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Table of Contents

Steps to Import CSV

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titleExpand...
  • 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 the option '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 below 'Data Dictionary' table.
  • 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 import job.

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Column Name

Datatype

Mandatory?

(Create)

Mandatory?

(Update)

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

Should be blank during add.

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 LabelStringDependsYesMandatory when the auto label generation is OFF OR 'Manual Input' is set to 'Yes'
It should be unique within the system or within CP - depending on the system setting.
BarcodeStringNoNo

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

TypeStringYesNo
Permissible values for specimen class-type
LineageStringNoNo
  • New
  • Derived
  • Aliquot
  • This field cannot be edited once the specimen is created.
  • This field is case-sensitive.
Parent Specimen LabelStringNoNoMandatory in case of derivatives and aliquots.
Should exist within the same CP → Participant→Visit
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 & TimeNoNo


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 created the sample
Should be an existing user

External IDs#1#Name

StringNoNoAdditional Identifiers source

External IDs#1#Value

StringNoNoAdditional IDs for specimen


Note

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.)

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