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Release from staging to master 2025-02-28. #1612

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merged 9 commits into from
Feb 28, 2025
Merged

Release from staging to master 2025-02-28. #1612

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fb7ec81
Added ncit & broader DRON terms in medication
arschat Jan 27, 2025
cb5adf6
Added ontology updates in docs & update_log.csv
arschat Jan 27, 2025
51af423
Removed DRON ontology & specified NCIT branches
arschat Feb 12, 2025
73b4323
Fixed ontology term typo
arschat Feb 13, 2025
fa31304
Uppercase in medication classes for consistency among ontology modules
arschat Feb 20, 2025
54e4df5
Ran release_prepare.py script.
arschat Feb 28, 2025
c96f658
Merge pull request #1605 from HumanCellAtlas/ac-medication-ncit-Issue…
arschat Feb 28, 2025
85fb896
Merge branch 'master' of github.com:HumanCellAtlas/metadata-schema in…
arschat Feb 28, 2025
3c31dce
Release from staging to master 2025-02-28.
arschat Feb 28, 2025
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12 changes: 12 additions & 0 deletions changelog.md
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Expand Up @@ -9,6 +9,18 @@ and (starting with v4.0.0) this project adheres to [Semantic Versioning](http://

## [Released](https://github.com/HumanCellAtlas/metadata-schema/)

### [module/ontology/medication_ontology.json - v2.0.0] - 2025-02-28
### Changed
Changed ontology source for the medication_ontology

### [module/biomaterial/medical_history.json - v8.0.0] - 2025-02-28
### Changed
Changed ontology source for the medication_ontology

### [type/biomaterial/donor_organism.json - v18.0.0] - 2025-02-28
### Changed
Changed ontology source for the medication_ontology

### [type/protocol/biomaterial_collection/dissociation_protocol.json - v6.3.0] - 2025-01-21
### Changed
Changed user_friendly name of reagent field
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6 changes: 3 additions & 3 deletions docs/jsonBrowser/module.md
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Expand Up @@ -232,9 +232,9 @@ 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
text | Medication(s) the individual was taking at time of biomaterial collection. | string | yes | | Medication | | Ibuprofen Lysine; Bisoprolol; Ambroxol Hydrochloride
ontology | An ontology term identifier in the form prefix:accession. | string | no | | Medication ontology ID | | NCIT:C72809; NCIT:C61653; NCIT:C78113
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 | | Ibuprofen Lysine; Bisoprolol; Ambroxol Hydrochloride

## File format ontology<a name='File format ontology'></a>
_A term that may be associated with a file format-related ontology term._
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2 changes: 1 addition & 1 deletion docs/jsonBrowser/required_fields.md
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Expand Up @@ -287,7 +287,7 @@ text | The name of the strain to which the organism belongs. | string | | Strai
### Medication ontology<a name='Medication ontology'></a>
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
text | Medication(s) the individual was taking at time of biomaterial collection. | string | | Medication | | Ibuprofen Lysine; Bisoprolol; Ambroxol Hydrochloride
### File format ontology<a name='File format ontology'></a>
Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example
--- | --- | --- | --- | --- | --- | ---
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10 changes: 5 additions & 5 deletions json_schema/module/ontology/medication_ontology.json
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Expand Up @@ -24,26 +24,26 @@
"description": "Medication(s) the individual was taking at time of biomaterial collection.",
"type": "string",
"user_friendly": "Medication",
"example": "bisoprolol; paracetamol; loratadine"
"example": "Ibuprofen Lysine; Bisoprolol; Ambroxol Hydrochloride"
},
"ontology": {
"description": "An ontology term identifier in the form prefix:accession.",
"type": "string",
"graph_restriction": {
"ontologies" : ["obo:dron"],
"classes": ["BFO:0000040"],
"ontologies" : ["obo:ncit"],
"classes": ["NCIT:C1505", "NCIT:C54060", "NCIT:C1909", "NCIT:C129986", "NCIT:C1899", "NCIT:C1913"],
"relations": ["rdfs:subClassOf"],
"direct": false,
"include_self": false
},
"user_friendly": "Medication ontology ID",
"example": "CHEBI:3127; CHEBI:46195; CHEBI:6538"
"example": "NCIT:C72809; NCIT:C61653; NCIT:C78113"
},
"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"
"example": "Ibuprofen Lysine; Bisoprolol; Ambroxol Hydrochloride"
}
}
}
8 changes: 4 additions & 4 deletions json_schema/versions.json
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@@ -1,5 +1,5 @@
{
"last_update_date": "2025-01-21T10:14:27Z",
"last_update_date": "2025-02-28T10:45:54Z",
"version_numbers": {
"core": {
"biomaterial": {
Expand All @@ -26,7 +26,7 @@
"familial_relationship": "6.0.3",
"growth_conditions": "6.4.2",
"human_specific": "1.0.11",
"medical_history": "7.0.0",
"medical_history": "8.0.0",
"medical_tests": "1.0.0",
"mouse_specific": "1.0.8",
"preservation_storage": "6.1.1",
Expand All @@ -51,7 +51,7 @@
"library_amplification_ontology": "1.2.5",
"library_construction_ontology": "1.2.5",
"mass_unit_ontology": "5.3.5",
"medication_ontology": "1.0.0",
"medication_ontology": "2.0.0",
"microscopy_ontology": "1.0.5",
"organ_ontology": "5.3.7",
"organ_part_ontology": "5.3.5",
Expand Down Expand Up @@ -95,7 +95,7 @@
"biomaterial": {
"cell_line": "16.0.0",
"cell_suspension": "14.0.0",
"donor_organism": "17.1.0",
"donor_organism": "18.0.0",
"imaged_specimen": "3.5.0",
"organoid": "11.5.0",
"specimen_from_organism": "10.9.0"
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