From c0057f175f7bf46c0d5814107d215c77d277803b Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Fri, 25 Oct 2024 14:33:41 +0100 Subject: [PATCH 1/5] Add medication ontology --- docs/jsonBrowser/module.md | 14 +++++- docs/jsonBrowser/required_fields.md | 4 ++ .../module/biomaterial/medical_history.json | 11 +++-- .../module/ontology/medication_ontology.json | 49 +++++++++++++++++++ json_schema/update_log.csv | 2 + json_schema/versions.json | 1 + 6 files changed, 75 insertions(+), 6 deletions(-) create mode 100644 json_schema/module/ontology/medication_ontology.json diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index af2e62d83..fe7f974f8 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -214,6 +214,17 @@ text | The name of the strain to which the organism belongs. | string | yes | | ontology | An ontology term identifier in the form prefix:accession. | string | no | | Strain ontology ID | | EFO:0004472; EFO:0000602 ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | | Strain ontology label | | C57BL/6; BALB/c +## Medication ontology +_A term that may be associated with a medication-related ontology term._ + +Location: module/ontology/medication_ontology.json + +Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example +--- | --- | --- | --- | --- | --- | --- | --- +text | Medication(s) the individual was taking at time of biomaterial collection. | string | yes | | Medication | | bisoprolol; paracetamol; loratadine +ontology | An ontology term identifier in the form prefix:accession. | string | no | | Medication ontology ID | | CHEBI:3127; CHEBI:46195; CHEBI:6538 +ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | | Medication ontology label | | bisoprolol; paracetamol; loratadine + ## File format ontology _A term that may be associated with a file format-related ontology term._ @@ -520,7 +531,7 @@ Location: module/biomaterial/medical_history.json Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example --- | --- | --- | --- | --- | --- | --- | --- alcohol_history | Estimated amount of alcohol consumed per day. | string | no | | Alcohol history | | 3-6 alcohol units/day; 1 drink per day -medication | Medications the individual was taking at time of biomaterial collection. | string | no | | Medications | | Naproxen 500mg/day; Citalopram 20mg/day +medication | Medication(s) the individual was taking at time of biomaterial collection. | array | no | [See module medication_ontology](module.md#medication-ontology) | Medication | | smoking_status | Whether the individual is actively, was formerly or never consumed smoking tobacco products like cigarettes, cigars, pipe etc. | string | no | | Smoking status | active, former, never | Should be one of: active, former, never. smoking_pack_years | Estimated number of packs (20 cigarettes) smoked per day multiplied by the number of years the individual was smoking. | number | no | | Smoking pack years | | 4.55 years_since_smoking_cessation | If smoking status is 'former', specify the number of years since smoking cessation. | integer | no | | Years since smoking cessation | | 12 @@ -636,3 +647,4 @@ Property name | Description | Type | Required? | Object reference? | User friend plate_label | A label or name for the plate on which the well is located. | string | yes | | Plate label | | 2217 well_label | A label or name for the well in which the cell is located. | string | no | | Well label | | A1 well_quality | Quality of well if imaged before sequencing. | string | no | | Well quality | OK, control, 2-cell well, control, empty well, low quality cell | Should be one of: 'OK', 'control, 2-cell well', 'control, empty well', or 'low quality cell'. + diff --git a/docs/jsonBrowser/required_fields.md b/docs/jsonBrowser/required_fields.md index 7ba742bae..e02cc763b 100644 --- a/docs/jsonBrowser/required_fields.md +++ b/docs/jsonBrowser/required_fields.md @@ -280,6 +280,10 @@ text | The text for the term as the user provides it. | string | | Disease | | Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example --- | --- | --- | --- | --- | --- | --- text | The name of the strain to which the organism belongs. | string | | Strain | | C57BL/6; BALB/c +### Medication ontology +Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example +--- | --- | --- | --- | --- | --- | --- +text | Medication(s) the individual was taking at time of biomaterial collection. | string | | Medication | | bisoprolol; paracetamol; loratadine ### File format ontology Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example --- | --- | --- | --- | --- | --- | --- diff --git a/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json index 224bc79e5..112e5587d 100644 --- a/json_schema/module/biomaterial/medical_history.json +++ b/json_schema/module/biomaterial/medical_history.json @@ -25,11 +25,12 @@ "guidelines": "Enter the amount consumed per day using units such as alcohol units (10mL or 8g of alcohol) or drinks (14g of alcohol)." }, "medication": { - "description": "Medications the individual was taking at time of biomaterial collection.", - "type": "string", - "user_friendly": "Medications", - "example": "Naproxen 500mg/day; Citalopram 20mg/day", - "guidelines": "Enter the medication and dosage. Separate multiple medications with commas." + "description": "Medication(s) the individual was taking at time of biomaterial collection.", + "type": "array", + "items": { + "$ref": "module/ontology/medication_ontology.json" + }, + "user_friendly": "Medication" }, "smoking_status": { "description": "Whether the individual is actively, was formerly or never consumed smoking tobacco products like cigarettes, cigars, pipe etc.", diff --git a/json_schema/module/ontology/medication_ontology.json b/json_schema/module/ontology/medication_ontology.json new file mode 100644 index 000000000..646af56d7 --- /dev/null +++ b/json_schema/module/ontology/medication_ontology.json @@ -0,0 +1,49 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema#", + "description": "A term that may be associated with a medication-related ontology term.", + "additionalProperties": false, + "required": [ + "text" + ], + "title": "Medication ontology", + "name": "medication_ontology", + "type": "object", + "properties": { + "describedBy" : { + "description": "The URL reference to the schema.", + "pattern" : "^(http|https)://schema.(.*?)humancellatlas.org/module/ontology/(([0-9]{1,}.[0-9]{1,}.[0-9]{1,})|([a-zA-Z]*?))/medication_ontology", + "type": "string" + }, + "schema_version": { + "description": "Version number in major.minor.patch format.", + "type": "string", + "pattern": "^[0-9]{1,}.[0-9]{1,}.[0-9]{1,}$", + "example": "4.6.1" + }, + "text": { + "description": "Medication(s) the individual was taking at time of biomaterial collection.", + "type": "string", + "user_friendly": "Medication", + "example": "bisoprolol; paracetamol; loratadine" + }, + "ontology": { + "description": "An ontology term identifier in the form prefix:accession.", + "type": "string", + "graph_restriction": { + "ontologies" : ["obo:dron"], + "classes": ["BFO:0000040"], + "relations": ["rdfs:subClassOf"], + "direct": false, + "include_self": false + }, + "user_friendly": "Medication ontology ID", + "example": "CHEBI:3127; CHEBI:46195; CHEBI:6538" + }, + "ontology_label": { + "description": "The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.", + "type": "string", + "user_friendly": "Medication ontology label", + "example": "bisoprolol; paracetamol; loratadine" + } + } +} \ No newline at end of file diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 3231ff199..6b9f2e170 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1 +1,3 @@ Schema,Change type,Change message,Version,Date +module/biomaterial/medical_history,major,"Update medication field with ontology Fix#1589",, +module/ontology/medication_ontology,major,"Created medication ontology module Fix#1589",, \ No newline at end of file diff --git a/json_schema/versions.json b/json_schema/versions.json index bcd03b5fc..3450d173b 100644 --- a/json_schema/versions.json +++ b/json_schema/versions.json @@ -50,6 +50,7 @@ "library_amplification_ontology": "1.2.5", "library_construction_ontology": "1.2.5", "mass_unit_ontology": "5.3.5", + "medication_ontology": "0.0.0", "microscopy_ontology": "1.0.5", "organ_ontology": "5.3.7", "organ_part_ontology": "5.3.5", From f4a27c81bcaa845c6a8ab601bdca1e43dba9ab5c Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Tue, 29 Oct 2024 09:20:49 +0000 Subject: [PATCH 2/5] Added change messages with keywords used in release_script.py --- json_schema/update_log.csv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 6b9f2e170..34c6d15e6 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date -module/biomaterial/medical_history,major,"Update medication field with ontology Fix#1589",, -module/ontology/medication_ontology,major,"Created medication ontology module Fix#1589",, \ No newline at end of file +module/biomaterial/medical_history,major,"Changed medication field type Fix#1589",, +module/ontology/medication_ontology,major,"Added medication ontology module Fix#1589",, \ No newline at end of file From 715b44fe014d7c72f30cb3a405ee975569c8b3d9 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Wed, 6 Nov 2024 17:01:03 +0000 Subject: [PATCH 3/5] Ran human_readable_json.py script --- docs/jsonBrowser/module.md | 6 +++--- docs/jsonBrowser/required_fields.md | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index fe7f974f8..eeb1db007 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -376,7 +376,7 @@ Location: module/project/hca_bionetwork.json Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example --- | --- | --- | --- | --- | --- | --- | --- name | HCA Bionetwork the project is a part of (e.g. Kidney). | string | no | | Official HCA Bionetwork | Adipose, Breast, Development, Eye, Genetic Diversity, Gut, Heart, Immune, Kidney, Liver, Lung, Musculoskeletal, Nervous System, Oral & Craniofacial, Organoid, Pancreas, Reproduction, Skin | Kidney; Lung -hca_tissue_atlas | A field describing if the project is part of a HCA Tissue Atlas (e.g. Brain Alzheimer Atlas). | string | no | | HCA Tissue Atlas | Adipose, Blood, Brain, Breast, Development, Eye, GDN, Gut, Heart, Immune, Kidney, Liver, Lung, MSK, ORCF, Organoid-Endoderm, Organoid-Neural, Pancreas Retina, Reproduction, Skin | Retina +hca_tissue_atlas | A field describing if the project is part of a HCA Tissue Atlas (e.g. Brain Alzheimer Atlas). | string | no | | HCA Tissue Atlas | Adipose, Blood, Brain, Breast, Development, Eye, GDN, Gut, Heart, Immune, Kidney, Liver, Lung, MSK, ORCF, Organoid-Endoderm, Organoid-Neural, Pancreas, Retina, Reproduction, Skin | Retina hca_tissue_atlas_version | A field describing which version of the HCA Tissue Atlas is associated with the project (e.g. v1.0; v2.0) | string | no | | Official HCA Tissue Atlas Version | | v1.0; v2.0 atlas_project | A field describing if this project is the HCA Tissue Atlas project which integrates data from other datasets. | boolean | no | | Project Tissue Atlas Status | | Yes; No @@ -478,12 +478,12 @@ Location: module/biomaterial/disease_profile.json Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example --- | --- | --- | --- | --- | --- | --- | --- -copd_gold_stage | Indicating current GOLD stage (Global Initiative for Chronic Obstructive Lung Disease). | integer | no | | GOLD stage | 1, 2, 3, 4 | 1; 2; 3; 4 +copd_gold_stage | Indicate the current GOLD stage (Global Initiative for Chronic Obstructive Lung Disease). | integer | no | | GOLD stage | 1, 2, 3, 4 | 1; 2; 3; 4 copd_mmrc_grade | Indicate the Modified British Medical Research Council (mMRC) dyspnea scale grade. | integer | no | | mMRC grade | 0, 1, 2, 3, 4 | 0, 1; 2; 3; 4 copd_cat_score | Indicate the COPD Assessment Test (CAT) score. | integer | no | | CAT score | | 2; 5; 37 copd_gold_abe_assessment | Indicate the Global Initiative for Chronic Obstructive Lung Disease (GOLD) A, B, C, D assessment group if available. | string | no | | GOLD ABE assessment | A, B, E | A; B; E copd_phenotype | Indicate the COPD disease phenotype(s) of donor. Please indicate all applicable phenotypes of donor. | array | no | | COPD phenotype | COPD not otherwise specified, COPD with emphysema, COPD with bronchitis, COPD with history of asthma, COPD with >300 eos in blood, COPD with allergy, COPD with Chronic Mucus Hypersecretion, COPD with frequent exacerbations | COPD with bronchitis; COPD with history of asthma; COPD with emphysema -copd_emphysema_percentage | Indicate the percentage of the lung that is affected by emphysema as judged based on non-invasive imaging, such as from a CT scan. | number | no | | Percentage of emphysema | | 30; 76; 92 +copd_emphysema_percentage | Indicate the percentage of the lung that is affected by emphysema as judged based on non-invasive imaging, such as from a CT scan. | number | no | | Percentage of emphysema | | ## Preservation and storage _Information relating to how a biomaterial was preserved and/or stored over a period of time._ diff --git a/docs/jsonBrowser/required_fields.md b/docs/jsonBrowser/required_fields.md index e02cc763b..7346337f6 100644 --- a/docs/jsonBrowser/required_fields.md +++ b/docs/jsonBrowser/required_fields.md @@ -357,7 +357,7 @@ _There are no required properties in schema Growth conditions_ ### Medical tests _There are no required properties in schema Medical tests_ ### Disease profile -_There are no required properties in schema disease profile_ +_There are no required properties in schema Disease profile_ ### Preservation and storage _There are no required properties in schema Preservation and storage_ ### Death From 443cb24c6ed4d60ce6f8474d033cebd2a8087b40 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Wed, 6 Nov 2024 17:02:20 +0000 Subject: [PATCH 4/5] Ran release_prepare.py script --- changelog.md | 12 ++++++++++++ json_schema/update_log.csv | 2 -- json_schema/versions.json | 8 ++++---- 3 files changed, 16 insertions(+), 6 deletions(-) diff --git a/changelog.md b/changelog.md index 91659deee..e7f3c796a 100644 --- a/changelog.md +++ b/changelog.md @@ -7,6 +7,18 @@ and (starting with v4.0.0) this project adheres to [Semantic Versioning](http:// ## [Unreleased](https://github.com/HumanCellAtlas/metadata-schema/tree/staging) +### [module/biomaterial/medical_history.json - v7.0.0] - 2024-11-06 +### Changed +Changed medication field type Fix#1589 + +### [module/ontology/medication_ontology.json - v1.0.0] - 2024-11-06 +### Added +Added medication ontology module Fix#1589 + +### [type/biomaterial/donor_organism.json - v17.0.0] - 2024-11-06 +### Changed +Changed medication field type Fix#1589 + ## [Released](https://github.com/HumanCellAtlas/metadata-schema/) ### [type/biomaterial/donor_organism.json - v16.4.0] - 2024-10-21 diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 34c6d15e6..3231ff199 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1 @@ Schema,Change type,Change message,Version,Date -module/biomaterial/medical_history,major,"Changed medication field type Fix#1589",, -module/ontology/medication_ontology,major,"Added medication ontology module Fix#1589",, \ No newline at end of file diff --git a/json_schema/versions.json b/json_schema/versions.json index 3450d173b..8e36fe0ef 100644 --- a/json_schema/versions.json +++ b/json_schema/versions.json @@ -1,5 +1,5 @@ { - "last_update_date": "2024-10-21T12:21:40Z", + "last_update_date": "2024-11-06T17:01:14Z", "version_numbers": { "core": { "biomaterial": { @@ -26,7 +26,7 @@ "familial_relationship": "6.0.3", "growth_conditions": "6.4.2", "human_specific": "1.0.11", - "medical_history": "6.0.0", + "medical_history": "7.0.0", "medical_tests": "1.0.0", "mouse_specific": "1.0.8", "preservation_storage": "6.1.1", @@ -50,7 +50,7 @@ "library_amplification_ontology": "1.2.5", "library_construction_ontology": "1.2.5", "mass_unit_ontology": "5.3.5", - "medication_ontology": "0.0.0", + "medication_ontology": "1.0.0", "microscopy_ontology": "1.0.5", "organ_ontology": "5.3.7", "organ_part_ontology": "5.3.5", @@ -94,7 +94,7 @@ "biomaterial": { "cell_line": "16.0.0", "cell_suspension": "14.0.0", - "donor_organism": "16.4.0", + "donor_organism": "17.0.0", "imaged_specimen": "3.5.0", "organoid": "11.5.0", "specimen_from_organism": "10.9.0" From dfa1e893672aed4803238cb24e99d5b7c0aa49c2 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Wed, 6 Nov 2024 17:09:01 +0000 Subject: [PATCH 5/5] Release from staging to master 2024-11-06. --- changelog.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/changelog.md b/changelog.md index e7f3c796a..8acf4103d 100644 --- a/changelog.md +++ b/changelog.md @@ -7,6 +7,8 @@ and (starting with v4.0.0) this project adheres to [Semantic Versioning](http:// ## [Unreleased](https://github.com/HumanCellAtlas/metadata-schema/tree/staging) +## [Released](https://github.com/HumanCellAtlas/metadata-schema/) + ### [module/biomaterial/medical_history.json - v7.0.0] - 2024-11-06 ### Changed Changed medication field type Fix#1589 @@ -19,8 +21,6 @@ Added medication ontology module Fix#1589 ### Changed Changed medication field type Fix#1589 -## [Released](https://github.com/HumanCellAtlas/metadata-schema/) - ### [type/biomaterial/donor_organism.json - v16.4.0] - 2024-10-21 ### Added Added comorbidities field in the donor_organism Fix#1569