Other TSVs
sample
Related files:
- 📝 Excel template: For metadata entry.
- 📝 TSV template: Alternative for metadata entry.
Metadata schema
Version 0 (use this one)
IDs
Donor
IDs
sample_id
(No description for this field was supplied.) Example: VAN0010-LK-152-162.
| constraint | value |
|---|---|
| required | True |
| pattern (regular expression) | ([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)? |
Donor
vital_state
Identify the vital state of the donor.
| constraint | value |
|---|---|
| required | True |
| enum | living or deceased |
health_status
Patient’s baseline physical condition prior to immediate event leading to organ/tissue acquisition. For example, if a relatively healthy patient suffers trauma, and as a result of reparative surgery, a tissue sample is collected, the subject will be deemed “relatively healthy”. Likewise, a relatively healthy subject may have experienced trauma leading to brain death. As a result of organ donation, a sample is collected. In this scenario, the subject is deemed “relatively healthy.”.
| constraint | value |
|---|---|
| required | True |
| enum | cancer, relatively healthy, or chronic illness |
Medical Procedure
organ_condition
Health status of the organ at the time of sample recovery.
| constraint | value |
|---|---|
| required | True |
| enum | healthy or diseased |
procedure_date
Date of procedure to procure organ.
| constraint | value |
|---|---|
| type | date |
| format | %Y-%m-%d |
| required | True |
perfusion_solution
Type of solution that was used to perfuse the organ.
| constraint | value |
|---|---|
| required | True |
| enum | UWS, HTK, Belzer MPS/KPS, Formalin, Perfadex, Unknown, or None |
pathologist_report
Further details on organ level QC checks.
| constraint | value |
|---|---|
| required | True |
warm_ischemia_time_value
Time interval between cessation of blood flow and cooling to 4C. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
warm_ischemia_time_unit
Time unit. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
| enum | minutes |
| required if | warm_ischemia_time_value present |
cold_ischemia_time_value
Time interval on ice to the start of preservation protocol. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
cold_ischemia_time_unit
Time unit. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
| enum | minutes |
| required if | cold_ischemia_time_value present |
Biospecimen
specimen_preservation_temperature
The temperature of the medium during the preservation process.
| constraint | value |
|---|---|
| required | True |
| enum | Liquid Nitrogen, Liquid Nitrogen Vapor, Freezer (-80 Celsius), Freezer (-20 Celsius), Refrigerator (4 Celsius), or Room Temperature |
specimen_quality_criteria
For example, RIN: 8.7. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
specimen_tumor_distance_value
If surgical sample, how far from the tumor was the sample obtained from. Typically a number of centimeters. Leave blank if not applicable or unknown. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
specimen_tumor_distance_unit
Distance unit. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
| enum | cm |
| required if | specimen_tumor_distance_value present |