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add multi submitter id validation #67

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6f857c5
add multi submitter id validation
Aug 14, 2026
dccb69f
Update to reflect data viewer instance
Aug 18, 2026
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92 changes: 88 additions & 4 deletions base/base.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -1130,6 +1130,31 @@ slots:
range: string
required: true
pattern: ^[A-Za-z0-9\-\._]{1,64}
submitter_participant_ids:

@lindaxiang lindaxiang Aug 31, 2026

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Any reason we fully duplicated slot definitions rather than using is_a slot inheritance feature, e.g,

  submitter_participant_ids:
    is_a: submitter_participant_id
    name: submitter_participant_ids
    description: A list of unique identifiers (min 1) for participants within the study, assigned by the data provider.
    multivalued: true
    minimum_cardinality: 1
    list_elements_unique: true

name: submitter_participant_ids
description: A list of Unique identifiers (min 1) for participants within the study, assigned by
the data provider.
title: Submitter Participant Ids
examples:
- value: '90234'
- value: BLD_donor_89
- value: AML-90
exact_mappings:
- ARGO.v1.34:donor.submitter_donor_id
- Beacon.v2.2.0:individual.id
- CQDG:submitter_participant_id
- FHIR.v5.0.0:Patient.identifier
- mCODE.v4.0.0:Patient.identifier
- MOHCCN.v3.1:Donor.submitter_donor_id
- Phenopackets.v2.0:Individual.id
annotations:
specifications: "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier"
range: string
required: true
pattern: ^[A-Za-z0-9\-\._]{1,64}
multivalued: true
minimum_cardinality: 1
list_elements_unique: true
vital_status:
name: vital_status
description: Participant's last known state of living or deceased.
Expand Down Expand Up @@ -1681,6 +1706,31 @@ slots:
range: string
required: true
pattern: ^[A-Za-z0-9\-\._]{1,64}$
submitter_specimen_ids:
name: submitter_specimen_ids
description: List of Unique identifiers (min 1) for specimens within the study, assigned by the
data provider.
title: Submitter Specimen Ids
examples:
- value: LAML_PO
- value: '00445'
- value: THY_099-tumour
exact_mappings:
- ARGO.v1.34:specimen.submitter_specimen_id
- Beacon.v2.2.0:biosample.id
- CQDG:submitter_biospecimen_id
- FHIR.v5.0.0:Specimen.identifier
- mCODE.v4.0.0:Specimen.identifier
- MOHCCN.v3.1:specimen.submitter_specimen_id
- Phenopackets.v2.0:Biosample.derived_from_id
annotations:
specifications: "FHIRSpec.v5.0.0:https://hl7.org/fhir/specimen-definitions.html#Specimen.identifier"
range: string
required: true
pattern: ^[A-Za-z0-9\-\._]{1,64}$
multivalued: true
minimum_cardinality: 1
list_elements_unique: true
age_at_diagnosis:
name: age_at_diagnosis
description: Age of participant (in days) at time of diagnosis of the condition.
Expand Down Expand Up @@ -1962,6 +2012,27 @@ slots:
range: string
required: true
pattern: ^[A-Za-z0-9\-\._]{1,64}$
submitter_sample_ids:
name: submitter_sample_ids
description: 'List of Unique identifiers (min 1) for samples within the study, assigned by the
data provider.

'
title: Submitter Sample Ids
examples:
- value: hnc_12
- value: CCG_34_94583
- value: BRCA47832-3239
exact_mappings:
- ARGO.v1.34:sample_registration.submitter_sample_id
- MOHCCN.v3.1:Sample_registration.submitter_sample_id
- Phenopackets.v2.0:Biosample.id
range: string
required: true
pattern: ^[A-Za-z0-9\-\._]{1,64}$
multivalued: true
minimum_cardinality: 1
list_elements_unique: true
sample_status:
name: sample_status
description: "Indicate the status of the sample for data analysis.\nCase sample refers to a sample that meets the disease or exposure criteria under investigation.\nControl sample refers to of the same type that does not meet the criteria, representing a normal or baseline state for comparison."
Expand All @@ -1978,6 +2049,19 @@ slots:
range: string
required: true
pattern: ^[A-Za-z0-9\-\._]{1,64}$
submitter_experiment_ids:
name: submitter_experiment_ids
description: A list of Unique identifiers (min 1) for experiments within the study, assigned by
the data provider.
title: Submitter Experiment Ids
exact_mappings:
- ARGO.v1.34:experiment.submitter_sequencing_experiment_id
range: string
required: true
pattern: ^[A-Za-z0-9\-\._]{1,64}$
multivalued: true
minimum_cardinality: 1
list_elements_unique: true
experiment_type:
name: experiment_type
description: "Indicate NCIt (NCI Thesaurus) code and term to denote the broad type of sequencing experiment performed. A mixture of library strategy and source."
Expand Down Expand Up @@ -4019,10 +4103,10 @@ classes:
title: Analysis
slots:
- submitter_analysis_id
- submitter_experiment_id
- submitter_participant_id
- submitter_sample_id
- submitter_specimen_id
- submitter_experiment_ids
- submitter_participant_ids
- submitter_sample_ids
- submitter_specimen_ids
- analysisType
- data_category
- genome_annotation
Expand Down
132 changes: 110 additions & 22 deletions custom/pcgl/pcgl_dh.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -1135,6 +1135,33 @@ slots:
range: string
required: true
pattern: ^[A-Za-z0-9\-\._]{1,64}
submitter_participant_ids:
name: submitter_participant_ids
annotations:
specifications:
tag: specifications
value: FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier
description: A list of Unique identifiers (min 1) for participants within the
study, assigned by the data provider.
title: submitter_participant_ids
examples:
- value: '90234'
- value: BLD_donor_89
- value: AML-90
exact_mappings:
- ARGO.v1.34:donor.submitter_donor_id
- Beacon.v2.2.0:individual.id
- CQDG:submitter_participant_id
- FHIR.v5.0.0:Patient.identifier
- mCODE.v4.0.0:Patient.identifier
- MOHCCN.v3.1:Donor.submitter_donor_id
- Phenopackets.v2.0:Individual.id
list_elements_unique: true
range: string
required: true
multivalued: true
pattern: ^[A-Za-z0-9\-\._]{1,64}
minimum_cardinality: 1
vital_status:
name: vital_status
annotations:
Expand Down Expand Up @@ -1821,6 +1848,33 @@ slots:
range: string
required: true
pattern: ^[A-Za-z0-9\-\._]{1,64}$
submitter_specimen_ids:
name: submitter_specimen_ids
annotations:
specifications:
tag: specifications
value: FHIRSpec.v5.0.0:https://hl7.org/fhir/specimen-definitions.html#Specimen.identifier
description: List of Unique identifiers (min 1) for specimens within the study,
assigned by the data provider.
title: submitter_specimen_ids
examples:
- value: LAML_PO
- value: '00445'
- value: THY_099-tumour
exact_mappings:
- ARGO.v1.34:specimen.submitter_specimen_id
- Beacon.v2.2.0:biosample.id
- CQDG:submitter_biospecimen_id
- FHIR.v5.0.0:Specimen.identifier
- mCODE.v4.0.0:Specimen.identifier
- MOHCCN.v3.1:specimen.submitter_specimen_id
- Phenopackets.v2.0:Biosample.derived_from_id
list_elements_unique: true
range: string
required: true
multivalued: true
pattern: ^[A-Za-z0-9\-\._]{1,64}$
minimum_cardinality: 1
age_at_diagnosis:
name: age_at_diagnosis
annotations:
Expand Down Expand Up @@ -2149,6 +2203,27 @@ slots:
range: string
required: true
pattern: ^[A-Za-z0-9\-\._]{1,64}$
submitter_sample_ids:
name: submitter_sample_ids
description: 'List of Unique identifiers (min 1) for samples within the study,
assigned by the data provider.

'
title: submitter_sample_ids
examples:
- value: hnc_12
- value: CCG_34_94583
- value: BRCA47832-3239
exact_mappings:
- ARGO.v1.34:sample_registration.submitter_sample_id
- MOHCCN.v3.1:Sample_registration.submitter_sample_id
- Phenopackets.v2.0:Biosample.id
list_elements_unique: true
range: string
required: true
multivalued: true
pattern: ^[A-Za-z0-9\-\._]{1,64}$
minimum_cardinality: 1
sample_status:
name: sample_status
description: 'Indicate the status of the sample for data analysis.
Expand All @@ -2171,6 +2246,19 @@ slots:
range: string
required: true
pattern: ^[A-Za-z0-9\-\._]{1,64}$
submitter_experiment_ids:
name: submitter_experiment_ids
description: A list of Unique identifiers (min 1) for experiments within the study,
assigned by the data provider.
title: submitter_experiment_ids
exact_mappings:
- ARGO.v1.34:experiment.submitter_sequencing_experiment_id
list_elements_unique: true
range: string
required: true
multivalued: true
pattern: ^[A-Za-z0-9\-\._]{1,64}$
minimum_cardinality: 1
experiment_type:
name: experiment_type
description: Indicate NCIt (NCI Thesaurus) code and term to denote the broad type
Expand Down Expand Up @@ -4409,13 +4497,13 @@ classes:
title: Analysis
slots:
- submitter_analysis_id
- submitter_experiment_id
- submitter_participant_id
- submitter_sample_id
- submitter_specimen_id
- analysisType
- data_category
- studyId
- submitter_experiment_ids
- submitter_participant_ids
- submitter_sample_ids
- submitter_specimen_ids
- genome_annotation
- genome_build
- variant_calling_strategy
Expand All @@ -4425,32 +4513,32 @@ classes:
name: submitter_analysis_id
rank: 1
slot_group: Database Identifiers
submitter_experiment_id:
name: submitter_experiment_id
rank: 2
slot_group: Database Identifiers
submitter_participant_id:
name: submitter_participant_id
rank: 3
slot_group: Database Identifiers
submitter_sample_id:
name: submitter_sample_id
rank: 4
slot_group: Database Identifiers
submitter_specimen_id:
name: submitter_specimen_id
rank: 5
slot_group: Database Identifiers
analysisType:
name: analysisType
rank: 6
rank: 2
slot_group: Analysis
data_category:
name: data_category
rank: 7
rank: 3
slot_group: Analysis
studyId:
name: studyId
rank: 4
slot_group: Analysis
submitter_experiment_ids:
name: submitter_experiment_ids
rank: 5
slot_group: Analysis
submitter_participant_ids:
name: submitter_participant_ids
rank: 6
slot_group: Analysis
submitter_sample_ids:
name: submitter_sample_ids
rank: 7
slot_group: Analysis
submitter_specimen_ids:
name: submitter_specimen_ids
rank: 8
slot_group: Analysis
genome_annotation:
Expand Down
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