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Table of Contents

Introduction

Using this template, you can create participants, visits, and specimens in one go. 

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Note
title

Note:

Only specimen custom fields are included in the template and registration or visit custom fields are not included. 

Steps to import CSV

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

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  • 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'.

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

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  • 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
  1. 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
  1. specific label tokens are not defined at any level (system, CP, SR)

  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
  1.  all the dates use the same format throughout the BO file.

  2. From v10.3 the master specimen template can also be used to only create/update participants and their respective visits, without any specimen data in it.

  3. All the values for field type ‘Permissible Values’ are case sensitive e.g., Lineage, Laterality, Pathology status, etc.

Data Dictionary

Column name

Data type

Mandatory

(Create)?

Description

Permissible Values

Validations

Collection Protocol (CP) Short Title

String

Yes

Protocol under which participants should be registered


Collection Protocol should exist within the system.

PPID

String

No

Participant 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
  1. new participant with specified PPID will be registered.

Registration Date

Date

Depends



  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

String

No

First Name of the participant



Last Name

String

No

Last Name of the participant



Middle Name

String

No

Middle Name of the participant



Date Of Birth

Date

No

Date of Birth of the participant


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

Death Date

Date

No



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

Gender

String

No


  • Female

  • Male

  • Unknown

  • Undifferentiated


Race#1

String

No

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

String

No


  • Alive

  • Dead

  • Unknown

  • Unspecified


Ethnicity

String

No


  • Hispanic or Latino

  • Not Hispanic or Latino

  • Not Reported

  • Unknown


SSN

Integer

No

Social Security Number for US locale.

National Identification Number for other countries.


It should be unique within OS.

eMPI

String

No

Enterprise Master Patient Index


It should be unique within OS.

PMI#1#Site Name

String

No

The site which issued the MRN


It should be an existing site within OS.

PMI#1#MRN

String

No

Medical Record Number (unique identification given by the site)


It should be unique within a site.

Event Label

String

Yes

Depends

Event 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

String

No

Auto-generated if left blank


It should be unique within OS.

Visit Date

String

No



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


Collection Site

String

No

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



Visit Status

String

No


  • Complete

  • Pending

Default: 'Complete'

Clinical Diagnosis

String

No


Permissible Values File - SNOMED

Permissible Values File - ICD 10

Default: 'Not Specified'

Clinical Status

String

No


  • 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

String

No

Surgical Pathology Number


Default: 'Not Specified'

Visit Comments

String

No




Specimen Requirement Code

String

No

Code 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 Label

String

No

It 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

Barcode

String

No



It should be unique within the system

Class

String

Depends

Exception- conditional mandatory filed
If 'Not specified' is selected in the 'type' field, in that case, the class field is mandatory.

  • Tissue

  • Molecular

  • Cell

  • Fluid


Type

String

Yes

Depends


Permissible Values File

  • From v10.3 mandatory only if creating specimens else optional

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

Lineage

String

No


  • New

  • Derived

  • Aliquot

Default: New

Parent Specimen Label

String

No

Required when creating child specimens



Anatomic Site

String

No


Permissible Values File

Default: 'Not Specified'

Laterality

String

No


  • Left

  • Right

  • Not Applicable

  • Not Specified

Default: 'Not Specified'

Pathological Status

String

No


  • Non-Malignant

  • Non-Malignant, Diseased

  • Pre-Malignant

  • Malignant, Pre-Invasive

  • Malignant, Invasive

  • Malignant

  • Metastatic

  • Not Specified

  • Clinically normal

Default: 'Not Specified'

Initial Quantity

Numeric

No

Default units:

  • Fluid: ml

  • Tissue: gm

  • Cell: cells

  • Molecular: µg


It should be greater than zero ("0")

Available Quantity

Numeric

No

Default units:

  • Fluid: ml

  • Tissue: gm

  • Cell: cells

  • Molecular: µg


It should be greater than zero ("0")

Concentration

Numeric

No

Concentration units are

  • Cells: cells,

  • Tissue: µg/ml

  • Molecular: µg/ml


It should be greater than zero ("0")

Freeze/Thaw Cycles



Numeric

No

The number of cycles carried out.



Created On

Date & Time

No

Mandatory for child specimens.



Comments

String

No




Collection Status



String

No

Status of the specimen to be collected

  • Pending

  • Complete

  • Missed Collection

  • Not Collected


Container

String

No

Name 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.

Row

String

No



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

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

Column

String

No



Position

Integer

No

Use this column if you do not use "row" and "column."


Collection Date

Date & Time

Yes

Depends

Required for primary specimens.


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


Collection Procedure

String

No


  • Lavage Needle

  • Aspirate

  • Needle Core Biopsy

  • Venipuncture

  • Indwelling Catheter

  • Surgical Resection

  • Not Specified


Collection Container

String

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


Collector

Email address

No



Valid user

Received Date

Date & Time

No

Date when specimens were received at the lab. If not specified, the current date/time is being used.




Received Quality

String

No


  • Acceptable

  • Thawed

  • Frozen

  • Quantity Not Sufficient

  • Clotted

  • Hemolyzed

  • Lipemic

  • Cauterized

  • Hemorrhagic

  • Damaged

  • Unacceptable, Not Specified

  • Not Specified


Receiver

Email address

No



Valid user


title
Note

Participant matching

The participant matching based on MRN and eMPI is implemented in v7.0.  (OPSMN-5190)

FAQ

Q. How to create parent and child specimens using the master specimen template when labels are auto-generated?

  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.