Introduction
Using this template, you can create participants, visits, and specimens in one go.
Note:
Only specimen custom fields are included in the template and registration or visit custom fields are not included.
Steps to import CSV
- Go to the collection protocols list page, click on the 'Import' button, and select the option 'Biospecimen Data' OR
- Go to the participants list page of the CP under which the participants, visits, and specimens have to be created, click on the 'More' button, and select the option 'Biospecimen Data'.
- Select 'Master Specimens' from the 'Select Record Type' dropdown and click on 'Download Template File' to download the template file.
- Enter all valid data in the template file as mentioned in the 'Data Dictionary' table.
- Upload the filled template file in the 'Input Records File' field.
- Select the correct 'Date and Time Format.'
- Click on the 'Validate and Import' button.
- Refer 'Import status' to check the status of the import job.
- You can both create and update records using the master template. If data already exists, the record is updated with the input specified in the CSV file. Otherwise, a new record is created.
- If the visit name is not specified, all specimens within the same "collection date" will be collected under one visit.
- Specimen labels cannot be auto-generated if you are going to include rows for aliquots and derivatives within the same file. i.e If labels are auto-generated, you need to upload parents and children in two different imports to export the labels generated from the first upload and use them as parent labels for uploading children.
Sample CSV
- You need to enter the actual PPIDs and Specimen labels when the auto-generation is disabled in bulk import.
- When the tokens are specified at the collection protocol level, the PPID and specimen label can be left blank.
- When entering the 'Event Label,' OpenSpecimen will correctly recognize and group the specimens into visits based on the participant.
- Make sure all the dates use the same format throughout the BO file.
Data Dictionary
| Column name | Data type | Mandatory (Create)? | Description | Permissible Values | Validations |
|---|---|---|---|---|---|
| Collection Protocol (CP) Short Title | String | Yes | Protocol under which participants should be registered | Collection Protocol should exist within the system. | |
| PPID | String | No | Participant Protocol ID |
| |
Registration Date | Date | Depends |
| ||
First Name | String | No | First Name of the participant | ||
Last Name | String | No | Last Name of the participant | ||
Middle Name | String | No | Middle Name of the participant | ||
Date Of Birth | Date | No | Date of Birth of the participant | Select the correct date format from UI based on the data in the file. | |
Death Date | Date | No | Select the correct date format from UI based on the data in the file. | ||
Gender | String | No |
| ||
| Race#1 | String | No | Add an extra column for the participant with multiple races. E.g. Race#1, Race#2, etc. |
| |
Vital Status | String | No |
| ||
Ethnicity | String | No |
| ||
| SSN | Integer | No | Social Security Number for US locale. National Identification Number for other countries. | It should be unique within OS. | |
| eMPI | String | No | Enterprise Master Patient Index | It should be unique within OS. | |
PMI#1#Site Name | String | No | The site which issued the MRN | It should be an existing site within OS. | |
PMI#1#MRN | String | No | Medical Record Number (unique identification given by the site) | It should be unique within a site. | |
Event Label | String | Yes | Event Point Label from the protocol for which this event corresponds. E.g., baseline, surgery, etc. | If left blank, an unplanned visit is collected. | |
Visit Name | String | No | Auto-generated if left blank | It should be unique within OS. | |
| Visit Date | String | No | If the visit date value is not specified, the system takes up the value of the collection date. | ||
| Collection Site | String | No | Maps to Visit site. It needs to be specified if no default is specified at the CP event level. | ||
| Visit Status | String | No |
| Default: 'Complete' | |
Clinical Diagnosis | String | No | Default: 'Not Specified' | ||
Clinical Status | String | No |
| Default: 'Not Specified' | |
Path. Number | String | No | Surgical Pathology Number | Default: 'Not Specified' | |
Visit Comments | String | No | |||
Specimen Requirement Code | String | No | Code defined in collection protocol for the corresponding specimen requirement. | If this is not specified, specimens are created as unplanned specimens. For enabling CP encoding, please refer to the wiki page | |
| Specimen Label | String | No | It needs to be specified when the auto label generation is OFF OR 'Manual Input' is set to 'Yes.' | It should be unique within the system | |
| Barcode | String | No | It should be unique within the system | ||
| Class | String | Depends | Exception- conditional mandatory filed If 'Not specified' is selected in the 'type' field, in that case, the class field is mandatory. |
| |
| Type | String | Yes | Permissible Values File | ||
| Lineage | String | No |
| Default: New | |
| Parent Specimen Label | String | No | Required when creating child specimens | ||
| Anatomic Site | String | No | Permissible Values File | Default: 'Not Specified' | |
| Laterality | String | No |
| Default: 'Not Specified' | |
| Pathological Status | String | No |
| Default: 'Not Specified' | |
| Initial Quantity | Numeric | No | Default units:
| It should be greater than zero ("0") | |
| Available Quantity | Numeric | No | Default units:
| It should be greater than zero ("0") | |
| Concentration | Numeric | No | Concentration units are
| It should be greater than zero ("0") | |
Freeze/Thaw Cycles | Numeric | No | The number of cycles carried out. | ||
| Created On | Date & Time | No | Mandatory for child specimens. | ||
| Comments | String | No | |||
Collection Status | String | No | Status of the specimen to be collected |
| |
| Container | String | No | Name of the existing container. |
| |
| Row | String | No | Position within the container at which the specimen is to be stored. If left blank, the system will allocate the next available position | ||
| Column | String | No | |||
| Position | Integer | No | Use this column if you do not use "row" and "column." | ||
| Collection Date | Date & Time | Yes | Required for primary specimens. | ||
| Collection Procedure | String | No |
| ||
| Collection Container | String | No | Type of container used for specimen collection |
| |
| Collector | Email address | No | Valid user | ||
| Received Date | Date & Time | No | Date when specimens were received at the lab. If not specified, the current date/time is being used. | ||
| Received Quality | String | No |
| ||
| Receiver | Email address | No | Valid user |
Participant matching
The participant matching based on MRN and eMPI is implemented in v7.0. (OPSMN-5190)
FAQ
Q. How to create parent and child specimens using the master specimen template when labels are auto-generated?
- Enable 'CP Coding' from Settings
- Add specimen requirement code at the CP level for all the parent and child samples.
- Download the master specimen template from the user interface.
- Add the required data in their respective columns and codes in the 'Specimen Requirement Code' column.
- Create patient, visit, and primary specimens in one go using the master template, and for child specimens, create separate imports using a master template or specimen template.
- If you receive information separately, it is easier to use separate templates: Participant registrations, Visits, and Specimens. The master template is used when participants visit, and specimens or visits and specimens under existing participants need to be created in one go.