Managing Sample Metadata

Each project in IRIDA may contain a collection of samples that corresponds to an isolate. Each sample can contain an indefinite number of metadata terms.

Viewing and modifying metadata on a sample

Metadata can be viewed and modified on the individual sample.

Bulk import of metadata for samples within a project

Administrators and project managers can directly upload Excel spreadsheets of metadata directly to a project. It is expected that one of the columns in the spreadsheet will map to the sample name within IRIDA, this can be selected at upload time.

Links to the upload page can be found:

  1. On the Project > Samples page, under the Sample Tools dropdown menu:
    Bulk upload on project sample page under sample tools menu.

  2. On the Project > Linelist page:
    Bulk upload on project linelist page using link.

Please not that this feature is still under development.

Excel Spreadsheet Example

Any excel spreadsheet containing metadata for samples in a project can be uploaded through the IRIDA web interface. One of the column in the table must correspond to the sample name within the project. In this example spreadsheet, the NLEP # column is the sample name.

THe first step is to select the Excel file containing the data. Either click on the square label Click or drop Excel file containing metadata for samples in this project. or drag and drop the file from your file browser.

Select spreadsheet

After uploading a spreadsheet, the column corresponding to the sample name must be selected. After selecting the column heading, press the Preivew metadata to be uploaded button.

Select name column.

Before the metadata upload is completed, metadata that matches sample names and ones that don’t are presented.

Preview Upload

Metadata that has a matching sample name are listed in the table Rows matcthings samples with the number of matching samples. Clicking on the Save valid metadata button will add the metadata to it’s sample and redirect to the linelist page.

Upload Preview Success

Metadata that do not have matching sample names are listed in the table Rows not matching samples with the number of non-matching samples. Currently nothing can be done about these. Try to check the sample names and re-importing the spreadsheet.

Upload Preview Errors

Example Upload

Demonstration of uploading Excel Spreadsheet

Project Metadata Line List

Line lists are tables that summarize the available metadata for samples within a project. Only samples that have associated metadata will not be shown in this table.

Basic Line List

Reorder Columns

To make it easier to see related information, columns can be re-ordered by dragging the the column header to the required position.

Line List Reorder

Toggle Metadata Columns

Some columns might not have information that is useful in a particular analysis. You can toggle any metadata field by clicking the Toggle Metadata Columns button, which will open a side panel where metadata fields can be toggled on and off.

Line List Metadata Toggle

Note: the first column cannot be toggled off directly. If that field needs to be hidden, drag it to a different column and then toggle the field.

Toggling metadata column

Once all the column visibility has been set, click the close button at the top of the side panel to hide these options.

Closing metadata panel by clicking 'close' button

Saving Column Order and Visible Metadata

Updating the column order and which metadata is visible can be saved as a Template so that the next time the line list is viewed the same settings can be applied quickly. Click the Save Template button which will open a dialog window. Add a name for the template (this cannot match the name of another template within the project).

Save Template Dialog

The name given to the template should be descriptive and must be more than 5 letters. The name must also not be used for another template within the project.

A warning is displayed if the name given for the template is too short or if the name is already used for a template within the current project.

After a unique name with more than 5 letters is provided the Save button will become enabled. Clicking it will save the template to the project.

After a template is created it can me modified or deleted under Project Settings > Sample Metadata Templates

Exporting Data from Metadata Table

Data can be exported as either Excel or CSV formats. Ony the fields currently in the table will be exported.

Clicking on the Export button which will reveal a dropdown where you can select from either CSV or Excel, the download will begin automatically.

Export Buttons