Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive.

High-throughput sequencing technology, also called next-generation sequencing (NGS), has the potential to revolutionize the whole process of genome sequencing, transcriptomics, and epigenetics. Sequencing data is captured in a public primary data archive, the Sequence Read Archive (SRA). As of Janua...

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Autores principales:	Takeru Nakazato, Tazro Ohta, Hidemasa Bono
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/1dd4c06327074da3961d4c3f3e82b2f0
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spelling	oai:doaj.org-article:1dd4c06327074da3961d4c3f3e82b2f02021-11-18T08:49:58ZExperimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive.1932-620310.1371/journal.pone.0077910https://doaj.org/article/1dd4c06327074da3961d4c3f3e82b2f02013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24167589/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203High-throughput sequencing technology, also called next-generation sequencing (NGS), has the potential to revolutionize the whole process of genome sequencing, transcriptomics, and epigenetics. Sequencing data is captured in a public primary data archive, the Sequence Read Archive (SRA). As of January 2013, data from more than 14,000 projects have been submitted to SRA, which is double that of the previous year. Researchers can download raw sequence data from SRA website to perform further analyses and to compare with their own data. However, it is extremely difficult to search entries and download raw sequences of interests with SRA because the data structure is complicated, and experimental conditions along with raw sequences are partly described in natural language. Additionally, some sequences are of inconsistent quality because anyone can submit sequencing data to SRA with no quality check. Therefore, as a criterion of data quality, we focused on SRA entries that were cited in journal articles. We extracted SRA IDs and PubMed IDs (PMIDs) from SRA and full-text versions of journal articles and retrieved 2748 SRA ID-PMID pairs. We constructed a publication list referring to SRA entries. Since, one of the main themes of -omics analyses is clarification of disease mechanisms, we also characterized SRA entries by disease keywords, according to the Medical Subject Headings (MeSH) extracted from articles assigned to each SRA entry. We obtained 989 SRA ID-MeSH disease term pairs, and constructed a disease list referring to SRA data. We previously developed feature profiles of diseases in a system called "Gendoo". We generated hyperlinks between diseases extracted from SRA and the feature profiles of it. The developed project, publication and disease lists resulting from this study are available at our web service, called "DBCLS SRA" (http://sra.dbcls.jp/). This service will improve accessibility to high-quality data from SRA.Takeru NakazatoTazro OhtaHidemasa BonoPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 10, p e77910 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Takeru Nakazato Tazro Ohta Hidemasa Bono Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive.
description	High-throughput sequencing technology, also called next-generation sequencing (NGS), has the potential to revolutionize the whole process of genome sequencing, transcriptomics, and epigenetics. Sequencing data is captured in a public primary data archive, the Sequence Read Archive (SRA). As of January 2013, data from more than 14,000 projects have been submitted to SRA, which is double that of the previous year. Researchers can download raw sequence data from SRA website to perform further analyses and to compare with their own data. However, it is extremely difficult to search entries and download raw sequences of interests with SRA because the data structure is complicated, and experimental conditions along with raw sequences are partly described in natural language. Additionally, some sequences are of inconsistent quality because anyone can submit sequencing data to SRA with no quality check. Therefore, as a criterion of data quality, we focused on SRA entries that were cited in journal articles. We extracted SRA IDs and PubMed IDs (PMIDs) from SRA and full-text versions of journal articles and retrieved 2748 SRA ID-PMID pairs. We constructed a publication list referring to SRA entries. Since, one of the main themes of -omics analyses is clarification of disease mechanisms, we also characterized SRA entries by disease keywords, according to the Medical Subject Headings (MeSH) extracted from articles assigned to each SRA entry. We obtained 989 SRA ID-MeSH disease term pairs, and constructed a disease list referring to SRA data. We previously developed feature profiles of diseases in a system called "Gendoo". We generated hyperlinks between diseases extracted from SRA and the feature profiles of it. The developed project, publication and disease lists resulting from this study are available at our web service, called "DBCLS SRA" (http://sra.dbcls.jp/). This service will improve accessibility to high-quality data from SRA.
format	article
author	Takeru Nakazato Tazro Ohta Hidemasa Bono
author_facet	Takeru Nakazato Tazro Ohta Hidemasa Bono
author_sort	Takeru Nakazato
title	Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive.
title_short	Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive.
title_full	Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive.
title_fullStr	Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive.
title_full_unstemmed	Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive.
title_sort	experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/1dd4c06327074da3961d4c3f3e82b2f0
work_keys_str_mv	AT takerunakazato experimentaldesignbasedfunctionalminingandcharacterizationofhighthroughputsequencingdatainthesequencereadarchive AT tazroohta experimentaldesignbasedfunctionalminingandcharacterizationofhighthroughputsequencingdatainthesequencereadarchive AT hidemasabono experimentaldesignbasedfunctionalminingandcharacterizationofhighthroughputsequencingdatainthesequencereadarchive
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Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive.

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