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2

User Guide

3

Searching and Filtering

4

Creating an Account/Logging In

5

Customizing email notifications

6

Submitting new metadata

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FAQ

8

Contact Information

1

Terms and Conditions

User Guide

This user guide provides a step-by-step manual about how to navigate and use the features on metadatacommons.com.

Searching and Filtering


To browse and search for project metadata, navigate to the Search Metadata Commons tab.

Search for a specific project or keyword by typing in the search bar (typing in parts of words will yield results).

Advanced Search

Click 'Advanced Search Filters'

Search for a specific project or keyword by typing in the search bar, making sure to type in entire words or phrases (typing in parts of words will not yield results).

The total number of projects matching your search is displayed at the top.

Click the Reset button to remove your search and filter selections.

Scroll down to see the list of projects or to browse.

To download your search results, click the Download CSV | Download PDF buttons at the bottom.

Advanced Filters

Filter for desired sorting categories by using the left panel.

Selecting multiple options within a category increases the scope of your search (results matching any of your selected options within a category will be displayed).
For example, filtering for both end-stage organ failure and acute heart failure within Diseases returns all four projects that contain end-stage organ failure OR acute heart failure.

Selecting multiple options across categories decreases the scope of your search (results matching all your selected options across categories will be displayed).
For example, filtering for end-stage organ failure within Diseases and kidney samples within Samples returns one project containing both that disease AND that sample type.

For Cohort Size, enter your desired cohort size from smallest to largest (inclusive).

For all other filters, click Show All to see all filter selections.

Click the three dots symbol then click ‘Filter’ to type in and search for a specific filter selection, if one exists.

For Sample Type and Omics Type, note that the Metadata Commons was designed to support projects utilizing multiple omics types (multiomics), which is why each sample type has an omics type. However, the current filtering capabilities of the platform cannot filter for a sample type that belongs to a specific omics type and vice versa.
For example, if you try to specifically filter projects with whole blood samples focused on metabolomics, the projects that appear will necessarily have whole blood samples and metabolomics-related samples, but not necessarily have them paired.


Creating an Account/Logging In


No login is required, excepting for submitting metadata.

Step 1

Click the Login button on the top right of the page then click Register.

Step 2

Enter your details, acknowledge the terms and conditions, and click Create User.

Step 3

Navigate back to the login page by clicking the Back to Login button.
Enter your username and the temporary password sent to your email. Set a personalized password on the screen when prompted.

Step 4

To log in, click the Login button again. Enter your username and new password, then click the Sign In button.
If you would like to change your account email or delete your account, please contact us.

Customizing Email Notifications

Please note that if no selections are made, no email notifications will be sent.

Step 1

Log in, go to the top right from the home screen, and click on your username. Select User Preferences.

Step 2

Choose whether you want to be notified if any of your criteria are met by selecting “OR”, or if you want all your criteria to be met by selecting “AND”. An email will be sent to you whenever a new project is submitted that matches this criteria. Please note that if only "OR" is selected and no other selections are made, email notifications will be sent for every newly added project.

Step 3

To save your preferences, click the Apply Changes button. You will now receive an email whenever a new submission matching your criteria is published.

Submission


Please note that if you are not the principal investigator of the project you want to submit, it is your responsibility to get their approval.

Step 1. Go to the Metadata Submission page

On the Health Metadata Common’s Home page, go to the navigation menu on top of the page and click on the Metadata Submission tab. Note that users who are submitting metadata need to create an account and login before being able to access the submission page.

Step 2. Start a new submission

On the right of the Metadata Submission page, open a new submission form by clicking on the Start a New Submission button.

Step 3. Create your draft

The project title is the only information that is required at this step. Once your project title is typed in, click the Create button.

Step 4. Fill out the form

We encourage you to provide as much information on the form as possible to facilitate future potential collaborations.


On the Metadata Submission page, find your draft in the summary list.
Click the icon to edit your draft and continue filling out the submission form at any time.
To delete a draft, click on the Delete button at the top. This action is permanent.
Click the icon beside each field to view its help text.
Note that the required fields are indicated on the form with an asterisk (*).

The form consists of 3 main sections:
Project: Information related to the study, investigators, funders.
Cohort: Information related to the enrolled patients, disease/condition studied, types of clinical data collected. If there is no specific name for the cohort, please enter the same as for project title
Samples/Omics: Information related to the sample types and if applicable, the omics datasets. This section consists of two linked interactive grids, meaning that every sample type has its own omics datasets. Make sure to select the sample type before filling out the related omics information.

Each section has the following required fields:
# Field Name Details
1 Project Title Title or name of the project
2 Project Description Describe the study (maximum 4,000 characters)
3 Project Investigator(s) First and last names of each investigator (check box or type in)
4 Contact Email address of the project leader
5 Data Access Request URL to Data Access Request
6 Cohort Size Number of patients in the cohort (or estimate)
7 Enrollment City and Country Please specify where the patients have been enrolled
8 Disease/Condition studied Please check the box in the drop-down menu, or type in if absent
9 Sample Type Select from the drop-down menu or click '+' sign and type in, if absent
10 Omics Type Select from the drop-down menu or click '+' sign and type in, if absent
11 Omics sub-type Select from the drop-down menu or click '+' sign and type in, if absent

Either an email address or a URL to data access request is required. Not both.
Omics sub-type is required only if omics type is not equal to 'Not analyzed'

Step 5. Submit for approval

Before submitting for approval, make sure you have saved your last changes by clicking the Apply Changes button.
Click the Submit for Approval button to submit your metadata.
If any of the required fields are not completed, a window will pop up on the top right corner of the page and specify what information is missing.

Next Steps

  1. The administrators of the platform will be notified upon your submission and will review it within a week.
  2. The result of the review will be sent by email to the user account holder:
    1. Rejected: Suggestions will be provided, and the submission form can be edited before re-submission.
    2. Approved: A data sharing certificate will be attached to the email. If minor changes have been made, they will be specified in the body of the email.
  3. Once approved, the project becomes available to the public on the Home and Search pages.
  4. If you would like to edit your submission after it is approved, open your project from the Metadata Submission tab and click the Request Update button. Your project will be hidden from the public and available as a draft until re-submission.

Frequently Asked Questions

How much time does it take to fill out the submission form?
Depending on the scope of the project, it will take about 10 to 30 minutes. The submission can be saved as draft and edited as many times as needed before submitting it for approval. Only the submitter can see and edit the draft.

How long does it take for my submission to be approved?
It will take up to one week for the administrators to review your submission.

How can I know if my submission is approved?
An email will be sent to the project PI after review. The data entry status will be updated in the table on the Metadata Submission page.

How do I edit my submission after it has been approved?
Open your project from the Metadata Submission page and click the ‘Request Update’ button. Your project will be hidden from the public and available to edit as a draft. After you are satisfied with your edits, click ‘Submit For Approval’. Once the administrators review and re-approve your project, it will become visible to the public again.

How do I delete my account or change my email/login information?
To change your account information, please contact the administrators of the Health Metadata Commons by clicking ‘Contact Us’ and filling out the form, or by emailing metadatacommons@genomebc.ca.

Should I be worried about data and participant privacy if I have contributed my project?
Only your project’s metadata is available to the public after you have submitted to the Metadata Commons—we do not collect data from your study, samples, or individual participants. Metadata related to the cohort of patients are at an aggregated level, not individual level.

How do I obtain data from a project in the Metadata Commons?
Researchers interested in using data from a specific project should follow the ‘Data Access Request URL’ or click on the ‘Contact Investigator…’ button on the project page. If the omics datasets have been deposited into a repository, the accession number is provided in the project description or Omics section.

Contact Information

If you would like to provide feedback on Health Metadata Commons, click on the speech bubble icon on the top right of the page to send feedback directly.

To request for help or provide feedback to Health Metadata Commons, please contact us at metadatacommons@genomebc.ca or go to the bottom of the page and click Contact Us to fill out a contact form.

Terms and Conditions

Terms and Conditions 

Last revised, December 2024 

URL to webpage : https://metadatacommons.ca/ords/r/genomebc/hmc/documentation 

By using, accessing, and browsing the website, you accept and acknowledge, without limitation or qualification, that you have read, understood, and agree to be bound by the Terms. 

Overview & Purpose 

The Health Metadata Commons serves as a centralized hub, providing researchers with seamless access to a comprehensive repository of human biological samples and omic research metadata. Our overarching goal is to democratize access to genomic data, nurture collaborative endeavors, and expedite breakthroughs within the health sector. By consolidating metadata from Genome BC-funded projects and beyond, our mission is to empower stakeholders with a unified platform, fostering data exchange, amplifying the visibility of research endeavors, and spurring interdisciplinary cooperation. Through facilitating researchers access to pertinent datasets and biobanked samples, our endeavor is to hasten discoveries, validate hypotheses, and propel scientific advancement across the globe. 

Within the Health Metadata Commons, we cultivate a synergistic ecosystem where health researchers, clinicians, data scientists, funding entities, policymakers, and other stakeholders seamlessly discover and request access to pertinent health and omics data, alongside human biological samples. Our vision is to establish the bedrock for future omics research, dismantling barriers to accessibility, and championing cross-institutional collaboration. Emphasizing collaborative spirit, when data is shared through the commons, we encourage users to engage closely and share co-authorship on resultant findings and publications, thereby fostering a culture of inclusive scientific progress. 

Disclaimer 

Metadata is provided by investigators and research funders.  It is their responsibility to ensure that studies have been approved by the relevant research ethics board and information uploaded is correct. Genome BC does not verify that metadata provided is correct and complete beyond a limited validation for apparent errors or inconsistencies. 

Metadata Submission and Collection 

  • Users of the platform agree that no one associated with metadatacommons.ca, can be held responsible for your use of the information contained in or linked to this metadata. 
  • Intellectual property resulting from the research findings resulting from accessing samples and data through the Health Metadata Commons is at the discretion of the metadata submitters and requesters and should be decided prior to the data access taking place. 

Metadata submitters rights and responsibilities: 

  • Submitters are responsible for the accuracy and quality of the metadata provided.  
  • Submitters are responsible for ensuring the studies follow relevant laws and regulations and have obtained research ethics board approval for the research study. 
  • Submitters are responsible for updating their submission by contacting metadatacommons@genomebc.ca 
  • The Health Metadata Commons staff do not verify the scientific validity of the submission,  the accuracy of the metadata.  However, data validation is performed for apparent errors of inconsistencies of the submitted metadata. 

Metadata requesters rights and responsibilities: 

  • In the process of asking to access biological samples and data for a project listed in the Health Metadata Commons, requesters provide information to the data custodians about themselves, such as name, affiliation; what clinical or research questions will be asked of the requested data; whether the required ethics approvals have been obtained; and what samples and data they would like to access. 

Aggregated Metadata 

  • Metadata are aggregated at the cohort level and do not identify any individual. 
  • Metadata types: 
  • Project related information, including title, description, investigators, funders  
  • Patient cohort related information: aggregated data on what was collected from the patients, number of subjects enrolled, inclusion/exclusion criteria, enrollment city/country, types of clinical data collected  
  • Sample related information: sample type, sample size, sample collection method 
  • Omics related information: omics type and sub-type, number of samples profiled, experimental design, data repository link (if available) 

Metadata Approval Process and Release 

After submission, the metadata will be reviewed by the admin of the metadata commons who will approve or reject the submission with or without edits/changes. Once approved, the metadata submission is released and made public on the website. 

Data Access 

Access to the home page, search function and resources is free and public.  However, access to metadata submission requires log in. This function allows users to go back to their draft submission, modify as many times as needed and view all of their submitted projects and their status.  

Data Storage 

All metadata provided are stored permanently in the Health Metadata Commons but could be removed at the request of the submitter. 

References 

https://www.genomebc.ca/terms/ 

https://www.genomebc.ca/privacy/ 

How to cite Metadata Commons 

https://metadatacommons.ca 

Health Metadata Commons, Genome British Columbia, Vancouver, BC  

Please mention the HMC unique identifier of each project 

Contact Information 

For any questions or concerns regarding the Terms and Conditions, write to: metadatacommons@genomebc.ca 

Genome British Columbia 

400-575 West 8th Avenue 

Vancouver, BC V5Z 0C4 

604-738-8072