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lzehllzehl
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first draft (TBD and further modified)
1 parent b33ae21 commit 717be83

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+167
-108
lines changed

‎schemas/research/TissueSampleCollectionStateStatistic.schema.tpl.json‎

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{
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"_type": "core:TissueSampleCollectionStateStatistic",
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"required": [
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"attribute",
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"count"
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],
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"properties": {
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"attribute": {
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"type": "array",
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"minItems": 1,
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"uniqueItems": true,
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"_instruction": "Add all attributes (including age) common for the specified tissue sample count within the tissue sample collection state.",
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"_linkedTypes": [
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"controlledTerms:Disease",
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"controlledTerms:DiseaseModel",
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"controlledTerms:TissueSampleAttribute",
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"core:SpecimenAge",
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"core:SpecimenWeight"
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]
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},
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"count": {
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"type": "integer",
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"_instruction": "Enter the tissue sample count within the tissue sample collection to which the defined state attribute(s) apply.",
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}
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}
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}

‎schemas/research/specimenAge.schema.tpl.json‎

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{
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"_type": "core:Age",
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"required": [
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"age",
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"reference"
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],
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"properties": {
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"age": {
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"_instruction": "Enter the age value.",
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"_embeddedTypes": [
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"core:QuantitativeValue",
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"core:QuantitativeValueRange"
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]
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},
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"reference": {
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"_instruction": "Enter the age reference for the specified age value.",
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"_linkedTypes": [
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"controlledTerms:AgeReference"
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]
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}
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}
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}

‎schemas/research/specimenSet.schema.tpl.json‎

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"type": "string",
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"_instruction": "Enter any additional remarks concerning this specimen set."
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},
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"biologicalSex": {
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"type": "array",
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"minItems": 1,
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"uniqueItems": true,
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"_instruction": "Add the biological sex of all specimen in this set.",
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"_linkedTypes": [
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"controlledTerms:BiologicalSex"
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]
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},
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"internalIdentifier": {
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"type": "string",
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"_instruction": "Enter the identifier (or label) of this specimen set that is used within the corresponding data files to identify this specimen set."
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},
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"lookupLabel": {
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"type": "string",
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"_instruction": "Enter a lookup label for this specimen set that may help you to find this instance more easily."
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},
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"species": {
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"type": "array",
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"minItems": 1,
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"uniqueItems": true,
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"_instruction": "Add the species and/or strain (a sub-type of a genetic variant of species) of all specimen in this set.",
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"_linkedTypes": [
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"controlledTerms:Species",
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"core:Strain"
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]
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}
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}
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}

‎schemas/research/specimenState.schema.tpl.json‎

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"additionalRemarks": {
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"type": "string",
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"_instruction": "Enter any additional remarks concerning the specimen (set) in this state."
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},
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"age": {
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"_instruction": "Enter the age of the specimen (set) in this state.",
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"_embeddedTypes": [
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"core:QuantitativeValue",
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"core:QuantitativeValueRange"
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]
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},
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}
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"internalIdentifier": {
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"type": "string",
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"_instruction": "Enter the identifier (or label) of this specimen (set) state that is used within the corresponding data files to identify this specimen (set) state."
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},
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"lookupLabel": {
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"type": "string",
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"_instruction": "Enter a lookup label for this specimen (set) state that may help you to find this instance more easily."
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},
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"pathology": {
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"type": "array",
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"minItems": 1,
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"uniqueItems": true,
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"_instruction": "Add all (human) diseases and/or conditions that the specimen (set) in this state has and/or is a model for.",
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"_linkedTypes": [
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"controlledTerms:Disease",
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"controlledTerms:DiseaseModel"
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]
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},
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}
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"relativeTimeIndication": {
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"_instruction": "If there is a temporal relation between the states of a specimen (set), enter the relative time that has passed between this and the preceding specimen (set) state referenced under 'descendedFrom'.",
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"_embeddedTypes": [
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"core:QuantitativeValue",
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"core:QuantitativeValueRange"
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]
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},
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"weight": {
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"_instruction": "Enter the weight of the specimen (set) in this state.",
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"_embeddedTypes": [
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"core:QuantitativeValue",
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"core:QuantitativeValueRange"
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]
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}
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}
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}

‎schemas/research/specimenWeight.schema.tpl.json‎

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{
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"_type": "core:SpecimenWeight",
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"required": [
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"age",
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"reference"
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],
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"properties": {
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"weight": {
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"_instruction": "Enter the age value.",
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"_embeddedTypes": [
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"core:QuantitativeValue",
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"core:QuantitativeValueRange"
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]
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},
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"type": {
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"_instruction": "Enter the age reference for the specified age value.",
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"_linkedTypes": [
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"controlledTerms:SpecimenWeightType"
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]
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}
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}
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}

‎schemas/research/subjectGroup.schema.tpl.json‎

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"required": [
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"studiedState"
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],
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"properties": {
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"properties": {
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"attributeStatistic": {
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"type": "array",
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"minItems": 1,
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"uniqueItems": true,
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"_instruction": "Add all known statistics for the attributes of this subject group.",
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"_embeddedTypes": [
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"core:SubjectGroupStatistic"
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]
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},
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"numberOfSubjects": {
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"type": "integer",
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"minimum": 2,

‎schemas/research/subjectGroupState.schema.tpl.json‎

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"_type": "core:SubjectGroupState",
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"_extends": "research/specimenState.schema.tpl.json",
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"required": [
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"ageCategory"
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"attributeStatistic"
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],
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"properties": {
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"ageCategory": {
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"attributeStatistic": {
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"type": "array",
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"minItems": 1,
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"uniqueItems": true,
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"_instruction": "Add the age category of the subject in this state.",
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"_linkedTypes": [
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"controlledTerms:AgeCategory"
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]
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},
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"attribute": {
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"type": "array",
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"minItems": 1,
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"uniqueItems": true,
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"_instruction": "Add all attributes that can be ascribed to this subject group state.",
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"_linkedTypes": [
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"controlledTerms:SubjectAttribute"
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"_instruction": "Add all known statistics for the attributes of this subject group state.",
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"_embeddedTypes": [
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"core:SubjectGroupStateStatistic"
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]
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},
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"descendedFrom": {
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"_instruction": "Add the previous subject group state.",
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"_linkedTypes": [
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"core:SubjectGroupState"
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]
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},
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"handedness": {
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"type": "array",
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"minItems": 1,
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"uniqueItems": true,
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"_instruction": "Add all preferred types of handedness of the subject group in this state.",
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"_linkedTypes": [
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"controlledTerms:Handedness"
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]
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}
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}
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}

‎schemas/research/subjectGroupStateStatistic.schema.tpl.json‎

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{
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"_type": "core:SubjectGroupStateStatistic",
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"required": [
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"attribute",
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"count"
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],
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"properties": {
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"attribute": {
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"type": "array",
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"minItems": 1,
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"uniqueItems": true,
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"_instruction": "Add all attributes (including age) common for the specified subject count within the subject group state.",
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"_linkedTypes": [
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"controlledTerms:AgeCategory",
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"controlledTerms:Disease",
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"controlledTerms:DiseaseModel",
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"controlledTerms:SubjectAttribute",
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"core:SpecimenAge",
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"core:SpecimenWeight"
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]
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},
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"count": {
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"type": "integer",
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"_instruction": "Enter the subject count within the subject group to which the defined state attribute(s) apply.",
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}
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}
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}

‎schemas/research/subjectGroupStatistic.schema.tpl.json‎

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{
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"_type": "core:SubjectGroupStatistic",
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"required": [
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"attribute",
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"count"
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],
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"properties": {
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"attribute": {
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"type": "array",
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"minItems": 1,
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"uniqueItems": true,
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"_instruction": "Add all attributes common for the specified subject count within the subject group.",
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"_linkedTypes": [
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"controlledTerms:SpecimenAttribute"
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]
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},
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"count": {
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"type": "integer",
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"_instruction": "Enter the subject count within the subject group to which the defined attribute(s) apply.",
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}
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}
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}

‎schemas/research/tissueSampleCollection.schema.tpl.json‎

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"type"
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],
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"properties": {
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"anatomicalLocation": {
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"attributeStatistic": {
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"type": "array",
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"minItems": 1,
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"uniqueItems": true,
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"_instruction": "Add all anatomical entities that describe the anatomical location of this tissue sample collection.",
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"_linkedCategories": [
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"anatomicalLocation"
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"_instruction": "Add all known statistics for the attributes of this tissue sample collection.",
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"_embeddedTypes": [
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"core:TissueSampleCollectionStatistic"
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]
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},
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"laterality": {
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"type": "array",
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"minItems": 1,
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"maxItems": 2,
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"uniqueItems": true,
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"_instruction": "Add one or both sides of the body, bilateral organ or bilateral organ part that this tissue sample collection originates from.",
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"_linkedTypes": [
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"controlledTerms:Laterality"
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]
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},
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},
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"numberOfTissueSamples": {
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"type": "integer",
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"minimum": 2,
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"_instruction": "Enter the number of tissue samples that belong to this tissue sample collection."
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},
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"origin": {
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"type": "array",
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"minItems": 1,
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"uniqueItems": true,
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"_instruction": "Add the biogical origin of all tissue samples in this collection.",
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"_linkedTypes": [
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"controlledTerms:CellType",
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"controlledTerms:Organ",
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"controlledTerms:OrganismSubstance"
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]
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},
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"studiedState": {
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"type": "array",
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"minItems": 1,
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"_linkedTypes": [
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"core:TissueSampleCollectionState"
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]
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},
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"type": {
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"type": "array",
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"minItems": 1,
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"uniqueItems": true,
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"_instruction": "Add the type of all tissue samples in this collection.",
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"_linkedTypes": [
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"controlledTerms:TissueSampleType"
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]
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}
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}
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}

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