson, E.O.; Perry, M.D. et al. (2011). "The modENCODE Data Coordination Center: Lessons in harvesting comprehensive experimental details". Database 2011: bar023. doi:10.1093/database/bar023. PMC PMC3170170. PMID 21856757. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3170170. 
  6. ↑ Bernstein, B.E.; Stamatoyannopoulos, J.A.; Costello, J.F. et al. (2010). "The NIH Roadmap Epigenomics Mapping Consortium". Nature Biotechnology 28 (10): 1045-8. doi:10.1038/nbt1010-1045. PMC PMC3607281. PMID 20944595. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3607281. 
  7. ↑ Kolesnikov, N.; Hastings, E.; Keays, M. et al. (2015). "ArrayExpress update -- Simplifying data submissions". Nucleic Acids Research 43 (D1): D1113-6. doi:10.1093/nar/gku1057. PMC PMC4383899. PMID 25361974. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383899. 
  8. ↑ Barrett, T.; Wilhite, S.E.; Ledoux, P. et al. (2013). "NCBI GEO: Archive for functional genomics data sets -- Update". Nucleic Acids Research 41 (D1): D991-5. doi:10.1093/nar/gks1193. PMC PMC3531084. PMID 23193258. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531084. 
  9. ↑ NCBI Resource Coordinators (2015). "Database resources of the National Center for Biotechnology Information". Nucleic Acids Research 43 (D1): D6–17. doi:10.1093/nar/gku1130. PMC PMC4383943. PMID 25398906. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383943. 

Notes

This presentation is faithful to the original, with only a few minor changes to presentation. In some cases important information was missing from the references, and that information was added.

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