AMED Data Utilization Platform User Manual

1 Common Information

1.1 Access URL

1.2 Screen Configuration

Each function consists of the following screens. For operating procedures for each screen, see the relevant page.

1.3 Session Timeout

2 Login

2.1 Login

2.2 Logging in via GakuNin

2.2.1 Select Your Institution

Select the institution you belong to.
When selecting an institution, the login screen for the selected institution will appear.

2.2.2 Authentication by Your Institution

On the login screen of the selected institution, perform the login authentication process.
If the institution does not require two-factor authentication on the AMED Data Utilization Platform, login is successful when this authentication process succeeds, and the Dashboard (TOP) screen appears.
When performing authentication with another institution, if this authentication process succeeds you will be taken to the Enter Email Address screen or the Enter One-Time Password (OTP) screen.

(The Orthros authentication screen is showed here as an example. The actual screen layout and entry fields will vary depending on the institution selected.)

2.2.3 Enter Email Address

When logging into AMED Data Utilization Platform for the first time, the Enter Email Address screen may appear.
Depending on the settings of your institution, it may not be displayed.


When this screen appears, please enter the e-mail address you submitted to AMED Data Utilization Platform office when applying for use.
This screen is displayed only for the first login, it is not displayed for the second and subsequent logins.


Enter your e-mail address and click the Send button. You will be taken to the Enter One-Time Password (OTP) screen.

2.2.4 Enter One-Time Password

After successfully passing authentication procedures for institutions that requires two-factor authentication, you will be sent an email containing the one-time password to the registered email address. If authentication is successful after entering the one-time password, the Dashboard (TOP) screen will appear.

2.3 Logging In With SecurID (First-Time Login)

When logging in for the first time, you will be asked to register a passcode number.
Enter your login ID and the initial passcode number provided to open the Register Passcode Number screen.
Register your own passcode number. * Enter the passcode number registered for subsequent login attempts.
If authentication fails on any screen, you will be returned to the Login screen (Enter ID).

2.3.1 Login (Enter ID)

Enter your login ID and click the [LOGIN] button.
If authentication is successful, the Enter Passcode Number screen will appear.

2.3.2 Login (Enter Passcode Number)

After entering in the login ID, the initial passcode number authentication process will begin.
If authentication is successful, the Register New Passcode Number screen will appear.


Once the new passcode number is registered, enter the passcode number again.
*Enter the passcode number registered, not the initial passcode number.
If authentication is successful, the Enter One-Time Password screen will appear.

2.3.3 Login (Register a New Passcode Number)

Enter the passcode number to register, and then click the [REGISTER PERSONAL IDENTIFICATION NUMBER (PIN)] button.
If registration is successful, the Enter Passcode Number screen will appear.
Passcode numbers must satisfy the following requirements to be registered.
・Be 4 to 8 digits long, containing half-width numerals.
・Not match the three most recent passcode numbers used.

2.3.4 Login (Enter One-Time Password)

An email containing the one-time password will be sent to the registered email address.
If authentication is successful, the Dashboard (TOP) screen will appear.
*If you wish to change your email address, please contact your system administrator.

2.4 Logging In With SecurID (Subsequent Logins)

Enter the passcode number registered when logging in for the first time for subsequent login attempts.
Complete the authentication process using the one-time password sent to the email address registered with the system.
*If you forget your passcode number, please contact your system administrator to reset your passcode number.

2.4.1 Login (Enter ID)

Enter your login ID and click the [LOGIN] button.
If authentication is successful, the Enter Passcode Number screen will appear.

2.4.2 Login (Enter Passcode Number)

Enter the passcode number registered when first logging in, and then click the [SEND PERSONAL IDENTIFICATION NUMBER (PIN)] button.
If authentication is successful, the Enter One-Time Password screen will appear.

2.4.3 Login (Enter One-Time Password)

Complete the authentication process using the one-time password sent to the email address registered with the system.
Enter the one-time password, and then click the [SEND ONE-TIME PASSWORD(OTP)] button to login.
If authentication is successful, the Dashboard (TOP) screen will appear.

3 Common Features

3.1 Header and Menu

Each screen features a common header and menu.

3.1.1 Header

You can perform the following actions from the header.
・Display the main page of the Japan Agency for Medical Research and Development website in a separate tab.
・Open and close the menu bar.
・Switch the language display between Japanese/English
・Display a link to the User Details screen.
・Display the [Logout] button.

3.1.2 JA/EN Switch

3.1.3 Logout

Click the [Logout] button to logout. Logout after your work is complete.

3.1.4 Menu

You can jump to any screen from the menu.


See below for details on each screen.
・4 Dashboard (TOP)
・5.2 Metadata Search
・5.10 Metadata Aggregation
・5.11 Dataset List
・6.2 Specifying Search Conditions
・6.5 Downloads
・7 Notebook
・8 Data Management
・9 Information

3.2 Breadcrumbs List

A [breadcrumbs list] showing page navigation is located at the top of each screen to show which screen is currently displayed. Click a link in the [breadcrumbs list] to jump to the corresponding screen.


List of link destinations

Screen name	Link name	Link destination
Common to all screens	TOP	Dashboard (TOP)
Metadata Search screen	Genome & Omics Metadata	Menu(Genome & Omics Metadata)
Metadata Search Results screen	Genome & Omics Metadata	Menu(Genome & Omics Metadata)
	Metadata Search	Metadata Search
Metadata Details screen (shared data for each)	Genome & Omics Metadata	Menu(Genome & Omics Metadata)
	Metadata Search	Metadata Search
	Metadata Search Results	Metadata Search Results
Metadata Details screen (shared data for each)	Genome & Omics Metadata	Menu(Genome & Omics Metadata)
	Metadata Search	Metadata Search
Metadata Aggregation screen (from menu)	Genome & Omics Metadata	Menu(Genome & Omics Metadata)
Metadata Aggregation screen (from Metadata Search Results screen)	Genome & Omics Metadata	Menu(Genome & Omics Metadata)
	Metadata Search	Metadata Search
	Metadata Search Results	Metadata Search Results
Dataset List screen	Genome & Omics Metadata	Menu(Genome & Omics Metadata)
Dataset Detail screen	Genome & Omics Metadata	Menu(Genome & Omics Metadata)
	Dataset List	Dataset List
Specifying Search Conditions screen	Variant Allele Frequency Data	Menu(Variant / Allele Frequency Data)
Variant List screen	Variant Allele Frequency Data	Menu(Variant / Allele Frequency Data)
	Specifying Search Conditions	Specifying Search Conditions
Variant Details screen	Variant Allele Frequency Data	Menu(Variant / Allele Frequency Data)
	Specifying Search Conditions	Specifying Search Conditions
	Variant List	Variant List
Downloads screen	Variant Allele Frequency Data	Menu(Variant / Allele Frequency Data)

3.3 Sort and Pager

Various lists, such as Metadata Search Results and Dataset List, are equipped with a pager function.
In addition, tabular lists, such as Aggregation by subject and Dataset List, also have a sorting function.

3.4 User Details

Click the [User Details] button in the header to jump to the User Details screen. You can view details on the login user and upload a profile image on the User Details screen. Uploaded image files will appear in the header. The following restrictions apply when uploading files.

Item name	Restriction
File size	2 MB or less
File extensions	Only .jpeg, .jpg, and .png file extensions accepted
Vertical size of file	560 px
Horizontal size of file	420 px

The registered profile image will appear in the header.

4 Dashboard (TOP)

This screen will appear when first logging on, and when clicking the [TOP] link on the menu.
[1]Area for emergency news

-> See 4.1 Emergency News.

[2]Area for displaying menu of Dashboard

-> See 4.2 Menu(Dashboard).

[3]Area for displaying Metadata Summary Information

-> See 4.3 Metadata Summary Information.

4.1 Emergency News

This is used by AMED to issue urgent news to users, such as in the event of a system failure.

4.2 Menu(Dashboard)

Click the [START] button to navigate to any screen.


See below for details on each screen.
・5.1 Menu(Genome & Omics Metadata)
・6.1 Menu(Variant / Allele Frequency Data)
・7 Notebook
・8 Data Management
・9 Information

If your Notebook's user storage is running low, the Data Management menu will display the message "Disk space is full."

If you exceed the available storage limit, your device will be locked, and you will no longer be able to save, update, or perform other operations.
Please delete any unnecessary files immediately.
For detailed information, please refer to the Data Management manual.
・8 Data Management

If "Important notice(s)" is displayed in the Information menu, there is an Important News from the AMED Data Utilization Platform (CANNDs) Secretariat.
Click the [START] button to go to the Information screen and check “Important News.”

4.3 Metadata Summary Information

This displays aggregate graphs of the number of registered Metadata entries, "Age", "Diseases", "Region", and "Gender".
Click on an element in the graph or the aggregate table link to perform a Metadata Search using the selected element as a Search Condition.

5 Genome & Omics Metadata

5.1 Menu(Genome & Omics Metadata)

Click the [START] button to display any screen.


See below for details on each screen.
・5.2 Metadata Search
・5.10 Metadata Aggregation
・5.11 Dataset List

5.2 Metadata Search

Enter Search Conditions to search for Metadata.
The following three search methods are available.
・Searching by entering search keywords.
・Searching previously searched Metadata from saved Search Conditions.
・Searching previously searched Metadata from Search Condition History.
・Only displaying analysis data not tied to a sample.


Data Provider Institution


When detailed conditions are displayed

5.2.1 Search Target Metadata

5.2.2 Keyword Search (Synonyms)

This extracts data for any search target entered as a keyword in the top box.
This excludes data as a target for extraction for any search target entered as a keyword in the bottom box.
Example: When searching for the keyword ”cancer” by entering the word in the top box, data containing the word “cancer” in any search target, such as the title or abstract of a study, will be retrieved.
When entering the keyword ”cancer” into the bottom box, data containing the word “cancer” in any search target, such as the title or abstract of a study, will not be retrieved.
* For details on search target items in a keyword search, see 10.1 Search Target Items in a Keyword Search

If the [Search including synonyms] check box is selected, synonyms of the keyword entered will also be retrieved in a search.
Example: When entering the keyword “Alzheimer’s disease,” data corresponding to synonym keywords such as “Alzheimer’s” and “Alzheimer dementia” will also be retrieved.
If you do not wish to include synonyms in the search results, uncheck the [Search including synonyms] check box before performing your search.
Example: Entering the keyword “Alzheimer’s disease” and unchecking the [Search including synonyms] check box before performing the search will limit search results to data matching the keyword “Alzheimer’s disease,” without retrieving data containing keywords such as “Alzheimer’s” and “Alzheimer dementia.”

5.2.3 Keyword Suggestions

A list of disease names that partially match the keyword entered in the keyword field will appear as suggested keywords.

5.2.4 Check the Number of Search Results

Click the [CHECK THE NUMBER OF SEARCH RESULTS] button to check the number of Metadata entries matching the Search Conditions entered.

5.2.5 Search Using Saved Search Conditions

You can perform a search using previously saved Search Conditions.
[Number of Search Results] shows the number of matches retrieved when the search was previously saved. If Metadata was added or deleted since the search was performed, the number of matches shown may not match the current number of matches in search results.
Click the [DOWNLOAD THE SEARCH CONDITIONS] button to download the file in JSON format.
Click the [DELETE] button to delete saved Search Conditions.
* For more information on saving Search Conditions, see 5.3.1 Save Search Conditions

5.2.6 Search Condition History Search

You can perform searches using previously entered Search Conditions (five most recent Search Conditions).
Number of Search Results shows the number of matches retrieved when the search was previously performed. If Metadata was added or deleted since the search was performed, the number of matches shown may not match the current number of matches in search results.

5.2.7 Searching Analysis Data Not Tied to a Sample

5.3 Metadata Search Results

The Search Metadata screen displays a list of samples tied to extracted data.
Example: When searching for the keyword ”cancer,” matching data samples will appear when the keyword appears in the title, abstract, or other part of a study.

5.3.1 Save Search Conditions

5.3.2 Aggregate by Subject or Disease

5.3.3 Expand Synonyms

When performing a searching with the [Search including synonyms ] check box selected as described in 5.2.2 Keyword Search (Synonyms), you can check synonyms.
You can also search any synonym to search again.
Example: When entering the keyword “Alzheimer’s disease,” keywords such as “Alzheimer’s” and “Alzheimer dementia” will also be used as synonyms. To exclude “Alzheimer dementia” from the search results retrieved, uncheck the “Alzheimer dementia” check box and perform the search again to only retrieve data for “Alzheimer’s disease” and “Alzheimer’s.”


The screenshot below shows an expanded view.

5.3.4 Display Graph

This displays a graph that aggregate the Search Results.


You can click on an element in the graph to refine Search Results.
The Search Condition will be overwritten when the same condition is clicked in the graph.
(For check boxes, a search will be performed as though all conditions other than the selected condition have not been checked)
Example: When clicking Kanto in the Region graph, Kanto will be the only Region Search Condition selected, and a search will be performed with all check boxes other than Kanto unchecked.
Click the [Re-display of initial search results] button to redisplay the initial results before Search Results were refined.

5.4 Show Metadata Details - Sample

The Metadata Search Results screen displays sample data tied to the data selected.
*Sample is a general term used to refer to data containing anonymized information about a subject used for research purposes.

5.5 Show Metadata Details - Experiment

The Metadata Search Results screen displays experiment data tied to the data selected.
*Experiment is a general term used to refer to data containing information on experiment procedures, questionnaires, library information, sequencers, and other experiment information used in research.

5.6 Show Metadata Details - Study

The Metadata Search Results screen displays study data tied to the data selected.
*Study is a general term used to refer to research information, including the content of studies, research expenses, and publication information.

5.7 Show Metadata Details - Data

The Metadata Search Results screen displays study data tied to the data selected.
*Data is a general term used to refer to data containing raw data information on experiment results for a specific experiment.

5.8 Show Metadata Details - Analysis

The Metadata Search Results screen displays study data tied to the data selected.
*Analysis is a general term used to refer to data containing analysis result information, including experiment result analysis and sample information analysis.

5.9 Show Metadata Details - Analysis (No Association)

Here you can check a list of analysis data entries not tied to a particular sample. This screen can be reached by clicking the [Click here for Analysis data not associated with Sample (without SAMPLE_REF registration)] link on the Search Metadata screen.

5.10 Metadata Aggregation

This displays the number of metadata entries, aggregate graphs for “Age,” “Diseases,” “Region,” and “Gender,” and aggregation tables of metadata by subject or disease.
Click on an element in the graph or the aggregate table link to perform a Metadata Search using the selected element as a Search Condition.


Aggregation by Disease


Study Details

5.11 Dataset List

A list of research projects (datasets) registered in this system will be displayed.

5.12 Dataset Detail

This screen displays details for the research project (dataset) selected on the Dataset List screen.

6 Variant / Allele Frequency Data

6.1 Menu(Variant / Allele Frequency Data)

A list of menus related to variant/allele frequency will be displayed.


See below for details on each screen.
・6.2 Specifying Search Conditions
・6.5 Downloads

6.2 Specifying Search Conditions

Since the amount of variant/allele frequency data is extremely large, it is necessary to narrow down the range of data by specifying conditions before moving to the variant list.
On this screen, specify conditions to narrow down variant/allele frequency data.
After specifying the conditions, press either "Execute search in current tab" or "Execute search in new tab" to display the variant list screen.


Enter three characters or more of the gene to display suggestions.


You can select multiple options from the drop-down list.
Each Search Condition is applied using the AND condition. Multiple values selected from the drop-down list are searched using the OR condition.

6.3 Variant List

This shows a list of variants for the allele frequency data selected on the Specifying Search Conditions screen.
・If a variant does not exist in a biobank, the Alt allele frequency will display "N/A".
・If a variant exists in a biobank, but the number of its samples is too small to reach the minimum number needed for frequency information, the Alt allele frequency will display "N/A(※)".

6.3.1 Variant Filter

On the Variant List screen, you can apply filters to narrow down and sort data.
You can specify multiple filters, and you can refine searches using multiple filters using the AND condition.
Filters can be applied by either specifying filters by keyword, selecting filters from the drop-down list, or by using expressions.
To specify filters by keyword, either enter the filter in the Keyword field and press the ENTER key, or click the filtering icon.


For items specified by keyword, enter three characters or more of the gene to display suggestions.


You can select multiple options from the drop-down list.
Once selected, click the filtering icon to filter the data.
Each filter is applied using the AND condition. Multiple values selected from the drop-down list are filtered using the OR condition.


To apply filters using expressions, select the numerical symbol from the drop-down list, and then input the value in the Keyword field.
Press the ENTER key, or click the filtering icon in the Keyword field to filter variants by a expression of the “selected numerical symbol” + “input value”.
For example, if “≧” is specified as the numerical symbol, and “0.0001” is specified in the Keyword field, the expression becomes “≧0.0001”, and variants with an allele frequency of 0.0001 or greater will be retrieved.


By default, results are sorted in ascending order by Region. Click the filter item header to sort in ascending order for the item.
Click items sorted in ascending order again to sort them in descending order. Clicking the item once more will revert to sorting the item in ascending order again.

6.4 Variant Details

This shows details of variants selected on the Variant List screen.

The preset data provides stratified allele frequency by age group, gender, residence or birthplace, and disease name. (However, data on allele frequency is not provided where there are less than 100 samples).
Under Frequency at the bottom of the screen, click the “Disease” “ Gender,” “Age,” “Region,”, or “Genetic Ancestry Group” buttons to show/hide subsets other than Overall.


When Disease results are shown, you can filter results by a partial match of the disease name.

6.5 Downloads

You can download some of the files from the Sites-Only VCF displayed on the variant list screen.
You must agree to the terms and conditions to download these files.
Click the “Terms of Use” link and read through its contents.



To agree to its contents, select the “I have read and understand the Terms of Use.” check box.
Once this check box is selected, the files will be available to download.

7 Notebook

When you click Notebook on the menu, JupyterLab will open in a separate tab in your web browser.
You can perform simple data processing and analysis using Python and R on this screen.
JupyterLab will be started with the following settings.

Settings
CPU	4 vCPU
Memory	28 GiB
Auto Stop Time	300 minutes

If this amount of time has passed since startup, JupyterLab will automatically stop even in the middle of processing.
If it stops, please start JupyterLab again from Notebook in the menu.

The saved file can be downloaded from Data Management.

7.1 Notes When Using Jupyter Notebook

8 Data Management

This displays a list of files created in Notebook.
The displayed files can be downloaded or deleted.

Hidden files, whose filenames begin with a dot(.), are normally hidden. Checking the "Show hidden attribute files" option will display these hidden attribute files in the list.


If the total size of the stored files exceeds the warning size, a warning will be displayed and
you will receive an email notification with the subject line "【CANNDs】ストレージ使用量が上限に近づいています".
Please delete any unnecessary files.

If the total size of the stored files exceeds the maximum size, a warning will be displayed,
and you will receive an email notification with the subject line "【CANNDs】10GBの上限を超過したため、ストレージがロックされました【制限通知】".
Your account's storage functionality is temporarily locked, which restricts file operations and notebook launches.
Please contact the support desk to have the lock removed.

9 Information

You can find important news, news, manuals, and contact information here.

10 Supplement

10.1 Search Target Items in a Keyword Search

11 FAQ