Data Dictionary

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.


PageAttribute NameDefinitionPermissible Values

Administrative Data

Users

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

Last NameLast name of the user.

First NameFirst Name of the User.

E-mail 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.

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.



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 site.

Default Roles:

  • Administrator
  • Coordinator
  • Principal Investigator
  • Researcher
  • Technician
  • Tissue Banker

Institutes

NameName of the Institution (Overarching authoritative entity).

Sites

InstituteInstitute name to which the site is associated.

Name

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.

Containers

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.

Barcode


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 is to indicate 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, who gets read access to all data of the protocol.

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

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

Carts


NameName of the cart

Share with usersUsers whom you want to share the cart.

Share with user groupsUsers 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

Participant

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.

Consents

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

ResponseExact participant response to the consent statement

Yes

No

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

Visits

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 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 in PDF/Txt formats.

Specimen

LabelHuman readable unique label/name assigned to a specimen.

Created OnThe date on which a specimen is created. For parent specimen, it is the same as collection date; for child specimen (derivatives and aliquots), it is the creation date.

Collection StatusStatus of collection of specimen

Collected

Missed Collection

Pending


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.

New

Derived

Aliquot


CommentComments about collected/created specimens.

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

LateralityLaterality of anatomic sites

Left

Right

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

Non-Malignant, Diseased

Pre-Malignant

Malignant, Pre-Invasive

Malignant, Invasive

Malignant

Metastatic

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 to a virtual position.

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

Gels


LabelLabel of the gel

SiteSite of gel loading

ImageImage of the gel

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

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 e-mail 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.

Site

Distributing site name. 


Distribution Order

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

Name

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

Executed

Pending

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

Shipment

Shipment LabelThe label of Shipment to be requested

Sender's site

The site to whom the shipment is being requested

Receiving SiteA site which have requested the specimens for shipment

Creation dateDate when the distribution order was created

Distribution datedate when the specimens are distributed

QuantityAmount of the specimen distributed

CommentsComments at time of requesting./receiving the shipment

Specimen Events

Collection Event

ProcedureMethod of specimen collection from participant

Lavage

Needle Aspirate

Needle Core Biopsy

Venipuncture

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

CPT

Paxgene

User CP defaults

Received Event

QualityGrossly 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 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.

Check-in

Check-out

Embedded Event

Embedding MediumType 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 TypeType of the fixation.

Neutral Buffered Formalin

Formaldehyde

Methanol

Ethanol, 70%

Methacarn

UM-Fix

RNALater

Bouin's

Not Specified


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

Frozen Event

MethodThe method applied on 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 URLA reference to the location of an electrophoretic gel image of the specimen.

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

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

Gel NumberA number corresponding 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 detail information of the customized processes.

NameName of the customized procedure.

Spun Event

G(Gravity) ForceThe rotational force 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 containers 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