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phenopacket.proto
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phenopacket.proto
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// org.phenopackets.api.PhenoPacket
// Message for org.phenopackets.api.PhenoPacket
message PhenoPacket {
optional string id = 1;
optional string title = 2;
repeated Entity entities = 3;
repeated Variant variants = 4;
repeated Person persons = 5;
repeated Organism organisms = 6;
repeated PhenotypeAssociation phenotype_profile = 7;
repeated DiseaseOccurrenceAssociation diagnosis_profile = 8;
repeated EnvironmentAssociation environment_profile = 9;
}
// Message for org.phenopackets.api.model.environment.Environment
message Environment {
repeated OntologyClass types = 1;
repeated OntologyClass negated_types = 2;
optional string description = 3;
}
// Message for org.phenopackets.api.model.condition.TemporalRegion
message TemporalRegion {
repeated OntologyClass types = 1;
repeated OntologyClass negated_types = 2;
optional string description = 3;
optional string start_time = 4;
optional string end_time = 5;
}
// Message for org.phenopackets.api.model.association.PhenotypeAssociation
message PhenotypeAssociation {
optional string entity = 1;
optional Phenotype phenotype = 2;
repeated Evidence evidence = 3;
}
// Message for org.phenopackets.api.model.meta.Evidence
message Evidence {
repeated OntologyClass types = 1;
repeated OntologyClass negated_types = 2;
optional string description = 3;
repeated string supporting_entities = 4;
repeated Publication source = 5;
}
// Message for org.phenopackets.api.model.entity.Variant
message Variant {
optional string descriptionHGVS = 1;
optional string id = 2;
optional string label = 3;
}
// Message for org.phenopackets.api.model.entity.Person
message Person {
optional OntologyClass strain = 1;
repeated OntologyClass types = 2;
repeated OntologyClass negated_types = 3;
optional string description = 4;
optional string id = 5;
optional string label = 6;
optional OntologyClass taxon = 7;
optional string sex = 8;
optional string date_of_birth = 9;
}
// Message for org.phenopackets.api.model.condition.ConditionSeverity
message ConditionSeverity {
repeated OntologyClass types = 1;
repeated OntologyClass negated_types = 2;
optional string description = 3;
}
// Message for org.phenopackets.api.model.entity.Entity
message Entity {
optional string id = 1;
optional string label = 2;
}
// Message for org.phenopackets.api.model.condition.OrganismalSite
message OrganismalSite {
repeated OntologyClass types = 1;
repeated OntologyClass negated_types = 2;
optional string description = 3;
}
// Message for org.phenopackets.api.model.association.EnvironmentAssociation
message EnvironmentAssociation {
optional Environment environment = 1;
optional string entity = 2;
repeated Evidence evidence = 3;
}
// Message for org.phenopackets.api.model.ontology.OntologyClass
message OntologyClass {
optional string id = 1;
optional string label = 2;
}
// Message for org.phenopackets.api.model.condition.Measurement
message Measurement {
optional OntologyClass unit = 1;
optional double magnitude = 2;
repeated OntologyClass types = 3;
repeated OntologyClass negated_types = 4;
optional string description = 5;
}
// Message for org.phenopackets.api.model.condition.DiseaseOccurrence
message DiseaseOccurrence {
optional DiseaseStage stage = 1;
repeated OntologyClass types = 2;
repeated OntologyClass negated_types = 3;
optional string description = 4;
optional OrganismalSite has_location = 5;
optional TemporalRegion onset = 6;
optional TemporalRegion offset = 7;
optional ConditionSeverity severity = 8;
optional Environment environment = 9;
}
// Message for org.phenopackets.api.model.association.DiseaseOccurrenceAssociation
message DiseaseOccurrenceAssociation {
optional DiseaseOccurrence diseaseOcurrence = 1;
optional string entity = 2;
repeated Evidence evidence = 3;
}
// Message for org.phenopackets.api.model.condition.DiseaseStage
message DiseaseStage {
repeated OntologyClass types = 1;
repeated OntologyClass negated_types = 2;
optional string description = 3;
optional OrganismalSite has_location = 4;
optional TemporalRegion onset = 5;
optional TemporalRegion offset = 6;
optional ConditionSeverity severity = 7;
optional Environment environment = 8;
}
// Message for org.phenopackets.api.model.entity.Organism
message Organism {
optional OntologyClass strain = 1;
repeated OntologyClass types = 2;
repeated OntologyClass negated_types = 3;
optional string description = 4;
optional string id = 5;
optional string label = 6;
optional OntologyClass taxon = 7;
optional string sex = 8;
optional string date_of_birth = 9;
}
// Message for org.phenopackets.api.model.condition.Phenotype
message Phenotype {
repeated Measurement measurements = 1;
repeated OntologyClass types = 2;
repeated OntologyClass negated_types = 3;
optional string description = 4;
optional OrganismalSite has_location = 5;
optional TemporalRegion onset = 6;
optional TemporalRegion offset = 7;
optional ConditionSeverity severity = 8;
optional Environment environment = 9;
}
// Message for org.phenopackets.api.model.meta.Publication
message Publication {
optional string title = 1;
optional string id = 2;
}