| Table of Contents |
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- Page: OpenSpecimen user interface page
- Attribute name: Fields displayed per page
- Definition: Description of the attribute
- Permissible Values: For certain 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.
| 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 |
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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. |
| |
| 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. |
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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. |
| |
| 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 | 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 | The custom fields of order. | ||
| Order Attachments | The attachments of the order | ||
| 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 the distribution report format. | ||
Distributing Sites | Institute | Distributing Institute name. | |
| Site | Distributing site name. | ||
Distribution Order | |||
| Distribution Protocol | Name of the Distribution Protocol from which the specimen is distributed |
| . | |||
Name | Name of the order. | ||
| Receiving Institute | Name of the |
| receiving institute. | |||
| Receiving Site | Name of the receiving site. | ||
| Requestor | Name of the requestor. | ||
| Execution Date | Date and time of specimen distribution | ||
| Courier tracking URL | URL for courier tracking. | ||
| 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 | ||