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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

Metadata as a hub for other data resources. Examples of the metadata are shown: (A) Metadata for processed data obtained from Arabidopsis (SE1_S01_M01_D01, the original metadata are available at http://metabolonote.kazusa.or.jp/SE1:/S01/M01/D01). A reciprocal link is made with the mass spectrum database Bio-MassBank. (B) Metadata with a link to the comparable data (SE12_MS1, the original metadata are available at http://metabolonote.kazusa.or.jp/SE12:/MS1). (C) Metadata with images representing analytical procedures (SE37, the original metadata are available at http://metabolonote.kazusa.or.jp/SE37:/). The metadata are used as Supplementary Material in the research article. (D) Metadata with a picture of the sample (SE4, the original metadata are available at http://metabolonote.kazusa.or.jp/SE4:/).
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Figure 4: Metadata as a hub for other data resources. Examples of the metadata are shown: (A) Metadata for processed data obtained from Arabidopsis (SE1_S01_M01_D01, the original metadata are available at http://metabolonote.kazusa.or.jp/SE1:/S01/M01/D01). A reciprocal link is made with the mass spectrum database Bio-MassBank. (B) Metadata with a link to the comparable data (SE12_MS1, the original metadata are available at http://metabolonote.kazusa.or.jp/SE12:/MS1). (C) Metadata with images representing analytical procedures (SE37, the original metadata are available at http://metabolonote.kazusa.or.jp/SE37:/). The metadata are used as Supplementary Material in the research article. (D) Metadata with a picture of the sample (SE4, the original metadata are available at http://metabolonote.kazusa.or.jp/SE4:/).

Mentions: By adding extra information in the free text area, a metadata can become a hub with rich information about related data resources. Figure 4A is an example of metadata of computationally analyzed data obtained from the liquid chromatography–MS analysis of leaves of a model plant, Arabidopsis (SE1_S01_M01_D01). Several links to the other databases are attached. In Metabolonote, all of the metadata at the upper levels of the hierarchy are displayed as a single webpage. A link to PGDBj (Asamizu et al., 2014), which provides integrated information around plant genome data, is attached to the metadata of the sample set (SE). At the metadata of the samples, a link to the record of KomicMarket (Sakurai et al., 2014), the peak annotation database is present. For the analytical methods metadata, a link to the corresponding raw data in MassBase (Sakurai et al., 2014) is present. Links to two databases are attached to the data analysis procedures metadata; namely, Bio-MassBank8, the mass spectrum library from organisms, and KomicMarket2’s temporary website (KM2)9, which provides peak annotation data in TogoMD format. The metadata in Metabolonote is referred from the record pages in Bio-MassBank by a URL link, which complements the detailed description of metadata in Bio-MassBank. Figure 4B shows an attachment of a link to the other data resource that is comparable. Figure 4C is an example of the attachment of an image representing the process of data generation. Detailed information about the process in Metabolonote is referred as a Supplementary Material from Kera et al. (2014). A link to the article website is also attached. Figure 4D is another example of attachment of pictures for aiding understanding about the analyzed samples. This information aids in the reuse of published data by the readers. As shown in Figure 4, the metadata prepared by the submitters becomes a hub of related data resources, and give rich information to the readers.


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)

Metadata as a hub for other data resources. Examples of the metadata are shown: (A) Metadata for processed data obtained from Arabidopsis (SE1_S01_M01_D01, the original metadata are available at http://metabolonote.kazusa.or.jp/SE1:/S01/M01/D01). A reciprocal link is made with the mass spectrum database Bio-MassBank. (B) Metadata with a link to the comparable data (SE12_MS1, the original metadata are available at http://metabolonote.kazusa.or.jp/SE12:/MS1). (C) Metadata with images representing analytical procedures (SE37, the original metadata are available at http://metabolonote.kazusa.or.jp/SE37:/). The metadata are used as Supplementary Material in the research article. (D) Metadata with a picture of the sample (SE4, the original metadata are available at http://metabolonote.kazusa.or.jp/SE4:/).
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Figure 4: Metadata as a hub for other data resources. Examples of the metadata are shown: (A) Metadata for processed data obtained from Arabidopsis (SE1_S01_M01_D01, the original metadata are available at http://metabolonote.kazusa.or.jp/SE1:/S01/M01/D01). A reciprocal link is made with the mass spectrum database Bio-MassBank. (B) Metadata with a link to the comparable data (SE12_MS1, the original metadata are available at http://metabolonote.kazusa.or.jp/SE12:/MS1). (C) Metadata with images representing analytical procedures (SE37, the original metadata are available at http://metabolonote.kazusa.or.jp/SE37:/). The metadata are used as Supplementary Material in the research article. (D) Metadata with a picture of the sample (SE4, the original metadata are available at http://metabolonote.kazusa.or.jp/SE4:/).
Mentions: By adding extra information in the free text area, a metadata can become a hub with rich information about related data resources. Figure 4A is an example of metadata of computationally analyzed data obtained from the liquid chromatography–MS analysis of leaves of a model plant, Arabidopsis (SE1_S01_M01_D01). Several links to the other databases are attached. In Metabolonote, all of the metadata at the upper levels of the hierarchy are displayed as a single webpage. A link to PGDBj (Asamizu et al., 2014), which provides integrated information around plant genome data, is attached to the metadata of the sample set (SE). At the metadata of the samples, a link to the record of KomicMarket (Sakurai et al., 2014), the peak annotation database is present. For the analytical methods metadata, a link to the corresponding raw data in MassBase (Sakurai et al., 2014) is present. Links to two databases are attached to the data analysis procedures metadata; namely, Bio-MassBank8, the mass spectrum library from organisms, and KomicMarket2’s temporary website (KM2)9, which provides peak annotation data in TogoMD format. The metadata in Metabolonote is referred from the record pages in Bio-MassBank by a URL link, which complements the detailed description of metadata in Bio-MassBank. Figure 4B shows an attachment of a link to the other data resource that is comparable. Figure 4C is an example of the attachment of an image representing the process of data generation. Detailed information about the process in Metabolonote is referred as a Supplementary Material from Kera et al. (2014). A link to the article website is also attached. Figure 4D is another example of attachment of pictures for aiding understanding about the analyzed samples. This information aids in the reuse of published data by the readers. As shown in Figure 4, the metadata prepared by the submitters becomes a hub of related data resources, and give rich information to the readers.

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