Other TSVs

sample

Related files:

Metadata schema

Version 0 (use this one)
IDs

sample_id

Donor

vital_state
health_status

Medical Procedure

organ_condition
procedure_date
perfusion_solution
pathologist_report
warm_ischemia_time_value
warm_ischemia_time_unit
cold_ischemia_time_value
cold_ischemia_time_unit

Biospecimen

specimen_preservation_temperature
specimen_quality_criteria
specimen_tumor_distance_value
specimen_tumor_distance_unit

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