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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

Implementation scheme of data model with SMW template. (A) Template dependencies. Each page in SSTAR use one or more template from SMW, the template points to different style sheets, calls semantic property and SSTAR plug-ins to deliver particular function. (B) Data flow from depositing the data file in MediaWiki server to render the page into the client. (C) Code snippet showing template call (EntrezGene) with the semantic properties to generate the page with EntrezGene:4602 http://fantom.gsc.riken.jp/5/sstar/EntrezGene:4602. (D) Statements in the ‘EntrezGene’ template to store template parameters as semantic properties. The statements will add the semantic properties ‘GeneID’, ‘LocusTag’ and ‘type_of_gene’. (E) An example of inline semantic query, retrieving the association between two categories (gene and CAGE peaks) and show the result in an unnumbered list. (F) An example of the inline semantic query modified to call SSTAR ucsc_gb_link function to provide the genomic view of the FFCP in UCSC genome browser.
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baw105-F2: Implementation scheme of data model with SMW template. (A) Template dependencies. Each page in SSTAR use one or more template from SMW, the template points to different style sheets, calls semantic property and SSTAR plug-ins to deliver particular function. (B) Data flow from depositing the data file in MediaWiki server to render the page into the client. (C) Code snippet showing template call (EntrezGene) with the semantic properties to generate the page with EntrezGene:4602 http://fantom.gsc.riken.jp/5/sstar/EntrezGene:4602. (D) Statements in the ‘EntrezGene’ template to store template parameters as semantic properties. The statements will add the semantic properties ‘GeneID’, ‘LocusTag’ and ‘type_of_gene’. (E) An example of inline semantic query, retrieving the association between two categories (gene and CAGE peaks) and show the result in an unnumbered list. (F) An example of the inline semantic query modified to call SSTAR ucsc_gb_link function to provide the genomic view of the FFCP in UCSC genome browser.

Mentions: The MediaWiki system stores the majority of data as Wiki markup text. It also supports a template scheme to specify presentation style. We used the template parameters to store data as semantic properties (see below), in addition to descriptive text (Figure 2A and B). The templates are used to specify a graphical layout and to set and query semantic properties. The process to generate semantic properties in a SWM system consists of two consecutive steps: (i) all data objects are imported as wiki markup (see ‘Data modeling and implementation of heterogeneous and complex biological states in SMW’ in the ‘Results and Discussion’ section), (ii) the imported markup text is then parsed by the SMW system to generate semantic properties.Figure 2.


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)

Implementation scheme of data model with SMW template. (A) Template dependencies. Each page in SSTAR use one or more template from SMW, the template points to different style sheets, calls semantic property and SSTAR plug-ins to deliver particular function. (B) Data flow from depositing the data file in MediaWiki server to render the page into the client. (C) Code snippet showing template call (EntrezGene) with the semantic properties to generate the page with EntrezGene:4602 http://fantom.gsc.riken.jp/5/sstar/EntrezGene:4602. (D) Statements in the ‘EntrezGene’ template to store template parameters as semantic properties. The statements will add the semantic properties ‘GeneID’, ‘LocusTag’ and ‘type_of_gene’. (E) An example of inline semantic query, retrieving the association between two categories (gene and CAGE peaks) and show the result in an unnumbered list. (F) An example of the inline semantic query modified to call SSTAR ucsc_gb_link function to provide the genomic view of the FFCP in UCSC genome browser.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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baw105-F2: Implementation scheme of data model with SMW template. (A) Template dependencies. Each page in SSTAR use one or more template from SMW, the template points to different style sheets, calls semantic property and SSTAR plug-ins to deliver particular function. (B) Data flow from depositing the data file in MediaWiki server to render the page into the client. (C) Code snippet showing template call (EntrezGene) with the semantic properties to generate the page with EntrezGene:4602 http://fantom.gsc.riken.jp/5/sstar/EntrezGene:4602. (D) Statements in the ‘EntrezGene’ template to store template parameters as semantic properties. The statements will add the semantic properties ‘GeneID’, ‘LocusTag’ and ‘type_of_gene’. (E) An example of inline semantic query, retrieving the association between two categories (gene and CAGE peaks) and show the result in an unnumbered list. (F) An example of the inline semantic query modified to call SSTAR ucsc_gb_link function to provide the genomic view of the FFCP in UCSC genome browser.
Mentions: The MediaWiki system stores the majority of data as Wiki markup text. It also supports a template scheme to specify presentation style. We used the template parameters to store data as semantic properties (see below), in addition to descriptive text (Figure 2A and B). The templates are used to specify a graphical layout and to set and query semantic properties. The process to generate semantic properties in a SWM system consists of two consecutive steps: (i) all data objects are imported as wiki markup (see ‘Data modeling and implementation of heterogeneous and complex biological states in SMW’ in the ‘Results and Discussion’ section), (ii) the imported markup text is then parsed by the SMW system to generate semantic properties.Figure 2.

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