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alfredompalfredomp
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Merge pull request #27 from alfredomp/fixAnnotation
Fix annotation
2 parents aaacc12 + 20e5001 commit 0fca4d5

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9 files changed

+350
-28
lines changed

9 files changed

+350
-28
lines changed

‎examples/annotation/multipleAnswer.json‎

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{
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"status": "SAVED",
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"reference": {
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"roiId": "7ba82ae63c95754352706fcca5039e1b",
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"materializedTaskId": "7ba82ae63c95754352706fcca5037a66",
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"taskId": "7ba82ae63c95754352706fcca5039e1b",
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"workflowId": "7ba82ae63c95754352706fcca5037a66",
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"questionId": "7ba82ae63c95754352706fcca5037a66"
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},
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"typeQuestion":"MULTIPLE_CHOICE_MULTIPLE_ANSWER",
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"typeAnnotation": "TEXT",
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"properties": {
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"values": [
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"Identification uncertain"
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],
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"isOntologyBased": false
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}
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}

‎examples/annotation/openEnded.json‎

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{
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"status": "SAVED",
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"reference": {
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"roiId": "7ba82ae63c95754352706fcca5039e1b",
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"materializedTaskId": "7ba82ae63c95754352706fcca5037a66",
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"taskId": "7ba82ae63c95754352706fcca5039e1b",
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"workflowId": "7ba82ae63c95754352706fcca5037a66",
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"questionId": "7ba82ae63c95754352706fcca5037a66"
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},
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"typeQuestion":"OPEN_ENDED",
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"typeAnnotation": "NUMBER",
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"properties": {
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"value": 3,
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"concept": "volume",
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"isOntologyBased": false
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}
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}

‎examples/annotation/singleAnswer.json‎

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{
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"typeQuestion":"MULTIPLE_CHOICE_SINGLE_ANSWER",
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"status": "SAVED",
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"reference": {
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"roiId": "7ba82ae63c95754352706fcca5039e1b",
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"materializedTaskId": "7ba82ae63c95754352706fcca5037a66",
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"taskId": "7ba82ae63c95754352706fcca5039e1b",
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"workflowId": "7ba82ae63c95754352706fcca5037a66",
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"questionId": "7ba82ae63c95754352706fcca5037a66"
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},
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"typeAnnotation": "TEXT",
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"properties": {
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"value": "Identification uncertain",
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"isOntologyBased": false
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}
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}

‎examples/question/multipleChoiceMultipleAnswerQuestion.json‎

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{
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"typeQuestion":"MULTIPLE_CHOICE_MULTIPLE_ANSWER",
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"propertiesAnnotation": {
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"typeAnnotationOptions":"TEXT",
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"isOntologyBased": false
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},
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"options": [
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{
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"value": "Cerebrum"
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},
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{
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"value": "Cerebellum"
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},
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{
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"value": "Brainstem"
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}
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]
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}

‎examples/question/multipleChoiceSingleAnswerQuestion.json‎

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{
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"typeQuestion":"MULTIPLE_CHOICE_SINGLE_ANSWER",
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"propertiesAnnotation": {
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"typeAnnotationOptions":"TEXT",
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"isOntologyBased": false
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},
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"options": [
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{
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"value": "Cerebrum"
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},
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{
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"value": "Cerebellum"
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},
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{
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"value": "Brainstem"
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}
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]
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}

‎examples/question/openEndedQuestion.json‎

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{
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"typeQuestion":"OPEN_ENDED",
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"propertiesAnnotation": {
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"typeAnnotationOptions":"TEXT",
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"isOntologyBased": false
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},
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"options": "Comments"
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}

‎schemas/annotation.schema.json‎

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"title": "Annotation Schema",
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"type": "object",
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"TODOS": [
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"Usually an annotation is a simple comment. In the future an annotation can be an image, for instance a probability mask."
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"Usually an annotation is a simple comment. In the future an annotation can be an image, for instance a probability mask. This can be the answer to the question, what is the probability for every voxel to be part of the corpus callosum."
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],
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"definitions": {
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"annotationBasic":{
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"$id": "#annotationBasic",
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"description": "Basic description of an annotation",
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"properties":{
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"typeAnnotationForm":{
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"$ref": "annotationForm.schema.json#/definitions/typeAnnotationForm"
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"typeQuestion":{
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"$ref": "question.schema.json#/definitions/typeQuestion"
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},
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"typeAnnotation": {
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"description": "",
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"type": "string",
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"enum": ["TEXT","IMAGE","NUMBER","BOOLEAN"]
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"$ref": "question.schema.json#/definitions/typeAnnotationOptions"
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},
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"status": {
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"description": "Status of the annotation: saved or submitted",
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"type": "string",
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"enum": ["SAVED","SUBMITTED"]
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},
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"reference": {
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"roiId": {
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"description": "Id of the ROI annotated by this annotation",
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"type": "string"
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"description": "References to main documents",
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"type": "object",
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"properties": {
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"roiId": {
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"description": "Id of the ROI annotated by this annotation",
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"type": "string"
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},
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"taskId": {
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"description": "Id of the task used to produce this annotation",
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"type": "string"
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},
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"workflowId": {
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"description": "Id of the workflow used to produce this annotation",
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"type": "string"
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},
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"materializedTaskId": {
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"description": "Id of the materialized task used to created the ROI. If not set then the materialized task has not been submitted.",
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"type": "string"
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},
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"questionId":{
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"description": "Id of the question related to this annotation. An annotation is an answer to a question.",
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"type": "string"
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}
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},
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"materializedTaskId":{
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"description": "Id of the materialized task used to created the ROI. If not set then the materialized task has not been submitted.",
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"type": "string"
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}
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"required": ["roiId", "materializedTaskId", "questionId"],
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"additionalProperties": false
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},
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"properties": {
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"description": "Properties of the annotation. The list of properties depends in the type of annotation.",
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"type": "object",
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"properties": {
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"isOntologyBased":{
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"description": "True if the annotation and its options are based on an ontology",
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"type": "boolean"
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"oneOf":[
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{
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"properties": {
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"isOntologyBased": {
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"description": "True if the annotation and its options are based on an ontology",
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"type": "boolean",
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"enum": [true]
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},
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"ontologyId": {
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"description": "Id of the ontology where the value of the annotation is retrieved.",
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"type": "string"
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}
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},
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"required": ["isOntologyBased", "ontologyId"]
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},
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"ontologyId": {
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"description": "Id of the ontology where the value of the annotation is retrieved.",
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"type": "string"
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{
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"properties": {
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"isOntologyBased": {
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"description": "True if the annotation and its options are based on an ontology",
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"type": "boolean",
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"enum": [false]
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}
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},
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"required": ["isOntologyBased"]
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}
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}
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]
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}
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},
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"required": ["typeAnnotationForm", "typeAnnotation", "status", "reference", "properties"]
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"required": ["typeQuestion", "typeAnnotation", "status", "reference", "properties"]
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},
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"annotationMultipleChoiceMultipleAnswer":{
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{ "$ref": "#/definitions/annotationBasic" },
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{
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"properties":{
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"typeAnnotationForm": {
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"typeQuestion": {
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"enum": ["MULTIPLE_CHOICE_MULTIPLE_ANSWER"]
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},
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"properties":{
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{ "$ref": "#/definitions/annotationBasic" },
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{
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"properties":{
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"typeAnnotationForm": {
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"typeQuestion": {
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"enum": ["MULTIPLE_CHOICE_SINGLE_ANSWER"]
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},
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"properties":{
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{ "$ref": "#/definitions/annotationBasic" },
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{
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"properties":{
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"typeAnnotationForm": {
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"typeQuestion": {
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"enum": ["OPEN_ENDED"]
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},
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"properties":{
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{ "$ref": "#/definitions/annotationMultipleChoiceMultipleAnswer" },
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{ "$ref": "#/definitions/annotationMultipleChoiceSingleAnswer" },
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{ "$ref": "#/definitions/annotationOpenEnded" }
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]
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}
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}

‎schemas/annotationForm.schema.json‎

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{
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"$id":"https://raw.githubusercontent.com/SPINEProject/SPINE-json-schema/master/schemas/annotationForm.schema.json",
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"$id":"https://raw.githubusercontent.com/SPINEProject/SPINE-json-schema/master/schemas/question.schema.json",
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"$schema": "http://json-schema.org/draft-07/schema#",
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"title": "Annotation Forms that describes the options for an annotation",
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"type": "object",

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