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Data Dictionary


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.

PageAttribute NameDefinitionPermissible Values

Administrative Data


TypeType of user.
  • Super Administrator
  • Institute Administrator
  • Contact
  • Regular

Last NameLast name of the user.

First NameFirst Name of the User.

Email AddressThe email address of the user.

Phone numberPhone number.

Domain NameBy 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 NameLogin name of the user.

InstituteInstitute name to which the user is associated.

Primary SiteThe 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 ZoneTime zone of the user.

Manage forms?Indicates whether the user can access custom forms or not.
  • Yes
  • No

Disable notificationIndicates whether the email notification for the user will be on or off.
  • Yes
  • No

AddressAddress of the user.

Indicates whether the user can access OpenSpecimen APIs
  • Yes
  • No

RoleDefines 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


NameName of the Institution (Overarching authoritative entity).


InstituteInstitute name to which the site is associated.


Name of the physical location (Biobank, repository, or hospital).

CodeShortcode, which can be used in container name generation.

TypeThe function of the site. It could be for collection, storage, experimentation, etc.
  • Collection Site
  • Repository
  • Laboratory
  • Not Specified
  • Not applicable

CoordinatorsCoordinators name.

AddressAddress of the site.

Container Types

NameName of the container type.

Name FormatIndicates the naming/labeling format of the container.

DimensionsDimensions of the container
  • Rows
  • Columns

Position labelingIndicates position labeling of the container.
  • Linear
  • Row and Column

Labeling schemeLabeling rows and columns
  • Numbers
  • Alphabetic Upper Case
  • Alphabetic Lower Case
  • Roman Upper Case
  • Roman Lower Case

Position assignmentIndicates 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 holdIndicates whether the current container will hold any other container.


CreateType of container User wants to create.
  • Single Container
  • Multiple Containers
  • Container Hierarchy

Number of containersThe number of containers to be created.

Used forUsage of Container.
  • Storage
  • Distribution

TypeName of Container Type.

NameName of the container.


Parent SiteThe site to which the container will belong.

Parent ContainerThe 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

DimensionsThe number of rows and number of columns.

Approximate capacityThe capacity of the container to hold specimens.

Position labelingIndicates how specimen labeling should be done.
  • Linear
  • Row and Column

Position assignmentIndicates how the specimens will be placed in the container.

Labeling schemeLabeling 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 SpecimensThis indicates at which level the specimens will be stored like a box.
  • Yes
  • No

Display in MapIndicated what label type should be displayed for a specimen.
  • Specimen Label
  • Specimen Barcode
  • PPID

Collection ProtocolRestrict to store specimens from specific collection protocols.

Specimen TypesRestrict specimen types to be stored in the container.

Collection Protocol

SitesSites with which the collection protocol is associated.

Site Code InformationCode of Site

TitleTitle of the protocol.

Short TitleShort title of the protocol. This will be displayed on all data entry pages.

CodeCollection Protocol Code. Usually used to generate Participants Ids.

Principal InvestigatorUser will be assigned PI role, which gets read access to all protocol data.

Protocol CoordinatorsUser will be assigned coordinator role, who gets all access to all protocol data.

Start/End DateStart date and end date of the collection protocol based on which protocol expiry reports are sent.

Ethics Approval/ IRB IDIRB ID assigned by the review board.

TypeType of Collection protocol
  • Participant Centric
  • Specimen Centric

'Expected Registrations'Number of Participants Anticipated to get registered in the protocol

SOP Document URLStandard operating procedure document link.

SOP Document fileStandard 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 FormatAllows setting PPI format according to which PPI of the future participants will be generated on registration.

Visit Name Format

Specimen Label FormatThe format in which the specimen label will be created.

Derivative Label Format

Aliquot Label Format

User inputs allowedManual inputs for labels.

Participant Protocol IDs

Visit Names

Specimen Labels


NameName of the cart

Share with usersUsers whom you want to share the cart.

Share with user groups.Users groups whom you want to share the cart.

DescriptionDescription of the cart.

SpecimensSpecimens that you want to add to your cart.
  • Specimen labels
  • Specimen barcodes

BioSpecimen Data


Registration DateDate of registration.

Participant Protocol ID

A unique Id assigned to a Participant within a protocol.

Registration SiteThe original hospital where the participant is registered.

External Subject IDID assigned to the participant by other participant registries.

NameName of the participant (Last name, First name, Middle name).

Email AddressEmail address of the participant.

Birth DateParticipant's date of birth.

National Identifier/ SSNSSN of the patient for the U.S and national IDs in other countries

Master Patient IndexMPI of the participant

GenderGender of the participant.
  • Castrate
  • Female
  • Male
  • Undifferentiated
  • Unknown

Vital status

Vital status of the participant.
  • Alive
  • Dead
  • Unknown
  • Unspecified

Death dateDate of death of the participant.

EthnicityEthnicity 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

RacePatient'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

SiteSite name at which the participant is registered.

Medical Record NumberParticipants' medical record numbers were used in their medical treatment.


StatementA statement that is used to define consent in free text format

ResponseExact participant response to the consent statement



Not specified

Consent Signature Date

Upload consent fileIt enables you to browse the files and choose the desired file to upload, edit, and delete.

Consent WitnessName of Witness for the consents

Consent comments


NameName of the visits.

StatusThe status of the visit as to whether it is collected or pending.
  • Complete
  • Pending
  • Missed Collection
  • Not Collected

Visit DateDate of visit.

Site of visitName of the visit site.

Clinical StatusIt 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 DiagnosisIt 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

Cohortcohort an A study is a particular form of a longitudinal study.

Surgical Pathological NumberIt is the unique number associated with Surgical Pathological Report.

CommentsAny comments related to the group of specimens.

Surgical Pathology Report

Upload Surgical Pathology ReportEnables upload SPRs, edit, lock, unlock and download PDF/Txt formats.


LabelHuman readable unique label/name assigned to a specimen.

Created OnThe 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 StatusStatus of collection of specimen


Missed Collection


Available QuantityThe current quantity of a specimen available in the system

LineageSpecimen's heredity status, like a specimen, could be original from the participant, derived from another specimen, aliquoted from another specimen.




CommentComments about collected/created specimens.

Anatomic SiteThe anatomical site from which a specimen is derived.Tissue Site list.xls

LateralityLaterality of anatomic sites



Not Applicable

Not Specified

Specimen TypeSub-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 StatusThe histopathological character of the specimen is required at the time of collection/distribution.


Non-Malignant, Diseased


Malignant, Pre-Invasive

Malignant, Invasive



Not Specified

Initial QuantityQuantity of specimen when collected from the patient

ConcentrationThe concentration of specimen, in the case of molecular specimens

Biohazard(s)Additional information about biohazard

Storage LocationDescribes the specimen allocation to the available storage or a virtual position.

External IDsIn some cases, the specimens are associated with other external IDs.


LabelLabel of the gel

SiteSite of gel loading

ImageImage of the gel

Distribution Protocols and Distribution Orders

Distribution Protocols

TitleThe 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 SiteThe receiving site of the project.

Principal InvestigatorName of the PI

Protocol CoordinatorName of the protocol coordinator of the distribution protocol.

IRB IDIRB ID assigned by the review board.

DateStart date and end date of the Distribution Protocol.

Label Format

Order Custom FieldsThe custom fields of order.

Order AttachmentsThe attachments of the order

Disable email notification CheckboxIndicates no email will be sent when orders are processed.

Order Report QueryA query is saved to set up the distribution report format.

Distributing Sites

InstituteDistributing Institute name.


Distributing site name. 

Distribution Order

Distribution ProtocolName of the Distribution Protocol from which the specimen is distributed.


Name of the order.

Receiving InstituteName of the receiving institute.

Receiving SiteName of the receiving site.

RequestorName of the requestor.

Execution DateDate and time of specimen distribution

Courier tracking URLURL for courier tracking.

Sender CommentsDescriptive information about the order request.

StatusStatus of the order item



Distribution Requests

Request IDIdentifier of the request

Requestor Email IDEmail address of the requestor

Requestor NameName of the requestor

Request DateDate of the request

Request Screening StatusStatus of request
  • Pending
  • Approved
  • Rejected

Request Screening DateDate of request screening

Request Processing DateDate of processing request

Request StatusStatus of the request
  • Active
  • Closed


NameShipment name

Name of shipment c

Shipment tracking number

Shipment tracking URL

Sender's siteThe site to whom the shipment is being requested

An institute that has requested the specimens for shipment

Receiving SiteA site that has requested the specimens for shipment

A user account with whom the shipment details will be shared and notified on operations

Shipped dateDate of shipment occurred.

Creation dateDate when the distribution order was created

Distribution datedate when the specimens are distributed

QuantityAmount of the specimen distributed.

Sender CommentsComments at time of requesting./receiving the shipment

Specimen Events

Collection Event

ProcedureMethod of specimen collection from participant


Needle Aspirate

Needle Core Biopsy


Indwelling Catheter

Surgical Resection

Not Specified

User CP defaults

ContainerContainer 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



User CP defaults

Received Event

QualityGrossly evaluated the quality of the received specimen.




Quantity Not Sufficient







Unacceptable, Not Specified

Not Specified

User CP defaults

Cell Review Event

Neo Plastic Cellularity PercentagePercentage of histologically evident neoplastic cells present in the specimen.

Viable Cell PercentagePercentage of viable cells in the specimen.

Check In Check Out Event

Storage StatusType of the movement, whether Check-in or Check-out.



Embedded Event

Embedding MediumType of medium in which specimen is embedded.


Low Melting Point Paraffin

Optimal Cutting Temperature Media

Freezing Media, Not Specified


Not Specified

Fixed Event

Fixation TypeType of the fixation.

Neutral Buffered Formalin



Ethanol, 70%





Not Specified

Duration In MinutesDuration, measured in minutes, for which fixation is performed on the specimen.

Frozen Event

MethodThe method is applied to a specimen to freeze it.

Liquid Nitrogen

Liquid Nitrogen / Isopentane

Liquid Nitrogen Vapor

Dry Ice

Dry Ice / Hydrocarbon Slurry



Aerosol Spray

Not Specified

Molecular Review Event

Gel Image URLA reference to the location of an electrophoretic gel image of the specimen.

Quality IndexA normalized quality score indicates the integrity of the specimen.

Lane NumberThe lane number within the electrophoretic gel image corresponds to the specimen.

Gel NumberA number corresponds to the gel on which the specimen was analyzed for QA purposes.

Absorbance At 260The absorbance of the specimen at 260 nanometers.

Absorbance At 280The absorbance of the specimen at 280 nanometers.

Ratio 28S To 18SA unitless ratio of the? Full-length 28S to 18S? Ribosomal RNA mass that is detected in a mammalian cellular RNA sample.

Procedure Event

URLURL to the document that describes detailed information of the customized processes.

NameName of the customized procedure.

Spun Event

G(Gravity) ForceThe rotational force was applied to the specimen.

Duration In MinutesDuration for which specimen is spun.

Tissue Review Event

Neoplastic Cellularity PercentagePercentage of histologically evident neoplastic cells present in the tissue specimen.

Necrosis PercentagePercentage of the specimen that is histologically necrotic.

Lymphocytic PercentagePercentage of histologically evident lymphocytes in the tissue specimen.

Total Cellularity PercentagePercentage of total cellularity of the specimen.

Histological QualityHistological 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 OneReference to dimensional position one of the specimens in previous storage containers before transfer.

From Position Dimension TwoReference to dimensional position two of the specimen in a previous storage container before transfer.

From ContainerName of the container from which the specimen is to be transferred

To Position Dimension OneReference to dimensional position one of the specimens in new storage containers after transfer.

To Position Dimension TwoReference to dimensional position two of the specimen in new storage containers after transfer.

To ContainerName of container to which the specimen is being transferred
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