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EEH-2506 - Modified "phenotypes" and "diseases" arrays #64

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Feb 3, 2023
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EEH-2506 - Modified "phenotypes" and "diseases" arrays #64

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bf04bf4
EEH-2506 - Added new ontologies to Disease
M-casado Feb 3, 2023
272863f
EEH-2506 - Modified Phenotypes and Diseases arrays and added "excluded"
M-casado Feb 3, 2023
81b553c
EEH-2506 - Amended "individual" objects in the JSON examples
M-casado Feb 3, 2023
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34 changes: 27 additions & 7 deletions examples/json_validation_tests/individual_valid-1.json
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Original file line number Diff line number Diff line change
Expand Up @@ -30,18 +30,38 @@
"biologicalSex": "male",
"diseases": [
{
"termId": "EFO:0003101",
"termLabel": "testicular seminoma"
"excluded": true,
"disease": {
"termId": "EFO:0003101",
"termLabel": "testicular seminoma"
}
},
{
"termId": "EFO:1000254",
"termLabel": "fibroadenoma"
"excluded": true,
"disease": {
"termId": "MONDO:0019808",
"termLabel": "aortic valve atresia"
}
},
{
"disease": {
"termId": "EFO:1000254",
"termLabel": "fibroadenoma"
}
},
{
"disease": {
"termId": "Orphanet:610",
"termLabel": "Bethlem myopathy"
}
}
],
"phenotypes": [
"phenotypicAbnormalities": [
{
"termId": "HP:0033403",
"termLabel": "Testicular ischemia"
"phenotypicAbnormality": {
"termId": "HP:0033403",
"termLabel": "Testicular ischemia"
}
}
],
"subjectId": "donor-NM305004"
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32 changes: 21 additions & 11 deletions examples/json_validation_tests/object-set_Covid19.json
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Expand Up @@ -16,25 +16,35 @@
"biologicalSex": "male",
"diseases": [
{
"termId": "MONDO:0100096",
"termLabel": "COVID-19"
"disease": {
"termId": "MONDO:0100096",
"termLabel": "COVID-19"
}
},
{
"termId": "EFO:0000400",
"termLabel": "Diabetes Mellitus"
"disease": {
"termId": "EFO:0000400",
"termLabel": "Diabetes Mellitus"
}
},
{
"termId": "EFO:0000318",
"termLabel": "Cardiomyopathy"
"disease": {
"termId": "EFO:0000318",
"termLabel": "Cardiomyopathy"
}
},
{
"termId": "EFO:0009909",
"termLabel": "Chronic Kidney Disease"
"disease": {
"termId": "EFO:0009909",
"termLabel": "Chronic Kidney Disease"
}
},
{
"termId": "EFO:0001073",
"termLabel": "Obesity"
}
"disease": {
"termId": "EFO:0001073",
"termLabel": "Obesity"
}
}
]
},
"organismDescriptor": {
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44 changes: 28 additions & 16 deletions examples/json_validation_tests/object-set_RareDisease.json
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Expand Up @@ -14,29 +14,39 @@
"minimalPublicAttributes": {
"subjectId": "Affected_proband_14y",
"biologicalSex": "male",
"phenotypes": [
"phenotypicAbnormalities": [
{
"termId": "HP:0001558",
"termLabel": "Decreased fetal movement"
"phenotypicAbnormality": {
"termId": "HP:0001558",
"termLabel": "Decreased fetal movement"
}
},
{
"termId": "HP:0031910",
"termLabel": "Abnormal cranial nerve physiology"
"phenotypicAbnormality": {
"termId": "HP:0031910",
"termLabel": "Abnormal cranial nerve physiology"
}
},
{
"termId": "HP:0012587",
"termLabel": "Macroscopic hematuria"
"phenotypicAbnormality": {
"termId": "HP:0012587",
"termLabel": "Macroscopic hematuria"
}
},
{
"termId": "HP:0001270",
"termLabel": "Motor delay"
}
"phenotypicAbnormality": {
"termId": "HP:0001270",
"termLabel": "Motor delay"
}
}
],
"diseases": [
{
"termId": "MONDO:0008029",
"termLabel": "Bethlem myopathy"
}
"disease": {
"termId": "MONDO:0008029",
"termLabel": "Bethlem myopathy"
}
}
]
},
"organismDescriptor": {
Expand Down Expand Up @@ -82,10 +92,12 @@
"minimalPublicAttributes": {
"subjectId": "Unaffected mother",
"biologicalSex": "female",
"phenotypes": [
"phenotypicAbnormalities": [
{
"termId": "NCIT:C94232",
"termLabel": "Unaffected"
"phenotypicAbnormality": {
"termId": "NCIT:C94232",
"termLabel": "Unaffected"
}
}
]
},
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22 changes: 21 additions & 1 deletion schemas/EGA.common-definitions.json
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Expand Up @@ -3799,7 +3799,7 @@
"title": "Ontology constraints for this specific termId",
"anyOf": [
{
"title": "Ontology validation of diseases",
"title": "Ontology validation of 'disease' - EFO",
"graphRestriction": {
"ontologies" : ["obo:efo"],
"classes": ["EFO:0000408"],
Expand All @@ -3808,6 +3808,26 @@
"include_self": false
}
},
{
"title": "Ontology validation of 'disease' - ORDO",
"graphRestriction": {
"ontologies" : ["obo:ordo"],
"classes": ["Orphanet:377788"],
"relations": ["rdfs:subClassOf"],
"direct": false,
"include_self": false
}
},
{
"title": "Ontology validation of 'human disease or disorder' - MONDO",
"graphRestriction": {
"ontologies" : ["obo:mondo"],
"classes": ["MONDO:0700096"],
"relations": ["rdfs:subClassOf"],
"direct": false,
"include_self": false
}
},
{
"title": "In case the phenotypic abnormality is unknown or there is none",
"enum": ["NCIT:C17998", "NCIT:C94232"],
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36 changes: 33 additions & 3 deletions schemas/EGA.individual.json
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Expand Up @@ -52,14 +52,29 @@
"biologicalSex": {
"$ref": "./EGA.common-definitions.json#/definitions/biologicalSex"
},
"phenotypes": {
"phenotypicAbnormalities": {
"type": "array",
"title": "Array of phenotypic abnormalities",
"minItems": 1,
"additionalProperties": false,
"uniqueItems": true,
"items": {
"$ref": "./EGA.common-definitions.json#/definitions/phenotypicAbnormality"
"type": "object",
"title": "Phenotypic abnormality item",
"description": "One individual Phenotypic abnormality of the array. Keep in mind that in order to correctly interprete the phenotype it is **imperative** to check the 'excluded' property: each item of the array can be either specifying that the phenotipic abnormality was present or the opposite (i.e. logical negation).",
"additionalProperties": false,
"required": [ "phenotypicAbnormality" ],
"properties": {
"excluded": {
"type": "boolean",
"title": "Excluded",
"description": "Property that specifies whether the phenotype was observed or not. Similar to phenopacket's 'excluded' property, by default it is 'false', which means that the phenotype was observed (i.e. not excluded). This flag is only required to indicate that the phenotype was looked for, but found to be absent. The terms 'not excluded' (i.e. false) and 'excluded' (i.e. true) correlate with the common notation of 'case' versus 'control', respectively.",
"default": false
},
"phenotypicAbnormality": {
"$ref": "./EGA.common-definitions.json#/definitions/phenotypicAbnormality"
}
}
}
},
"diseases": {
Expand All @@ -69,7 +84,22 @@
"additionalProperties": false,
"uniqueItems": true,
"items": {
"$ref": "./EGA.common-definitions.json#/definitions/disease"
"type": "object",
"title": "Disease item",
"description": "One individual disease of the array. Keep in mind that in order to correctly interprete the disease it is **imperative** to check the 'excluded' property: each item of the array can be either specifying that the disease was present or the opposite (i.e. logical negation).",
"additionalProperties": false,
"required": [ "disease" ],
"properties": {
"excluded": {
"type": "boolean",
"title": "Excluded",
"description": "Property that specifies whether the disease was observed or not. Similar to phenopacket's 'excluded' property, by default it is 'false', which means that the disease was observed (i.e. not excluded). This flag is only required to indicate that the disease was looked for, but found to be absent. The terms 'not excluded' (i.e. false) and 'excluded' (i.e. true) correlate with the common notation of 'case' versus 'control', respectively.",
"default": false
},
"disease": {
"$ref": "./EGA.common-definitions.json#/definitions/disease"
}
}
}
}
},
Expand Down