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FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki.

Abugessaisa I, Shimoji H, Sahin S, Kondo A, Harshbarger J, Lizio M, Hayashizaki Y, Carninci P, FANTOM consortiumForrest A, Kasukawa T, Kawaji H - Database (Oxford) (2016)

Bottom Line: To make the heterogeneous data set accessible and useful for investigators, we developed a web-based database called Semantic catalog of Samples, Transcription initiation And Regulators (SSTAR).SSTAR utilizes the open source wiki software MediaWiki along with the Semantic MediaWiki (SMW) extension, which provides flexibility to model, store, and display a series of data sets produced during the course of the FANTOM5 project.Our use of SMW demonstrates the utility of the framework for dissemination of large-scale analysis results.

View Article: PubMed Central - PubMed

Affiliation: Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Kanagawa 230-0045, Japan.

No MeSH data available.


Related in: MedlinePlus

SSTAR data model. SSTAR data model consists of six classes, those represents the main ‘categories’ in SMW. The oval represents a class and the kind of the data stored. Relationship between any two categories is represented as an arrow. The direction of the arrow indicates which of the two classes stores the relationship (indicated by the end of the arrow) as a class attribute. The head and color of the arrow indicates the type of relationship.
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baw105-F1: SSTAR data model. SSTAR data model consists of six classes, those represents the main ‘categories’ in SMW. The oval represents a class and the kind of the data stored. Relationship between any two categories is represented as an arrow. The direction of the arrow indicates which of the two classes stores the relationship (indicated by the end of the arrow) as a class attribute. The head and color of the arrow indicates the type of relationship.

Mentions: SSTAR stores and manages two kinds of data sets: original (raw and processed) data generated by the FANTOM5 consortium and external data supporting interpretation of the FANTOM5 data (Figure 1). The original raw data set consists of sample RNA and sequencing library metadata in sample and data relationship format (SDRF), sequence data in the FASTQ format, genome mapping data in the BAM format and CTSS (CAGE tag starting site) profiles in the BED format. The raw data had been deposited to DDBJ DRA under accession number DRA000991, DRA001026, DRA001027, DRA001028, DRA001101, DRA002216, DRA002711, DRA002747, DRA002748 (17, 22).Figure 1.


FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki.

Abugessaisa I, Shimoji H, Sahin S, Kondo A, Harshbarger J, Lizio M, Hayashizaki Y, Carninci P, FANTOM consortiumForrest A, Kasukawa T, Kawaji H - Database (Oxford) (2016)

SSTAR data model. SSTAR data model consists of six classes, those represents the main ‘categories’ in SMW. The oval represents a class and the kind of the data stored. Relationship between any two categories is represented as an arrow. The direction of the arrow indicates which of the two classes stores the relationship (indicated by the end of the arrow) as a class attribute. The head and color of the arrow indicates the type of relationship.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4940433&req=5

baw105-F1: SSTAR data model. SSTAR data model consists of six classes, those represents the main ‘categories’ in SMW. The oval represents a class and the kind of the data stored. Relationship between any two categories is represented as an arrow. The direction of the arrow indicates which of the two classes stores the relationship (indicated by the end of the arrow) as a class attribute. The head and color of the arrow indicates the type of relationship.
Mentions: SSTAR stores and manages two kinds of data sets: original (raw and processed) data generated by the FANTOM5 consortium and external data supporting interpretation of the FANTOM5 data (Figure 1). The original raw data set consists of sample RNA and sequencing library metadata in sample and data relationship format (SDRF), sequence data in the FASTQ format, genome mapping data in the BAM format and CTSS (CAGE tag starting site) profiles in the BED format. The raw data had been deposited to DDBJ DRA under accession number DRA000991, DRA001026, DRA001027, DRA001028, DRA001101, DRA002216, DRA002711, DRA002747, DRA002748 (17, 22).Figure 1.

Bottom Line: To make the heterogeneous data set accessible and useful for investigators, we developed a web-based database called Semantic catalog of Samples, Transcription initiation And Regulators (SSTAR).SSTAR utilizes the open source wiki software MediaWiki along with the Semantic MediaWiki (SMW) extension, which provides flexibility to model, store, and display a series of data sets produced during the course of the FANTOM5 project.Our use of SMW demonstrates the utility of the framework for dissemination of large-scale analysis results.

View Article: PubMed Central - PubMed

Affiliation: Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Kanagawa 230-0045, Japan.

No MeSH data available.


Related in: MedlinePlus