Metadata
Metadata is information about the source of the DNA sequences (e.g., GPS coordinates, pH, patient, disease status, age, weight).
A. Metadata File Format
The top row of the metadata file specifies the names of the metadata categories for the project (e.g., library, specimen, time). One column must list library names exactly as they appear in the OTU file. This column maps the library names to the metadata values for that library. The column position of the library names within the metadata file does not matter, but the column must be present. The column fields must be delimited by either tabs, commas, or spaces.
B. Import Metadata
- Metadata import is fully incremental, so new metadata may be loaded at any time during the life of a project.
- Note: The import date, time, and file location of metadata are logged in Edit → Project Settings.
File → Import → Metadata
- Select file
Click Open
- A pop-up window will open
- The upper left pane of the window shows the metadata fields found by Explicet in the metadata file
When Libraries not found is selected, any libraries found in the metadata import file that are not in the project appear in the upper right pane.
When Libraries found is selected, any libraries found in the metadata import file that already exist in the project appear in the upper right pane.
By default, Add missing libraries to the project is deselected so that metadata import doesn’t force empty libraries into projects. By selecting Add missing libraries to the project, any library found in the metadata import file that is not in the project will be added to the project and populated with imported metadata. However, because there are no sequences associated with these libraries, the data columns will be filled with zeros in the hierarchy and OTU panes.
Metadata in the selected file that does not match the format of metadata already in the project appears in the bottom pane. For example, if “Age” is a metadata category containing numerical data, attempting to import text data into the “Age” category will be noted in the bottom pane.
- In the upper left pane, select the column that contains the library name
Click Import
A new pop-up window will open displaying the imported metadata, the details of which are presented in the following section. This window can be re-accessed via Data → Metadata.
C. Add New Metadata
- Instead of importing metadata from an outside source, the user can create new metadata from within Explicet.
Data → Metadata
- A window with three sections will open
The left pane: Defined Metadata, the right pane: Assigned Metadata, the bottom area: Metadata Definition. The bottom section, Metadata Definition, allows creation of new metadata fields.
Enter the desired name of the new metadata category next to the box labeled Name
Choose the Type of metadata from the drop down menu
String that may be more than 8 characters: words or strings of text longer than 8 characters (e.g., umbilicus)
String that is 8 characters or less: words or strings of text 8 characters or less (e.g., male)
64 bit Integer: whole number/number with no fractional part (e.g., 21, 4, or -2)
Double precision number: number with a fractional part (e.g., 3.75 or 5.5)
(optional) If there are only a few, distinct metadata values for the new definition, enter them as enumerated values; type each value under Enumerated Values, and click Add Value
To remove an enumerated value, select the value and click Remove Value.
To clear all enumerated values for a particular definition in one click, click Clear Values.
Click Add in bottom right corner to add the new metadata definition to Defined Metadata list
Select new metadata definition in the Defined Metadata pane
Click Add button between panes to add it to Assigned Metadata
For each library in the Assigned Metadata pane, enter the corresponding value
If Enumerated Values were entered, the values will appear in a drop down menu for each library.
To fill values for multiple libraries at once, use the Copy and Paste functions.
To select whole rows, click on the first value to select, then Shift-click on the last value; to select whole columns, click on the title of the column. Click the Copy button (the values are copied to an internal clipboard). To paste the copied values to other cells, select the cells you want to paste to, and click the Paste button. Note: If the clipboard contains a multi-row and/or multi-column selection, the number of rows and columns to paste to must match the number of rows and columns copied to the clipboard. If they don't match, an error message will appear, and nothing will be copied.
To copy one value to multiple cells, select the cell to copy, click Copy. Select the cells to paste to, click Paste.
Click Apply to keep the changes; click Done without clicking Apply to discard the changes
Note: All operations are performed on the libraries displayed in the Assigned Metadata pane. Only the libraries selected by the filter in the current workspace are shown in this pane. To edit all libraries in the project, instead of just those selected by the current filter, create a new workspace with No filter assigned.
D. Modify Current Metadata
To set or change values in the Assigned Metadata pane, click on the value to change, and type in a new value. If the metadata values are enumerated values, a drop down from which to pick one of the Enumerated Values will appear.
To modify an existing metadata definition, click on it in the Defined Metadata pane. Its definition will show in the box labeled Metadata Definition. Make any desired changes; change the Name, the Type, or add Enumerated Values, then click Replace. Keep the changes by clicking Apply.
To create new metadata from existing metadata, select the metadata in the Defined Metadata pane. The name MUST be changed. Then make any other changes to Type or Enumerations, and click Add.
Note: All operations are performed on the libraries displayed in the Assigned Metadata pane. Only the libraries selected by the filter in the current workspace are shown in this pane. To edit all libraries in the project, instead of just those selected by the current filter, create a new workspace with No filter assigned.
E. Export Metadata
- Metadata is exported as a tab-delimited (.txt) file. There are 2 different ways to export metadata:
1. File → Export → Metadata
- Enter desired metadata output file name and location
Click Save
2. Data → Metadata
Click Export in upper right corner of pop-up window
- Enter desired metadata output file name and location
Click Save
F. View Metadata
Data → Metadata
A window with three sections will open. The left pane, Defined Metadata, has the libraries and columns describing each metadata point associated. The right pane, Assigned Metadata, has the metadata titles. The bottom area, Metadata Definition, allows you to create new metadata fields (instead of importing them from elsewhere).
G. Remove Metadata Assignment
- This will remove the metadata assignment to the selected libraries shown in the Assigned Metadata pane.
Data → Metadata
- A pop-up window will appear
Select the unwanted metadata column in the right, Assigned Metadata, pane of the window
Click Remove button between panels
- A pop-up message will appear to warn you that you are about to delete data
Click OK to remove metadata
Note: Explicet does not store the metadata values for each library once it is removed from the Assigned Metadata pane and Apply is clicked. Therefore, if you decide to Add the metadata item back to Assigned Metadata after clicking Apply, the values for each library will appear blank.
H. Remove Metadata from Project
- This will remove a metadata definition from the project.
Data → Metadata
- A pop-up window will appear
Select the unwanted metadata item in the Defined Metadata pane of the window
Click Delete button to the right of the Metadata Definition
- A pop-up message will appear to warn you that you are about to delete data
Click OK to remove metadata