phenopackets

erDiagram Phenopacket { string id } Individual { stringList alternateIds string dateOfBirth string id KaryotypicSex karyotypicSex Sex sex } VitalStatus { Status status integer survivalTimeInDays } TimeElement { string timestamp } OntologyClass { string id string label } TimeInterval { string end string start } GestationalAge { integer days integer weeks } AgeRange { } Age { string iso8601duration } PhenotypicFeature { string description boolean excluded } Evidence { } ExternalReference { string description string id string reference } MetaData { string created string createdBy string phenopacketSchemaVersion string submittedBy } Update { string comment string timestamp string updatedBy } Resource { string id string iriPrefix string name string namespacePrefix string url string version } MedicalAction { } Treatment { DrugType drugType } DoseInterval { } Quantity { double value } ReferenceRange { double high double low } TherapeuticRegimen { RegimenStatus regimenStatus } RadiationTherapy { integer dosage integer fractions } Procedure { } Measurement { string description } Value { } ComplexValue { } TypedQuantity { } Interpretation { string id ProgressStatus progressStatus string summary } Diagnosis { } GenomicInterpretation { InterpretationStatus interpretationStatus string subjectOrBiosampleId } VariantInterpretation { AcmgPathogenicityClassification acmgPathogenicityClassification TherapeuticActionability therapeuticActionability } VariationDescriptor { stringList alternateLabels string description string id string label MoleculeContext moleculeContext string vrsRefAlleleSeq stringList xrefs } VcfRecord { string alt string chrom string filter string genomeAssembly string id string info integer pos string qual string ref } Variation { } VariationSet { } Text { string definition string id } Haplotype { } CopyNumber { string curie string id } RepeatedSequenceExpression { } Number { integer value } LiteralSequenceExpression { string sequence } IndefiniteRange { string comparator integer value } DerivedSequenceExpression { boolean reverseComplement } SequenceLocation { string id string sequenceId } SequenceInterval { } DefiniteRange { integer max integer min } Gene { string geneId } Allele { string curie string id } ChromosomeLocation { string chr string id string speciesId } CytobandInterval { string end string start } GeneDescriptor { stringList alternateIds stringList alternateSymbols string description string symbol string valueId stringList xrefs } Extension { string name stringList value } Expression { string syntax string value string version } File { string uri } Dictionary { } Disease { boolean excluded } Biosample { string derivedFromId string description string id string individualId } Phenopacket ||--}o Biosample : "biosamples" Phenopacket ||--}o Disease : "diseases" Phenopacket ||--}o File : "files" Phenopacket ||--}o Interpretation : "interpretations" Phenopacket ||--}o Measurement : "measurements" Phenopacket ||--}o MedicalAction : "medicalActions" Phenopacket ||--|| MetaData : "metaData" Phenopacket ||--}o PhenotypicFeature : "phenotypicFeatures" Phenopacket ||--|o Individual : "subject" Individual ||--|o OntologyClass : "gender" Individual ||--|o OntologyClass : "taxonomy" Individual ||--|o TimeElement : "timeAtLastEncounter" Individual ||--|o VitalStatus : "vitalStatus" VitalStatus ||--|o OntologyClass : "causeOfDeath" VitalStatus ||--|o TimeElement : "timeOfDeath" TimeElement ||--|o Age : "age" TimeElement ||--|o AgeRange : "ageRange" TimeElement ||--|o GestationalAge : "gestationalAge" TimeElement ||--|o TimeInterval : "interval" TimeElement ||--|o OntologyClass : "ontologyClass" AgeRange ||--|o Age : "end" AgeRange ||--|o Age : "start" PhenotypicFeature ||--}o Evidence : "evidence" PhenotypicFeature ||--}o OntologyClass : "modifiers" PhenotypicFeature ||--|o TimeElement : "onset" PhenotypicFeature ||--|o TimeElement : "resolution" PhenotypicFeature ||--|o OntologyClass : "severity" PhenotypicFeature ||--|o OntologyClass : "type" Evidence ||--|o OntologyClass : "evidenceCode" Evidence ||--|o ExternalReference : "reference" MetaData ||--}o ExternalReference : "externalReferences" MetaData ||--}o Resource : "resources" MetaData ||--}o Update : "updates" MedicalAction ||--}o OntologyClass : "adverseEvents" MedicalAction ||--|o Procedure : "procedure" MedicalAction ||--|o RadiationTherapy : "radiationTherapy" MedicalAction ||--|o OntologyClass : "responseToTreatment" MedicalAction ||--|o TherapeuticRegimen : "therapeuticRegimen" MedicalAction ||--|o Treatment : "treatment" MedicalAction ||--|o OntologyClass : "treatmentIntent" MedicalAction ||--|o OntologyClass : "treatmentTarget" MedicalAction ||--|o OntologyClass : "treatmentTerminationReason" Treatment ||--|o OntologyClass : "agent" Treatment ||--|o Quantity : "cumulativeDose" Treatment ||--}o DoseInterval : "doseIntervals" Treatment ||--|o OntologyClass : "routeOfAdministration" DoseInterval ||--|o TimeInterval : "interval" DoseInterval ||--|o Quantity : "quantity" DoseInterval ||--|o OntologyClass : "scheduleFrequency" Quantity ||--|o ReferenceRange : "referenceRange" Quantity ||--|o OntologyClass : "unit" ReferenceRange ||--|o OntologyClass : "unit" TherapeuticRegimen ||--|o TimeElement : "endTime" TherapeuticRegimen ||--|o ExternalReference : "externalReference" TherapeuticRegimen ||--|o OntologyClass : "ontologyClass" TherapeuticRegimen ||--|o TimeElement : "startTime" RadiationTherapy ||--|| OntologyClass : "bodySite" RadiationTherapy ||--|| OntologyClass : "modality" Procedure ||--|o OntologyClass : "bodySite" Procedure ||--|o OntologyClass : "code" Procedure ||--|o TimeElement : "performed" Measurement ||--|o OntologyClass : "assay" Measurement ||--|o ComplexValue : "complexValue" Measurement ||--|o Procedure : "procedure" Measurement ||--|o TimeElement : "timeObserved" Measurement ||--|o Value : "value" Value ||--|o OntologyClass : "ontologyClass" Value ||--|o Quantity : "quantity" ComplexValue ||--}o TypedQuantity : "typedQuantities" TypedQuantity ||--|o Quantity : "quantity" TypedQuantity ||--|o OntologyClass : "type" Interpretation ||--|o Diagnosis : "diagnosis" Diagnosis ||--|o OntologyClass : "disease" Diagnosis ||--}o GenomicInterpretation : "genomicInterpretations" GenomicInterpretation ||--|o GeneDescriptor : "gene" GenomicInterpretation ||--|o VariantInterpretation : "variantInterpretation" VariantInterpretation ||--|o VariationDescriptor : "variationDescriptor" VariationDescriptor ||--|o OntologyClass : "allelicState" VariationDescriptor ||--}o Expression : "expressions" VariationDescriptor ||--}o Extension : "extensions" VariationDescriptor ||--|o GeneDescriptor : "geneContext" VariationDescriptor ||--|o OntologyClass : "structuralType" VariationDescriptor ||--|o Variation : "variation" VariationDescriptor ||--|o VcfRecord : "vcfRecord" Variation ||--|o Allele : "allele" Variation ||--|o CopyNumber : "copyNumber" Variation ||--|o Haplotype : "haplotype" Variation ||--|o Text : "text" Variation ||--|o VariationSet : "variationSet" CopyNumber ||--|o Allele : "allele" CopyNumber ||--|o DefiniteRange : "definiteRange" CopyNumber ||--|o DerivedSequenceExpression : "derivedSequenceExpression" CopyNumber ||--|o Gene : "gene" CopyNumber ||--|o Haplotype : "haplotype" CopyNumber ||--|o IndefiniteRange : "indefiniteRange" CopyNumber ||--|o LiteralSequenceExpression : "literalSequenceExpression" CopyNumber ||--|o Number : "number" CopyNumber ||--|o RepeatedSequenceExpression : "repeatedSequenceExpression" RepeatedSequenceExpression ||--|o DefiniteRange : "definiteRange" RepeatedSequenceExpression ||--|o DerivedSequenceExpression : "derivedSequenceExpression" RepeatedSequenceExpression ||--|o IndefiniteRange : "indefiniteRange" RepeatedSequenceExpression ||--|o LiteralSequenceExpression : "literalSequenceExpression" RepeatedSequenceExpression ||--|o Number : "number" DerivedSequenceExpression ||--|o SequenceLocation : "location" SequenceLocation ||--|o SequenceInterval : "sequenceInterval" SequenceInterval ||--|o DefiniteRange : "endDefiniteRange" SequenceInterval ||--|o IndefiniteRange : "endIndefiniteRange" SequenceInterval ||--|o Number : "endNumber" SequenceInterval ||--|o DefiniteRange : "startDefiniteRange" SequenceInterval ||--|o IndefiniteRange : "startIndefiniteRange" SequenceInterval ||--|o Number : "startNumber" Allele ||--|o ChromosomeLocation : "chromosomeLocation" Allele ||--|o DerivedSequenceExpression : "derivedSequenceExpression" Allele ||--|o LiteralSequenceExpression : "literalSequenceExpression" Allele ||--|o RepeatedSequenceExpression : "repeatedSequenceExpression" Allele ||--|o SequenceLocation : "sequenceLocation" ChromosomeLocation ||--|o CytobandInterval : "interval" File ||--|o Dictionary : "fileAttributes" File ||--|o Dictionary : "individualToFileIdentifiers" Disease ||--}o OntologyClass : "clinicalTnmFinding" Disease ||--}o OntologyClass : "diseaseStage" Disease ||--|o OntologyClass : "laterality" Disease ||--|o TimeElement : "onset" Disease ||--|o OntologyClass : "primarySite" Disease ||--|o TimeElement : "resolution" Disease ||--|o OntologyClass : "term" Biosample ||--}o OntologyClass : "diagnosticMarkers" Biosample ||--}o File : "files" Biosample ||--|o OntologyClass : "histologicalDiagnosis" Biosample ||--|o OntologyClass : "materialSample" Biosample ||--}o Measurement : "measurements" Biosample ||--|o OntologyClass : "pathologicalStage" Biosample ||--}o OntologyClass : "pathologicalTnmFinding" Biosample ||--}o PhenotypicFeature : "phenotypicFeatures" Biosample ||--|o Procedure : "procedure" Biosample ||--|o OntologyClass : "sampleProcessing" Biosample ||--|o OntologyClass : "sampleStorage" Biosample ||--|o OntologyClass : "sampleType" Biosample ||--|o OntologyClass : "sampledTissue" Biosample ||--|o OntologyClass : "taxonomy" Biosample ||--|o TimeElement : "timeOfCollection" Biosample ||--|o OntologyClass : "tumorGrade" Biosample ||--|o OntologyClass : "tumorProgression"