Table of Contents

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

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

Note

If the visit name is not specified, all specimens within the same "collection date" will be collected under one visit.
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 label for uploading children.

Sample CSV

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Note
In bulk import, you need to enter the actual PPIDs and Specimen labels when the auto-generation is disabled. When the tokens are specified at the collection protocol level, the PPID and specimen label can be left blank. When you enter the 'Event Label,' OpenSpecimen will correctly recognize and group the specimens into visits based on the participant.

Data Dictionary

Added in	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 be existing within the system
	PPID	String	No	Participant Protocol ID	Blank - The New participant with auto-generated PPID is registered. Existing - Specimens will get collected under participants of specified PPID. New participant PPID - The New participant with specified PPID will be registered.
	Registration Date	Date	Yes
v3.4	First Name	String	No
v3.4	Last Name	String	No
v3.4	Middle Name	String	No
v3.4	Date Of Birth	Date	No
v3.4	Death Date	Date	No
v3.4	Gender	String	No		Female Male Unknown Undifferentiated
v3.4	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
v3.4	Vital Status	String	No		Alive Dead Unknown Unspecified
v3.4	Ethnicity	String	No		Hispanic or Latino Not Hispanic or Latino Not Reported Unknown
v3.4	SSN	Integer	No	Social Security Number for US locale. National Identification Number for other countries.		Should be unique within OS
v3.4	eMPI	String	No	Enterprise Master Patient Index		Should be unique within OS
v3.4	PMI#1#Site Name	String	No	The site which issued the MRN		Should be an existing site within OS
v3.4	PMI#1#MRN	String	No	Medical Record Number (unique identification given by the site)		Should be unique within a site
v3.4	Event Label	String	No	Event Point Label from the protocol for which this event corresponds. E.g. baseline, surgery, etc.
v3.4	Visit Name	String	No	Auto-generated if left blank		Should be unique within OS
v3.4	Visit Date	String	No			Select the correct date format from UI based on the data in the file
	Collection Site	String	No	Maps to Visit site. Needs to be specified if no default is specified at the CP event level.
v3.4	Visit Status	String	No		Complete Pending	Default: 'Complete'
v3.4	Clinical Diagnosis	String	No		Permissible Values File - SNOMED Permissible Values File - ICD 10	Default: 'Not Specified'
v3.4	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'
v3.4	Path. Number	String	No	Surgical Pathology Number		Default: 'Not Specified'
v3.4	Visit Comments	String	No
v3.4	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	Needs to be specified when the auto label generation is OFF OR 'Manual Input' is set to 'Yes'		Should be unique within the system
	Barcode	String	No			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		Permissible Values File
	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'
	Quantity	Numeric	Yes	Default units: Fluid: ml Tissue: gm Cell: cells Molecular: µg		Should be greater than zero ("0")
	Concentration	Numeric	No	Concentration units are Cells: cells, Tissue: µg/ml Molecular: µg/ml		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.		Container specified should be existing Suitable to hold the specimen (based on type and protocol) 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	Required for primary specimens.
	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

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Enable 'CP Coding' from Settings
Add specimen requirement code at the CP level for all the parent and child samples.
Download the master specimen template from the user interface.
Add the required data in their respective columns and codes in the 'Specimen Requirement Code' column to link the parent and child specimens. Refer to the example sheet attached.
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.

Versions Compared

Old Version 49

New Version 50

Key

Sample CSV

Data Dictionary

Page Comparison

Versions Compared

Old Version 49

New Version 50

Key

Sample CSV

Data Dictionary