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@namespace("org.gel.models.participant.avro")
/**
This protocol defines the `CancerParticipant`
*/
protocol CancerParticipants {
import idl "CommonParticipant.avdl";
import idl "VersionControl.avdl";
/**
This defines a pair of germline and tumor, this pair should/must be analyzed together
*/
record MatchedSamples{
/**
Sample identifier (e.g, LP00012645_5GH)) for the germline
*/
union {null, string} germlineSampleId;
/**
Sample identifier (e.g, LP00012643_7JS)) for the tumor
*/
union {null, string} tumourSampleId;
}
record Tumour{
/**
TumourId in GMS
*/
string tumourId;
/**
Local hospital tumour ID from the GLH Laboratory Information Management System (LIMS) in GMS
*/
string tumourLocalId;
/**
tumourType
*/
TumourType tumourType;
/**
Parent Tumour UID if this tumour is metastatic
*/
union {null, string} tumourParentId;
/**
Date of Diagnosis of the specific tumour
*/
union {null, Date} tumourDiagnosisDate;
/**
Description of the tumour
*/
union {null, string} tumourDescription;
/**
Morphology of the tumour
*/
union {null, array} tumourMorphologies;
/**
Topography of the tumour
*/
union {null, array} tumourTopographies;
/**
Associated primary topography for metastatic tumours
*/
union {null, array} tumourPrimaryTopographies;
/**
Grade of the Tumour
*/
union {null, string} tumourGrade;
/**
Stage of the Tumour
*/
union {null, string} tumourStage;
/**
Prognostic Score of the Tumour
*/
union {null, string} tumourPrognosticScore;
/**
In GMS, tumour presentation
*/
union {null, TumourPresentation} tumourPresentation;
/**
In GMS, primary or metastatic
*/
union {null, PrimaryOrMetastatic} primaryOrMetastatic;
}
/**
This defines a Cancer Participant
*/
record CancerParticipant{
/**
Year of birth for the cancer participant
*/
union {null, int} yearOfBirth;
/**
Morphology of any tumours
NOTE: In GMS, this field is deprecated as morphology will be in sample or with respect to a tumour record
*/
union {null, array} morphology;
/**
Flag indicating if the participant is ready for analysis
NOTE: In GMS, this will default to true
*/
boolean readyForAnalysis;
/**
What has this participant consented to?
A participant that has been consented to the programme should also have sequence data associated with them; however
this needs to be programmatically checked
*/
union {null, ConsentStatus} consentStatus;
/**
What has this participant consented in the context of a Genomic Test?
*/
union {null, GmsConsentStatus} testConsentStatus;
/**
Center
NOTE: In GMS, this will be taken from the ReferralTest and duplicated here
*/
union {null, string} center;
/**
Individual identifier
*/
union {null, string} individualId;
/**
This is a human readable participant ID
*/
union {null, string} participantId;
/**
This should be an enumeration when it is well defined
blood, breast, prostate, colorectal, cll, aml, renal, ovarian, skin, lymphNode, bone, saliva //for individual - there could be more than I have listed here, in fact there definitely will.
In GMS, this field is deprecated
*/
union {null, array} primaryDiagnosisDisease;
/**
This should be an enumeration when it is well defined
blood, breast, prostate, colorectal, cll, aml, renal, ovarian, skin, lymphNode, bone, saliva //for individual - there could be more than I have listed here, in fact there definitely will.
In GMS, this field is deprecated
*/
union {null, array} primaryDiagnosisSubDisease;
/**
Sex
*/
Sex sex;
/**
We could add a map here to store additional information for example URIs to images, ECGs, etc
*/
union {null, map} additionalInformation;
/**
assigned ICD10 code
IN GMS, this is deprecated
*/
union {null, array} assignedICD10;
/**
List of tumour samples
IN GMS, this is deprecated and moved to ReferralTest
*/
union {null, array} tumourSamples;
/**
List of germline samples
IN GMS, this is deprecated and moved to ReferralTest
*/
union {null, array} germlineSamples;
/**
Model version number
*/
union {null, VersionControl} versionControl;
/**
Individual UID in GMS
*/
union {null, string} participantUid;
/**
In GMS, for all tumours for the CancerParticipant, independent of any samples
*/
union {null, array} tumours;
/**
In GMS, any previous treatment recorded in TOMs
*/
union {null, array} previousTreatment;
}
}
