Metabolonote


25905099	Metabolonote: a wiki-based database for managing hierarchical metadata of metabolome analyses. [PMID: 25905099] Ara T, Enomoto M, Arita M, Ikeda C, Kera K, Yamada M, Nishioka T, Ikeda T, Nihei Y, Shibata D, Kanaya S, Sakurai N. 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/. Front Bioeng Biotechnol. 2015:3() \| 21 Citations (from Europe PMC, 2025-03-22)

Metabolonote: a wiki-based database for managing hierarchical metadata of metabolome analyses. [PMID: 25905099]

Ara T, Enomoto M, Arita M, Ikeda C, Kera K, Yamada M, Nishioka T, Ikeda T, Nihei Y, Shibata D, Kanaya S, Sakurai N.

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/.

Front Bioeng Biotechnol. 2015:3() | 21 Citations (from Europe PMC, 2025-03-22)

URL:	http://metabolonote.kazusa.or.jp
Full name:
Description:	Metabolonote is a specialized database system for metadata management. This system aims to promote the publication and utilization of metabolomics data by simplifying the metadata record process. Separation of the management of metadata from experimental data has the following two advantages: (1) Multiple databases can share the same metadata, and (2) Data can easily be publicized.
Year founded:	2015
Last update:
Version:
Accessibility:	Accessible
Country/Region:	Japan

Data type:	Other
Data object:	Animal
Database category:	Raw bio-data
Major species:	Homo sapiens
Keywords:	meta data

University/Institution:	Kazusa DNA Research Institute
Address:	Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Japan
City:
Province/State:
Country/Region:	Japan
Contact name (PI/Team):	Takeshi Ara
Contact email (PI/Helpdesk):	ara@kais.kyoto-u.ac.jp

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Database Commons a catalog of worldwide biological databases