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MetaRNA-Seq: An Interactive Tool to Browse and Annotate Metadata from RNA-Seq Studies.

Kumar P, Halama A, Hayat S, Billing AM, Gupta M, Yousri NA, Smith GM, Suhre K - Biomed Res Int (2015)

Bottom Line: Most of these publically available RNA-Seq studies are deposited in NCBI databases, but their metadata are scattered throughout four different databases: Sequence Read Archive (SRA), Biosample, Bioprojects, and Gene Expression Omnibus (GEO).Moreover, project- and study-level metadata lack manual or automatic curation by categories, such as disease type, time series, case-control, or replicate type, which are vital to comprehending any RNA-Seq study.Here we describe "MetaRNA-Seq," a new tool for interactively browsing, searching, and annotating RNA-Seq metadata with the capability of semiautomatic curation at the study level.

View Article: PubMed Central - PubMed

Affiliation: Weill Cornell Medical College in Qatar, Education City, Doha, Qatar.

ABSTRACT
The number of RNA-Seq studies has grown in recent years. The design of RNA-Seq studies varies from very simple (e.g., two-condition case-control) to very complicated (e.g., time series involving multiple samples at each time point with separate drug treatments). Most of these publically available RNA-Seq studies are deposited in NCBI databases, but their metadata are scattered throughout four different databases: Sequence Read Archive (SRA), Biosample, Bioprojects, and Gene Expression Omnibus (GEO). Although the NCBI web interface is able to provide all of the metadata information, it often requires significant effort to retrieve study- or project-level information by traversing through multiple hyperlinks and going to another page. Moreover, project- and study-level metadata lack manual or automatic curation by categories, such as disease type, time series, case-control, or replicate type, which are vital to comprehending any RNA-Seq study. Here we describe "MetaRNA-Seq," a new tool for interactively browsing, searching, and annotating RNA-Seq metadata with the capability of semiautomatic curation at the study level.

No MeSH data available.


Related in: MedlinePlus

The MetaRNA-Seq web interface. On the left it has the search functionality for RNA-Seq studies. Below the search, the table contains all RNA-Seq study details, including name, title, number of samples, number of experiments, and number of runs, allowing one to quickly scroll through all of the studies. The table is filtered based on the search. The table can be sorted by double clicking any column. Upon clicking any study in the table, the study details are populated at the upper right. A tree-like data structure containing biosamples, experiments, and runs for the selected study is populated in the lower right.
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Related In: Results  -  Collection


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fig1: The MetaRNA-Seq web interface. On the left it has the search functionality for RNA-Seq studies. Below the search, the table contains all RNA-Seq study details, including name, title, number of samples, number of experiments, and number of runs, allowing one to quickly scroll through all of the studies. The table is filtered based on the search. The table can be sorted by double clicking any column. Upon clicking any study in the table, the study details are populated at the upper right. A tree-like data structure containing biosamples, experiments, and runs for the selected study is populated in the lower right.

Mentions: The MetaRNA-Seq web tool provides enhanced utilization of metadata for RNA-Seq studies in NCBI resources with semiautomatic curation, restructures the presentation, and allows convenient browsing of all of the details in a single window with a study-level search. MetaRNA-Seq currently has metadata information for 1508 human RNA-Seq studies and is updated every quarter. The main web interface of MetaRNA-Seq is shown in Figure 1. The interface has a desktop application-like design and behavior.


MetaRNA-Seq: An Interactive Tool to Browse and Annotate Metadata from RNA-Seq Studies.

Kumar P, Halama A, Hayat S, Billing AM, Gupta M, Yousri NA, Smith GM, Suhre K - Biomed Res Int (2015)

The MetaRNA-Seq web interface. On the left it has the search functionality for RNA-Seq studies. Below the search, the table contains all RNA-Seq study details, including name, title, number of samples, number of experiments, and number of runs, allowing one to quickly scroll through all of the studies. The table is filtered based on the search. The table can be sorted by double clicking any column. Upon clicking any study in the table, the study details are populated at the upper right. A tree-like data structure containing biosamples, experiments, and runs for the selected study is populated in the lower right.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4561952&req=5

fig1: The MetaRNA-Seq web interface. On the left it has the search functionality for RNA-Seq studies. Below the search, the table contains all RNA-Seq study details, including name, title, number of samples, number of experiments, and number of runs, allowing one to quickly scroll through all of the studies. The table is filtered based on the search. The table can be sorted by double clicking any column. Upon clicking any study in the table, the study details are populated at the upper right. A tree-like data structure containing biosamples, experiments, and runs for the selected study is populated in the lower right.
Mentions: The MetaRNA-Seq web tool provides enhanced utilization of metadata for RNA-Seq studies in NCBI resources with semiautomatic curation, restructures the presentation, and allows convenient browsing of all of the details in a single window with a study-level search. MetaRNA-Seq currently has metadata information for 1508 human RNA-Seq studies and is updated every quarter. The main web interface of MetaRNA-Seq is shown in Figure 1. The interface has a desktop application-like design and behavior.

Bottom Line: Most of these publically available RNA-Seq studies are deposited in NCBI databases, but their metadata are scattered throughout four different databases: Sequence Read Archive (SRA), Biosample, Bioprojects, and Gene Expression Omnibus (GEO).Moreover, project- and study-level metadata lack manual or automatic curation by categories, such as disease type, time series, case-control, or replicate type, which are vital to comprehending any RNA-Seq study.Here we describe "MetaRNA-Seq," a new tool for interactively browsing, searching, and annotating RNA-Seq metadata with the capability of semiautomatic curation at the study level.

View Article: PubMed Central - PubMed

Affiliation: Weill Cornell Medical College in Qatar, Education City, Doha, Qatar.

ABSTRACT
The number of RNA-Seq studies has grown in recent years. The design of RNA-Seq studies varies from very simple (e.g., two-condition case-control) to very complicated (e.g., time series involving multiple samples at each time point with separate drug treatments). Most of these publically available RNA-Seq studies are deposited in NCBI databases, but their metadata are scattered throughout four different databases: Sequence Read Archive (SRA), Biosample, Bioprojects, and Gene Expression Omnibus (GEO). Although the NCBI web interface is able to provide all of the metadata information, it often requires significant effort to retrieve study- or project-level information by traversing through multiple hyperlinks and going to another page. Moreover, project- and study-level metadata lack manual or automatic curation by categories, such as disease type, time series, case-control, or replicate type, which are vital to comprehending any RNA-Seq study. Here we describe "MetaRNA-Seq," a new tool for interactively browsing, searching, and annotating RNA-Seq metadata with the capability of semiautomatic curation at the study level.

No MeSH data available.


Related in: MedlinePlus