From 3fb3a4652bd755899db8e695c60852e0ff790740 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Wed, 6 Nov 2024 16:57:31 +0000 Subject: [PATCH 1/4] Add dissociation solution, time and temperature fields. --- .../dissociation_protocol.json | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) diff --git a/json_schema/type/protocol/biomaterial_collection/dissociation_protocol.json b/json_schema/type/protocol/biomaterial_collection/dissociation_protocol.json index 3a87aad3a..e3afbc7bb 100644 --- a/json_schema/type/protocol/biomaterial_collection/dissociation_protocol.json +++ b/json_schema/type/protocol/biomaterial_collection/dissociation_protocol.json @@ -55,6 +55,55 @@ "$ref": "module/process/purchased_reagents.json" }, "user_friendly": "Protocol reagents" + }, + "digestion_time": { + "description": "Time of digestion of the specimen.", + "type": "integer", + "example": "2; 5; 10", + "user_friendly": "Digestion time" + }, + "digestion_time_unit": { + "description": "The unit in which the digestion time is expressed.", + "type": "object", + "$ref": "module/ontology/time_unit_ontology.json", + "user_friendly": "Digestion time unit" + }, + "digestion_temperature": { + "description": "Temperature of digestion in Celsius or in general terms (i.e. cold, warm, room temperature)", + "pattern": "\\d+|frozen|cold|room temperature|warm", + "type": "string", + "example": "4; 37.5; cold", + "user_friendly": "Digestion temperature" + }, + "digestion_solution": { + "description": "Enzyme(s) or reagent(s) of the solution that was used for the digestion of the specimen.", + "type": "array", + "items": { + "type": "string", + "enum": [ + "Citric-acid based", + "Detergent-based", + "Lysis buffer", + "Collagenase", + "Collagenase A", + "Collagenase B", + "Collagenase complex", + "Collagenase D", + "Collagenase I", + "Collagenase II", + "Collagenase IV", + "Dispase", + "Dispase II", + "DNAse", + "DNAse I", + "Elastase", + "Liberase", + "Protease", + "Trypsin-like", + "Trypsin" + ] + }, + "user_friendly": "Digestion solution" } } } From da456686da035f1beb7db72599306af50da75b31 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Thu, 21 Nov 2024 16:53:17 +0200 Subject: [PATCH 2/4] Add dissociation fields - init commit --- docs/jsonBrowser/type.md | 6 +++++- .../dissociation_protocol.json | 12 ++++++------ json_schema/update_log.csv | 5 +++++ 3 files changed, 16 insertions(+), 7 deletions(-) diff --git a/docs/jsonBrowser/type.md b/docs/jsonBrowser/type.md index 5a181e708..0ee3d6e75 100644 --- a/docs/jsonBrowser/type.md +++ b/docs/jsonBrowser/type.md @@ -190,7 +190,11 @@ schema_type | The type of the metadata schema entity. | string | yes | | | pro provenance | Provenance information provided by the system. | object | no | [See provenance](.md#provenance) | | | protocol_core | Core protocol-level information. | object | yes | [See core protocol_core](core.md#protocol-core) | Protocol core | | method | How cells or organelles were dissociated. | object | yes | [See module process_type_ontology](module.md#process-type-ontology) | Dissociation method | | -reagents | A list of purchased reagents used in this protocol. | array | no | [See module purchased_reagents](module.md#purchased-reagents) | Protocol reagents | | +reagents | A list of purchased reagents used in this protocol. | array | no | [See module purchased_reagents](module.md#purchased-reagents) | Purchased reagents | | +digestion_time | Time of digestion of the specimen. | integer | no | | Digestion time | | 2; 5; 10 +digestion_time_unit | The unit in which the digestion time is expressed. | object | no | [See module time_unit_ontology](module.md#time-unit-ontology) | Digestion time unit | | +digestion_temperature | Temperature of digestion in Celsius or in general terms (i.e. cold, warm, room temperature). | string | no | | Digestion temperature | | 4; 37; cold +digestion_solution | Enzyme(s) or reagent(s) of the solution that was used for the digestion of the specimen. | array | no | | Digestion solution | Citric-acid based, Detergent-based, Lysis buffer, Collagenase, Collagenase A, Collagenase B, Collagenase complex, Collagenase D, Collagenase I, Collagenase II, Collagenase IV, Dispase, Dispase II, DNAse, DNAse I, Elastase, Liberase, Protease, Trypsin, Trypsin-like | ## iPSC induction protocol _Information about how a biomaterial is treated to become an induced pluripotent stem cell._ diff --git a/json_schema/type/protocol/biomaterial_collection/dissociation_protocol.json b/json_schema/type/protocol/biomaterial_collection/dissociation_protocol.json index e3afbc7bb..f21ff4b55 100644 --- a/json_schema/type/protocol/biomaterial_collection/dissociation_protocol.json +++ b/json_schema/type/protocol/biomaterial_collection/dissociation_protocol.json @@ -54,7 +54,7 @@ "type": "object", "$ref": "module/process/purchased_reagents.json" }, - "user_friendly": "Protocol reagents" + "user_friendly": "Purchased reagents" }, "digestion_time": { "description": "Time of digestion of the specimen.", @@ -69,10 +69,10 @@ "user_friendly": "Digestion time unit" }, "digestion_temperature": { - "description": "Temperature of digestion in Celsius or in general terms (i.e. cold, warm, room temperature)", - "pattern": "\\d+|frozen|cold|room temperature|warm", + "description": "Temperature of digestion in Celsius or in general terms (i.e. cold, warm, room temperature).", + "pattern": "\\d+(\\.\\d+)|frozen|cold|room temperature|warm", "type": "string", - "example": "4; 37.5; cold", + "example": "4; 37; cold", "user_friendly": "Digestion temperature" }, "digestion_solution": { @@ -99,8 +99,8 @@ "Elastase", "Liberase", "Protease", - "Trypsin-like", - "Trypsin" + "Trypsin", + "Trypsin-like" ] }, "user_friendly": "Digestion solution" diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 3231ff199..de80d6269 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1 +1,6 @@ Schema,Change type,Change message,Version,Date +type/protocol/biomaterial_collection/dissociation_protocol,minor,Change of user_friendly name of reagent field,, +type/protocol/biomaterial_collection/dissociation_protocol,minor,Add digestion_time field,, +type/protocol/biomaterial_collection/dissociation_protocol,minor,Add digestion_time_unit field,, +type/protocol/biomaterial_collection/dissociation_protocol,minor,Add digestion_temperature field,, +type/protocol/biomaterial_collection/dissociation_protocol,minor,Add digestion_solution field,, From 8a31c751971347fe53fbf7d6fb0fbc615c78f6ec Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Fri, 22 Nov 2024 15:51:30 +0200 Subject: [PATCH 3/4] Updated log message --- json_schema/update_log.csv | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index de80d6269..ada2da410 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,6 +1,6 @@ Schema,Change type,Change message,Version,Date -type/protocol/biomaterial_collection/dissociation_protocol,minor,Change of user_friendly name of reagent field,, -type/protocol/biomaterial_collection/dissociation_protocol,minor,Add digestion_time field,, -type/protocol/biomaterial_collection/dissociation_protocol,minor,Add digestion_time_unit field,, -type/protocol/biomaterial_collection/dissociation_protocol,minor,Add digestion_temperature field,, -type/protocol/biomaterial_collection/dissociation_protocol,minor,Add digestion_solution field,, +type/protocol/biomaterial_collection/dissociation_protocol,minor,Changed of user_friendly name of reagent field,, +type/protocol/biomaterial_collection/dissociation_protocol,minor,Added optional digestion_time field,, +type/protocol/biomaterial_collection/dissociation_protocol,minor,Added optional digestion_time_unit field,, +type/protocol/biomaterial_collection/dissociation_protocol,minor,Added optional digestion_temperature field,, +type/protocol/biomaterial_collection/dissociation_protocol,minor,Added optional digestion_solution field,, From 95952dda8df168e56338420156efc4b7c4546a44 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Fri, 20 Dec 2024 13:18:53 +0200 Subject: [PATCH 4/4] Fix pattern for digestion_temperature --- .../biomaterial_collection/dissociation_protocol.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/json_schema/type/protocol/biomaterial_collection/dissociation_protocol.json b/json_schema/type/protocol/biomaterial_collection/dissociation_protocol.json index f21ff4b55..b6fbcf07d 100644 --- a/json_schema/type/protocol/biomaterial_collection/dissociation_protocol.json +++ b/json_schema/type/protocol/biomaterial_collection/dissociation_protocol.json @@ -57,7 +57,7 @@ "user_friendly": "Purchased reagents" }, "digestion_time": { - "description": "Time of digestion of the specimen.", + "description": "Time of digestion of the specimen.", "type": "integer", "example": "2; 5; 10", "user_friendly": "Digestion time" @@ -70,7 +70,7 @@ }, "digestion_temperature": { "description": "Temperature of digestion in Celsius or in general terms (i.e. cold, warm, room temperature).", - "pattern": "\\d+(\\.\\d+)|frozen|cold|room temperature|warm", + "pattern": "\\d+(\\.\\d+)?|frozen|cold|room temperature|warm", "type": "string", "example": "4; 37; cold", "user_friendly": "Digestion temperature"