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Table of Contents

Introduction

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

  • Go to the participants list page of the CP under which the participants, visits, and specimens have to be created, click on the 'More' button, and select the option 'Biospecimen Data'.

  • Select 'Master 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.
  • Upload the filled template file in the 'Input Records File' field.
  • Select the correct 'Date and Time Format.'
  • Click on the 'Validate and Import' button.
  • Refer 'Import status' to check the status of the import job.
  • You can both create and update records using the master template. If data already exists, the record is updated with the input specified in the CSV file. Otherwise, a new record is created.
Note
  1. If the visit name is not specified, all specimens within the same "collection date" will be collected under one visit.
  2. Specimen labels cannot be auto-generated if you are going to include rows for aliquots and derivatives within the same file.  i.e If labels are auto-generated, you need to upload parents and children in two different imports to export the labels generated from the first upload and use them as parent labels for uploading children.


Sample CSV

Download

Note
  1. You need to enter the actual PPIDs and Specimen labels when the auto-generation is disabled in bulk import. 
  2. When the tokens are specified at the collection protocol level, the PPID and specimen label can be left blank.
  3. When entering the 'Event Label,' OpenSpecimen will correctly recognize and group the specimens into visits based on the participant.
  4. Make sure all the dates use the same format throughout the BO file.
  5. From v10.3 the master specimen template can be used only to create/update participants and their respective visits, without any specimen data in it.

Data Dictionary

Column nameData type

Mandatory

(Create)?

DescriptionPermissible ValuesValidations
Collection Protocol (CP) Short TitleStringYesProtocol under which participants should be registered

Collection Protocol should exist within the system.

PPIDStringNoParticipant Protocol ID
  1. Blank - The New participant with auto-generated PPID is registered.
  2. Existing - Specimens will get collected under participants of specified PPID.
  3. New participant PPID - The new participant with specified PPID will be registered.

Registration Date

DateDepends

  1. The visit date value is taken if the registration date is not specified and the visit date is specified.
  2. The collection date value is taken if the registration date and the visit date are not specified.
  3. From v10.3 if the registration date is mandatory if creating only new participants 

First Name

StringNoFirst Name of the participant

Last Name

StringNoLast Name of the participant

Middle Name

StringNoMiddle Name of the participant

Date Of Birth

DateNoDate of Birth of the participant

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

Death Date

DateNo

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

Gender

StringNo
  • Female
  • Male
  • Unknown
  • Undifferentiated

Race#1StringNo

Add an extra column for the participant with multiple races. E.g.

Race#1, Race#2, etc.

  • American Indian or Alaska Native
  • Asian
  • Black or African American
  • Native Hawaiian or other Pacific Islander
  • Not Reported
  • Unknown
  • White

Vital Status

StringNo
  • Alive
  • Dead
  • Unknown
  • Unspecified

Ethnicity

StringNo
  • Hispanic or Latino
  • Not Hispanic or Latino
  • Not Reported
  • Unknown

SSNIntegerNo

Social Security Number for US locale.

National Identification Number for other countries.


It should be unique within OS.
eMPIStringNoEnterprise Master Patient Index
It should be unique within OS.

PMI#1#Site Name

StringNoThe site which issued the MRN
It should be an existing site within OS.

PMI#1#MRN

StringNoMedical Record Number (unique identification given by the site)
It should be unique within a site.

Event Label

StringYesDependsEvent Point Label from the protocol for which this event corresponds. E.g., baseline, surgery, etc.

If left blank, an unplanned visit is collected.


Visit Name

StringNoAuto-generated if left blank
It should be unique within OS.
Visit DateStringNo

If the visit date value is not specified, the system takes up the value of the collection date.


Collection SiteStringNoMaps to Visit site. It needs to be specified if no default is specified at the CP event level.

Visit StatusStringNo
  • Complete
  • Pending
Default: 'Complete'

Clinical Diagnosis

StringNo

Permissible Values File - SNOMED

Permissible Values File - ICD 10

Default: 'Not Specified'

Clinical Status

StringNo
  • No Diagnosis / Control
  • New Diagnosis
  • Pre-Therapy
  • Post-Therapy
  • Pre-Operative
  • Operative
  • Post-Operative
  • Remission
  • Relapse, Primary Site
  • Relapse, Distant Site
  • Relapse, Not Specified
  • Not Specified
Default: 'Not Specified'

Path. Number

StringNoSurgical Pathology Number
Default: 'Not Specified'

Visit Comments

StringNo


Specimen Requirement Code

StringNoCode defined in collection protocol for the corresponding specimen requirement.

If this is not specified, specimens are created as unplanned specimens.

For enabling CP encoding, please refer to the wiki page

Specimen LabelStringNoIt needs to be specified when the auto label generation is OFF OR 'Manual Input' is set to 'Yes.'
It should be unique within the system
BarcodeStringNo

It should be unique within the system
ClassStringDependsException- conditional mandatory filed
If 'Not specified' is selected in the 'type' field, in that case, the class field is mandatory.
  • Tissue
  • Molecular
  • Cell
  • Fluid

TypeStringYesDepends
Permissible Values FileFrom v10.3 mandatory only if creating specimens else optional
LineageStringNo
  • New
  • Derived
  • Aliquot
Default: New
Parent Specimen LabelStringNoRequired when creating child specimens

Anatomic SiteStringNo
Permissible Values FileDefault: 'Not Specified'
LateralityStringNo
  • Left
  • Right
  • Not Applicable
  • Not Specified
Default: 'Not Specified'
Pathological StatusStringNo
  • Non-Malignant
  • Non-Malignant, Diseased
  • Pre-Malignant
  • Malignant, Pre-Invasive
  • Malignant, Invasive
  • Malignant
  • Metastatic
  • Not Specified
  • Clinically normal

Default: 'Not Specified'

Initial QuantityNumericNo

Default units:

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

It should be greater than zero ("0")

Available QuantityNumericNo

Default units:

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

It should be greater than zero ("0")
ConcentrationNumericNo

Concentration units are

  • Cells: cells,
  • Tissue: µg/ml
  • Molecular: µg/ml

It should be greater than zero ("0")

Freeze/Thaw Cycles



NumericNoThe number of cycles carried out.

Created OnDate & TimeNo

Mandatory for child specimens.



CommentsStringNo


Collection Status



StringNoStatus of the specimen to be collected
  • Pending
  • Complete
  • Missed Collection
  • Not Collected

ContainerStringNoName of the existing container.
  1. The container specified should be existing.
  2. Suitable to hold the specimen (based on type and protocol)
  3. Should have available positions.
RowStringNo

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

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

ColumnStringNo

PositionIntegerNoUse this column if you do not use "row" and "column."
Collection DateDate & TimeYesDepends

Required for primary specimens.


From V10.3 collection date is mandatory while creating specimens else optional


Collection ProcedureStringNo
  • Lavage Needle
  • Aspirate
  • Needle Core Biopsy
  • Venipuncture
  • Indwelling Catheter
  • Surgical Resection
  • Not Specified

Collection ContainerStringNoType 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

CollectorEmail addressNo

Valid user
Received DateDate & TimeNoDate when specimens were received at the lab. If not specified, the current date/time is being used.



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

ReceiverEmail addressNo

Valid user

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  1. Enable 'CP Coding' from Settings
  2. Add specimen requirement code at the CP level for all the parent and child samples.
  3. Download the master specimen template from the user interface.
  4. Add the required data in their respective columns and codes in the 'Specimen Requirement Code' column.
  5. Create patient, visit, and primary specimens in one go using the master template, and for child specimens, create separate imports using a master template or specimen template. 
  6. If you receive information separately, it is easier to use separate templates:  Participant registrations, Visits, and Specimens.  The master template is used when participants visit, and specimens or visits and specimens under existing participants need to be created in one go.