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Hierarchical Structure of Metadata and Rules for ID Assignment

The structure of metabolomics metadata can be separated to several layers. Metabolonote manages metadata by separating it into four basic layers, namely information about sample sets (SE), samples (S), analytical methods (M), and data analyses (D). According to these layer structures, IDs are given to metadata.

(Example) Metadata assigned 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. http://webs2.kazusa.or.jp/metabolonote/index.php/SE1:/S01/M01/D01

Hierarchical Structure of Metadata

Metabolonote manages metadata for experimental data sets based on the hierarchical structure shown below. This structure is based on the Togo Metabolome Data Format (TogoMD) we defined.

 SE (Sample Set information)
  |- S (Sample information)
  |  |- M (Method of Instrumental Analysis information)
  |     |- D (Data Analysis information)
  |       (|- P (Peak information）*Not used in the Metabolonote)
  |- SS (Detailed information of Sample Preaparation)
  |- MS (Detailed information of Method of Instrumental Analysis)
  |- DS (Detailed information of Data Analysis)
  |- AM (Detailed information of Metabolite Annotation)

One sample set (SE) could include multiple samples (S), one sample could be analyzed by multiple instruments and their settings (M), and one analytical data could be processed by multiple computational tools (D) to generate peak data (P).

ID Label	Classification	Description
SE	Sample Set information	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.
S	Sample information	Information about sample preparation methods.
M	Method of Instrumental Analysis information	Information about methods of instrumental analysis.
D	Data Analysis information	Information about data analysis methods by using computational tools, etc.
P	Peak information	Information about metabolite peaks obtained by data analysis. (This class is not used in Metabolonote, defined for databases that store peak information)
SS	Detailed information regarding sample preparation Analysis details information	Detailed information regarding sample preparations commonly applied to several samples, including information about growth conditions, drug treatments, etc. Referred to by S (Sample information).
MS	Detailed information regarding Method of Instrumental Analysis	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).
DS	Detailed information regarding Data Analysis	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).
AM	Annotation Method information	Information about method of metabolite peak annotation Referred to by P (Peak information).

Rules for ID Assignment

The ID label on each layer (see table above) is numbered and connected with an underscore in accordance with the hierarchical structure. This becomes the ID of each set of metadata.

(Example)

Metadata ID	Description
SE1_S01	Information regarding the sample S01 preparation.
SE1_S01_M01	Information regarding the method of instrumental analysis of the sample S01. Raw data file obtained through the analysis is accompanied by this metadata.
SE1_S01_M01_D01	Information regarding the computational analysis of data obtained by M01. In databases storing peak data, information regarding each peak is accompanied by this metadata.

Numbering

The system administrator assigns the appropriate serial number for SE when data is released. A tentative ID is used instead while data is being prepared by the user.

When it comes to other classifications (S, M, D, MS, DS, AM), a user can assign any serial number that is not used on the same layer. Zerofill can be used in the serial number. However, for example, M01 would be distinguished from M1.

ID Notation in Metabolonote

Page Title

In Metabolonote, page titles are represented in the MediaWiki page scheme, as shown below.

(Example)

SE1:/S01/M01/D01

Describing the URL as shown below can create a link to the corresponding page.

http://metabolonote.kazusa.or.jp/SE1:/S01/M01/D01

ID Specification by Using API

When retrieving metadata information via API, describe the URL using the ID connected with underscores, as shown below.

http://metabolonote.kazusa.or.jp/mnapi.php?action=getDataByMetadataID&id=SE1_S01_M01&output=xml
http://metabolonote.kazusa.or.jp/mnapi.php?action=getDataByMetadataID&id=SE1_S01_M01_D01&output=txt

See here for details about API.