Iz heart tier2 by idazucchi · Pull Request #1651 · HumanCellAtlas/metadata-schema

idazucchi · 2026-02-11T15:31:44Z

Release notes

This PR adds the tier 2 fields requested by the Heart bionetwork (reference sheet here) - none of the fields added in this PR are required

Please note that the modules blood_test, lifestyle are introduced in the Adipose PR which will be merged before the Heart PR, I pulled them into this branch because I need to add fields to them

New optional fields

For module/biomaterial/medical_history.json :

diseases_history
device_treatment
cardioplegia

For module/biomaterial/lifestyle.json :

substance_type
substance_frequency
substance_use_duration
substance_duration_since_last_use

For module/biomaterial/medical_tests.json :

ecg_heart_rate
ecg_heart_rhythm
ecg_pr_interval_duration
ecg_qrs_complex_duration
ecg_lbbb_rbbb_ivcd
ecg_qt_interval_corrected
ecg_time_offset
echo_aortic_stenosis
echo_aortic_regurgitation
echo_mitral_regurgitation
echo_mitral_stenosis
echo_tricuspid_regurgitation
echo_estimated_rvsp
echo_lvedv
echo_lvedv_indexed
echo_lvesv
echo_lvesv_indexed
echo_lvef
echo_lv_mass
echo_lv_mass_indexed
echo_rv_fac
echo_tapse
echo_lv_septum_thickness
echo_pw_thickness
echo_la_dimension
echo_lav_indexed
echo_time_offset
mri_lvedv
mri_lvedv_indexed
mri_lvesv
mri_lvesv_indexed
mri_lvef
mri_lv_mass
mri_lv_mass_indexed
mri_rv_ejection_fraction
mri_mid_wall_lge
mri_epicardial_lge
mri_infarct_pattern_lge
mri_myocardial_oedema
mri_time_offset
mps_lvef
mps_inducible_ischaemic
mps_scar
mps_time_offset

For module/biomaterial/blood_test.json :

sodium
sodium_unit
potassium
potassium_unit
urea
urea_unit
creatinine
creatinine_unit
total_bilirubin
total_bilirubin_unit

For type/biomaterial/specimen_from_organism.json :

transplant_rejection_reason"

Changes to existing fields

For specimen_from_organism.json:

transplant_organ : changed the type from boolean to enum. The enum validation is not compatible with the boolean, but the mapping between boolean and enum is clear so moving to a more recent version of the schema will be easy if needed

Reviews requested

Need 4 Reviewers to approve because this is a major update

It's already part of the gut pr

hannes-ucsc

Many of the regexes in here are buggy and pass on nonsensical inputs

I believe I posted a working alternative on one your other PRs.

…time_to_laboratory

# Conflicts: # docs/jsonBrowser/type.md # json_schema/type/biomaterial/specimen_from_organism.json # json_schema/type/protocol/biomaterial_collection/collection_protocol.json # json_schema/versions.json

idazucchi · 2026-02-27T16:16:19Z

Hi @hannes-ucsc
I've addressed the regex issue, please let me know if you have other comments

Copilot

Pull request overview

This PR expands the metadata schema to support additional (mostly optional) tier-2 biomaterial and clinical fields (notably for Heart), introduces new biomaterial modules, and updates associated docs/tests and CI configuration to match the schema changes.

Changes:

Added new schema properties across biomaterial modules/types (e.g., expanded medical tests/history, transplant metadata updates).
Introduced new biomaterial modules (blood_test, lifestyle) and wired them into existing schemas and docs.
Updated testing/tooling docs and CI to run Python tests with pytest, plus updated some example project test JSONs.

Reviewed changes

Copilot reviewed 21 out of 25 changed files in this pull request and generated 10 comments.

Show a summary per file

File	Description
tests/schema_test_files/project/test_pass_project_0.json	Updates project example to schema v20 and adds required `data_use_restriction`.
tests/schema_test_files/project/test_fail_project_0.json	Updates failing project example to schema v20 and adds required `data_use_restriction`.
tests/README.md	Updates Node instructions and adds VS Code test-running guidance.
requirements.txt	Adds `pytest` for Python test execution.
package-lock.json	Adds a root lockfile (separate from `tests/package-lock.json`).
json_schema/versions.json	Registers new biomaterial modules in the version map.
json_schema/update_log.csv	Adds release-log entries for some schema changes.
json_schema/type/protocol/sequencing/library_preparation_protocol.json	Adds `processing_time`.
json_schema/type/protocol/biomaterial_collection/collection_protocol.json	Adds `biopsy_procedure` enum.
json_schema/type/biomaterial/specimen_from_organism.json	Changes `transplant_organ` to enum; adds transplant and other new fields.
json_schema/type/biomaterial/cell_suspension.json	Adds `nuclei_yield`.
json_schema/module/biomaterial/reproductive_history.json	Fixes `describedBy` pattern; adds `menstrual_cycle_stage`.
json_schema/module/biomaterial/medical_tests.json	Adds ECG/ECHO/MRI/MPS heart-related metrics.
json_schema/module/biomaterial/medical_history.json	Adds fasting time, disease history, device treatment, cardioplegia, and blood test module ref.
json_schema/module/biomaterial/lifestyle.json	New schema module for lifestyle/substance-use fields.
json_schema/module/biomaterial/human_specific.json	Updates BMI representation; adds waist metrics and lifestyle module ref.
json_schema/module/biomaterial/blood_test.json	New schema module for blood-test results and units.
docs/jsonBrowser/type.md	Updates generated type docs for new/changed fields.
docs/jsonBrowser/required_fields.md	Updates generated required-fields docs for new modules.
docs/jsonBrowser/module.md	Updates generated module docs for new/changed fields.
.vscode/settings.json	Adds local editor test runner + pytest configuration.
.pullapprove.yml	Adjusts reviewer lists/groups.
.gitignore	Adds `*.pyc`.
.github/workflows/schema-tests.yml	Switches Python test invocation to `pytest`.

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

json_schema/module/biomaterial/human_specific.json

json_schema/update_log.csv

tests/README.md

json_schema/type/biomaterial/specimen_from_organism.json

json_schema/module/biomaterial/blood_test.json

json_schema/update_log.csv

tests/README.md

json_schema/type/protocol/biomaterial_collection/collection_protocol.json

…cursor's Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

.github/workflows/schema-tests.yml

hannes-ucsc

I had to abandon my review because it appears that both this PR and https://github.com/HumanCellAtlas/metadata-schema/pull/1638/changes touch some of the same files. The overlap is significant, so I think we should focus on on PR at a time. I won't be able to review this again until the other has been merged.

hannes-ucsc · 2026-03-10T17:49:00Z

json_schema/type/biomaterial/cell_suspension.json

+        },
+        "nuclei_yield": {
+            "description": "Number of nuclei sequenced per mg of tissue.",
+            "type": "integer",


Suggested change

"type": "integer",

"type": "integer",

"minimum": 0,

hannes-ucsc · 2026-03-10T17:49:30Z

json_schema/module/biomaterial/medical_history.json

        },
+        "fasting_time": {
+            "description": "Duration of the donor's fasting period (in hours) prior to sample collection.",
+            "type": "integer",


Suggested change

"type": "integer",

"type": "integer",

"minimum": 0,

hannes-ucsc · 2026-03-10T17:50:09Z

json_schema/module/biomaterial/blood_test.json

+        },
+        "androstenedione": {
+            "description": "Androstenedione in the last blood test of the donor before collection.",
+            "type": "number",


Suggested change

"type": "number",

"type": "number",

"minimum": 0,

hannes-ucsc · 2026-03-10T17:50:29Z

json_schema/module/biomaterial/blood_test.json

+        },
+        "dhea": {
+            "description": "Dehydroepiandrosterone (DHEA) in the last blood test of the donor before collection.",
+            "type": "number",


Suggested change

"type": "number",

"type": "number",

"minimum": 0,

hannes-ucsc · 2026-03-10T17:50:36Z

json_schema/module/biomaterial/blood_test.json

+        },
+        "estrogen": {
+            "description": "Estrogen in the last blood test of the donor before collection.",
+            "type": "number",


Suggested change

"type": "number",

"type": "number",

"minimum": 0,

hannes-ucsc · 2026-03-10T17:50:56Z

json_schema/module/biomaterial/blood_test.json

+        },
+        "free_fatty_acid": {
+            "description": "Free Fatty Acid (FFA) in the last blood test of the donor before collection.",
+            "type": "number",


Suggested change

"type": "number",

"type": "number",

"minimum": 0,

hannes-ucsc · 2026-03-10T17:51:03Z

json_schema/module/biomaterial/blood_test.json

+        },
+        "haematocrit": {
+            "description": "Percentage of red blood cells in whole blood from the donor's last blood test prior to biopsy collection.",
+            "type": "number",


Suggested change

"type": "number",

"type": "number",

"minimum": 0,

hannes-ucsc · 2026-03-10T17:51:13Z

json_schema/module/biomaterial/blood_test.json

+        },
+        "haemoglobin": {
+            "description": "Concentration of haemoglobin in whole blood from the donor's last blood test prior to biopsy collection.",
+            "type": "number",


Suggested change

"type": "number",

"type": "number",

"minimum": 0,

hannes-ucsc · 2026-03-10T17:51:21Z

json_schema/module/biomaterial/blood_test.json

+        },
+        "hba1c": {
+            "description": "Concentration of glycated hemoglobin (HbA1c) from the donor's last blood test prior to biopsy collection.",
+            "type": "number",


Suggested change

"type": "number",

"type": "number",

"minimum": 0,

hannes-ucsc · 2026-03-10T17:51:36Z

json_schema/module/biomaterial/blood_test.json

+        },
+        "homa_ir": {
+            "description": "Homeostatic Model Assessment of Insulin Resistance (HOMA-IR) in the last blood test of the donor before collection.",
+            "type": "number",


Suggested change

"type": "number",

"type": "number",

"minimum": 0,

idazucchi added 30 commits December 11, 2025 15:53

extend body_mass_index validation to number ranges

b8ca334

add menstrual_cycle_stage

fdce2cd

fix reproductive_history pattern

519b650

added new blood_test module

93fcea3

added androstenedione blood test

1d312d8

added dhea blood test

1b571c8

added estrogen blood test

80e0b27

added fasting_glucose blood test

a49ef9f

added fasting_insulin blood test

ce857c5

added free_fatty_acid blood test

2714381

added haematocrit blood test

a147c2f

added haemoglobin blood test

7fe06c1

added hba1c blood test

5b9be09

added hdl blood test

c0a6371

added homa_ir blood test

c07d5d6

added ldl blood test

bf95fa2

added platelet_count blood test

b023f71

added shbg blood test

fbe20fe

added testosterone blood test

6255f42

added triglycerides blood test

42611da

added white_blood_cell_count blood test

0245b5b

added bloodtest_time_offset blood test

b1ba63c

added biopsy_procedure to collection protocol

96febde

added nuclei_yield to cell suspension

f84da97

added fasting_time, previous_surgery

be1bbc5

added lifestyle module

8f50781

remove previous_surgery

0c66db3

It's already part of the gut pr

added physical_activity

83a55a4

added waist_circumference, waist_hip_ratio

11fade6

added time_to_laboratory

fab7985

idazucchi added 5 commits February 17, 2026 17:32

Added creatinine blood test

aaba0f6

Added total_bilirubin blood test

56710fd

update project test files

981eafd

Added substance use fields

72ee25d

Expanded transplant fields

e8d84b9

idazucchi self-assigned this Feb 18, 2026

idazucchi added the content Any PR that incorporates changes to the schema label Feb 18, 2026

pullapprove bot requested review from ESapenaVentura, NoopDog, amnonkhen, hannes-ucsc and ncalvanese1 February 18, 2026 15:47

hannes-ucsc requested changes Feb 23, 2026

View reviewed changes

idazucchi and others added 4 commits February 26, 2026 16:11

Merge branch 'staging' into iz-adipose-tier2

0a41472

fix linting errors

95f9ab0

fix regex for body_mass_index, waist_circumference, waist_hip_ratio, …

92548ff

…time_to_laboratory

Merge branch 'iz-adipose-tier2' into iz-heart-tier2

be6035d

# Conflicts: # docs/jsonBrowser/type.md # json_schema/type/biomaterial/specimen_from_organism.json # json_schema/type/protocol/biomaterial_collection/collection_protocol.json # json_schema/versions.json

idazucchi requested a review from hannes-ucsc February 27, 2026 16:16

ncalvanese1 approved these changes Feb 27, 2026

View reviewed changes

NoopDog requested a review from Copilot February 27, 2026 17:59

Copilot started reviewing on behalf of NoopDog February 27, 2026 17:59 View session

Copilot AI reviewed Feb 27, 2026

View reviewed changes

idazucchi and others added 2 commits March 5, 2026 15:01

fix linting comments

92341b3

Apply suggestion from @Copilot - use vscode market place rather than …

9b058c4

…cursor's Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

amnonkhen reviewed Mar 6, 2026

View reviewed changes

.github/workflows/schema-tests.yml Outdated Show resolved Hide resolved

Update .github/workflows/schema-tests.yml to use node 18

ce939af

amnonkhen approved these changes Mar 6, 2026

View reviewed changes

NoopDog approved these changes Mar 6, 2026

View reviewed changes

hannes-ucsc requested changes Mar 10, 2026

View reviewed changes

Conversation

idazucchi commented Feb 11, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Release notes

New optional fields

Changes to existing fields

Reviews requested

Uh oh!

hannes-ucsc left a comment

Choose a reason for hiding this comment

Uh oh!

idazucchi commented Feb 27, 2026

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Reviewed changes

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

hannes-ucsc left a comment

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

6 participants

idazucchi commented Feb 11, 2026 •

edited

Loading