cidc_schemas/schemas/templates/manifests/pbmc_template.json
{
"title": "Biospecimen manifest for PBMC samples",
"description": "Biospecimen manifest for transferring Peripheral Blood Mononuclear Cell (PBMC) samples.",
"properties": {
"worksheets": {
"Shipment": {
"prism_preamble_object_schema": "clinical_trial.json",
"prism_preamble_object_pointer": "/shipments/0",
"prism_data_object_pointer": "/shipped",
"preamble_rows": {
"manifest id": {
"merge_pointer": "/manifest_id",
"type_ref": "shipping_core.json#properties/manifest_id"
},
"protocol identifier": {
"merge_pointer": "2/protocol_identifier",
"type_ref": "clinical_trial.json#properties/protocol_identifier"
},
"assay priority": {
"merge_pointer": "/assay_priority",
"type_ref": "shipping_core.json#properties/assay_priority",
"allow_empty": true
},
"assay type": {
"merge_pointer": "/assay_type",
"type_ref": "shipping_core.json#properties/assay_type"
},
"receiving party": {
"merge_pointer": "/receiving_party",
"type_ref": "shipping_core.json#properties/receiving_party",
"allow_empty": true
},
"courier": {
"merge_pointer": "/courier",
"type_ref": "shipping_core.json#properties/courier",
"allow_empty": true
},
"tracking number": {
"merge_pointer": "/tracking_number",
"type_ref": "shipping_core.json#properties/tracking_number",
"allow_empty": true
},
"account number": {
"merge_pointer": "/account_number",
"type_ref": "shipping_core.json#properties/account_number",
"allow_empty": true
},
"shipping condition": {
"merge_pointer": "/shipping_condition",
"type_ref": "shipping_core.json#properties/shipping_condition",
"allow_empty": true
},
"date shipped": {
"merge_pointer": "/date_shipped",
"type_ref": "shipping_core.json#properties/date_shipped",
"allow_empty": true
},
"date received": {
"merge_pointer": "/date_received",
"type_ref": "shipping_core.json#properties/date_received",
"allow_empty": true
},
"quality of shipment": {
"merge_pointer": "/quality_of_shipment",
"type_ref": "shipping_core.json#properties/quality_of_shipment",
"allow_empty": true
},
"ship from": {
"merge_pointer": "/ship_from",
"type_ref": "shipping_core.json#properties/ship_from",
"allow_empty": true
},
"ship to": {
"merge_pointer": "/ship_to",
"type_ref": "shipping_core.json#properties/ship_to",
"allow_empty": true
}
}
},
"Essential Patient Data": {
"prism_preamble_object_schema": "clinical_trial.json",
"prism_preamble_object_pointer": "#",
"prism_data_object_pointer": "/participants/0/samples/0",
"data_columns": {
"Path Concordance Verification": {
"entry (#)": {
"do_not_merge": true,
"allow_empty": true,
"type": "string"
},
"participant ID": {
"merge_pointer": "2/participant_id",
"type_ref": "participant.json#properties/participant_id"
},
"CIMAC ID": {
"merge_pointer": "/cimac_id",
"type_ref": "sample.json#properties/cimac_id",
"process_as": [
{
"merge_pointer": "2/cimac_participant_id",
"type_ref": "participant.json#properties/cimac_participant_id",
"parse_through": "lambda x: x[:7]"
}
]
},
"surgical pathology report id": {
"merge_pointer": "/surgical_pathology_report_id",
"type_ref": "sample.json#properties/surgical_pathology_report_id"
},
"clinical report id": {
"merge_pointer": "/clinical_report_id",
"type_ref": "sample.json#properties/clinical_report_id"
},
"collection event name": {
"merge_pointer": "/collection_event_name",
"type_ref": "sample.json#properties/collection_event_name"
},
"diagnosis verification": {
"merge_pointer": "/diagnosis_verification",
"type_ref": "sample.json#properties/diagnosis_verification"
}
},
"ICD-0-3 Code/Description": {
"Site Description": {
"merge_pointer": "/site_description",
"type_ref": "sample.json#properties/site_description"
},
"Topography Code": {
"merge_pointer": "/topography_code",
"type_ref": "sample.json#properties/topography_code"
},
"Topography Description": {
"merge_pointer": "/topography_description",
"type_ref": "sample.json#properties/topography_description"
},
"Histology/Behavior": {
"merge_pointer": "/histology_behavior",
"type_ref": "sample.json#properties/histology_behavior"
},
"Histology/Behavior Description": {
"merge_pointer": "/histology_behavior_description",
"type_ref": "sample.json#properties/histology_behavior_description"
}
},
"Demographics": {
"Sex": {
"merge_pointer": "2/gender",
"type_ref": "participant.json#properties/gender"
},
"Race": {
"merge_pointer": "2/race",
"type_ref": "participant.json#properties/race"
},
"Ethnic Group": {
"merge_pointer": "2/ethnicity",
"type_ref": "participant.json#properties/ethnicity"
}
}
}
},
"Samples": {
"prism_preamble_object_schema": "clinical_trial.json",
"prism_preamble_object_pointer": "#",
"prism_data_object_pointer": "/participants/0/samples/0",
"data_columns": {
"IDs": {
"entry (#)": {
"merge_pointer": "/shipping_entry_number",
"type_ref": "sample.json#properties/shipping_entry_number"
},
"collection event name": {
"merge_pointer": "/collection_event_name",
"type_ref": "sample.json#properties/collection_event_name"
},
"cohort name": {
"merge_pointer": "2/cohort_name",
"type_ref": "participant.json#properties/cohort_name"
},
"participant ID": {
"merge_pointer": "2/participant_id",
"type_ref": "participant.json#properties/participant_id"
},
"parent sample ID": {
"merge_pointer": "/parent_sample_id",
"type_ref": "sample.json#properties/parent_sample_id"
},
"processed sample ID": {
"allow_empty": true,
"merge_pointer": "/processed_sample_id",
"type_ref": "sample.json#properties/processed_sample_id"
},
"CIMAC ID": {
"merge_pointer": "/cimac_id",
"type_ref": "sample.json#properties/cimac_id",
"process_as": [
{
"merge_pointer": "2/cimac_participant_id",
"type_ref": "participant.json#properties/cimac_participant_id",
"parse_through": "lambda x: x[:7]"
}
]
}
},
"Filled by Biorepository": {
"box number": {
"merge_pointer": "/box_number",
"type_ref": "sample.json#properties/box_number",
"allow_empty": true
},
"sample location": {
"merge_pointer": "0/sample_location",
"type_ref": "sample.json#properties/sample_location",
"allow_empty": true
},
"type of sample": {
"merge_pointer": "0/type_of_sample",
"type_ref": "sample.json#properties/type_of_sample"
},
"sample collection procedure": {
"merge_pointer": "/sample_collection_procedure",
"type_ref": "sample.json#properties/sample_collection_procedure"
},
"type of primary container": {
"merge_pointer": "0/type_of_primary_container",
"type_ref": "sample.json#properties/type_of_primary_container"
},
"processed sample type": {
"merge_pointer": "/processed_sample_type",
"type_ref": "sample.json#properties/processed_sample_type"
},
"processed sample volume": {
"merge_pointer": "/processed_sample_volume",
"type_ref": "sample.json#properties/processed_sample_volume",
"allow_empty": true
},
"processed sample volume units": {
"merge_pointer": "/processed_sample_volume_units",
"type_ref": "sample.json#properties/processed_sample_volume_units",
"allow_empty": true
},
"processed sample concentration": {
"merge_pointer": "/processed_sample_concentration",
"type_ref": "sample.json#properties/processed_sample_concentration",
"allow_empty": true
},
"processed sample concentration units": {
"merge_pointer": "/processed_sample_concentration_units",
"type_ref": "sample.json#properties/processed_sample_concentration_units",
"allow_empty": true
},
"processed sample derivative": {
"merge_pointer": "/processed_sample_derivative",
"type_ref": "sample.json#properties/processed_sample_derivative",
"allow_empty": true
},
"sample derivative volume": {
"merge_pointer": "/sample_derivative_volume",
"type_ref": "sample.json#properties/sample_derivative_volume",
"allow_empty": true
},
"sample derivative volume units": {
"merge_pointer": "/sample_derivative_volume_units",
"type_ref": "sample.json#properties/sample_derivative_volume_units"
},
"sample derivative concentration": {
"merge_pointer": "/sample_derivative_concentration",
"type_ref": "sample.json#properties/sample_derivative_concentration",
"allow_empty": true
},
"sample derivative concentration units": {
"merge_pointer": "/sample_derivative_concentration_units",
"type_ref": "sample.json#properties/sample_derivative_concentration_units",
"allow_empty": true
}
},
"Filled by CIMAC Lab": {
"pbmc viability": {
"merge_pointer": "/pbmc_viability",
"type_ref": "sample.json#properties/pbmc_viability",
"allow_empty": true
},
"pbmc recovery": {
"merge_pointer": "/pbmc_recovery",
"type_ref": "sample.json#properties/pbmc_recovery",
"allow_empty": true
},
"pbmc resting period used": {
"merge_pointer": "/pbmc_resting_period_used",
"type_ref": "sample.json#properties/pbmc_resting_period_used",
"allow_empty": true
},
"material used": {
"merge_pointer": "/material_used",
"type_ref": "sample.json#properties/material_used",
"allow_empty": true
},
"material remaining": {
"merge_pointer": "/material_remaining",
"type_ref": "sample.json#properties/material_remaining",
"allow_empty": true
},
"material storage condition": {
"merge_pointer": "/material_storage_condition",
"type_ref": "sample.json#properties/material_storage_condition",
"allow_empty": true
},
"quality of sample": {
"merge_pointer": "/quality_of_sample",
"type_ref": "sample.json#properties/quality_of_sample",
"allow_empty": true
},
"sample replacement": {
"merge_pointer": "/sample_replacement",
"type_ref": "sample.json#properties/sample_replacement",
"allow_empty": true
},
"residual sample use": {
"merge_pointer": "/residual_sample_use",
"type_ref": "sample.json#properties/residual_sample_use",
"allow_empty": true
},
"comments": {
"merge_pointer": "/comments",
"type_ref": "sample.json#properties/comments",
"allow_empty": true
}
}
}
}
}
}
}