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Table of Contents

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  • 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 under which the participants, visits, and specimens have to be created, click on the 'More' button, and select 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 parent and children in two different imports so that you can export the labels generated from first upload and use as parent labels for uploading children.


Sample CSV

Download

Note
  1. In bulk import, you need to enter the actual PPIDs and Specimen labels when the auto-generation is disabled. 
  2. When the tokens are specified at the collection protocol level, the PPID and specimen label can be left blank.
  3. When you enter 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.

Data Dictionary

Column nameData type

Mandatory

(Create)?

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

Collection Protocol should be existing 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

DateNoCan be left blank if PPID is specified.Depends

Mandatory for registering new participants. 

First Name

StringNo


Last Name

StringNo


Middle Name

StringNo


Date Of Birth

DateNo



Death Date

DateNo



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.


Should be unique within OS
eMPIStringNoEnterprise Master Patient Index
Should be unique within OS

PMI#1#Site Name

StringNoThe site which issued the MRN
Should be an existing site within OS

PMI#1#MRN

StringNoMedical Record Number (unique identification given by the site)
Should be unique within a site

Event Label

StringYesEvent Point Label from the protocol for which this event corresponds. E.g., baseline, surgery, etc.
If left blank, unplanned visit is collected.

Visit Name

StringNoAuto-generated if left blank
Should be unique within OS
Visit DateStringNo

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

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'
Should be unique within the system
BarcodeStringNo

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

TypeStringYes
Permissible Values File
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'

QuantityNumericYes

Default units:

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

Should be greater than zero ("0")

ConcentrationNumericNo

Concentration units are

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

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. 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 & TimeYes

Required for primary specimens.




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

...

  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 import 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.