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Metabolonote: a wiki-based database for managing hierarchical metadata of metabolome analyses.

Ara T, Enomoto M, Arita M, Ikeda C, Kera K, Yamada M, Nishioka T, Ikeda T, Nihei Y, Shibata D, Kanaya S, Sakurai N - Front Bioeng Biotechnol (2015)

Bottom Line: Among the reasons for this are difficulty precisely recording information about complicated analytical experiments (metadata), existence of various databases with their own metadata descriptions, and low reusability of the published data, resulting in submitters (the researchers who generate the data) being insufficiently motivated.Hence, this aspect of Metabolonote, as a metadata preparation tool, is complementary to high-quality and persistent data repositories such as MetaboLights.A total of 808 metadata for analyzed data obtained from 35 biological species are published currently.

View Article: PubMed Central - PubMed

Affiliation: Department of Technology Development, Kazusa DNA Research Institute , Kisarazu , Japan ; National Bioscience Database Center (NBDC), Japan Science and Technology Agency (JST) , Tokyo , Japan.

ABSTRACT
Metabolomics - technology for comprehensive detection of small molecules in an organism - lags behind the other "omics" in terms of publication and dissemination of experimental data. Among the reasons for this are difficulty precisely recording information about complicated analytical experiments (metadata), existence of various databases with their own metadata descriptions, and low reusability of the published data, resulting in submitters (the researchers who generate the data) being insufficiently motivated. To tackle these issues, we developed Metabolonote, a Semantic MediaWiki-based database designed specifically for managing metabolomic metadata. We also defined a metadata and data description format, called "Togo Metabolome Data" (TogoMD), with an ID system that is required for unique access to each level of the tree-structured metadata such as study purpose, sample, analytical method, and data analysis. Separation of the management of metadata from that of data and permission to attach related information to the metadata provide advantages for submitters, readers, and database developers. The metadata are enriched with information such as links to comparable data, thereby functioning as a hub of related data resources. They also enhance not only readers' understanding and use of data but also submitters' motivation to publish the data. The metadata are computationally shared among other systems via APIs, which facilitate the construction of novel databases by database developers. A permission system that allows publication of immature metadata and feedback from readers also helps submitters to improve their metadata. Hence, this aspect of Metabolonote, as a metadata preparation tool, is complementary to high-quality and persistent data repositories such as MetaboLights. A total of 808 metadata for analyzed data obtained from 35 biological species are published currently. Metabolonote and related tools are available free of cost at http://metabolonote.kazusa.or.jp/.

No MeSH data available.


Related in: MedlinePlus

System architecture of Metabolonote. The core system of Metabolonote, OmicsnoteCore is developed as an extension of Semantic MediaWiki, an extension of the content management system MediaWiki, which is written in PHP. A part of SemanticMediaWiki and its extension Semantic Forms was modified. By defining other corresponding formats apart from TogoMD, the system can manage other metadata. OmicsnoteCore implements TogoMD format-dependent and -independent APIs for semantic search and retrieval of metadata from other systems. The program and settings files for implementing Metabolonote in a local server (*) are available from the Metabolonote website.
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Figure 1: System architecture of Metabolonote. The core system of Metabolonote, OmicsnoteCore is developed as an extension of Semantic MediaWiki, an extension of the content management system MediaWiki, which is written in PHP. A part of SemanticMediaWiki and its extension Semantic Forms was modified. By defining other corresponding formats apart from TogoMD, the system can manage other metadata. OmicsnoteCore implements TogoMD format-dependent and -independent APIs for semantic search and retrieval of metadata from other systems. The program and settings files for implementing Metabolonote in a local server (*) are available from the Metabolonote website.

Mentions: Metabolonote is constructed as an extension called “OmicsnoteCore” for Semantic MediaWiki3, a content management system written in PHP, and a set of wiki page data (Properties, Templates, and Forms) prepared based on the “Togo Metabolome Data” (TogoMD) metadata format (described in the Section “The TogoMD Format”) (Figure 1). Functions related to form-editing, property displaying, and data storage in the extensions of MediaWiki4, Semantic MediaWiki, and Semantic Forms, are partially modified. The Metabolonote website is currently running on Red Hat Enterprise Linux Server release 5.6 with Apache 2.2, PHP 5.3, and MySQL 5.0. A sample program called “MNSearchDemo,” which includes practical examples of API usage for semantic searching and retrieving of metadata, is written in PHP. These programs and settings files are available free of cost at Metabolonote’s help page5.


Metabolonote: a wiki-based database for managing hierarchical metadata of metabolome analyses.

Ara T, Enomoto M, Arita M, Ikeda C, Kera K, Yamada M, Nishioka T, Ikeda T, Nihei Y, Shibata D, Kanaya S, Sakurai N - Front Bioeng Biotechnol (2015)

System architecture of Metabolonote. The core system of Metabolonote, OmicsnoteCore is developed as an extension of Semantic MediaWiki, an extension of the content management system MediaWiki, which is written in PHP. A part of SemanticMediaWiki and its extension Semantic Forms was modified. By defining other corresponding formats apart from TogoMD, the system can manage other metadata. OmicsnoteCore implements TogoMD format-dependent and -independent APIs for semantic search and retrieval of metadata from other systems. The program and settings files for implementing Metabolonote in a local server (*) are available from the Metabolonote website.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4388006&req=5

Figure 1: System architecture of Metabolonote. The core system of Metabolonote, OmicsnoteCore is developed as an extension of Semantic MediaWiki, an extension of the content management system MediaWiki, which is written in PHP. A part of SemanticMediaWiki and its extension Semantic Forms was modified. By defining other corresponding formats apart from TogoMD, the system can manage other metadata. OmicsnoteCore implements TogoMD format-dependent and -independent APIs for semantic search and retrieval of metadata from other systems. The program and settings files for implementing Metabolonote in a local server (*) are available from the Metabolonote website.
Mentions: Metabolonote is constructed as an extension called “OmicsnoteCore” for Semantic MediaWiki3, a content management system written in PHP, and a set of wiki page data (Properties, Templates, and Forms) prepared based on the “Togo Metabolome Data” (TogoMD) metadata format (described in the Section “The TogoMD Format”) (Figure 1). Functions related to form-editing, property displaying, and data storage in the extensions of MediaWiki4, Semantic MediaWiki, and Semantic Forms, are partially modified. The Metabolonote website is currently running on Red Hat Enterprise Linux Server release 5.6 with Apache 2.2, PHP 5.3, and MySQL 5.0. A sample program called “MNSearchDemo,” which includes practical examples of API usage for semantic searching and retrieving of metadata, is written in PHP. These programs and settings files are available free of cost at Metabolonote’s help page5.

Bottom Line: Among the reasons for this are difficulty precisely recording information about complicated analytical experiments (metadata), existence of various databases with their own metadata descriptions, and low reusability of the published data, resulting in submitters (the researchers who generate the data) being insufficiently motivated.Hence, this aspect of Metabolonote, as a metadata preparation tool, is complementary to high-quality and persistent data repositories such as MetaboLights.A total of 808 metadata for analyzed data obtained from 35 biological species are published currently.

View Article: PubMed Central - PubMed

Affiliation: Department of Technology Development, Kazusa DNA Research Institute , Kisarazu , Japan ; National Bioscience Database Center (NBDC), Japan Science and Technology Agency (JST) , Tokyo , Japan.

ABSTRACT
Metabolomics - technology for comprehensive detection of small molecules in an organism - lags behind the other "omics" in terms of publication and dissemination of experimental data. Among the reasons for this are difficulty precisely recording information about complicated analytical experiments (metadata), existence of various databases with their own metadata descriptions, and low reusability of the published data, resulting in submitters (the researchers who generate the data) being insufficiently motivated. To tackle these issues, we developed Metabolonote, a Semantic MediaWiki-based database designed specifically for managing metabolomic metadata. We also defined a metadata and data description format, called "Togo Metabolome Data" (TogoMD), with an ID system that is required for unique access to each level of the tree-structured metadata such as study purpose, sample, analytical method, and data analysis. Separation of the management of metadata from that of data and permission to attach related information to the metadata provide advantages for submitters, readers, and database developers. The metadata are enriched with information such as links to comparable data, thereby functioning as a hub of related data resources. They also enhance not only readers' understanding and use of data but also submitters' motivation to publish the data. The metadata are computationally shared among other systems via APIs, which facilitate the construction of novel databases by database developers. A permission system that allows publication of immature metadata and feedback from readers also helps submitters to improve their metadata. Hence, this aspect of Metabolonote, as a metadata preparation tool, is complementary to high-quality and persistent data repositories such as MetaboLights. A total of 808 metadata for analyzed data obtained from 35 biological species are published currently. Metabolonote and related tools are available free of cost at http://metabolonote.kazusa.or.jp/.

No MeSH data available.


Related in: MedlinePlus