Premium Resource - Specimen functionality is a legacy feature available with Premium Editions of LabKey Server. For new installations, we recommend using
Sample Manager instead.
Learn more or
contact LabKey.
The simplest method for importing specimen data is to use a
Standard Specimen Repository and paste data from a simple specimen spreadsheet, described in this topic.
To instead use an advanced specimen repository and manage the transfer of specimens between labs, see the topic
Import a Specimen Archive.
Select Standard Specimen Repository
- On the Study project home page, select the Manage tab.
- Under Specimen Repository Settings, click Change Repository Type.
- Select Standard Specimen Repository.
- Click Submit.
Import Specimen Spreadsheet Data
- Go to the Study project home page and select the Specimen Data tab.
- In the Specimens web part, expand the Administration section.
- Click Import Specimens to open the Upload Specimens page.
Show Expected Data Fields
To view data fields expected in the upload, click
Show Expected Data Fields.
This will expand a display of column names, types, brief descriptions, and whether the field is required for a successful upload. If your study is set up to use visits instead of date-based timepoints, you will see a
Visit field here in addition to
Draw Timestamp and draw timestamps will not be required.
Note that in cases where the Sample ID and/or Participant ID are the same as your Global Unique ID, you need only supply the Global Unique ID and leave the others null. They are still required fields, but will be populated on import automatically.
Download a Template Workbook
- Click Download a Template Workbook.
- Open the downloaded spreadsheet to confirm that your column headings match those in the template.
- Copy and paste your data into this template spreadsheet. In practice, you could download this template in advance and enter the original data into it.
- Note: if you would like to include location information on your uploaded spreadsheet, see the instructions below for how to add a lab column to hold this information.
Download and view the specimen template here:
specimen_template.xlsAn example of entering data into the template, some optional fields have been omitted for brevity:
| global_unique_specimen_id | specimen_number | draw_timestamp | visit_value | ptid | volume | volume_units | additive_type |
|---|
| vial1 | 101 | 10/10/2010 | 1 | pt101 | 10 | mL | Whole Blood |
| vial2 | 102 | 10/11/2010 | 1 | pt102 | 10 | mL | Whole Blood |
| vial3 | 103 | 10/12/2010 | 1 | pt103 | 10 | mL | Whole Blood |
Simpler, alternative templates for testing:
| vial id | ptid | visit | date |
|---|
| v1 | 101 | 1 | 10/10/2010 |
| specimen_number | ptid | visit | date |
|---|
| v2 | 101 | 1 | 10/10/2010 |
Select Replace or Merge
When uploading specimen data from a spreadsheet, you can either replace the existing repository with the new data, or merge new data into the existing repository. The
Merge option will use the primary key to determine if a row is in the repository already. If so, it will delete and replace it. Otherwise, it will add new rows but leave any unchanged rows in place.
Warning. Specimen import via
Replace replaces all specimens in the repository with a new list of specimens. Make sure not to accidentally delete needed specimen information when importing new specimen records.
Copy and Upload Data
- Copy the contents of the filled-in template file and paste this data into the text box on the Upload Specimens page.
- Select Replace or Merge, and click Submit.
- When the import is complete, click Specimens to see a grid view of all imported specimens.
Add Lab Information to Spreadsheet
The default template does not include a column for specifying a laboratory ID, but support is included for this field. To add location information to the spreadsheet:
- The field name should be "lab" (lower case, no quote marks).
- The value should be the text name of the lab, e.g. ABC Lab (no quotes are permitted in a TSV file). If any value in the name column is new, a new location will be added to the Locations table.
Customize Specimen Repository Data Fields
To add additional fields to the default Specimen Repository:
- Switch the repository to an advanced repository.
- Update the Specimen repository with the desired additional fields (aka, "properties").
- If desired, switch back to a basic repository. (This is an optional step.)
- Now, when importing specimen data, additional fields in your spreadsheet will be captured by the new properties in the specimen repository.
