Specimens CSV

Steps to Import CSV

 Expand...
  • 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)

DescriptionPermissible ValuesValidations
IdentifierNumberNoDependsSystem auto-generated unique number for every specimen.

Mandatory while updating.

CP Short TitleStringYesNoThe collection protocol short title under which specimen is collected

Visit NameStringYesNoThe name of the visit under which the specimen has to be created.
Should be an existing visit name
Specimen Requirement CodeStringNoNo

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.


Should be a valid code defined in the CP.

If blank, the specimen will be collected as unplanned.


Specimen LabelStringDependsYes

Depending on the system setting, it should be unique within the system or CP.

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

BarcodeStringNoNo

It should be unique within the system.
ClassStringNoNo
  • Tissue
  • Molecular
  • Cell
  • Fluid

TypeStringDependsNo
Permissible values for specimen class-type
  • Mandatory while creating unplanned specimens.
LineageStringNoNo
  • New
  • Derived
  • Aliquot
  • This field cannot be edited once the specimen is created.
  • This field is case-sensitive.
Parent Specimen LabelStringNoNo

Should exist within the same CP → Participant→Visit.

Mandatory in the case of derivatives and aliquots.

Anatomic SiteStringNoNo
Permissible values for anatomic site


Default value: 'Not Specified'

LateralityStringNoNo
  • Left
  • Right
  • Not Applicable
  • Not Specified
Default value: 'Not Specified'
Collection StatusStringNoNo


  • Collected
  • Pending
  • Missed Collection
Default value: 'Collected'
Pathological StatusStringNoNo
  • Non-Malignant
  • Non-Malignant, Diseased
  • Pre-Malignant
  • Malignant, Pre-Invasive
  • Malignant, Invasive
  • Malignant
  • Metastatic
  • Not Specified

Default value: 'Not Specified'

Initial QuantityDoubleNoNo


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

ConcentrationDoubleNoNo


BiohazardStringNoNo

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 CyclesIntegerNoNoNumber of freeze-thaw cycles

Created OnDate & TimeNoNoNeeds to be entered for child specimens.

It takes the current date if left blank.

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

CommentsStringNoNo


Location#ContainerStringNoNoName of the container. It needs to be specified if the specimen is not virtually located.
  • Should be an existing container
  • Suitable to hold the specimen (based on type and protocol).
  • Should have available slots.
Location#RowStringNoNo

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

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

Location#ColumnStringNoNo

Location#PositionIntegerNoNoLinear position in its parent container

Collection Event#Date and TimeDate & TimeNoNo

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

Collection Event#CommentsStringNoNo


Collection Event#ProcedureStringNoNoThe procedure used during specimen collection
  • Lavage Needle
  • Aspirate
  • Needle Core Biopsy
  • Venipuncture
  • Indwelling Catheter
  • Surgical Resection
  • Not Specified

Collection Event#ContainerStringNoNoType 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 AddressEmail AddressNoNo

Should be an existing user
Received Event#Date and TimeDate & TimeNoNo

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#CommentsStringNoNo


Received Event#QualityStringNoNo
  • Acceptable
  • Thawed
  • Frozen
  • Quantity Not Sufficient
  • Clotted
  • Hemolyzed
  • Lipemic
  • Cauterized
  • Hemorrhagic
  • Damaged
  • Unacceptable, Not Specified
  • Not Specified

Received Event#User#Email AddressEmail AddressNoNo

Should be an existing user
Activity statusStringNoNoUsed to close or reopen the specimens in bulk
  • Active
  • Closed
  • Disabled
  • The value should be 'Disabled' to delete the specimens.
  • Values are case-sensitive.


Reason

StringNoNoReason for closing the specimen

Created By#Email Address

StringNoNoEmail address of the user who processed the sample
Should be an existing user

External IDs#1#Name

StringNoNoAdditional Identifiers source

External IDs#1#Value

StringNoNoAdditional IDs for specimen

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.)