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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

Guided search using annotated fields. The search is performed to identify RNA-Seq studies involving breast cancer with cell line as the sample type and annotation status as completed. The result output is a filtered table, with rows highlighted in green because it searched for completed annotation. The user can obtain additional details about any of the filtered studies by simply clicking on them.
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Related In: Results  -  Collection


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fig3: Guided search using annotated fields. The search is performed to identify RNA-Seq studies involving breast cancer with cell line as the sample type and annotation status as completed. The result output is a filtered table, with rows highlighted in green because it searched for completed annotation. The user can obtain additional details about any of the filtered studies by simply clicking on them.

Mentions: RNA-Seq studies can be searched precisely for annotated fields using guided search. This can help identify RNA-Seq studies just by clicking various checkboxes and options rather than typing queries into different fields. A search combining multiple fields can be performed easily for studies meeting all or any criteria. Studies in the MetaRNA-Seq study table are filtered based on the search output. One example of searching annotated RNA-Seq studies related to breast cancer with “cell line” as the sample type is shown in Figure 3.


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)

Guided search using annotated fields. The search is performed to identify RNA-Seq studies involving breast cancer with cell line as the sample type and annotation status as completed. The result output is a filtered table, with rows highlighted in green because it searched for completed annotation. The user can obtain additional details about any of the filtered studies by simply clicking on them.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig3: Guided search using annotated fields. The search is performed to identify RNA-Seq studies involving breast cancer with cell line as the sample type and annotation status as completed. The result output is a filtered table, with rows highlighted in green because it searched for completed annotation. The user can obtain additional details about any of the filtered studies by simply clicking on them.
Mentions: RNA-Seq studies can be searched precisely for annotated fields using guided search. This can help identify RNA-Seq studies just by clicking various checkboxes and options rather than typing queries into different fields. A search combining multiple fields can be performed easily for studies meeting all or any criteria. Studies in the MetaRNA-Seq study table are filtered based on the search output. One example of searching annotated RNA-Seq studies related to breast cancer with “cell line” as the sample type is shown in Figure 3.

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