Introduction
‘Specimen Type’ is the most important and specialized dropdown. Each specimen type corresponds to a 'Specimen class,' such as Fluid, Molecular, Tissue, Cell, and others. In recent updates, OpenSpecimen has begun incorporating several frequently requested customizations, like the ability to create custom specimen classes and support for multiple specimen units per specimen type per Collection Protocol."
Create custom ‘Specimen Class’ (v10.3 onwards)
Before v10.3, only 4 specimen class (Fluid, Molecular, Tissue and Cell) were supported. From v10.3 onwards you can add different specimen class like plants, microbes, etc. depending on your requirement.
You can now add new specimen classes from v10.3 onwards
Go to 'Dropdown Manager'. Select 'Specimen Type'
Click on 'Add'
Enter the Class name in ‘Dropdown value', leaving 'Parent Dropdown’ blank.
Add the mandatory properties: ‘quantity_unit', ‘concentration_unit’, and ’container_color_coding’:
Once new class is added, this can be used as ‘Parent Dropdown' for new specimen types.
Below are the specimen-type properties
Attribute | Property Name | Property Value | Description |
|---|---|---|---|
Specimen Type | quantity_unit | Quantity units for the specific specimen type | Used to display the units on the specimen pages. Value can only be plain text. If special characters like symbols need to be used, it needs to be specified under quantity_display_unit. For e.g., μg/m3 By default, the units are set at classes level which will apply to all types under it:
|
Specimen Type | concentration_unit | Concentration unit for the specific specimen type | For example - microgram/ml |
Specimen Type | container_color_coding | The color representing the specimen class in the container location view | For example - background=red,opacity=0.5 |
Specimen Units (Dropdown)
From v11.x, you can define a list of Units which you want to use in the system. You can use the units defined in this dropdown to define specimen quantity/ concentration units for specimen class/ type on system/CP level.
Specimen Units (Define specimen class/ CP specific units)
From v11.x, OpenSpecimen supports specimen units per CP. A common issue for clients with multiple groups was to make units uniform across the collection protocols. E.g., some groups wanted to use ul vs ml as units for fluids like serum/ plasma. With this feature, users will be able to keep the units specific per specimen type within one collection protocol.
Configure specimen quantity/ concentration units using the UI
System level
Navigate to Home → Extras → Specimen Units
Add
Add all relevant values and add quantity and concentration units for any specimen class/ type for selected CP.
CP level
Navigate to Home → Collection Protocols → View CP details → Settings → Specimen units
Follow steps #2 and #3 similar to system level
Working with units for live clients
With v11.x upgrade, the system will automatically pick up all the specimen units defined at individual specimen level in specimen units (dropdown as well as the Extras card). Manual intervention not required.
If units are updated after specimens are collected, then the existing specimens won't be automatically recalculated. E.g., if blood is changed from ml to μL, then the system won't change the values proportionately to μL. 1 ml won’t be updated to 1000 μL automatically. Users will have to change it manually via bulk upload.
Display the unit using the following logic:
Use the units specified either at the CP level or system level using the following fallback mechanisms: (cp, class, type) -> (cp, class, *) -> (*, class, type) -> (*, class, *)
where * represents all of that category
E.g., (cp, class, *): All specimen types of a given class for a specific CP.When specimen type is changed, use the units specified either at the CP or system level for the selected type/class using the above mechanism.
There is no support for displaying specimen units in the query results view nor in the query exported CSV
Units are not stored with the specimen or specimen requirements. Their units are auto computed based on what is configured either at the system or CP level
There is no mechanism to allow the lab user to override the units for any particular or selected specimens. Any update to the unit is applicable to all the specimens of that type.