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Specimens CSV

Steps to Import CSV

  • Go to the collection protocols list page, click on the 'Import' button, and select option 'Biospecimen Data' OR

  • Go to the participants' list page of the CP whose specimens have to be created/updated, click on the 'More' button, and select 'Biospecimen Data'.

  • Select 'Specimens' from the 'Select Record Type' dropdown and click on 'Download Template File' to download the template file.

  • Enter all valid data in the template file as mentioned in the 'Data Dictionary' table below.

  • Upload the filled template file in the 'Input Records File' field, select 'Import Type' as 'Create' to create or 'Update' to update specimens or 'Update Else Create' to either create or update record. For the 'Update Else create' feature, please refer to Create & Update in Single Bulk Operation.

  • Click on the 'Validate and Import' button.

  • Refer'Import status'to check the status of the import job.

Sample CSV

Download

Moving Form Data while Moving Specimens

  • Export the form data for the specimens being moved. Refer to the wiki page for more information on exporting form data.

  • Move the specimen using bulk import update.

  • Delete the older form records to avoid confusion. For this, you can run a bulk import update by using the older record ID and activity status as 'Disabled'.

  • You have to choose 'Create' as bulk import type to move the forms data since you are creating new form records under the second CP. Using the form data exported in the first step, remove the record ID column.

Note:

Ensure that the form is attached to the CP at the required level.

Data Dictionary

Column Name

Datatype

Mandatory?

(Create)

Mandatory?

(Update)

Description

Permissible Values

Validations

Column Name

Datatype

Mandatory?

(Create)

Mandatory?

(Update)

Description

Permissible Values

Validations

Identifier

Number

No

Depends

System auto-generated unique number for every specimen.



Mandatory while updating specimen label

CP Short Title

String

Yes

Yes

The collection protocol short title under which specimen is collected



Mandatory while updating SR of a specimen.

Visit Name

String

Yes

No

The name of the visit under which the specimen has to be created.



It should be an existing visit name.

It can be blank if it is a specimen centric CP.

Specimen Requirement Code

String

No

No

Code defined in collection protocol for the corresponding specimen requirement.

If not specified, specimens are created as unplanned specimens.

For enabling CP encoding, please refer to the wiki page.



It should be a valid code defined in the CP.

If blank, the specimen will be collected as unplanned.



Specimen Label

String

Depends

Yes





It should be unique within the system or CP, depending on the system setting.

Mandatory when the auto-label generation is OFF OR 'Manual Input' is set to 'Yes'.

Note: For manual Input = Yes, make sure the label format matches with what is mentioned at CP/System level

Additional Label(V9.1.RC2)

String

Depends

Yes





It should be unique within the system or CP, depending on the system setting.

Mandatory when the auto-label generation is OFF OR 'Manual Input' is set to 'Yes.'

Barcode

String

No

No





It should be unique within the system.

Class

String

No

No



  • Tissue

  • Molecular

  • Cell

  • Fluid



Type

String

Depends

No



Permissible values for specimen class-type

  • Mandatory while creating unplanned specimens.

  • Field not applicable to the aliquot as aliquot type would always be same as that of parent

Lineage

String

No

No



  • New

  • Derived

  • Aliquot

  • This field cannot be edited once the specimen is created.

  • This field is case-sensitive.

Parent Specimen Label

String

No

No





Should exist within the same CP → Participant→Visit.

Mandatory in the case of derivatives and aliquots.

Anatomic Site

String

No

No



Permissible values for anatomic site



Default value: 'Not Specified'

Laterality

String

No

No



  • Left

  • Right

  • Not Applicable

  • Not Specified

Default value: 'Not Specified'

Collection Status

String

No

No



  • Collected

  • Pending

  • Missed Collection

Default value: 'Collected'

Pathological Status

String

No

No



  • Non-Malignant

  • Non-Malignant, Diseased

  • Pre-Malignant

  • Malignant, Pre-Invasive

  • Malignant, Invasive

  • Malignant

  • Metastatic

  • Not Specified

Default value: 'Not Specified'

Initial Quantity

Double

No

No







Available Quantity

Double

No

No

If not specified, it takes the same value as 'Initial Quantity.'





Concentration

Double

No

No







Quantity unit (v11.x)

-

No

No

Value will be auto-computed based on ‘Specimen type

 

 

Concentration unit (v11.x)

-

No

No

Value will be auto-computed based on ‘Specimen type

 

 

Biohazard

String

No

No

Multiple values can be specified as:

Biohazard#1,

Biohazard#2,

Biohazard#3 and so on

  • Hepatitis A

  • Hepatitis B

  • Hepatitis C

  • HIV

  • Tuberculosis



Freeze/Thaw Cycles

Integer

No

No

Number of freeze-thaw cycles





Created On

Date & Time

Depends

No

Needs to be entered for child specimens.



It takes the current date if left blank. Mandatory if creating child specimens

Note: Created On date for child specimens is the processing date for parent specimens.

Comments

String

No

No







Location#Container

String

No

No

Name of the container. It needs to be specified if the specimen is not virtually located.



  • It should be an existing container

  • Suitable to hold the specimen (based on type and protocol).

  • Should have available slots.

Location#Row

String

No

No





Position within the container in which the specimen is to be stored.

If left blank, the system will allocate the next available position.

Location#Column

String

No

No





Location#Position

Integer

No

No

Linear position in its parent container





Collection Event#Date and Time

Date & Time

No

No





If left blank, it will take the current date and time.

Collection Event#Comments

String

No

No







Collection Event#Procedure

String

No

No

The procedure used during specimen collection

  • Lavage Needle

  • Aspirate

  • Needle Core Biopsy

  • Venipuncture

  • Indwelling Catheter

  • Surgical Resection

  • Not Specified



Collection Event#Container

String

No

No

Type of container used for specimen collection

  • ACD Vacutainer

  • Citrate Vacutainer

  • CPT

  • EDTA Vacutainer

  • Heparin Vacutainer

  • No Additive Vacutainer

  • Paxgene

  • Serum Separator Vacutainer

  • Sterile Specimen Container

  • Streck

  • Not Specified



Collection Event#User#Email Address

Email Address

No

No





Should be an existing user

Received Event#Date and Time

Date & Time

No

No





Select the correct date and time format from UI based on the data in the file.

If left blank, it will take the current date and time.

Received Event#Comments

String

No

No







Received Event#Quality

String

No

No



  • Acceptable

  • Thawed

  • Frozen

  • Quantity Not Sufficient

  • Clotted

  • Hemolyzed

  • Lipemic

  • Cauterized

  • Hemorrhagic

  • Damaged

  • Unacceptable, Not Specified

  • Not Specified



Received Event#User#Email Address

Email Address

No

No





Should be an existing user

Activity status

String

No

No

Used to close or reopen the specimens in bulk

  • Active

  • Closed

  • Disabled

  • The value should be 'Disabled' to delete the specimens.

  • 'Disabled' status cannot be used when creating specimen.

  • Values are case-sensitive.

Checkout

 

No

No

Used to checkout the specimens in bulk. Refer to wiki page for more details.

  • TRUE/Yes

  • FALSE/No

 

Reason

String

No

No

Reason for closing the specimen





Created By#Email Address

String

No

No

Email address of the user who processed the sample



Should be an existing user

External IDs#1#Name

String

No

No

Additional Identifiers source





External IDs#1#Value

String

No

No

Additional IDs for specimen





Important points to remember about auto-generated formats (specimen label)

  1. Label formats take precedence where they are defined, in order: Specimen requirement > Collection Protocol > System

  2. If label format is left blank at SR/ CP level, it will still be validated against format defined in global 'Settings’

  3. User Inputs Allowed = Yes (for specimen labels) in CP settings does not bypass the validation if format is defined at any level.

Use '##set_to_blank##' for the fields which need to be updated to blank. 

Collection event and received event date/time fields of a collected specimen cannot be blanked out or set to empty. If you attempt to do that, no change is made. You can blank out dates for any custom field. (Make sure the form is attached to ALL CPs. Otherwise, it won't appear under the csv file.)



Got feedback or spotted a mistake?

Leave a comment at the end of this page or email contact@krishagni.com