Other TSVs

organ

Related files:

📝 Excel template: For metadata entry.
📝 TSV template: Alternative for metadata entry.

Metadata schema

Version 2 (use this one)

organ_id
lab_id
laterality
organ_condition
perfusion_solution
transport_solution
warm_ischemic_time_value
warm_ischemic_time_unit
cold_ischemic_time_value
cold_ischemic_time_unit
total_ischemic_time_value
total_ischemic_time_unit
pathology_report
organ_weight_value
weight_unit
organ_height_value
organ_height_unit
organ_width_value
organ_width_unit
organ_length_value
organ_length_unit
organ_volume_value
organ_volume_unit

`organ_id`

Unique HuBMAP identifier for the organ. This can be found in the Submission ID section of a registered donor on the Ingest UI. Example: TEST0001-RK.

constraint	value
required	`True`
pattern (regular expression)	`([A-Z]+[0-9]+)-[A-Z]{2}`

An internal field labs can use it to add whatever ID(s) they want or need for dataset validation and tracking. This could be a single ID (e.g., “Visium_9OLC_A4_S1”) or a delimited list of IDs (e.g., “9OL; 9OLC.A2; Visium_9OLC_A4_S1”). This field will not be accessible to anyone outside of the consortium and no effort will be made to check if IDs provided by one data provider are also used by another. Leave blank if not applicable.

constraint	value
required	`False`

`laterality`

The side of the body from which the organ came. This would be ‘N/A’ for blood, whereas an organ like the uterus would have a value of ‘midline’.

constraint	value
required	`True`
enum	`Left`, `Right`, `Midline`, or `N/A`

`organ_condition`

Health status of the organ at the time of sample recovery.

constraint	value
required	`True`
enum	`Healthy` or `Diseased`

`perfusion_solution`

Type of solution that was used to perfuse the organ. Leave blank if not applicable.

constraint	value
required	`False`
enum	`Miltenyi Tissue Preservation Buffer`, `UWS`, `HTK`, `Belzer MPS/KPS`, `None`, or `Unknown`

`transport_solution`

Type of solution used during transport. Leave blank if not applicable.

constraint	value
required	`False`
enum	`RPMI`, `PBS (1x)`, `Miltenyi Tissue Preservation Buffer`, `UWS`, `HTK`, `Belzer MPS/KPS`, `Saline (Buffered)`, `DMEM`, `None`, or `Unknown`

`warm_ischemic_time_value`

Time interval from interruption of blood supply of tissue to cooling to 4C: For organ donor: cessation of blood flow to perfusion of organ (cooled to 4C) For surgical specimen/biopsy: cessation of blood flow to specimen (time biopsy taken or blood supply is interrupted) to cooling of specimen to 4C.

constraint	value
type	`number`
required	`True`

`warm_ischemic_time_unit`

Time unit for the previous element. Leave blank if not applicable.

constraint	value
required	`False`
enum	`hours` or `minutes`
required if	`warm_ischemic_time_value` present

`cold_ischemic_time_value`

Time interval from cooling to 4C to final preservation. For organ donor: organ preservation flush (cooled to 4C) to final preservation (freezing or fixation). For surgical specimen/biopsy: time specimen is placed at 4C to final preservation (freezing or fixation.

constraint	value
type	`number`
required	`True`

`cold_ischemic_time_unit`

Time unit for the previous element. Leave blank if not applicable.

constraint	value
required	`False`
enum	`hours` or `minutes`
required if	`cold_ischemic_time_value` present

`total_ischemic_time_value`

Total time prior to tissue dissection.

constraint	value
type	`number`
required	`True`

`total_ischemic_time_unit`

Time unit for the previous element. Leave blank if not applicable.

constraint	value
required	`False`
enum	`hours` or `minutes`
required if	`total_ischemic_time_value` present

`pathology_report`

General pathologist report. Further details on organ level QC checks.

constraint	value
required	`True`

`organ_weight_value`

The total organ weight. Leave blank if not applicable.

constraint	value
type	`number`
required	`False`

`weight_unit`

Weight unit. Leave blank if not applicable.

constraint	value
required	`False`
enum	`g` or `kg`

`organ_height_value`

The height value of the organ. Leave blank if not applicable.

constraint	value
type	`number`
required	`False`

`organ_height_unit`

Height unit. Leave blank if not applicable.

constraint	value
required	`False`
enum	`cm` or `mm`
required if	`organ_height_value` present

`organ_width_value`

The width value of the organ. Leave blank if not applicable.

constraint	value
type	`number`
required	`False`

`organ_width_unit`

Width unit. Leave blank if not applicable.

constraint	value
required	`False`
enum	`cm` or `mm`
required if	`organ_width_value` present

`organ_length_value`

The length value of the organ. Leave blank if not applicable.

constraint	value
type	`number`
required	`False`

`organ_length_unit`

Length unit. Leave blank if not applicable.

constraint	value
required	`False`
enum	`cm` or `mm`
required if	`organ_length_value` present

`organ_volume_value`

A measure of the organ volume via buffer/water displacement by submerging the organ to reflect the volume of the organ. (May reflect gas trapping in lung with obstructed airways.) Leave blank if not applicable.

constraint	value
type	`number`
required	`False`

`organ_volume_unit`

Volume unit. Leave blank if not applicable.

constraint	value
required	`False`
enum	`ml`
required if	`organ_volume_value` present