Editing metadata

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Editing metadata
Steps to edit metadata

Overview

Once samples are uploaded into the CZ GEN EPI platform, you will manage your data through the Sample page (main dashboard). One of the things you can do is update sample metadata. Below are steps to edit metadata from your Sample page. The steps described below use examples from the SARS-CoV-2 workspace, but the same instructions apply to workspaces for other viruses.

After reading this user guide, you will be able to:

Understand which metadata can be edited
Edit metadata manually
Edit metadata by downloading, completing, and uploading a metadata template

If you need to update sample metadata within the CZ GEN EPI platform at any point, you can edit sample information from your Sample page. You will be able to edit the following metadata:

Public ID: Refers to an ID that will be visible to other groups if the data is public. Preferably, a GISAID ID or GenBank Isolate Name for SARS-CoV-2 or GenBank Accession ID for Mpox. Public IDs from GISAID or GenBank can be obtained after submitting samples to the GISAID or GenBank public repositories, respectively. However, if a GISAID or GenBank ID is not available, you will notice that the CZ GEN EPI platform will automatically generate a Public ID based on when the sample was uploaded (sequential number/year). Note that private samples will also receive a Public ID. However, private samples will not be visible to other groups. Since a GISAID or GenBank ID is the preferred Public ID, we encourage users to submit sequences to GISAID and/or GenBank and update sample Public IDs by editing metadata within the platform whenever possible. This is important given that GISAID and GenBank IDs are the only ones used to detect and remove duplicates from downstream phylogenetic analyses.
- - SARS-CoV-2 Public ID: Please provide the GISAID ID (e.g., hCoV-19/USA/MS-MSPHL-0012/2023) or GenBank Isolate Name without the "SARS-CoV-2/human" prefix that is commonly associated with isolate names. For example, for GenBank Isolate Name "SARS-CoV-2/human/AUS/VIC14483/2020", you should use "AUS/VIC14483/2020" as the Public ID.
  - Mpox Public ID: Please provide the GenBank Accession ID (e.g., NC_063383). Note that you have to strip the sequence version from the GenBank Accession ID. The sequence version is specified within accession IDs using a period followed by a version number. For example, for GenBank Accession ID "OP535341.1", you should use "OP535341" as the Public ID.
Collection Date: The month and year the sample was originally collected.
- Required format: YYYY-MM-DD
Collection Location: The location where samples were originally collected. Following the general format below will ensure that your specific location is found in the reference data from GISAID.
- General format: Continent or Region/Country/State or Province/Division. Examples:
  - North America/USA/California/San Francisco County
  - North America/USA/California
  - North America/USA/Illinois/Chicago
Sequencing Date: Optional entry specifying the month and year the sample was sequenced.
- Required format: YYYY-MM-DD
Privacy: You will be able to edit privacy settings for your samples under "Sample is Private". Remember that "Public" within CZ GEN EPI means that your data will be visible to groups or organizations with which you already have a data sharing relationship.

Steps to edit metadata

Select the samples you wish to edit and select "Edit Samples" from the "More actions" dropdown menu on the right-hand side of the Sample page.

Once you select samples to edit, you will be able to click on the "More Actions" dropdown menu on the right-hand side of the Sample page.

Select "Edit Samples" from the dropdown menu.
An "Edit Sample Metadata" dialog box will appear where you can edit selected samples.

Dialog box for editing metadata. Note that only selected samples will appear in the dialog box.

When editing metadata, remember to follow required formats for dates (YYYY-MM-DD) and locations (Continent or Region/Country/State or Province/Division). You can edit metadata through the "Enter Sample Metadata" dialog box in one of two ways:

1. Manually through the web interface (recommended when you have a small number of samples to edit)
2. By downloading, completing, and uploading a metadata table with updated information.

Entering updated metadata manually

If you only have a few pieces of metadata you wish to update, it’s usually easiest to use the CZ GEN EPI interface to edit those metadata entries. Edited fields within the table will be highlighted with a purple background for easy visualization. Once you finish updating the metadata within the provided entry fields, you will be able to save your edits. Note that once you save the edits, existing metadata will be replaced with the updated information.

Metadata entries can be directly edited through the web interface. Note that existing metadata will show on the entry fields. Only enter information for entry fields that need to be updated.

If applicable, you will be able to apply edits for a given field to all samples by clicking ‘Apply to All’. Once you finish updating the information you will be able to "Continue".

Review the updated metadata and accept the terms regarding sample privacy and CZ GEN EPI policies.

Once you accept the terms, you will be able to save the updated metadata. Note that once you save the updated information, the edited metadata will overwrite the existing data.

Message indicating that samples have been successfully updated. Click on "Go to Samples" to go back to the Sample page.

Downloading, completing, and uploading a metadata template with updated information

If you have a lot of metadata you wish to edit, we recommend that you update your metadata by downloading, updating, and uploading a metadata template. This would be an efficient way to update Public IDs if you now have GISAID IDs for your samples. To edit samples through a metadata template file:

Download the metadata template from the "Edit Sample Metadata" dialog box by clicking on "Download Metadata Template (TSV)"

Download metadata table template from "Edit Sample Metadata" dialog box.
When you open the downloaded metadata template file, you will notice that the file contains instructions, metadata fields, reference examples, and your selected samples.

Example downloaded metadata template after selecting 2 samples to edit.

Edit the metadata you wish to update on the downloaded metadata file and save it locally on your computer.

Example metadata template after editing information for "Sequencing Date" (edited information for both samples) and "Sample is Private" (edited privacy status for one sample). Blank metadata fields will retain the existing metadata on the platform and will not be edited.
Upload the updated metadata template by clicking the "Select Metadata File" icon within the "Edit Sample Metadata" dialog box.

To upload the updated metadata template, click "Select Metadata File" and select the saved metadata template file from the file browser.
If the metadata file upload is successful, you will be able to review the updated information through the web interface and continue on to save the changes. If you have trouble uploading the metadata file, see the updating metadata troubleshooting guide for common error and warning messages and how to resolve them.

After successfully uploading the metadata template file, continue to the next page to review the updated information and save changes.

Review the updated metadata and accept the terms regarding sample privacy and CZ GEN EPI policies. When there are changes to privacy settings you will see a warning message to highlight the changes. If you agree with the changes, continue to accept the terms and save the information.

Once you accept the terms, you will be able to save the updated metadata. Note that once you save the updated information, the edited metadata will overwrite the existing data on the platform.