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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

Form-editing window of Metabolonote. (A) Metadata and attachment of additional information can be edited using forms. (B) The function “Search Ontology Terms,” available at the button represented by the red round circle in (A), is used to search for ontology terms in BioPortal in NCBO.
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Figure 3: Form-editing window of Metabolonote. (A) Metadata and attachment of additional information can be edited using forms. (B) The function “Search Ontology Terms,” available at the button represented by the red round circle in (A), is used to search for ontology terms in BioPortal in NCBO.

Mentions: Creation and editing of the metadata can be done via web browsers without installing any special software. Figure 3A shows a form-editing interface for an SE-instance with a minimized number of description items in TogoMD format. The submitters can search ontology terms in the BioPortal at the National Center for Biomedical Ontology (NCBO) (Whetzel et al., 2011) by clicking the “Search Ontology Terms” button (Figure 3B). Submitters currently do not have to use the proper ontology terms for fields such as species names, but the function helps to reduce incidents of misspelling of specific terms, and helps to query the ID in the Taxonomy database of the National Center for Biotechnology Information (NCBI) (Federhen, 2012). In the “Free text” area, submitters can attach additional information in HTML or MediaWiki’s markup language. This area can be used, for example, to make links to the record of other databases in which data related to the metadata are deposited. Metabolonote provides several wiki templates to facilitate the creation of links by users. To prevent inappropriate writing and the creation of links to malicious websites, only system administrators are currently allowed to change the public/private state of the metadata.


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)

Form-editing window of Metabolonote. (A) Metadata and attachment of additional information can be edited using forms. (B) The function “Search Ontology Terms,” available at the button represented by the red round circle in (A), is used to search for ontology terms in BioPortal in NCBO.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Form-editing window of Metabolonote. (A) Metadata and attachment of additional information can be edited using forms. (B) The function “Search Ontology Terms,” available at the button represented by the red round circle in (A), is used to search for ontology terms in BioPortal in NCBO.
Mentions: Creation and editing of the metadata can be done via web browsers without installing any special software. Figure 3A shows a form-editing interface for an SE-instance with a minimized number of description items in TogoMD format. The submitters can search ontology terms in the BioPortal at the National Center for Biomedical Ontology (NCBO) (Whetzel et al., 2011) by clicking the “Search Ontology Terms” button (Figure 3B). Submitters currently do not have to use the proper ontology terms for fields such as species names, but the function helps to reduce incidents of misspelling of specific terms, and helps to query the ID in the Taxonomy database of the National Center for Biotechnology Information (NCBI) (Federhen, 2012). In the “Free text” area, submitters can attach additional information in HTML or MediaWiki’s markup language. This area can be used, for example, to make links to the record of other databases in which data related to the metadata are deposited. Metabolonote provides several wiki templates to facilitate the creation of links by users. To prevent inappropriate writing and the creation of links to malicious websites, only system administrators are currently allowed to change the public/private state of the metadata.

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