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Table of Contents

Info
titleFor Enterprise Edition Only

This feature is available only in the Enterprise Edition

Introduction

Using this plugin, super admins can update any dropdown list values in the application. To access, go to Home → Extras → Dropdown Manager.

Features include:

  1. Add a new dropdown
  2. Add new value
  3. Edit or delete existing values
  4. Import/Export values
  5. Set properties like units for specimen types, abbreviations, etc.

Add a new dropdown

...

Users can add a new dropdown altogether. Follow the below steps:

  1. Go to: Home → Extras → Dropdown Manager.
  2. Click on the "+Add" button.
    Image Removed
  3. Enter the value of the 3 mandatory fields present on the screen
    Unique ID: The unique attribute name of the dropdown. This is how the dropdown name will be saved in the database.
    This appears in brackets once you click on an existing dropdown
    Image Removed
    Name: Name of the dropdown
    Definition: Information regarding the dropdown
    The name and definition appear on the dropdown list page as follows
    Image Removed
  4. Fill in all the three values and click on Add.
    Image Removed

Add values

...

  1. Go to: Home → Extras → Dropdown Manager.

  2. Look for the field of interest.  E.g., 'Collection Container'.

  3. Click on the '+Add' to add new values.

Image Removed

...

If you want to assign a code to the value. E.g. SNOMED code, ICD code, or your own code (like 1 for Male, 2 for Female). If the concept code is set, it is displayed in the dropdown for that value. E.g.

Image Removed

This is useful especially in dropdowns like clinical diagnosis which has 1) a lot of values 2) standard vocabulary like SNOMED or ICD etc. During data entry, you can search by concept code rather than free text to avoid errors (since often you get SNOMED codes from the labs rather than text).

In the future, this will be available in the query interface to include the codes in the query results.

...

Warning
titleParent Dropdown in case of Specimen Type

In order to add a new specimen type, it is mandatory to add it under one of these 4 parent dropdowns: Cell, Fluid, Molecular, or Tissue. If you include it under any other parent class, there are some functionalities that might break.

Edit values

...

To edit, go to the overview page of the dropdown value and click 'Edit'. 

Image Removed

Delete values

Expand

Deleting of values is supported only if the value is not used. A value cannot be deleted if it is used in previous records.

To delete, go to the overview page of the dropdown value and click 'Delete'. 

Image Removed

To delete all the values in a dropdown, go to the required dropdown → click on "Delete All".

Image Removed

Archive values 

Expand

From v6.2, it is possible to archive the drop-down values which are no longer in use. To archive, a value, go to the overview page of the value and click 'Archive'. When a parent PV is archived, all its descendants are archived too.

Image Removed

Re-activate the archived values 

Expand

The archived values can be searched by selecting the activity status as 'Archived' in the search filter. 
Image Removed
To reactivate the archived value search the archived value and click 'Reactivate'.  

Image Removed

Import CSV

...

To add multiple values, OpenSpecimen supports the upload of these values. To add multiple values

  1. Click on 'Extras' → 'Dropdown Manager'.
  2. Click Import → Dropdown values.
  3. Download the template CSV file.
  4. Enter the details as mentioned in the below table. 
  5. Upload the file and click ' Validate and import'. 

Example CSV

Fields description

...

Attribute

...

Should be 'Active' while adding a value 

To delete: set to 'Disabled'.

To archive: set to 'Closed'

Properties

For some fields, there are extra properties that can be set. Below are the specimen-type properties

...

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

  • Tissue: gm
  • Fluid: ml
  • Molecular: µg
  • Cell: count

...

For example - µg/ml.

...

Table of Contents

Info
titleFor Enterprise Edition Only

This feature is available only in the Enterprise Edition

Introduction

Using this plugin, super admins can update any dropdown list values in the application. To access, go to Home → Extras → Dropdown Manager.

Features include:

  1. Add a new dropdown
  2. Add new value
  3. Edit or delete existing values
  4. Import/Export values
  5. Set properties like units for specimen types, abbreviations, etc.

Add a new dropdown

Expand


Users can add a new dropdown altogether. Follow the below steps:

  1. Go to: Home → Extras → Dropdown Manager.
  2. Click on the "+Add" button.
    Image Added
  3. Enter the value of the 3 mandatory fields present on the screen
    Unique ID: The unique attribute name of the dropdown. This is how the dropdown name will be saved in the database.
    This appears in brackets once you click on an existing dropdown
    Image Added
    Name: Name of the dropdown
    Definition: Information regarding the dropdown
    The name and definition appear on the dropdown list page as follows
    Image Added
  4. Fill in all the three values and click on Add.
    Image Added

Add values

Expand

  1. Go to: Home → Extras → Dropdown Manager.

  2. Look for the field of interest.  E.g., 'Collection Container'.

  3. Click on the '+Add' to add new values.

Image Added

FieldsDescription
Parent DropdownUsed only in the case of "Specimen Type" fields. This is to configure the parent-child relationship between dropdown values. 
Dropdown valueThe value of the field.
Concept code

If you want to assign a code to the value. E.g. SNOMED code, ICD code, or your own code (like 1 for Male, 2 for Female). If the concept code is set, it is displayed in the dropdown for that value. E.g.

Image Added

This is useful especially in dropdowns like clinical diagnosis which has 1) a lot of values 2) standard vocabulary like SNOMED or ICD etc. During data entry, you can search by concept code rather than free text to avoid errors (since often you get SNOMED codes from the labs rather than text).


In the future, this will be available in the query interface to include the codes in the query results.

PropertiesSome fields could have extra properties, like specimen type abbreviations, units, etc. Read the Properties section below.


Warning
titleParent Dropdown in case of Specimen Type

In order to add a new specimen type, it is mandatory to add it under one of these 4 parent dropdowns: Cell, Fluid, Molecular, or Tissue. If you include it under any other parent class, there are some functionalities that might break.


Add properties to the values

Expand

  1. Go to: Home → Extras → Dropdown Manager.

  2. Look for the field of interest.  E.g., 'Specimen Type'.

  3. Click on the '+Add' to add new values.

Image Added


Below are the specimen-type properties


Attribute
Property Name
Property Value
Description
Specimen TypeabbreviationAbbreviation for the specific specimen typeUsed for replacing the value of %SP_TYPE% token for specimen label auto-generation.
Specimen Typequantity_unitQuantity units for the specific specimen typeUsed 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:

  • Tissue: gm
  • Fluid: ml
  • Molecular: µg
  • Cell: count
Specimen Typequantity_display_unitQuantity display unit for the specific specimen typeUsed to display the units on the specimen pages. For example - µg. If both quantity_unit and quantity_display_unit are specified, quantity_display_unit is used to display unit in all pages.
Specimen Typeconcentration_unitConcentration unit for the specific specimen typeFor example - microgram/ml
Specimen Typeconcentration_display_unitConcentration display unit for the specific specimen type

For example - µg/ml.

Similar to quantity unit, concentration_display_unit is only used when special symbols or characters need to be displayed. If its only plain text, then specifying concentration_unit is sufficient.


Edit values

Expand

Since v6.2, editing of dropdown values is supported via Dropdown manager - even if it is already used. All the records are automatically updated if the value is already used.

To edit, go to the overview page of the dropdown value and click 'Edit'. 

Image Added

Delete values

Expand

Deleting of values is supported only if the value is not used. A value cannot be deleted if it is used in previous records.

To delete, go to the overview page of the dropdown value and click 'Delete'. 

Image Added

To delete all the values in a dropdown, go to the required dropdown → click on "Delete All".

Image Added

Archive values 

Expand

From v6.2, it is possible to archive the drop-down values which are no longer in use. To archive, a value, go to the overview page of the value and click 'Archive'. When a parent PV is archived, all its descendants are archived too.

Image Added

Re-activate the archived values 

Expand

The archived values can be searched by selecting the activity status as 'Archived' in the search filter. 
Image Added
To reactivate the archived value search the archived value and click 'Reactivate'.  

Image Added

Import CSV

Expand

To add multiple values, OpenSpecimen supports the upload of these values. To add multiple values

  1. Click on 'Extras' → 'Dropdown Manager'.
  2. Click Import → Dropdown values.
  3. Download the template CSV file.
  4. Enter the details as mentioned in the below table. 
  5. Upload the file and click ' Validate and import'. 

Example CSV

Fields description

Column nameDescription

Attribute

Attribute the name for which the value is to be added
ValueValue to be added
Parent ValueIn the case of specimen type, mention the class (parent)
Property#1#Name
Property#1#Value
Activity Status

Should be 'Active' while adding a value 

To delete: set to 'Disabled'.

To archive: set to 'Closed'

Properties

For some fields, there are extra properties that can be set. Please refer to the 'Add properties to the values' section

Export CSV (New in v6.1)

Expand

This is useful to move the dropdown values from test to production servers or use for reference during bulk imports. 

To export values for one or more fields, select the fields from the list and click on the 'Export' option:

Update Dropdown Values

Expand

To bulk update the concept code of existing PVs:

  1. Navigate to Extras → Dropdown. Export the PVs of one or more selected attributes.
  2. In the downloaded CSV file, change the values for the concept code.

  3. Click on Import → Dropdown Value → Upload the file as an update option.

To bulk update the properties of existing PVs:

  1. Export the PVs of one or more selected attributes.
  2. In the downloaded CSV file, change the values or properties of PVs.
  3. Upload the file as PV update option.

Example file: Update_DropDown.CSV

Info

Do not delete any columns from the exported file when importing for the update operation.


Bulk Delete

Expand

To bulk delete the value on the basis of identifier set activity status as "Disabled" in the exported file.

  1. Navigate to Extras → Dropdown. Export the dropdown whose values need to be deleted.
  2. In the downloaded CSV file, change the Activity Status to disabled → Import using Update Option.

Image Modified

Example file: Delete_Dropdown_Values.CSV

Changing Specimen Type's Units

Expand
  • Go to 'Dropdown Manager'. Select 'Specimen Type'
  • Search for the type 'Fixed Tissue Slide'
  • Click on it and 'Edit'
  • Add a new property for 'quantity_unit' and set it to 'microns' like below:

  • Once you update the type, refresh the data entry page once if you don't see the new values.

...

Expand

Below are the default values during installation. 

NameCodingPermissible Values
Anatomic SiteICD-O-3Permissible values for anatomic site
Specimen Type
Permissible values for specimen class-type
Clinical DiagnosisICD-10

Permissible Values File - SNOMED (before v2.2)

Permissible Values File - ICD 10 (since v2.2)

Frozen Event Methods
Permissible values


...