Add transplant_organ field in specimen_from_organism

[arschat]

For which schema is a change/update being suggested?

I would like to request an update to the specimen_from_organism.json schema.

What should the change/update be?

I would like to add a new field - transplant_organ - to this schema to allow data contributors to record whether the specimen_from_organism was collected after an organ donation.

This update constitutes a minor change to the schema it affects.

What new field(s) need to be changed/added?

• Field name: transplant_organ
• Field description: Was the specimen collected after extraction for organ transplantation?
• Field type: boolean
• Required: no
• Examples: yes; no
• CV or enum: no

Why is the change requested?

We would like to record if donor organism donated their organs but their organs were considered not fit for transplantation. The quality of the samples is different compared to surgical donors (i.e. biopsy, blood draw) or post-mortem donors. Is one of the upcoming Tier 1 metadata proposed from HCA Integration Teams & Bionetworks

The source of the sample (whether the sample comes from a surgical donor; an organ donor; or deceased subject) can result in different cellular profiles and hence batch effects.

[arschat]

PR #1548

[arschat]

After discussing with HCA execs, they are including 3 options for "sample_source" field.

• post-mortem donor
• organ donor
• surgical donor

Since we already record whether donor was deceased at the time of collection in donor_organism.is_living and on Tier 1, we are interested in recording the quality of the collection (there are very strict guidelines for organs collected for transplantation compared to specimens collected post-mortem) therefore, a boolean value for organ_donor should be enough.

We record the death type of organ donation in donor_organism.death.organ_donation_death_type (after circulatory or brainstem death) but it is in the death module. Organ donation, however can be done from living donors too (i.e. kidney donor), so the new field is not included in the death module.

[arschat]

Moved field at the specimen_from_organism level.