From e8802dcd7aec78df59103c4068ca050087bbef8a Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Wed, 14 Aug 2024 17:37:07 +0100 Subject: [PATCH 1/3] Add comorbidities field --- docs/jsonBrowser/type.md | 1 + json_schema/type/biomaterial/donor_organism.json | 9 +++++++++ json_schema/update_log.csv | 1 + 3 files changed, 11 insertions(+) diff --git a/docs/jsonBrowser/type.md b/docs/jsonBrowser/type.md index 1c02aed5e..e2048e926 100644 --- a/docs/jsonBrowser/type.md +++ b/docs/jsonBrowser/type.md @@ -431,6 +431,7 @@ organism_age | Age of organism in Age units measured since birth. | string | no organism_age_unit | The unit in which Age is expressed. | object | no | [See module time_unit_ontology](module.md#time-unit-ontology) | Age unit | | development_stage | A classification of the developmental stage of the organism. | object | yes | [See module development_stage_ontology](module.md#development-stage-ontology) | Development stage | | diseases | Short description of known disease(s) of the organism. | array | no | [See module disease_ontology](module.md#disease-ontology) | Known disease(s) | | +comorbidities | Short description of comorbidity(-ies) or secondary disease(s) of the organism. | array | no | [See module disease_ontology](module.md#disease-ontology) | Comorbidities | | death | Information about conditions of death of the organism. | object | no | [See module death](module.md#death) | Death conditions | | familial_relationships | Information about other organisms related to this organism. | array | no | [See module familial_relationship](module.md#familial-relationship) | Familial relationship | | medical_tests | Information about the medical tests of the organism. | object | no | [See module medical_tests](module.md#medical-tests) | Medical tests | | diff --git a/json_schema/type/biomaterial/donor_organism.json b/json_schema/type/biomaterial/donor_organism.json index f53e4f72e..5d6e3838b 100644 --- a/json_schema/type/biomaterial/donor_organism.json +++ b/json_schema/type/biomaterial/donor_organism.json @@ -117,6 +117,15 @@ "user_friendly": "Known disease(s)", "guidelines": "Enter 'normal' if no known disease." }, + "comorbidities": { + "description": "Short description of comorbidity(-ies) or secondary disease(s) of the organism.", + "type": "array", + "items": { + "$ref": "module/ontology/disease_ontology.json" + }, + "user_friendly": "Comorbidities", + "guidelines": "Primary disease should be described in Known diseases field. Leave empty if no known comorbidities." + }, "death": { "description": "Information about conditions of death of the organism.", "type": "object", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 3231ff199..a52180dd7 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1 +1,2 @@ Schema,Change type,Change message,Version,Date +type/biomaterial/donor_organism,minor,Added comorbidities field in the donor_organism Fix#1569,, \ No newline at end of file From 44d95013f93d8b7ad83909a9ee936b1d21e8e3c2 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Wed, 18 Sep 2024 15:35:58 +0100 Subject: [PATCH 2/3] Rephrase comorbidities guidelines --- json_schema/type/biomaterial/donor_organism.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/json_schema/type/biomaterial/donor_organism.json b/json_schema/type/biomaterial/donor_organism.json index 5d6e3838b..28e90f89b 100644 --- a/json_schema/type/biomaterial/donor_organism.json +++ b/json_schema/type/biomaterial/donor_organism.json @@ -124,7 +124,7 @@ "$ref": "module/ontology/disease_ontology.json" }, "user_friendly": "Comorbidities", - "guidelines": "Primary disease should be described in Known diseases field. Leave empty if no known comorbidities." + "guidelines": "Primary disease should be described in Known diseases field. Leave empty if no comorbidities are known." }, "death": { "description": "Information about conditions of death of the organism.", From a1c7f170c7c6e9c10e503c836ce7f4234b41df40 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 21 Oct 2024 12:23:45 +0100 Subject: [PATCH 3/3] Ran release_prepare.py script. --- changelog.md | 4 ++++ json_schema/update_log.csv | 1 - json_schema/versions.json | 4 ++-- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/changelog.md b/changelog.md index 6312d58b1..0fa51f01b 100644 --- a/changelog.md +++ b/changelog.md @@ -7,6 +7,10 @@ and (starting with v4.0.0) this project adheres to [Semantic Versioning](http:// ## [Unreleased](https://github.com/HumanCellAtlas/metadata-schema/tree/staging) +### [type/biomaterial/donor_organism.json - v16.4.0] - 2024-10-21 +### Added +Added comorbidities field in the donor_organism Fix#1569 + ## [Released](https://github.com/HumanCellAtlas/metadata-schema/) ### [module/project/hca_bionetwork.json - v1.0.2] - 2024-10-14 diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index a52180dd7..3231ff199 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,2 +1 @@ Schema,Change type,Change message,Version,Date -type/biomaterial/donor_organism,minor,Added comorbidities field in the donor_organism Fix#1569,, \ No newline at end of file diff --git a/json_schema/versions.json b/json_schema/versions.json index 9eb283285..bcd03b5fc 100644 --- a/json_schema/versions.json +++ b/json_schema/versions.json @@ -1,5 +1,5 @@ { - "last_update_date": "2024-10-14T10:11:29Z", + "last_update_date": "2024-10-21T12:21:40Z", "version_numbers": { "core": { "biomaterial": { @@ -93,7 +93,7 @@ "biomaterial": { "cell_line": "16.0.0", "cell_suspension": "14.0.0", - "donor_organism": "16.3.0", + "donor_organism": "16.4.0", "imaged_specimen": "3.5.0", "organoid": "11.5.0", "specimen_from_organism": "10.9.0"