Browsing Sample Sheets
This section details the user interface for browsing sample sheets in a project and accessing related files.
For modeling study data, SODAR uses the ISA-Tab model, which is a part of the ISA framework. In ISA-Tab, experiment data is grouped under an investigation into one or more studies, which in turn contain one or more assays. The data is generally visualized as spreadsheet-style tables for studies and assays. Basic knowledge of the ISA-Tab model is helpful in reading this part of the manual. For further information on providing ISA-Tab into SODAR, see Metadata Recording.
Upon entering the Sample Sheets app with existing sheets, you will see a tabular layout of study and assay tables along with a set of controls. In this view, one study is presented on each screen. In case of a project with multiple studies, they will appear as tabs in the navigation section.
From top to bottom, you will see the following elements:
- Navigation and Operations
This section contains a navigation menu for switching between studies and the sample sheet overview. The Sheet Operations dropdown lists actions to be performed depending on the user’s role in the project. Temporary status messages for e.g. editing are also displayed here.
- Study Title
The study title is displayed here. To the right hand side you will find a badge listing iRODS file statistics for the study. The rightmost buttons link out to iRODS storage on the study level.
- Study Table
The study table lists the study sources (e.g. patients or donors), sample collection processes and samples derived from the sources. The table header provides links for column visibility selection, table export as Excel and filtering visible table rows. The table itself displays tabular ISA-Tab data for the study table together with additional iRODS and IGV links.
- Assay Title
For each assay, the assay title is displayed. Similar to the study title, iRODS links on the assay level are included.
- Assay Shortcuts
The assay shortcuts card provides iRODS links to specific collections on the assay level.
- Assay Table
The assay table is similar to the study table, presenting processes and materials derived from the sample onwards.
Sheet Operations Dropdown
Operations to be performed on the project’s sample sheets can be found under the Sheet Operations dropdown. These actions will be detailed in further sections under the manual. An example of the dropdown can be seen below. Note that available operations depend on the user’s membership role in the project and the current status of the project sample sheets.
Study and Assay Tables
The study and assay tables follow ISA-Tab conventions with certain enhancements. Sources, samples, materials and processes are colour coded in the topmost table header to clarify navigation.
Tables offer the following functionality:
- Column Resizing
All columns in the tables can be freely resized by dragging on their edges.
- Row Sorting
Tables can be sorted by a specific column by clicking its header.
- Row Filtering
For filtering rows, a string can be entered into the Filter text input in the table header.
- Drag Selection
Multiple cells can be selected by holding down the left mouse button and “painting” cells. They can be copied into the clipboard with
In SODAR certain cells offer special notation of data:
- Cells with Units
Columns accompanied by units are grouped into a single column for display purposes. If the unit is set for a cell, it is displayed after the value using a different colour.
Contact columns are rendered as links to the contact email, if email is present in the values.
- HPO Terms
HPO terms are a special case, where a “copy to clipboard” button is included for copying the actual HPO term IDs, while the textual representations are displayed in the cell for users.
- External Links
The “external links” columns are a special case where key-value pairs are displayed as badges. If configured on the server side for a specific key, the badges will link out to the ID on the appropriate service.
- Simple Links
Generic text cells may also contain arbitrary hyperlinks which can target either internal or external resources.
Cells in file columns link out to iRODS files if present. For more details, see the “iRODS File Linking” section.
The maximum height of study and assay tables can be set in your user settings in the User Profile.
Toggling Column Visibility
Columns in a table can be displayed or hidden by the user. Not all available columns may be initially visible. For example, columns with no data appear hidden by default.
To choose which columns to display, click the eye icon in the table header, displayed in the screenshot below.
Clicking the button opens a modal in which you can hide or unhide columns using the accompanying checkboxes. Columns can be toggled individually or for an entire material or process. Name columns, or protocol columns in the case of unnamed processes, will always be displayed and can’t be hidden.
For assay tables, study table columns (up to sample) are hidden by default. However, they can be made visible as needed using the assay table’s modal.
Upon exiting the modal, your choices for column visibility are saved for the project. They will remain as previously set when you next navigate to the project, except if the sample sheets are replaced.
Filtering for specific columns in the modal can be done using the Filter text input in the modal title bar. For project owners and delegates, there is also a button for saving current column visibility choices as the default for all project members.
The overview tab displays additional information on the investigation, studies and assays, as well as statistics about the study contents.