From fb7ec8117cdbfef8caed36e8b0464a8fb4402980 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 27 Jan 2025 14:21:11 +0000 Subject: [PATCH 1/7] Added ncit & broader DRON terms in medication --- json_schema/module/ontology/medication_ontology.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/json_schema/module/ontology/medication_ontology.json b/json_schema/module/ontology/medication_ontology.json index 646af56d..6dee247b 100644 --- a/json_schema/module/ontology/medication_ontology.json +++ b/json_schema/module/ontology/medication_ontology.json @@ -24,20 +24,20 @@ "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; salbutamol suspension" }, "ontology": { "description": "An ontology term identifier in the form prefix:accession.", "type": "string", "graph_restriction": { - "ontologies" : ["obo:dron"], - "classes": ["BFO:0000040"], + "ontologies" : ["obo:ncit","obo:dron"], + "classes": ["ncit:C1908", "bfo:0000002"], "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; DRON:00001511" }, "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.", From cb5adf66d990577a40c77a979028f3907a2f2df1 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 27 Jan 2025 14:26:49 +0000 Subject: [PATCH 2/7] Added ontology updates in docs & update_log.csv --- docs/jsonBrowser/module.md | 4 ++-- docs/jsonBrowser/required_fields.md | 2 +- json_schema/module/ontology/medication_ontology.json | 2 +- json_schema/update_log.csv | 1 + 4 files changed, 5 insertions(+), 4 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 430e1b72..e46f6b61 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -232,8 +232,8 @@ 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 +text | Medication(s) the individual was taking at time of biomaterial collection. | string | yes | | Medication | | Ibuprofen Lysine; Bisoprolol; salbutamol suspension +ontology | An ontology term identifier in the form prefix:accession. | string | no | | Medication ontology ID | | NCIT:C72809; NCIT:C61653; DRON:00001511 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 diff --git a/docs/jsonBrowser/required_fields.md b/docs/jsonBrowser/required_fields.md index 0078d693..0fe164b3 100644 --- a/docs/jsonBrowser/required_fields.md +++ b/docs/jsonBrowser/required_fields.md @@ -287,7 +287,7 @@ text | The name of the strain to which the organism belongs. | string | | Strai ### 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 +text | Medication(s) the individual was taking at time of biomaterial collection. | string | | Medication | | Ibuprofen Lysine; Bisoprolol; salbutamol suspension ### File format ontology Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example --- | --- | --- | --- | --- | --- | --- diff --git a/json_schema/module/ontology/medication_ontology.json b/json_schema/module/ontology/medication_ontology.json index 6dee247b..4aa379cd 100644 --- a/json_schema/module/ontology/medication_ontology.json +++ b/json_schema/module/ontology/medication_ontology.json @@ -43,7 +43,7 @@ "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; salbutamol suspension" } } } \ No newline at end of file diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 3231ff19..13660fbf 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1 +1,2 @@ Schema,Change type,Change message,Version,Date +module/ontology/medication_ontology,major,Changed ontology source for the medication_ontology,, \ No newline at end of file From 51af4236317e447653fc4e14ecda0eb0b58c1c2e Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Wed, 12 Feb 2025 15:18:31 +0000 Subject: [PATCH 3/7] Removed DRON ontology & specified NCIT branches --- docs/jsonBrowser/module.md | 6 +++--- docs/jsonBrowser/required_fields.md | 2 +- json_schema/module/ontology/medication_ontology.json | 10 +++++----- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index e46f6b61..68e2ef8d 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -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 | | Ibuprofen Lysine; Bisoprolol; salbutamol suspension -ontology | An ontology term identifier in the form prefix:accession. | string | no | | Medication ontology ID | | NCIT:C72809; NCIT:C61653; DRON:00001511 -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 term that may be associated with a file format-related ontology term._ diff --git a/docs/jsonBrowser/required_fields.md b/docs/jsonBrowser/required_fields.md index 0fe164b3..d892a351 100644 --- a/docs/jsonBrowser/required_fields.md +++ b/docs/jsonBrowser/required_fields.md @@ -287,7 +287,7 @@ text | The name of the strain to which the organism belongs. | string | | Strai ### 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 | | Ibuprofen Lysine; Bisoprolol; salbutamol suspension +text | Medication(s) the individual was taking at time of biomaterial collection. | string | | Medication | | Ibuprofen Lysine; Bisoprolol; Ambroxol Hydrochloride ### File format ontology Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example --- | --- | --- | --- | --- | --- | --- diff --git a/json_schema/module/ontology/medication_ontology.json b/json_schema/module/ontology/medication_ontology.json index 4aa379cd..c72f34b3 100644 --- a/json_schema/module/ontology/medication_ontology.json +++ b/json_schema/module/ontology/medication_ontology.json @@ -24,26 +24,26 @@ "description": "Medication(s) the individual was taking at time of biomaterial collection.", "type": "string", "user_friendly": "Medication", - "example": "Ibuprofen Lysine; Bisoprolol; salbutamol suspension" + "example": "Ibuprofen Lysine; Bisoprolol; Ambroxol Hydrochloride" }, "ontology": { "description": "An ontology term identifier in the form prefix:accession.", "type": "string", "graph_restriction": { - "ontologies" : ["obo:ncit","obo:dron"], - "classes": ["ncit:C1908", "bfo:0000002"], + "ontologies" : ["obo:ncit"], + "classes": ["ncit:C1505", "ncit:C54060", "ncit:C1909", "ncit:C129986", "ncit:C1899", "ncit:C913"], "relations": ["rdfs:subClassOf"], "direct": false, "include_self": false }, "user_friendly": "Medication ontology ID", - "example": "NCIT:C72809; NCIT:C61653; DRON:00001511" + "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": "Ibuprofen Lysine; Bisoprolol; salbutamol suspension" + "example": "Ibuprofen Lysine; Bisoprolol; Ambroxol Hydrochloride" } } } \ No newline at end of file From 73b432394d02035753f526d4e8d84ae6ef69b2b2 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Thu, 13 Feb 2025 16:12:33 +0000 Subject: [PATCH 4/7] Fixed ontology term typo --- json_schema/module/ontology/medication_ontology.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/json_schema/module/ontology/medication_ontology.json b/json_schema/module/ontology/medication_ontology.json index c72f34b3..27e5bb79 100644 --- a/json_schema/module/ontology/medication_ontology.json +++ b/json_schema/module/ontology/medication_ontology.json @@ -31,7 +31,7 @@ "type": "string", "graph_restriction": { "ontologies" : ["obo:ncit"], - "classes": ["ncit:C1505", "ncit:C54060", "ncit:C1909", "ncit:C129986", "ncit:C1899", "ncit:C913"], + "classes": ["ncit:C1505", "ncit:C54060", "ncit:C1909", "ncit:C129986", "ncit:C1899", "ncit:C1913"], "relations": ["rdfs:subClassOf"], "direct": false, "include_self": false From fa313043d1dd26369ccda611d05c533db7df9a4a Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Thu, 20 Feb 2025 14:30:19 +0000 Subject: [PATCH 5/7] Uppercase in medication classes for consistency among ontology modules --- json_schema/module/ontology/medication_ontology.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/json_schema/module/ontology/medication_ontology.json b/json_schema/module/ontology/medication_ontology.json index 27e5bb79..469b7e51 100644 --- a/json_schema/module/ontology/medication_ontology.json +++ b/json_schema/module/ontology/medication_ontology.json @@ -31,7 +31,7 @@ "type": "string", "graph_restriction": { "ontologies" : ["obo:ncit"], - "classes": ["ncit:C1505", "ncit:C54060", "ncit:C1909", "ncit:C129986", "ncit:C1899", "ncit:C1913"], + "classes": ["NCIT:C1505", "NCIT:C54060", "NCIT:C1909", "NCIT:C129986", "NCIT:C1899", "NCIT:C1913"], "relations": ["rdfs:subClassOf"], "direct": false, "include_self": false From 54e4df5bf5a5e66fa4e48a4bd78ab253019ef5b7 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Fri, 28 Feb 2025 10:58:49 +0000 Subject: [PATCH 6/7] Ran release_prepare.py script. --- changelog.md | 12 ++++++++++++ json_schema/update_log.csv | 1 - json_schema/versions.json | 8 ++++---- 3 files changed, 16 insertions(+), 5 deletions(-) diff --git a/changelog.md b/changelog.md index cc0403f8..866b9ee2 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/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 + ## [Released](https://github.com/HumanCellAtlas/metadata-schema/) ### [type/protocol/biomaterial_collection/dissociation_protocol.json - v6.3.0] - 2025-01-21 diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 13660fbf..3231ff19 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,2 +1 @@ Schema,Change type,Change message,Version,Date -module/ontology/medication_ontology,major,Changed ontology source for the medication_ontology,, \ No newline at end of file diff --git a/json_schema/versions.json b/json_schema/versions.json index 62299a6e..4e42b6a6 100644 --- a/json_schema/versions.json +++ b/json_schema/versions.json @@ -1,5 +1,5 @@ { - "last_update_date": "2025-01-21T10:14:27Z", + "last_update_date": "2025-02-28T10:45:54Z", "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": "7.0.0", + "medical_history": "8.0.0", "medical_tests": "1.0.0", "mouse_specific": "1.0.8", "preservation_storage": "6.1.1", @@ -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", @@ -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" From 3c31dce690742daba159b7a969142310018ce5d9 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Fri, 28 Feb 2025 11:07:57 +0000 Subject: [PATCH 7/7] Release from staging to master 2025-02-28. --- changelog.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/changelog.md b/changelog.md index 866b9ee2..6c79c377 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/ontology/medication_ontology.json - v2.0.0] - 2025-02-28 ### Changed Changed ontology source for the medication_ontology @@ -19,8 +21,6 @@ Changed ontology source for the medication_ontology ### Changed Changed ontology source for the medication_ontology -## [Released](https://github.com/HumanCellAtlas/metadata-schema/) - ### [type/protocol/biomaterial_collection/dissociation_protocol.json - v6.3.0] - 2025-01-21 ### Changed Changed user_friendly name of reagent field