Introduction

This document provides information about all the attributes used in OpenSpecimen and their description listed on each user interface page.

Description of the fields in the below table:

Page: OpenSpecimen user interface page
Attribute name: Fields displayed per page
Definition: Description of the attribute
Permissible Values: For specific fields in OpenSpecimen, the user is restricted to use a set of permissible values (shown as dropdown fields on the interface). This column lists these permissible values.

Page	Attribute Name	Definition	Permissible Values
Administrative Data
Users	Type	Type of user.	Super Administrator Institute Administrator Contact Regular
	Last Name	Last name of the user.
	First Name	First Name of the User.
	Email Address	The email address of the user.
	Phone number	Phone number.
	Domain Name	By default, this is an openspecimen to support normal logins. If the system is integrated with LDAP, then the domain can be selected based on that.	openspecimen
	Login Name	Login name of the user.
	Institute	Institute name to which the user is associated.
	Primary Site	The primary site user belongs to. This is just for information and is not used to assign any privileges to the user. (Available in the version before v8.1)
	Time Zone	Time zone of the user.
	Manage forms?	Indicates whether the user can access custom forms or not.	Yes No
	Disable notification	Indicates whether the email notification for the user will be on or off.	Yes No
	Address	Address of the user.
	API User?	Indicates whether the user can access OpenSpecimen APIs	Yes No
	Role	Defines user role according to which the privileges get assigned within one or more sites. A role can also be restricted to one or more collection protocols within the site.	Default Roles: Administrator Coordinator Principal Investigator Researcher Technician Tissue Banker
Institutes	Name	Name of the Institution (Overarching authoritative entity).
Sites	Institute	Institute name to which the site is associated.
	Name	Name of the physical location (Biobank, repository, or hospital).
	Code	Shortcode, which can be used in container name generation.
	Type	The function of the site. It could be for collection, storage, experimentation, etc.	Collection Site Repository Laboratory Not Specified Not applicable
	Coordinators	Coordinators name.
	Address	Address of the site.
Container Types	Name	Name of the container type.
	Name Format	Indicates the naming/labeling format of the container.
	Dimensions	Dimensions of the container	Rows Columns
	Position labeling	Indicates position labeling of the container.	Linear Row and Column
	Labeling scheme	Labeling rows and columns	Numbers Alphabetic Upper Case Alphabetic Lower Case Roman Upper Case Roman Lower Case
	Position assignment	Indicates how the specimens will be placed in the container.
	Temperature (Celsius)	The temperature of the container.
	Store specimen?	Indicates whether the container will hold specimens or not.	Yes No
	Can hold	Indicates whether the current container will hold any other container.
Containers	Create	Type of container User wants to create.	Single Container Multiple Containers Container Hierarchy
	Number of containers	The number of containers to be created.
	Used for	Usage of Container.	Storage Distribution
	Type	Name of Container Type.
	Name	Name of the container.
	Barcode
	Parent Site	The site to which the container will belong.
	Parent Container	The site with which the container is associated.	Select parent container if creating child container.
	Dimensionless?	Indicates if the container will have dimensions or not.	Yes No
	Dimensions	The number of rows and number of columns.
	Approximate capacity	The capacity of the container to hold specimens.
	Position labeling	Indicates how specimen labeling should be done.	Linear Row and Column
	Position assignment	Indicates how the specimens will be placed in the container.
	Labeling scheme	Labeling rows and columns.	Numbers Alphabetic Upper Case Alphabetic Lower Case Roman Upper Case Roman Lower Case
	Temperature (Celsius)	The temperature of the current type of storage container.
	Stores Specimens	This indicates at which level the specimens will be stored like a box.	Yes No
	Display in Map	Indicated what label type should be displayed for a specimen.	Specimen Label Specimen Barcode PPID
	Collection Protocol	Restrict to store specimens from specific collection protocols.
	Specimen Types	Restrict specimen types to be stored in the container.
Collection Protocol	Sites	Sites with which the collection protocol is associated.
	Site Code Information	Code of Site
	Title	Title of the protocol.
	Short Title	Short title of the protocol. This will be displayed on all data entry pages.
	Code	Collection Protocol Code. Usually used to generate Participants Ids.
	Principal Investigator	User will be assigned PI role, which gets read access to all protocol data.
	Protocol Coordinators	User will be assigned coordinator role, who gets all access to all protocol data.
	Start/End Date	Start date and end date of the collection protocol based on which protocol expiry reports are sent.
	Ethics Approval/ IRB ID	IRB ID assigned by the review board.
	Type	Type of Collection protocol	Participant Centric Specimen Centric
	'Expected Registrations'	Number of Participants Anticipated to get registered in the protocol
	SOP Document URL	Standard operating procedure document link.
	SOP Document file	Standard operating procedure document file.
	Store SPR's	Indicates whether to store surgical pathology reports or not.	Yes No Use system Settings
	Extract Text from SPR PDF Docs?	Indicates whether to Extract Text from SPR PDF Documents or not.	Yes No
	Participant Protocol Identifier Format	Allows setting PPI format according to which PPI of the future participants will be generated on registration.
	Visit Name Format
	Specimen Label Format	The format in which the specimen label will be created.
	Derivative Label Format
	Aliquot Label Format
	User inputs allowed	Manual inputs for labels.	Participant Protocol IDs Visit Names Specimen Labels
Carts
	Name	Name of the cart
	Share with users	Users whom you want to share the cart.
	Share with user groups.	Users groups whom you want to share the cart.
	Description	Description of the cart.
	Specimens	Specimens that you want to add to your cart.	Specimen labels Specimen barcodes
BioSpecimen Data
Participant	Registration Date	Date of registration.
	Participant Protocol ID	A unique Id assigned to a Participant within a protocol.
	Registration Site	The original hospital where the participant is registered.
	External Subject ID	ID assigned to the participant by other participant registries.
	Name	Name of the participant (Last name, First name, Middle name).
	Email Address	Email address of the participant.
	Birth Date	Participant's date of birth.
	National Identifier/ SSN	SSN of the patient for the U.S and national IDs in other countries
	Master Patient Index	MPI of the participant
	Gender	Gender of the participant.	Castrate Female Male Undifferentiated Unknown
	Vital status	Vital status of the participant.	Alive Dead Unknown Unspecified
	Death date	Date of death of the participant.
	Ethnicity	Ethnicity of the participant.	African American Ashkenazi Jewish Cambodian Canadian Fijian Indian Hispanic or Latino Jewish Heritage Maori Norwegian Not Hispanic or Latino Not Reported Other Singaporean Spanish or Latino Thai Unknown
	Race	Patient's racial origination.	White Black or African American American Indian or Alaska Native Asian Native Hawaiian or other Pacific Islander Not Reported Unknown Caucasian Hispanic Iranian Other Spanish/Filipino
	Site	Site name at which the participant is registered.
	Medical Record Number	Participants' medical record numbers were used in their medical treatment.
Consents	Statement	A statement that is used to define consent in free text format
	Response	Exact participant response to the consent statement	Yes No Not specified
	Consent Signature Date
	Upload consent file	It enables you to browse the files and choose the desired file to upload, edit, and delete.
	Consent Witness	Name of Witness for the consents
	Consent comments
Visits	Name	Name of the visits.
	Status	The status of the visit as to whether it is collected or pending.	Complete Pending Missed Collection Not Collected
	Visit Date	Date of visit.
	Site of visit	Name of the visit site.
	Clinical Status	It describes the participant's current position at a particular time point in the collection protocol—for example, Pre-Surgery, Post-Surgery, or Control.	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
	Clinical Diagnosis	It describes the determination of a disease in a participant based on the study of signs and symptoms—the diagnoses map to the ICD-10 codes.	Clinical Diagnosis list.xls
	Cohort	A cohort an A study is a particular form of a longitudinal study.
	Surgical Pathological Number	It is the unique number associated with Surgical Pathological Report.
	Comments	Any comments related to the group of specimens.
Surgical Pathology Report	Upload Surgical Pathology Report	Enables upload SPRs, edit, lock, unlock and download PDF/Txt formats.
Specimen	Label	Human readable unique label/name assigned to a specimen.
	Created On	The date on which a specimen is created. It is the same as the collection date; for child specimen (derivatives and aliquots), it is the creation date.
	Collection Status	Status of collection of specimen	Collected Missed Collection Pending
	Available Quantity	The current quantity of a specimen available in the system
	Lineage	Specimen's heredity status, like a specimen, could be original from the participant, derived from another specimen, aliquoted from another specimen.	New Derived Aliquot
	Comment	Comments about collected/created specimens.
	Anatomic Site	The anatomical site from which a specimen is derived.	Tissue Site list.xls
	Laterality	Laterality of anatomic sites	Left Right Not Applicable Not Specified
	Specimen Type	Sub-classification of a class of specimens based on their type. Type of specimen involves Serum, Plasma, Blood, Fresh Tissue, Fixed Tissue, etc.	Tissue Type.xls
	Pathological Status	The histopathological character of the specimen is required at the time of collection/distribution.	Non-Malignant Non-Malignant, Diseased Pre-Malignant Malignant, Pre-Invasive Malignant, Invasive Malignant Metastatic Not Specified
	Initial Quantity	Quantity of specimen when collected from the patient
	Concentration	The concentration of specimen, in the case of molecular specimens
	Biohazard(s)	Additional information about biohazard
	Storage Location	Describes the specimen allocation to the available storage or a virtual position.
	External IDs	In some cases, the specimens are associated with other external IDs.
Gels
	Label	Label of the gel
	Site	Site of gel loading
	Image	Image of the gel
Distribution Protocols and Distribution Orders
Distribution Protocols	Title	The long title of the distribution protocol.
	Short title	The short title of the distribution protocol.
	Receiving Institute	Name of the institute to which the distribution protocol is associated. Note: Institute of the Distribution protocol should be the same as that of the site of Collection Protocol through which the specimens are to be distributed.
	Receiving Site	The receiving site of the project.
	Principal Investigator	Name of the PI
	Protocol Coordinator	Name of the protocol coordinator of the distribution protocol.
	IRB ID	IRB ID assigned by the review board.
	Date	Start date and end date of the Distribution Protocol.
	Label Format
	Order Custom Fields	The custom fields of order.
	Order Attachments	The attachments of the order
	Disable email notification Checkbox	Indicates no email will be sent when orders are processed.
	Order Report Query	A query is saved to set up the distribution report format.
Distributing Sites	Institute	Distributing Institute name.
	Site	Distributing site name.
Distribution Order	Distribution Protocol	Name of the Distribution Protocol from which the specimen is distributed.
	Name	Name of the order.
	Receiving Institute	Name of the receiving institute.
	Receiving Site	Name of the receiving site.
	Requestor	Name of the requestor.
	Execution Date	Date and time of specimen distribution
	Courier tracking URL	URL for courier tracking.
	Sender Comments	Descriptive information about the order request.
	Status	Status of the order item	Executed Pending
Distribution Requests	Request ID	Identifier of the request
	Requestor Email ID	Email address of the requestor
	Requestor Name	Name of the requestor
	Request Date	Date of the request
	Request Screening Status	Status of request	Pending Approved Rejected
	Request Screening Date	Date of request screening
	Request Processing Date	Date of processing request
	Request Status	Status of the request	Active Closed
Shipment	Name	Shipment name
	Courier Name	Name of shipment courier
	Tracking Number	Shipment tracking number
	Tracking URL	Shipment tracking URL
	Sender's site	The site to whom the shipment is being requested
	Receiving Institute	An institute that has requested the specimens for shipment
	Receiving Site	A site that has requested the specimens for shipment
	Notify Users	A user account with whom the shipment details will be shared and notified on operations
	Shipped date	Date of shipment occurred.
	Creation date	Date when the distribution order was created
	Distribution date	date when the specimens are distributed
	Quantity	Amount of the specimen distributed.
	Sender Comments	Comments at time of requesting./receiving the shipment
Specimen Events
Collection Event	Procedure	Method of specimen collection from participant	Lavage Needle Aspirate Needle Core Biopsy Venipuncture Indwelling Catheter Surgical Resection Not Specified User CP defaults
	Container	Container type in which specimen is collected	No Additive Vacutainer Serum Separator Vacutainer EDTA Vacutainer Citrate Vacutainer ACD Vacutainer Heparin Vacutainer Sterile Specimen Container Not Specified CPT Paxgene User CP defaults
Received Event	Quality	Grossly evaluated the quality of the received specimen.	Acceptable Thawed Frozen Quantity Not Sufficient Clotted Hemolyzed Lipemic Cauterized Hemorrhagic Damaged Unacceptable, Not Specified Not Specified User CP defaults
Cell Review Event	Neo Plastic Cellularity Percentage	Percentage of histologically evident neoplastic cells present in the specimen.
	Viable Cell Percentage	Percentage of viable cells in the specimen.
Check In Check Out Event	Storage Status	Type of the movement, whether Check-in or Check-out.	Check-in Check-out
Embedded Event	Embedding Medium	Type of medium in which specimen is embedded.	Paraffin Low Melting Point Paraffin Optimal Cutting Temperature Media Freezing Media, Not Specified Plastic Not Specified
Fixed Event	Fixation Type	Type of the fixation.	Neutral Buffered Formalin Formaldehyde Methanol Ethanol, 70% Methacarn UM-Fix RNALater Bouin's Not Specified
	Duration In Minutes	Duration, measured in minutes, for which fixation is performed on the specimen.
Frozen Event	Method	The method is applied to a specimen to freeze it.	Liquid Nitrogen Liquid Nitrogen / Isopentane Liquid Nitrogen Vapor Dry Ice Dry Ice / Hydrocarbon Slurry Cryobath Cryostat Aerosol Spray Not Specified
Molecular Review Event	Gel Image URL	A reference to the location of an electrophoretic gel image of the specimen.
	Quality Index	A normalized quality score indicates the integrity of the specimen.
	Lane Number	The lane number within the electrophoretic gel image corresponds to the specimen.
	Gel Number	A number corresponds to the gel on which the specimen was analyzed for QA purposes.
	Absorbance At 260	The absorbance of the specimen at 260 nanometers.
	Absorbance At 280	The absorbance of the specimen at 280 nanometers.
	Ratio 28S To 18S	A unitless ratio of the? Full-length 28S to 18S? Ribosomal RNA mass that is detected in a mammalian cellular RNA sample.
Procedure Event	URL	URL to the document that describes detailed information of the customized processes.
	Name	Name of the customized procedure.
Spun Event	G(Gravity) Force	The rotational force was applied to the specimen.
	Duration In Minutes	Duration for which specimen is spun.
Tissue Review Event	Neoplastic Cellularity Percentage	Percentage of histologically evident neoplastic cells present in the tissue specimen.
	Necrosis Percentage	Percentage of the specimen that is histologically necrotic.
	Lymphocytic Percentage	Percentage of histologically evident lymphocytes in the tissue specimen.
	Total Cellularity Percentage	Percentage of total cellularity of the specimen.
	Histological Quality	Histological quality of the specimen.	Excellent- Definable Nuclear Detail Good- Definable Cellular Detail Fair- Definable Tissue Architecture Poor- No Definable Features Not Specified
Transfer Event	From Position Dimension One	Reference to dimensional position one of the specimens in previous storage containers before transfer.
	From Position Dimension Two	Reference to dimensional position two of the specimen in a previous storage container before transfer.
	From Container	Name of the container from which the specimen is to be transferred
	To Position Dimension One	Reference to dimensional position one of the specimens in new storage containers after transfer.
	To Position Dimension Two	Reference to dimensional position two of the specimen in new storage containers after transfer.
	To Container	Name of container to which the specimen is being transferred

Data Dictionary

Introduction

Administrative Data

Users

Institutes

Sites

Container Types

Containers

Collection Protocol

Carts

BioSpecimen Data

Participant

Consents

Visits

Surgical Pathology Report

Specimen

Gels

Distribution Protocols and Distribution Orders

Distribution Protocols

Distributing Sites

Distribution Order

Distribution Requests

Shipment

Specimen Events

Collection Event

Received Event

Cell Review Event

Check In Check Out Event

Embedded Event

Fixed Event

Frozen Event

Molecular Review Event

Procedure Event

Spun Event

Tissue Review Event

Transfer Event