CIMAC-CIDC/cidc-schemas

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cidc_schemas/schemas/templates/manifests/pbmc_template.json

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{
    "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
                        }
                    }
                }
            }
        }
    }
}