Using this template, you can create participants, visits, and specimens in one-go.
Note: Currently, only specimen custom fields are included in the template. An enhancement is logged for this OPSMN-4391
Steps to import CSV
- Go to the collection protocols list page, click on 'Import' button and select option 'Biospecimen Data' OR
- Go to participants list page of the CP under which the participants, visits, and specimens have to be created, click on 'More' button and select option 'Biospecimen Data'
- Select 'Master Specimens' from '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 below 'Data Dictionary' table
- Upload the filled template file in 'Input Records File' field
- Click on 'Validate and Import' button
- Refer 'Import status' to check the status of import job
- If visit name is not specified, all specimens within the same "collection date" will be collected under one visit.
- Specimen label cannot be auto-generated if you are going to include rows for aliquots and derivatives within the same file.
Sample CSV
Data Dictionary
| Added in | 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 be existing within the system | ||
| PPID | String | No |
| |||
Registration Date | Date | Yes | ||||
| v3.4 | First Name | String | No | |||
| v3.4 | Last Name | String | No | |||
| v3.4 | Middle Name | String | No | |||
| v3.4 | Date Of Birth | Date | No | |||
| v3.4 | Death Date | Date | No | |||
| v3.4 | Gender | String | No |
| ||
| v3.4 | Race#1 | String | No | Add an extra column for the participant with multiple races. E.g. Race#1, Race#2, etc. |
| |
| v3.4 | Vital Status | String | No |
| ||
| v3.4 | Ethnicity | String | No |
| ||
| v3.4 | SSN | Integer | No | Social Security Number for US locale National Identification Number for other countries | Should be unique within OS | |
| v3.4 | eMPI | String | No | Enterprise Master Patient Index | Should be unique within OS | |
| v3.4 | PMI#1#Site Name | String | No | The site which issued the MRN | Should be an existing site within OS | |
| v3.4 | PMI#1#MRN | String | No | Medical Record Number (unique identification given by the site) | Should be unique within a site | |
| v3.4 | Event Label | String | No | Event Point Label from the protocol for which this event corresponds. E.g. baseline, surgery, etc. | ||
| v3.4 | Visit Name | String | No | Auto-generated if left blank | Should be unique within OS | |
| v3.4 | Visit Date | String | No | Select the correct date format from UI based on the data in the file | ||
| Collection Site | String | No | Maps to Visit site. Needs to be specified if no default is specified at CP event level. | |||
| v3.4 | Visit Status | String | No |
| Default: 'Complete' | |
| v3.4 | Clinical Diagnosis | String | No | Default: 'Not Specified' | ||
| v3.4 | Clinical Status | String | No |
| Default: 'Not Specified' | |
| v3.4 | Path. Number | String | No | Surgical Pathology Number | Default: 'Not Specified' | |
| v3.4 | Visit Comments | String | No | |||
| v3.4 | 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 | Needs to be specified when the auto label generation is OFF OR 'Manual Input' is set to 'Yes' | Should be unique within the system | ||
| Barcode | String | No | 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' | ||
| Quantity | Numeric | Yes | Default units:
| Should be greater than zero ("0") | ||
| Concentration | Numeric | No | Concentration units are
| 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, 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
How to create parent and child specimens using master specimen template when labels are autogenerated?
- 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 user interface
- Add required data in their respective columns and codes in the 'Specimen Requirement Code' column to link the parent and child specimens. Refer to the example sheet attached