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Introduction

‘Specimen Type’ is the most an important and specialized dropdown. Each specimen type corresponds belongs to a 'Specimen class,' such as Fluid, Molecular, Tissue, Cell, and others. In the recent updatesversions, OpenSpecimen has begun incorporating several frequently requested implemented customizations, like the ability to create custom specimen classes and support for multiple specimen units per specimen type per Collection Protocol."

Create a custom ‘Specimen Class’

Before v10.3, only 4 specimen class classes (Fluid, Molecular, Tissue, and Cell) were supported. From v10.3 onwards you can add different specimen class classes like plants, microbes, etc. depending on your requirementrequirements.

You can now classes from v10.3 onwards
Expand
titleClick to expand
to view steps to add new specimen
class

  • 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 the new class is added, this can be used as a ‘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, then it needs to be specified under quantity_display_unit. For eE.g., μg/m3

By default, the units are set at classes class level which will apply to all types under it:

  • Tissue: gm

  • Fluid: ml

  • Molecular: µg

  • Cell: count

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.x0 onwards, you can define a list of Units which configure the units 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.x0, 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 can keep the units specific per specimen type within one collection protocol.

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titleClick here to expand

Configure specimen quantity/ concentration units using the UI

System-level

  1. Navigate to Home → Extras → Specimen Units

    Screen Shot 2024-04-17 at 4.48.57 pm-20240417-111920.png

    Add

  2. Click on ‘Add’

    Screen Shot 2024-04-17 at 4.51.30 pm-20240417-112203.png

  3. Add all relevant values and add quantity and concentration units for any specimen class/ type for the selected CP.

    Screen Shot 2024-04-17 at 4.54.10 pm-20240417-112415.png

CP level

  1. Navigate to Home → Collection Protocols → View CP details → Settings → Specimen units

    Screen Shot 2024-04-17 at 5.00.32 pm-20240417-113101.png


    Follow steps #2 and #3 similar to system level

Working with units for live clients

  1. With From v11.x upgrade, 0 onwards the system will automatically pick up all the specimen units defined at individual specimen level levels in specimen units (dropdown as well as the Extras cardCP or system level). Manual intervention is not required.

  2. If units are updated after specimens are collected, then the existing specimens won't be automatically recalculated. E.g.For example, 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.

  3. Display the unit using the following logic:

    1. 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.

    2. 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.

  4. There is no support for displaying specimen units in the query results view nor in the query exported CSV

  5. 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

  6. 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 applies to all the specimens of that type.