ArticleFrontiers in bioengineering and biotechnology2015
Metabolonote: a wiki-based database for managing hierarchical metadata of metabolome analyses.
Article in Frontiers in bioengineering and biotechnology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
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Who cites it
23 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of clinical metabolic profiling studies in cancer: challenges and opportunities.EMBO molecular medicine · 2016Pooled it
- Current status and challenges of multi-omics research using animal models of atherosclerosis.Journal of molecular and cellular cardiology plus · 2025Review
- MetaboSERV-a platform for selecting, exchanging, and visualizing metabolomics data with controlled data access.GigaScience · 2025Article
- The Thing Metabolome Repository family (XMRs): comparable untargeted metabolome databases for analyzing sample-specific unknown metabolites.Nucleic acids research · 2023Article
- iDMET: network-based approach for integrating differential analysis of cancer metabolomics.BMC bioinformatics · 2022Article
- A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics.Metabolites · 2022Review
- Development of RIKEN Plant Metabolome MetaDatabase.Plant & cell physiology · 2022Article
- Plants Metabolome Study: Emerging Tools and Techniques.Plants (Basel, Switzerland) · 2021Review
- Pharmacometabolomics by NMR in Oncology: A Systematic Review.Pharmaceuticals (Basel, Switzerland) · 2021Review
- Identification of potential biomarkers and metabolic pathways based on integration of metabolomic and transcriptomic data in the development of breast cancer.Archives of gynecology and obstetrics · 2021Article
- TOMATOMET: A metabolome database consists of 7118 accurate mass values detected in mature fruits of 25 tomato cultivars.Plant direct · 2021Article
- MassBase: A large-scaled depository of mass spectrometry datasets for metabolome analysis.Plant biotechnology (Tokyo, Japan) · 2021Article
- Metabolome analysis revealed that soybean-Aspergillus oryzae interaction induced dynamic metabolic and daidzein prenylation changes.PloS one · 2021Article
- Data Management and Modeling in Plant Biology.Frontiers in plant science · 2021Review
- Metabolome profile of Negi-Nira chive, an interspecies hybrid of green spring onion (Plant biotechnology (Tokyo, Japan) · 2020Article
- Metabolome analysis using multiple data mining approaches suggests luteolin biosynthesis inPlant biotechnology (Tokyo, Japan) · 2020Article
- Cloud-based archived metabolomics data: A resource for in-source fragmentation/annotation, meta-analysis and systems biology.Analytical science advances · 2020Article
- Metabolome Analysis Identified Okaramines in the Soybean Rhizosphere as a Legacy of Hairy Vetch.Frontiers in genetics · 2020Article
- Lipid remodeling regulator 1 (LRL1) is differently involved in the phosphorus-depletion response from PSR1 in Chlamydomonas reinhardtii.The Plant journal : for cell and molecular biology · 2019Article
- Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community.Metabolites · 2019Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
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/.
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