Metabolonote
2016/06/22Web Site: http://metabolonote.kazusa.or.jp/
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/metabolonote/
A database specified for managing information on experimental methods (metadata) which is accompanied with the experimental data obtained from metabolomics studies.
README Content
1. Database Component
- README
- Sample Set (SE)
- Sample (S)
- Analytical Method (M)
- Data Analysis (D)
- Analytical Method Details (MS)
- Data Analysis Details (DS)
- Annotation Method (AM)
- Sample Preparation (SS)
- Experimental Conditions
2. Data Description
2.1 README
| Data name | README |
| Description of data contents | HTML file to describe "Metabolonote" data. |
| File | README_e.html(English) |
2.2 Sample Set (SE)
| Data name | Sample Set (SE) |
| Description of data contents | Information about a set of experimental data corresponding to the study purpose, including information regarding data interpretation and handling, such as which sample should be compared with which control, etc. |
| File | metabolonote_sample_set.zip (41 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Sample Set ID | Sample set ID |
| Title | Sample set name |
| Description | Describes important concepts for interpreting data, such as experiment purposes and relevancy between samples. |
| Authors | Author |
| Reference | Related reference information |
| Comment | Comment |
| Experimental Conditions | Link to Experimental Conditions (only in Simple search) |
2.3 Sample (S)
| Data name | Sample (S) |
| Description of data contents | Information about sample preparation methods. |
| File | metabolonote_sample.zip (110 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Sample Set ID | Sample Set ID ("Sample Set ID" and "Sample ID" are merged into "ID" in the Simple search.) |
| Sample ID | Sample ID ("Sample Set ID" and "Sample ID" are merged into "ID" in the Simple search.) |
| Title | Sample name |
| Organism - Scientific Name | Scientific name |
| Organism - ID | Classification ID of the organism. |
| Compound - ID | Compound ID |
| Compound - Source | Information about the availability of the reagent: the company name and catalog id. |
| Preparation | Growing methods, conditions, particular processing, sampling portions, sampling methods, and preparation methods for reagents |
| Comment | Comment |
| Analytical Method IDs | Link to Analytical Method (M) (only in Simple search) |
2.4 Analytical Method (M)
| Data name | Analytical Method (M) |
| Description of data contents | Information about methods of instrumental analysis. |
| File | metabolonote_analytical_method.zip (269 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Sample Set ID | Sample Set ID ("Sample Set ID", "Analytical Method ID" and "Sample ID" are merged into "ID" in the Simple search.) |
| Analytical Method ID | Analysis method ID ("Sample Set ID", "Analytical Method ID" and "Sample ID" are merged into "ID" in the Simple search.) |
| Title | Analysis method name |
| Analytical Method Details ID | Detailed analysis information ID (MS) applied. ("Analytical Method Details ID" and "Sample ID" are merged into "ID" in the Simple search.) |
| Sample Amount | An amount of sample used. This information is necessary for normalizing quantitative data to compare with other samples. |
| Comment | Comment |
| Data Analysis IDs | Link to Data Analysis (D) (only in Simple search) |
2.5 Data Analysis (D)
| Data name | Data Analysis (D) |
| Description of data contents | Information about data analysis methods by using computational tools, etc. |
| File | metabolonote_data_analysis.zip (444 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Sample Set ID | Sample Set ID ("Sample Set ID", "Data Analysis ID", "Sample ID" and "Analytical Method ID" are merged into "ID" in the Simple search.) |
| Data Analysis ID | Data analysis method ID ("Sample Set ID", "Data Analysis ID", "Sample ID" and "Analytical Method ID" are merged into "ID" in the Simple search.) |
| Title | Data analysis method name |
| Data Analysis Details ID | Detailed data analysis method information ID (DS) applied. ("Data Analysis Details ID" and "Sample ID" are merged into "ID" in the Simple search.) |
| Recommended decimal places of mass | Number of significant figures. |
| Comment | Comment |
2.6 Analytical Method Details (MS)
| Data name | Analytical Method Details (MS) |
| Description of data contents | Detailed information regarding analysis methods commonly applied to several analysis experiments, including information about what kind of devices were used under what kind of settings, etc. Referred to by M (Method of Instrumental Analysis information). |
| File | metabolonote_analytical_method_details.zip (73 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Sample Set ID | Sample Set ID ("Sample Set ID" and "Analytical Method Details ID" are merged into "ID" in the Simple search.) |
| Analytical Method Details ID | Detailed analysis information ID ("Sample Set ID" and "Analytical Method Details ID" are merged into "ID" in the Simple search.) |
| Title | Detailed analysis information name |
| Instrument | Instrument name and vendor name |
| Instrument Type | Instrument type |
| Ionization Method | Ionization method |
| Ion Mode | Distinction of positive analysis and negative analysis |
| Description | Details about methods of instrumental analysis. Describes all details regarding analytical instruments and analysis conditions. |
| Comment_of_details | Comment |
2.7 Data Analysis Details (DS)
| Data name | Data Analysis Details (DS) |
| Description of data contents | Detailed information regarding data analysis methods commonly applied to several data analysis cases, including information about what kind of software programs were used with what kind of parameters, etc. Referred to by D (Data analysis information). |
| File | metabolonote_data_analysis_details.zip (67 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Sample Set ID | Sample Set ID ("Sample Set ID" and "Data Analysis Details ID" are merged into "ID" in the Simple search.) |
| Data Analysis Details ID | Detailed analysis method information ID ("Sample Set ID" and "Data Analysis Details ID" are merged into "ID" in the Simple search.) |
| Title | Detailed analysis method information name |
| Description | Describes all details regarding data analysis methods such as software programs used and the parameters adopted. |
| Comment_of_details | Comment |
2.8 Annotation Method (AM)
| Data name | Annotation Method (AM) |
| Description of data contents | Information about method of metabolite peak annotation. |
| File | metabolonote_annotation_method_details.zip (26 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Sample Set ID | Sample Set ID ("Sample Set ID" and "Annotation Method Details ID" are merged into "ID" in the Simple search.) |
| Annotation Method Details ID | Annotation method ID ("Sample Set ID" and "Annotation Method Details ID" are merged into "ID" in the Simple search.) |
| Title | Annotation method name |
| Description | Describes details regarding annotation methods. Describes standards by which annotation has been assigned. |
| Comment_of_details | Comment |
2.9 Sample Preparation (SS)
| Data name | Sample Preparation (SS) |
| Description of data contents | Detailed information regarding sample preparations commonly applied to several samples, including information about growth conditions, drug treatments, etc. Referred to by S (Sample information). |
| File | metabolonote_sample_preparation_details.zip (13 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Sample Set ID | Sample Set ID ("Sample Set ID" and "Sample Preparation ID" are merged into "ID" in the Simple search.) |
| Sample Preparation ID | The sample preparation details ID ("Sample Set ID" and "Sample Preparation ID" are merged into "ID" in the Simple search.) |
| Title | Sample preparation name |
| Description | Details about sample preparation. In the case of biological samples, for example, details of growth conditions and drug treatments are described. Descriptions that depend on analytical methods should not be included here, and they should be included in the details of analytical methods (MS). |
| Comment_of_details | Comment |
2.10 Experimental Conditions
| Data name | Experimental Conditions |
| Description of data contents | It is the list of sample (S) with Analytical Method (M) and Data Analysis (D) etc. |
| File | metabolonote_experimental_conditions.zip (15 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Data Analysis ID | Data analysis method ID |
| Sample Set ID | Sample Set ID (Not shown in the Simple search) |
| Sample Set | Sample set name |
| Sample ID | Sample ID (Not shown in the Simple search) |
| Sample | Sample name |
| Analytical Method ID | Analytical Method ID (Not shown in the Simple search) |
| Sample Amount | An amount of sample used. |
| Sample Comment | Sample comment |
| Analytical Method Details ID | Detailed analysis information ID (MS) applied. (Not shown in the Simple search) |
| Analytical Method Details | Detailed analysis information name |
| Data Analysis Details ID | Detailed analysis method information ID (Not shown in the Simple search) |
| Data Analysis Details | Detailed analysis method information name |
| Recommended decimal places of mass | Number of significant figures. |
| Annotation Method ID | Annotation method ID (Not shown in the Simple search) |
| Annotation Method | Annotation method name |
| Sample Preparation ID | The sample preparation details ID (Not shown in the Simple search) |
| Sample Preparation | Sample preparation name |
3. License
Last updated : 2016/06/22
You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.
The license for this database is specified in the Creative Commons Attribution-Share Alike 4.0 International.
If you use data from this database, please be sure attribute this database as follows: "Metabolonote licensed under CC Attribution-Share Alike 4.0 International".
The summary of the Creative Commons Attribution-Share Alike 4.0 International is found here.
With regard to this database, you are licensed to:
- freely access part or whole of this database, and acquire data;
- freely redistribute part or whole of the data from this database; and
- freely create and distribute database and other adapted materials based on part or whole of the data from this database,
under the license, as long as you comply with the following conditions:
- You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any adapted material.
- You must distribute any adapted material based on part or whole of the data from this database under CC Attribution-Share Alike 4.0 (or later), or CC Attribution-Share Alike Compatible License (the list is here).
- You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.
Nozomu Sakurai
Kazusa DNA Research Institute
2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan
E-mail: metabolonote[at]kazusa[dot]or[dot]jp
4. Update History
| Date | Update contents |
|---|---|
| 2016/06/22 | Metabolonote English archive site is opened. |
| 2012/12/28 | Metabolonote (http://webs2.kazusa.or.jp/metabolonote/) is opened. |
5. Literature
Ara T, Enomoto M, Arita M, Ikeda C, Kera K, Yamada M, Nishioka T, Ikeda T, Nihei Y, Shibata D, Kanaya S and Sakurai N (2015)Metabolonote: a wiki-based database for managing hierarchical metadata of metabolome analyses.
Front Bioeng Biotechnol 3: 38
PMID: 25905099
6. Contact address
When you have any question about "Metabolonote", contact the following:
Kazusa DNA Research Institute
2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan
Tel: +81-438-52-3900
Mail: metabolonote[at]kazusa[dot]or[dot]jp