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

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  • Page: OpenSpecimen user interface page
  • Attribute name: Fields displayed per page
  • Definition: Description of the attribute
  • Permissible Values: For certain 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.

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Vital status

  • White
  • Black or African American
  • American Indian or Alaska Native
  • Asian
  • Native Hawaiian or other Pacific Islander
  • Not Reported
  • Unknown
  • PageAttribute NameDefinitionPermissible Values

    Administrative Data

    Users

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

    Last NameLast name of the Useruser.

    First NameFirst Name of the User.

    E-mail AddressThe email address of the Useruser.

    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 Useruser.

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

    Disable notificationIndicates whether the email notification for the User 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 the 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).



    CodeShort code Shortcode, 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/labelling labeling format of the container.

    DimensionsDimensions of the container
    • Rows
    • Columns

    Position labellinglabelingIndicates position labelling 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 containersNumber The 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

    DimensionsNumber The number of rows and number of columns.

    Approximate capacityThe capacity of the container to hold specimens.

    Position labellinglabelingIndicates how specimen labelling 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 to set 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

    BioSpecimen Data

    Carts

    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 U.S and national IDs in other countriesMaster Patient IndexMPI of the participantGenderGender of the participant.
    • Castrate
    • Female
    • Male
    • Undifferentiated
    • Unknown
    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.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 NumberParticipantParticipants' s 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 fileEnables It enables you to browse the files and then choose the desired file to upload, edit, and deleteddelete.

    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 of the participant at a particular time point in the collection protocol. For 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 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 to 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.

    Distribution Protocols and Distribution Orders

    Distribution Protocols

    TitleThe long title of the distribution protocol.Short title

    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..

    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 order.Receiving InstituteName of the receiving institute.Receiving SiteName of the receiving site.RequestorName of the requestor.Execution DateDate and time of specimen distributionCourier tracking URLURL for courier tracking.Sender CommentsDescriptive information about the order request.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 order itemrequestExecuted
    • Active
    Pending
    • 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 a 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

    ...