Table of Contents |
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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 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 U.S and national IDs in other 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. |
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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. | |||||
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 the visit as to whether it is collected or pending. |
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Visit Date | Date of visit. | |||||
Site of visit | Name of the visit site. | |||||
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. |
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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 study is a particular form of a longitudinal study. | |||||
Surgical Pathological Number | It is the unique number associated with Surgical Pathological Report 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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