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Concept and Features of Metabolonote

Metabolonote is a specialized database system that manages "metadata" accompanied with the experimental data of Metabolomics studies. This system aims to promote the publication and utilization of Metabolomics data by simplifying the metadata record process.

Structure and ID Notation

The structure of metabolomics metadata can be separated into several layers. Metabolonote manages metadata by separating it mainly into four layers, namely information about sample sets (SE), samples (S), analytical methods (M), and data analysis procedures (D). According to these layer structures, IDs are given to metadata. In order to learn more about browsing Metabolonote, check the rules for assigning IDs and information of how to name each Wiki page.

(Example) Metadata with the ID "SE1_S01_M01_D01" is described on the Wiki page entitled "SE1:/S01/M01/D01", which can be accessed through the following URL.

TogoMD: The Togo Metabolome Data Format

The hierarchical structure of Metabolonote is based on the Togo Metabolome Data Format (TogoMD) we defined.

Browsing Metadata

You can browse public metadata released on Metabolonote. The browsing screen follows the hierarchical structure of metadata. This section is mainly an explanation of how to view the screen.

Registering and Editing Metaata

You can register your own metadata by simply creating your own user account.

Creating a User Account

Registration and Editing of Metadata

Making Metadata Public/Private

Advanced Usage

Use of Data from the External System via API

Use of Application Programming Interface (API) provided by Metabolonote enables other databases and applications to program access Metabolonote data.

Setup of Metabolonote

The Metabolonote system is released and available free of charge. By downloading and setting up core programs, you can install the Metabolonote system on your own server. Moreover, by creating your own personal settings for properties, templates and forms, you can design a universal system that manages metadata of fields other than metabolomics.



Administrator's Manual

Related tools and links

KomicMarket2 Temporary Website

This site distribute the experimental data obtained by metabolomics analyses (such as peak lists, and MS/MS data) in the TogoMD format. The APIs of Metabolonote is used in the metadata search function of this site, and no management system of metadata are implemented there.


A simple web application written in PHP for demonstrating usage of Metabolonote APIs. Web sites that have metadata search functions like "KomicMarket2 Temporary Website" can be setup easily. Use for checking and testing the functions of Metabolonote APIs.

  Download      (44 KB)   


Find answers to commonly asked questions.


Development staff and research project contacts and information.

Personal tools
View and Edit Metadata