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Introduction

‘Specimen Type’ is an important dropdowndropdown defines the available list of specimens types. Each specimen type belongs to a 'Specimen class,' such as Fluid, Molecular, Tissue, Cell, and others. In the recent versions, OpenSpecimen has implemented customizations, like added the ability to create custom specimen classes and support for multiple specimen units per specimen type per Collection Protocol.

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Expand
titleClick to view steps to add new specimen class

  • Go to 'Dropdown Manager'. Select

  • Click on the 'Specimen Type' value

  • Click on 'Add'

  • Enter the Class name in ‘Dropdown value', leaving 'Parent Dropdown’ blank.

  • Add the mandatory properties: ‘quantity_unit', ‘concentration_unit’, and ’container‘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. E.g., μg/m3

By default, the units are set at 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

 

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From v11.0, you can create/update a list of the units you want to use in the system (Extras → Dropdown Manager → Specimen Unit). This list can be used to define specimen quantity/concentration units for specimen class/ type on system/CP level.

Note: After upgrading to v11, all the values present in the specimen type properties for quantity and concentration will be added to this list automatically.

Expand
titleClick here to view steps to add new units

  1. Navigate to Home → Extras → Dropdown Manager→ Specimen Unit

  2. You will be navigated to the below page which has all the units

image-20240516-065420.pngImage Added

Specimen Units (Define specimen class/ CP specific units)

From v11.0, 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 ‘ul’ vs ml ‘ml’ as units for fluids like serum/ plasma or capture quantity of DNA or RNA in ‘ul’ vs ‘ug’. With this feature, users can keep have the ability to configure the units specific per to each specimen type within one a single 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

  2. User will be navigated to the list of current unit setup. The units visible here are being populated from the list configured in the ‘Dropdown manager’→ ‘Specimen Unit’ attribute

    image-20240516-070631.pngImage Added

  3. In this list, users can edit any of the existing unit values by clicking on the edit icon

    Screenshot 2024-05-16 124620.pngImage Added

  4. Click on ‘Add’

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

  5. 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.pngImage Removed

CP level

  1. to setup new unit configuration

    new.pngImage Added

Specimen Class Units

  • To add units at the specimen class level across the system, select specimen class and units from the dropdown.

    image-20240516-072950.pngImage Added

Specimen Type Units

  • To add units per specimen type across the system, select specimen class and type and the units from the dropdown

    image-20240516-073548.pngImage Added

CP level

There are 2 methods to add the CP specific units

  1. Select the collection protocol from the list. Select specimen class and/or type for which you want to add quantity and concentration units.

    image-20240516-073922.pngImage Added

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

    Screen Shot 2024-04-17 at 5.00.32 pm-20240417-113101.pngFollow steps #2 and #3 similar to system level

Working with units for live clients

Expand
titleClick here to expand

  1. From v11.0 onwards, the system will automatically pick all the specimen units defined

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  1. for specimen

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  1. types in the dropdown manager to the specimen units

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  1. . Manual intervention is not required.

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

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    1. mechanisms: (cp, class, type)

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    1. → (cp, class, *)

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    1. → (*, class, type)

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    1. → (*, 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.

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

  3. 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

  4. There is no mechanism to allow the lab user to override the units for any particular or selected specimens. Any update to the unit applies to all the specimens of that type.

  5. On making any changes to the specimen units, please refresh your browser page once for the new configuration to be shown