Table of Contents |
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Introduction
This document provides information about all the attributes used in OpenSpecimen
Table of Contents |
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Introduction
This document provides information about all the attributes used in OpenSpecimen along with their description listed by each user interface page.
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Page | Attribute Name | Definition | Permissible Values | ||||||
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Administrative Data | |||||||||
Users | Type | Type of user. |
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Last Name | Last name of the User. | ||||||||
First Name | First Name of the User. | ||||||||
E-mail 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 not used to assign any privileges to the user. | ||||||||
Time Zone | Time zone of the User. | ||||||||
Manage forms? | Indicates whether the User can access custom forms or not. |
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Disable notification | Indicates whether the email notification for the User will be on or off. |
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Address | Address of the user. | ||||||||
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:
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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 | Short code which can be used in container name generation. | ||||||||
Type | The function of the site. It could be for collection, storage, experimentation, etc. |
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Coordinators | Coordinators name. | ||||||||
Address | Address of the site. | ||||||||
Container Types | Name | Name of the container type. | |||||||
Name Format | Indicates the naming/labelling format of the container. | ||||||||
Dimensions | Dimensions of the container |
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Position labelling | Indicates position labelling of the container. |
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Labeling scheme | Labeling rows and columns |
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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. |
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Can hold | Indicates whether the current container will hold any other container. | ||||||||
Containers | Create | Type of container User wants to create. |
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Number of containers | Number of containers to be created. | ||||||||
Used for | Usage of Container. |
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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. |
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Dimensions | Number of rows and number of columns. | ||||||||
Approximate capacity | The capacity of the container to hold specimens. | ||||||||
Position labelling | Indicates how specimen labelling should be done. |
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Position assignment | Indicates how the specimens will be placed in the container. | ||||||||
Labeling scheme | Labeling rows and columns. |
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Temperature (Celsius) | The temperature of the current type of storage container. | ||||||||
Stores Specimens | This is to indicate at which level the specimens will be stored like a box. |
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Display in Map | Indicated what label type should be displayed for a specimen. |
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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, who gets read access to all data of the protocol. | ||||||||
Protocol Coordinators | User will be assigned coordinator role, who gets all access to all data of the protocol. | ||||||||
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 review board. | ||||||||
Type | Type of Collection protocol |
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'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. |
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Extract Text from SPR PDF Docs? | Indicates whether to Extract Text from SPR PDF Documents or not. |
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Participant Protocol Identifier Format | Allows to set 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 | |||||||
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 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 of the patient for U.S and national IDs in other countries | Master Patient Index | MPI of the participant | Gender | Male Gender Female Gender Unspecified Unknown | Ethnicity | Hispanic or Latinoother countries | ||
Master Patient Index | MPI of the participant | ||||||||
Gender | Gender of the participant. |
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Vital status | Vital status of the participant. |
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Death date | Date of death of the participant. | ||||||||
Ethnicity | Ethnicity of the participant. |
| Vital status | Alive Dead Unknown Unspecified | Death date
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Race | Patient's racial origination. |
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Site | Site name at which the participant is registered. | ||||||||
Medical Record Number | Participant's medical record numbers used in their medical treatment. | Site | Site name at which the participant is registered | Registration Site | The original hospital where the participant is registered | External Subject ID | ID assigned to participant by other participant registries | ||
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 | Enables you to browse the files and then choose the desired file to upload, edit and deleted | ||||||||
Consent Witness | Name of Witness for the consents | ||||||||
Consent comments | |||||||||
Visits | Name | Name of the visits | |||||||
Site of visit | Name of the visit site | ||||||||
Status | The status of visit as to whether it is collected or pending | Complete Pending Missed Collection | |||||||
Visit Date | |||||||||
Clinical Status | It describes the current position of the participant 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 | |||||||
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 to upload SPRs, edit, lock, unlock, and download in PDF/Txt formats. | |||||||
Specimen | Label | Human readable unique label/name assigned to a specimen. | |||||||
Created On | The 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 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 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 case of molecular specimens | ||||||||
Biohazard(s) | Additional information about biohazard | ||||||||
Storage Location | Describes the specimen allocation to the available storage or to a virtual position. | ||||||||
Distribution Protocols and Distribution Orders | |||||||||
Distribution Protocols | Title | ||||||||
Short title | |||||||||
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 | ||||||||
Principal Investigator | Name of the PI | ||||||||
IRB ID | |||||||||
Date | Start date and end date of the Distribution Protocol | ||||||||
Order Report Query | A query is saved to set up distribution report format | ||||||||
Distribution Order | Name | Name of the order | |||||||
Distribution Protocol | Name of the Distribution Protocol from which the specimen is distributed | ||||||||
Requestor | Name of the requestor | ||||||||
Receiving Site | Name of the receiving site | ||||||||
Execution Date | Date of specimen distribution | ||||||||
Courier tracking URL | |||||||||
Sender Comments | Descriptive information about the order request | ||||||||
Status | Status of the order item | Executed Pending | |||||||
Shipment | Shipment Label | The label of Shipment to be requested | |||||||
Sender's site | The site to whom the shipment is being requested | ||||||||
Receiving Site | A site which have requested the specimens for shipment | ||||||||
Creation date | Date when the distribution order was created | ||||||||
Distribution date | date when the specimens are distributed | ||||||||
Quantity | Amount of the specimen distributed | ||||||||
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 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 URL | A reference to the location of an electrophoretic gel image of the specimen. | |||||||
Quality Index | A normalized quality score that indicates the integrity of the specimen. | ||||||||
Lane Number | The lane number within the electrophoretic gel image that corresponds to the specimen. | ||||||||
Gel Number | A number corresponding 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 detail information of the customized processes. | |||||||
Name | Name of the customized procedure. | ||||||||
Spun Event | G(Gravity) Force | The rotational force 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 a previous storage containers before transfer. | |||||||
From Position Dimension Two | Reference to dimensional position two of the specimen in a previous storage containers 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 |
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