Table of Contents |
---|
...
Page | Attribute Name | Definition | Permissible Values | ||
---|---|---|---|---|---|
Administrative Data | |||||
Users | Type | Type of user. |
| ||
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. |
| |||
Disable notification | Indicates whether the email notification for the User will be on or off. |
| |||
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:
| |||
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. |
| |||
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 |
| |||
Position labelling | Indicates position labelling of the container. |
| |||
Labeling scheme | Labeling rows and columns |
| |||
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. |
| |||
Can hold | Indicates whether the current container will hold any other container. | ||||
Containers | Create | Type of container User wants to create. |
| ||
Number of containers | Number of containers to be created. | ||||
Used for | Usage of Container. |
| |||
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. |
| |||
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. |
| |||
Position assignment | Indicates how the specimens will be placed in the container. | ||||
Labeling scheme | Labeling rows and columns. |
| |||
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. |
| |||
Display in Map | Indicated what label type should be displayed for a specimen. |
| |||
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 |
| |||
'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. |
| |||
Extract Text from SPR PDF Docs? | Indicates whether to Extract Text from SPR PDF Documents or not. |
| |||
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. |
| |||
Vital status | Vital status of the participant. |
| |||
Death date | Date of death of the participant. | ||||
Ethnicity | Ethnicity of the participant. |
| |||
Race | Patient's racial origination. |
| |||
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. | |||
Status | The status of the visit as to whether it is collected or pending. |
| |||
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. |
| |||
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. | ||||
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 The 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 Site | The receiving site of the project. | ||||
Principal Investigator | Name of the PI | ||||
Protocol Coordinator | Name of the protocol coordinator of the distribution protocol. | ||||
IRB ID | IRB ID assigned by the review board. | ||||
Date | Start date and end date of the Distribution Protocol. | ||||
Label Format | |||||
Order Custom Fields | |||||
Order Attachments | |||||
Disable e-mail notification Checkbox | Indicates no email will be sent when orders are processed. | ||||
Order Report Query | A query is saved to set up distribution report format. | ||||
Distributing Sites | Institute | Distributing Institute name. | |||
Site | Distributing site name. | ||||
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 |
...