{"AlignedReads": {"$id": "/profiles/aligned_reads.json", "title": "Aligned Reads", "properties": {"submitted_id": {"pattern": "^[A-Z0-9]{3,}_ALIGNED-READS_[A-Z0-9-_.]{4,}$", "title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "is_required": true}, "submitted_md5sum": {"title": "Submitted MD5", "description": "Submitted MD5 checksum of the file", "type": "string", "format": "hex"}, "external_quality_metrics": {"description": "Link to externally-generated QC metrics associated with file", "items": {"description": "Associated QC report", "linkTo": "ExternalQualityMetric", "title": "Quality Metric", "type": "string"}, "minItems": 1, "title": "External Quality Metrics", "type": "array", "uniqueItems": true}, "file_format": {"ff_flag": "filter:valid_item_types", "linkTo": "FileFormat", "title": "File Format", "type": "string", "description": "Format for the file", "is_required": true}, "filename": {"description": "The local file name used at time of submission. 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"description": "Instrument used for RNA integrity assessment", "type": "string", "suggested_enum": ["Agilent Bioanalyzer", "Agilent 4200 TapeStation", "Agilent 5300 Fragment Analyzer", "Caliper Life Sciences LabChip GX"], "also_requires": ["rna_integrity_number"]}, "sample_quantity": {"title": "Sample Quantity", "description": "The amount of sample used to generate the analyte", "type": "number", "minimum": 0, "also_requires": ["sample_quantity_unit"]}, "sample_quantity_unit": {"title": "Sample Quantity Unit", "description": "Unit of the sample quantity", "type": "string", "enum": ["cells", "uL", "mL", "ng", "ug", "mg", "g"], "also_requires": ["sample_quantity"]}, "volume": {"title": "Volume", "description": "Analyte volume", "type": "number", "minimum": 0, "also_requires": ["volume_unit"]}, "volume_unit": {"title": "Volume Unit", "description": "Unit of the volume", "type": "string", "enum": ["uL", "mL"], "also_requires": ["volume"]}, "analyte_preparation": {"title": "Analyte Preparation", "description": "Link to associated analyte preparation", "type": "string", "linkTo": "AnalytePreparation"}, "samples": {"title": "Samples", "description": "Link to associated samples (e.g. Tissue Sample, Cell Culture Sample, etc.)", "type": "array", "minItems": 1, "maxItems": 1000, "uniqueItems": true, "items": {"type": "string", "linkTo": "Sample"}, "is_required": true}, "total_yield": {"title": "Total Yield", "description": "Total yield of analyte from sample (ug)", "type": "number", "minimum": 0}, "yield_per_unit": {"title": "Yield Per Unit", "description": "Yield per unit of sample", "type": "number", "minimum": 0, "also_requires": ["yield_unit"]}, "yield_unit": {"title": "Yield Unit", "description": "Unit used for measuring yield per unit of sample", "type": "string", "enum": ["ug/million cells", "ug/mg", "ug/vial of cells"], "also_requires": ["yield_per_unit"]}}}, "AnalytePreparation": {"$id": "/profiles/analyte_preparation.json", "title": "Analyte Preparation", "properties": {"submitted_id": {"pattern": "^[A-Z0-9]{3,}_ANALYTE-PREPARATION_[A-Z0-9-_.]{4,}$", "title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "is_required": true}, "preparation_kits": {"title": "Preparation Kits", "description": "Links to associated preparation kits", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "linkTo": "PreparationKit"}}, "treatments": {"title": "Treatments", "description": "Link to associated treatments performed during library preparation", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "linkTo": "Treatment"}}, "description": {"title": "Description", "description": "Plain text description of the item", "type": "string", "formInput": "textarea"}, "cell_lysis_method": {"title": "Cell Lysis Method", "description": "Cell lysis method for analyte extraction, if applicable. Relevant for extraction for single-cell assays", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "enum": ["Chemical", "Enzymatic", "Mechanical", "Thermal"]}}, "cell_selection_method": {"title": "Cell Selection Method", "description": "Cell selection method for analyte extraction, if applicable. Relevant for extraction for single-cell assays", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "enum": ["Fluoresence-activated Cell Sorting", "Magnetic-activated Cell Sorting", "Selective Media", "Laser Capture Microdissection", "Micromanipulation", "Isopycnic Sedimentation", "Velocity Sedimentation", "Centrifugation", "Cell Raft", "Size Selection", "Microfluidics"]}}, "extraction_method": {"title": "Extraction Method", "description": "Method of analyte extraction", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "enum": ["Density Gradient Centrifugation", "Magnetic Beads", "Mechanical Dissociation", "Not Applicable", "Organic Chemicals", "Silica Column"]}}, "homogenization_method": {"title": "Homogenization method", "description": "Method of sample homogenization, if applicable", "type": "string"}, "suspension_type": {"title": "Suspension Type", "description": "Type of cell suspension. Relevant for extraction for single-cell assays", "type": "string", "enum": ["Whole Cell", "Nucleus"]}}}, "BrainPathologyReport": {"$id": "/profiles/brain_pathology_report.json", "title": "Brain Pathology Report", "properties": {"submitted_id": {"pattern": "^[A-Z0-9]{3,}_BRAIN-PATHOLOGY-REPORT_[A-Z0-9-_.]{4,}$", "title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "is_required": true}, "additional_notes": {"title": "Additional Notes", "description": "Additional notes or other findings related to the sample", "type": "string"}, "final_review_determination": {"title": "Final Review Determination", "description": "Whether a final review determination was made for the sample", "type": "string", "enum": ["Yes", "No"]}, "is_indeterminate": {"title": "Is Indeterminate", "description": "Whether the tissue sample is indeterminate", "type": "string", "enum": ["Yes", "No"]}, "outcome": {"title": "Outcome", "description": "Outcome of the pathology report", "type": "string", "enum": ["Acceptable", "Unacceptable"], "is_required": true}, "tissue_name": {"title": "Tissue Name", "description": "Name of the type of tissue the sample was taken from", "type": "string", "enum": ["Brain"], "is_required": true}, "unacceptable_description": {"title": "Unacceptable Description", "description": "Description of unacceptable review determination", "type": "string"}, "tissue_samples": {"title": "Tissue Samples", "description": "Link to associated tissue samples", "type": "array", "items": {"type": "string", "linkTo": "TissueSample"}, "is_required": true}, "version": {"title": "Version", "description": "Version for the item", "type": "string", "pattern": "^([0-9]+.)*[0-9]+$"}, "description": {"title": "Description", "description": "Plain text description of the item", "type": "string", "formInput": "textarea"}, "brain_subregions": {"title": "Brain Subregions", "type": "array", "items": {"properties": {"subregion": {"type": "string", "enum": ["Cerebellum Left Hemisphere", "Frontal Lobe Left Hemisphere", "Hippocampus Left Hemisphere", "Hippocampus Right Hemisphere", "Temporal Lobe Left Hemisphere"]}, "is_present": {"type": "string", "enum": ["Yes", "No"]}, "tissue_autolysis_score": {"title": "Tissue Autolysis Score", "description": "Tissue autolysis score of the sample or region. 0=None, 1=mild , 2=moderate, 3=severe", "type": "integer", "minimum": 0, "maximum": 3}}}}, "developmental_neuropathology_present": {"type": "string", "description": "Whether a developmental neuropathologic or unexpected finding was present or absent.", "enum": ["Yes", "No"]}, "developmental_neuropathology_description": {"type": "string", "description": "Description of developmental neuropathology."}, "infectious_neuropathology_present": {"type": "string", "description": "Whether an infectious neuropathologic or unexpected finding was present or absent.", "enum": ["Yes", "No"]}, "infectious_neuropathology_description": {"type": "string", "description": "Description of infectious neuropathology."}, "inflammatory_neuropathology_present": {"type": "string", "description": "Whether an inflammatory neuropathologic or unexpected finding was present or absent.", "enum": ["Yes", "No"]}, "inflammatory_neuropathology_description": {"type": "string", "description": "Description of inflammatory neuropathology."}, "neoplastic_neuropathology_present": {"type": "string", "description": "Whether a neoplastic neuropathologic or unexpected finding was present or absent.", "enum": ["Yes", "No"]}, "neoplastic_neuropathology_description": {"type": "string", "description": "Description of neoplastic neuropathology."}, "tbi_neuropathology_present": {"type": "string", "description": "Whether a traumatic brain injury finding was present or absent.", "enum": ["Yes", "No"]}, "tbi_neuropathology_description": {"type": "string", "description": "Description of traumatic brain injury."}, "vascular_neuropathology_present": {"type": "string", "description": "Whether a vascular neuropathologic or unexpected finding was present or absent.", "enum": ["Yes", "No"]}, "vascular_neuropathology_description": {"type": "string", "description": "Description of vascular neuropathology."}, "neurodegenerative_neuropathology_present": {"type": "string", "description": "Whether a neurodegenerative neuropathologic or unexpected finding was present or absent.", "enum": ["Yes", "No"]}, "neurodegenerative_neuropathology_description": {"type": "string", "description": "Description of neurodegenerative neuropathology."}, "metabolic_neuropathology_present": {"type": "string", "description": "Whether a metabolic neuropathologic or unexpected finding was present or absent.", "enum": ["Yes", "No"]}, "metabolic_neuropathology_description": {"type": "string", "description": "Description of metabolic neuropathology."}, "artifacts_present": {"type": "string", "description": "Whether artifacts were present or absent.", "enum": ["Yes", "No"]}, "artifacts_description": {"type": "string", "description": "Description of artifacts."}, "other_pathology_present": {"type": "string", "description": "Whether any other neuropathologic or unexpected findings were present.", "enum": ["Yes", "No"]}, "other_pathology_description": {"type": "string", "description": "Description of other neuropathology."}, "additional_age-related_staining_performed": {"type": "string", "description": "Whether additional dementia-related or age-related staining was conducted.", "enum": ["Yes", "No"]}, "abc_score_A": {"title": "ABC Score A", "type": "integer", "description": "Assesses the distribution of A\u03b2/amyloid plaques, 0 = none, 3 = severe", "minimum": 0, "maximum": 3}, "abc_score_B": {"title": "ABC Score B", "type": "integer", "description": "Stages the distribution of neurofibrillary tangle, 0 = none, 3 = severe", "minimum": 0, "maximum": 3}, "abc_score_C": {"title": "ABC Score C", "type": "integer", "description": "Scores the density of neuritic plaques, 0 = none, 1= sparse, 2= moderate, 3 = frequent", "minimum": 0, "maximum": 3}, "cerad_score": {"title": "CERAD", "type": "integer", "description": "Consortium to Establish a Registry for Alzheimer's Disease (CERAD) score of neuritic (usually dense-core) plaques.", "minimum": 0, "maximum": 100}, "ad_neuropathologic_change_level": {"title": "Level of AD Neuropathologic change", "type": "string", "description": "Amount of Alzheimer's disease-related neuropathologic change observed.", "enum": ["None", "Low", "Intermediate", "High"]}, "braak_pd": {"title": "Braak PD", "type": "integer", "description": "Braak staging of Parkinson's disease.", "minimum": 0, "maximum": 6}, "small_vessel_disease": {"title": "Small Vessel Disease", "type": "string", "description": "Amount of small vessel disease observed.", "enum": ["None", "Mild", "Moderate", "Severe"]}, "braak_and_braak_ad": {"title": "Braak & Braak AD", "type": "string", "description": "A semiquantitative measure of distribution and severity of neurofibrillary tangle (NFT) pathology", "enum": ["I", "II", "III", "IV", "V", "VI"]}, "thal": {"title": "Thal", "type": "integer", "description": "Thal phases refer to any amyloid deposits based on anti-A\u03b2 immunohistochemistry", "minimum": 0, "maximum": 5}, "caa_vonsattel": {"title": "CAA VonSattel", "type": "integer", "description": "Cerebral amyloid angiopathy (CAA) using VonSattel system (1= Mild, 2= Moderate, 3 to 4= Severe) ", "minimum": 0, "maximum": 4}, "mckeith": {"title": "McKeith", "type": "integer", "description": "McKeith staging system for Lewy body dementia.", "minimum": 0, "maximum": 4}, "vonsattel_hd": {"title": "VonSattel (Huntington's disease)", "type": "integer", "description": "Von Sattel grading system for Huntington's disease.", "minimum": 0, "maximum": 4}, "final_neuropathological_diagnosis": {"type": "string", "description": "Final summary of neuropathological diagnoses."}}}, "CellCulture": {"$id": "/profiles/cell_culture.json", "title": "Cell Culture", "properties": {"submitted_id": {"pattern": "^[A-Z0-9]{3,}_CELL-CULTURE_[A-Z0-9-_.]{4,}$", "title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "is_required": true}, "sample_count": {"title": "Sample Count", "description": "Number of samples produced for this source", "type": "integer", "minimum": 1}, "external_id": {"title": "External ID", "description": "External ID for the item provided by submitter", "type": "string", "pattern": "^[A-Za-z0-9-_]{3,}$"}, "description": {"title": "Description", "description": "Plain text description of the item", "type": "string", "formInput": "textarea"}, "culture_duration": {"title": "Culture Duration", "description": "Total number of culturing days", "type": "integer", "minimum": 0}, "culture_harvest_date": {"title": "Culture Harvest Date", "description": "YYYY-MM-DD format date for cell culture harvest", "type": "string", "format": "date"}, "culture_start_date": {"title": "Culture Start Date", "description": "YYYY-MM-DD format date for cell culture start date", "type": "string", "format": "date"}, "growth_medium": {"title": "Growth Medium", "description": "Medium used for cell culture", "type": "string"}, "karyotype": {"title": "Karyotype", "description": "Chromosome count and any noted rearrangements or copy number variation", "type": "string"}, "lot_number": {"title": "Lot Number", "description": "Lot number of cell line", "type": "array", "items": {"type": "string"}}, "passage_number": {"title": "Passage Number", "description": "Number of times the cell line has been passaged since the culture start date until harvest", "type": "integer", "minimum": 0}, "cell_line": {"title": "Cell Line", "description": "Cell line used for the cell culture", "type": "array", "items": {"type": "string", "linkTo": "CellLine"}, "required_if_not_one_of": ["tissue_samples"]}, "tissue_samples": {"title": "Tissue Samples", "description": "Tissue samples the cell culture was derived from", "type": "array", "minItem": 1, "uniqueItems": true, "items": {"type": "string", "linkTo": "Sample"}, "required_if_not_one_of": ["cell_line"]}}}, "CellCultureMixture": {"$id": "/profiles/cell_culture_mixture.json", "title": "Cell Culture Mixture", "properties": {"title": {"title": "Title", "description": "Name of the cell culture mixture", "type": "string", "minLength": 3}, "submitted_id": {"title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "pattern": "^[A-Z0-9]{3,}_CELL-CULTURE-MIXTURE_[A-Z0-9-_.]{4,}$", "is_required": true}, "external_id": {"title": "External ID", "description": "External ID for the item provided by submitter", "type": "string", "pattern": "^[A-Za-z0-9-_]{3,}$"}, "description": {"title": "Description", "description": "Plain text description of the item", "type": "string", "formInput": "textarea"}, "components": {"title": "Components", "description": "Cultures in the mixture and their corresponding ratios", "type": "array", "minItems": 1, "items": {"properties": {"ratio": {"title": "Ratio", "description": "Ratio of the cell culture to the total mixture (percentage)", "type": "number", "minimum": 0}, "cell_culture": {"title": "Cell Culture", "description": "Link to associated cell culture", "type": "string", "linkTo": "CellCulture"}}}, "is_required": true}}}, "CellCultureSample": {"$id": "/profiles/cell_culture_sample.json", "title": "Cell Culture Sample", "properties": {"submitted_id": {"pattern": "^[A-Z0-9]{3,}_CELL-CULTURE-SAMPLE_[A-Z0-9-_.]{4,}$", "title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "is_required": true}, "sample_sources": {"title": "Sample Sources", "description": "Link to associated sample sources (e.g. tissue, cell culture, etc.)", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "linkTo": "SampleSource"}, "is_required": true}, "preservation_type": {"title": "Preservation Type", "description": "Method of preservation", "type": "string", "enum": ["Fixed", "Fresh", "Frozen", "Snap Frozen"]}, "preservation_medium": {"title": "Preservation Medium", "description": "Medium used for preservation", "type": "string"}, "parent_samples": {"title": "Parent Samples", "description": "Link to associated parent samples from which this sample was derived", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "linkTo": "Sample"}}, "external_id": {"title": "External ID", "description": "External ID for the item provided by submitter", "type": "string", "pattern": "^[A-Za-z0-9-_]{3,}$"}, "description": {"title": "Description", "description": "Plain text description of the item", "type": "string", "formInput": "textarea"}, "cell_count": {"title": "Cell Count", "description": "The number of cells in the sample to be analyzed", "type": "integer", "minimum": 1}, "cell_density": {"title": "Cell Density", "description": "The number of cells per mL of storage medium", "type": "number", "minimum": 0}, "volume": {"title": "Volume", "description": "The volume of the sample in mL", "type": "number", "minimum": 0}}}, "CellLine": {"$id": "/profiles/cell_line.json", "title": "Cell Line", "properties": {"title": {"title": "Title", "description": "Name of the cell line", "type": "string", "minLength": 3, "is_required": true}, "submitted_id": {"title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "pattern": "^[A-Z0-9]{3,}_CELL-LINE_[A-Z0-9-_.]{4,}$", "is_required": true}, "description": {"title": "Description", "description": "Plain text description of the item", "type": "string", "formInput": "textarea"}, "source": {"title": "Source", "description": "Source of the cells (vendor or institution)", "type": "string", "is_required": true}, "url": {"title": "Url", "description": "URL for vendor information on the cell line", "type": "string", "format": "uri"}, "parent_cell_lines": {"title": "Parent Cell Lines", "description": "Cell lines the cell line was derived from", "type": "array", "minItem": 1, "uniqueItems": true, "items": {"type": "string", "linkTo": "CellLine"}}, "tissue_samples": {"title": "Tissue Samples", "description": "Tissue samples the cell line  was derived from", "type": "array", "minItem": 1, "uniqueItems": true, "items": {"type": "string", "linkTo": "Sample"}}, "donor": {"title": "Donor", "description": "Donor associated with the cell line", "type": "string", "linkTo": "Donor"}}}, "CellSample": {"$id": "/profiles/cell_sample.json", "title": "Cell Sample", "properties": {"submitted_id": {"pattern": "^[A-Z0-9]{3,}_CELL-SAMPLE_[A-Z0-9-_.]{4,}$", "title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "is_required": true}, "sample_sources": {"title": "Sample Sources", "description": "Link to associated sample sources (e.g. tissue, cell culture, etc.)", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "linkTo": "SampleSource"}, "is_required": true}, "preservation_type": {"title": "Preservation Type", "description": "Method of preservation", "type": "string", "enum": ["Fixed", "Fresh", "Frozen", "Snap Frozen"]}, "preservation_medium": {"title": "Preservation Medium", "description": "Medium used for preservation", "type": "string"}, "parent_samples": {"title": "Parent Samples", "description": "Link to associated parent samples from which this sample was derived", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "linkTo": "Sample"}}, "external_id": {"title": "External ID", "description": "External ID for the item provided by submitter", "type": "string", "pattern": "^[A-Za-z0-9-_]{3,}$"}, "description": {"title": "Description", "description": "Plain text description of the item", "type": "string", "formInput": "textarea"}, "cell_count": {"title": "Cell Count", "description": "The number of cells in the sample to be analyzed", "type": "integer", "minimum": 1}, "cell_ontology_id": {"title": "Cell Ontology ID", "description": "Cell Ontology identifier for the cell sample", "type": "string", "pattern": "^CL:[0-9]{7}$", "url": "https://cell-ontology.github.io/", "is_required": true}}}, "DeathCircumstances": {"$id": "/profiles/death_circumstances.json", "title": "Death Circumstances", "properties": {"submitted_id": {"title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "pattern": "^[A-Z0-9]{3,}_DEATH-CIRCUMSTANCES_[A-Z0-9-_.]{4,}$", "is_required": true}, "blood_transfusion": {"title": "Blood Transfusion", "description": "Whether donor received a blood transfusion within 48 hours of death", "type": "string", "enum": ["Yes", "No", "Unknown"]}, "blood_transfusion_products": {"title": "Blood Transfusion Products", "description": "Blood transfusion products received by donor within 48 hours", "type": "array", "uniqueItems": true, "minItems": 1, "items": {"type": "string", "suggested_enum": ["Cryoprecipitate", "Fresh Frozen Plasma", "Packed Red Blood Cells", "Platelets"]}}, "cause_of_death_immediate": {"title": "Cause Of Death Immediate", "description": "Immediate cause of death", "type": "string"}, "cause_of_death_immediate_interval": {"title": "Cause Of Death Immediate Interval", "description": "Interval of time from immediate cause of death to death (hours)", "type": "number", "minimum": 0}, "cause_of_death_initial": {"title": "Cause Of Death Initial", "description": "Initial cause of death", "type": "string"}, "cause_of_death_last_underlying": {"title": "Cause Of Death Last Underlying", "description": "Last underlying cause of death", "type": "string"}, "circumstances_of_death": {"title": "Circumstances of Death", "type": "string", "enum": ["Accidental", "Homicide", "Natural", "Suicide", "Undetermined", "Unreported"]}, "death_pronounced_interval": {"title": "Death Pronounced Interval", "description": "Interval of time between death pronouncement and witness of death (hours)", "type": "number", "minimum": 0}, "donor_stream": {"title": "Donor Stream", "description": "Status of donor when enrolled in the study", "type": "string", "enum": ["Brain Dead", "Donation Ater Circulatory Death", "Postmortem"]}, "place_of_death": {"title": "Place Of Death", "description": "Place of death of the donor", "type": "string", "enum": ["Home", "Hospital", "Other"]}, "region_of_death": {"title": "Region Of Death", "description": "Region of death of the donor", "type": "string", "enum": ["Midwest: East North Central", "Midwest: West North Central", "Northeast: Middle Atlantic", "Northeast: New England", "Other", "South: East South Central", "South: South Atlantic", "South: West South Central", "West: Mountain", "West: Pacific"]}, "season_of_death": {"title": "Season Of Death", "description": "Season of death of the donor", "type": "string", "enum": ["Fall", "Spring", "Summer", "Winter"]}, "sepsis_at_death": {"title": "Sepsis At Death", "description": "Whether the donor had sepsis at the time of death", "type": "string", "enum": ["No", "Unknown", "Yes"]}, "ventilator_at_death": {"title": "Ventilator At Death", "description": "Whether the donor was on a ventilator immediately prior to death", "type": "string", "enum": ["Yes", "No", "Unknown"]}, "ventilator_time": {"title": "Ventilator Time", "description": "Time the donor was on a ventilator prior to death (hours)", "type": "number", "minimum": 0}, "donor": {"title": "Donor", "description": "Link to the associated donor", "type": "string", "linkTo": "AbstractDonor", "is_required": true}}}, "Demographic": {"$id": "/profiles/demographic.json", "title": "Demographic", "properties": {"submitted_id": {"title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "pattern": "^[A-Z0-9]{3,}_DEMOGRAPHIC_[A-Z0-9-_.]{4,}$", "is_required": true}, "international_military_base": {"title": "International Military Base", "description": "Whether the donor lived or worked on an international U.S. military base", "type": "string", "enum": ["No", "Unknown", "Yes"]}, "international_military_base_details": {"title": "International Military Base Details", "description": "Additional information about the donor's association with an international military base", "type": "string"}, "military_association": {"title": "Military Association", "description": "Association of the donor with the military, either as a member, employee, or a dependent of a member of the military", "type": "string", "enum": ["No", "Unknown", "Yes"]}, "donor": {"title": "Donor", "description": "Link to the associated donor", "type": "string", "linkTo": "AbstractDonor", "is_required": true}}}, "Diagnosis": {"$id": "/profiles/diagnosis.json", "title": "Diagnosis", "properties": {"submitted_id": {"title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "pattern": "^[A-Z0-9]{3,}_DIAGNOSIS_[A-Z0-9-_.]{4,}$", "is_required": true}, "age_at_diagnosis": {"title": "Age At Diagnosis", "description": "Age when the disease was diagnosed (years). Note: age above 89 is represented as 89 to remove identifiable information.", "type": "integer", "minimum": 0, "maximum": 89}, "age_at_resolution": {"title": "Age At Resolution", "description": "Age when the disease was determined to have resolved (years). Note: age above 89 is represented as 89 to remove identifiable information.", "type": "integer", "minimum": 0, "maximum": 89}, "comments": {"title": "Comments", "description": "Additional information on the diagnosis", "type": "string"}, "disease": {"title": "Disease", "description": "Link to associated disease ontology term", "type": "string", "is_required": true}, "medical_history": {"title": "Medical History", "description": "Link to the associated medical history", "type": "string", "linkTo": "MedicalHistory", "is_required": true}}}, "Donor": {"$id": "/profiles/donor.json", "title": "Donor", "properties": {"external_id": {"submissionComment": "For donors from the TPC, this should be the TPC donor ID. Otherwise, the submitter's internal identifier can be used.", "type": "string", "pattern": "^[A-Za-z0-9-_]{2,}$", "is_required": true}, "submitted_id": {"pattern": "^[A-Z0-9]{3,}_DONOR_[A-Z0-9-_.]{4,}$", "title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "is_required": true}, "age": {"title": "Age", "description": "Age of the donor (years). Note: donor age above 89 is represented as 89 to remove identifiable information.", "type": "integer", "minimum": 0, "maximum": 89, "is_required": true}, "eligibility": {"title": "Eligibility", "description": "Whether donor was deemed eligible for the study", "type": "string", "enum": ["Yes", "No", "Unknown"]}, "hardy_scale": {"title": "Hardy Scale", "description": "Death classification based on the 4-point Hardy Scale", "type": "integer", "minimum": 0, "maximum": 4}, "sex": {"title": "Sex", "description": "Sex of the donor", "type": "string", "enum": ["Male", "Female", "Unknown"], "is_required": true}, "tpc_submitted": {"title": "TPC Submitted", "description": "Whether the donor was submitted by the TPC", "type": "string", "enum": ["True", "False"], "is_required": true}, "protected_donor": {"title": "Protected Donor", "description": "Link to protected donor", "type": "string", "linkTo": "ProtectedDonor"}}}, "DonorSpecificAssembly": {"$id": "/profiles/donor_specific_assembly.json", "title": "Donor Specific Assembly", "properties": {"version": {"title": "Version", "description": "Version of the assembly", "type": "string", "pattern": "^([0-9]+.)*[0-9]+$", "is_required": true}, "submitted_id": {"title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "pattern": "^[A-Z0-9]{3,}_DONOR-SPECIFIC-ASSEMBLY_[A-Z0-9-_.]{4,}$", "is_required": true}, "title": {"title": "Title", "description": "Title of the assembly (e.g. ST001_DSA)", "type": "string", "minLength": 3, "is_required": true}, "description": {"title": "Description", "description": "Plain text description of the item", "type": "string", "formInput": "textarea"}, "genome_size": {"title": "Genome Size", "description": "The size of both combined assembled haplotypes (bp)", "type": "integer", "minimum": 0, "allow_commas": true, "allow_multiplier_suffix": true}, "ploidy": {"title": "Ploidy", "description": "Ploidy of the assembly", "type": "string", "suggested_enum": ["Diploid", "Haploid", "Aneuploid"]}, "derived_from": {"title": "Derived From", "description": "Link to files used as input to generate the assembly", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "linkTo": "File"}, "is_required": true}}}, "Exposure": {"$id": "/profiles/exposure.json", "title": "Exposure", "properties": {"submitted_id": {"title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "pattern": "^[A-Z0-9]{3,}_EXPOSURE_[A-Z0-9-_.]{4,}$", "is_required": true}, "category": {"title": "Exposure Category", "description": "Category of the substance to which the donor was exposed", "type": "string", "enum": ["Alcohol", "Chemical", "Environmental", "Toxic Exposure", "Illicit Drug", "Occupational", "Tobacco", "Other"], "is_required": true}, "cessation": {"title": "Cessation", "description": "Whether exposure ceased prior to death", "type": "string", "enum": ["No", "Unknown", "Yes"]}, "cessation_duration": {"title": "Cessation Duration", "description": "Duration since exposure ceased (years)", "type": "integer", "minimum": 0}, "comments": {"title": "Comments", "description": "Additional information on the exposure", "type": "string"}, "duration": {"title": "Duration", "description": "Duration of the exposure (years)", "type": "number", "minimum": 0}, "frequency_category": {"title": "Exposure Frequency", "description": "Frequency of the exposure", "type": "string", "enum": ["Light", "Heavy", "Moderate", "Social", "Unknown"]}, "quantity": {"title": "Quantity", "description": "Quantity of the substance to which the donor was exposed", "type": "integer"}, "quantity_unit": {"title": "Quantity Unit", "description": "Unit of the quantity of the substance to which the donor was exposed", "type": "string", "suggested_enum": ["Drinks Per Day", "Drinks Per Week", "Packs Per Day", "Packs Per Year"]}, "route": {"title": "Exposure Route", "description": "Route of the exposure", "type": "string", "enum": ["Intranasal", "Transdermal", "Inhalation", "Ingestion", "IV", "Unknown"]}, "substance": {"title": "Substance", "description": "Substance to which the donor was exposed", "type": "string", "is_required": true}, "medical_history": {"title": "Medical History", "description": "Link to the associated medical history", "type": "string", "linkTo": "MedicalHistory", "is_required": true}}}, "ExternalOutputFile": {"$id": "/profiles/external_output_file.json", "title": "External Output File", "properties": {"submitted_id": {"pattern": "^[A-Z0-9]{3,}_EXTERNAL-OUTPUT-FILE_[A-Z0-9-_.]{4,}$", "title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "is_required": true}, "submitted_md5sum": {"title": "Submitted MD5", "description": "Submitted MD5 checksum of the file", "type": "string", "format": "hex"}, "external_quality_metrics": {"description": "Link to externally-generated QC metrics associated with file", "items": {"description": "Associated QC report", "linkTo": "ExternalQualityMetric", "title": "Quality Metric", "type": "string"}, "minItems": 1, "title": "External Quality Metrics", "type": "array", "uniqueItems": true}, "file_format": {"ff_flag": "filter:valid_item_types", "linkTo": "FileFormat", "title": "File Format", "type": "string", "description": "Format for the file", "is_required": true}, "filename": {"description": "The local file name used at time of submission. Must be alphanumeric, with the exception of the following special characters: '+=,.@-_'", "pattern": "^[\\w+=,.@-]*$", "title": "File Name", "type": "string", "is_required": true}, "analysis_details": {"title": "Analysis Details", "description": "Details of analysis performed on file", "type": "array", "items": {"type": "string", "enum": ["Aligned", "Filtered", "Sorted", "Phased", "Unphased"], "default": ["Unphased"]}}, "data_category": {"title": "Data Category", "description": "Category for information in the file", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "enum": ["Germline Variant Calls", "Somatic Variant Calls"]}, "is_required": true}, "data_type": {"title": "Data Type", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "enum": ["CNV", "Indel", "MEI", "SNV", "SV", "Fingerprint"]}, "is_required": true}, "reference_genome": {"title": "Reference Genome", "description": "Reference genome used for alignment", "type": "string", "linkTo": "ReferenceGenome"}, "analysis_runs": {"title": "Analysis Runs", "description": "Link to analysis runs associated with this file", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "linkTo": "AnalysisRun"}}, "derived_from": {"title": "Derived From", "description": "Link to files used as input to create this file", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "linkTo": "File"}}, "file_sets": {"title": "File Sets", "description": "Link to file sets associated with this file", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "linkTo": "FileSet"}, "required_if_not_one_of": ["tissues", "source_donors"]}, "software": {"title": "Software", "description": "Link to software used to create this file", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "linkTo": "Software"}}, "description": {"title": "Description", "description": "Plain text description of the item", "type": "string", "formInput": "textarea"}, "data_description": {"title": "Data Description", "description": "More detailed description of file", "type": "string", "enum": ["Phased Germline Variant", "Filtered Somatic Variant", "Unfiltered Somatic Variant"]}, "tissues": {"title": "Tissues", "description": "Tissues used to generate the file", "type": "array", "items": {"type": "string", "linkTo": "SampleSource"}, "required_if_not_one_of": ["file_sets", "source_donors"]}, "source_donors": {"title": "Donors", "description": "Donors used to generate the file", "type": "array", "items": {"type": "string", "linkTo": "Donor"}, "required_if_not_one_of": ["file_sets", "tissues"]}}}, "ExternalQualityMetric": {"$id": "/profiles/external_quality_metric.json", "title": "ExternalQualityMetric", "properties": {"submitted_id": {"title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "pattern": "^[A-Z0-9]{3,}_EXTERNAL-QUALITY-METRIC_[A-Z0-9-_.]{4,}$", "is_required": true}, "description": {"title": "Description", "description": "Plain text description of the item", "type": "string", "formInput": "textarea"}, "category": {"title": "Category", "comment": "Intended for primary classification of an item, i.e. as a property to use instead of file_type for File", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "suggested_enum": ["DuplexSeq"]}}, "qc_values": {"type": "array", "title": "QC Values", "description": "QC values and their associated metadata", "items": {"properties": {"key": {"type": "string", "title": "QC Name", "description": "Name of the QC metric"}, "value": {"type": ["array", "boolean", "integer", "number", "string"], "title": "QC value", "description": "Value of the QC metric"}, "derived_from": {"type": "string", "title": "Identifier for the QC value"}, "tooltip": {"type": "string", "title": "Tooltip"}}}, "is_required": true}}}, "FamilyHistory": {"$id": "/profiles/family_history.json", "title": "Family History", "properties": {"submitted_id": {"title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "pattern": "^[A-Z0-9]{3,}_FAMILY-HISTORY_[A-Z0-9-_.]{4,}$", "is_required": true}, "disease": {"title": "Disease", "description": "The disease or condition that is being reported", "type": "string", "is_required": true}, "relatives": {"title": "Relatives", "description": "The relatives affected by the disease", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "enum": ["Aunt", "Aunts", "Brother", "Brothers", "Child", "Children", "Cousin", "Cousins", "Daughter", "Daughters", "Father", "Grandfather", "Grandfathers", "Grandmother", "Grandmothers", "Grandparent", "Grandparents", "Mother", "Nephew", "Nephews", "Niece", "Nieces", "Parent", "Parents", "Son", "Sons", "Sibling", "Siblings", "Sister", "Sisters", "Uncle", "Uncles", "Unspecified"]}, "is_required": true}, "donor": {"title": "Donor", "description": "The donor of the family history", "type": "string", "linkTo": "AbstractDonor", "is_required": true}}}, "FileSet": {"$id": "/profiles/file_set.json", "title": "File Set", "properties": {"submitted_id": {"title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "pattern": "^[A-Z0-9]{3,}_FILE-SET_[A-Z0-9-_.]{4,}$", "is_required": true}, "description": {"title": "Description", "description": "Plain text description of the item", "type": "string", "formInput": "textarea"}, "submitter_comments": {"title": "Submitter Comments", "description": "Submitter comments on data quality related to the file set", "type": "array", "items": {"type": "string"}}, "libraries": {"title": "Libraries", "description": "Link to associated libraries", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "linkTo": "Library"}, "is_required": true}, "samples": {"title": "Samples", "description": "Link to associated samples. Only to be used for single-cell data sets when many samples are associated with a single library.", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "linkTo": "CellSample"}}, "sequencing": {"title": "Sequencing", "description": "Link to associated sequencing", "type": "string", "linkTo": "Sequencing", "is_required": true}}}, "HistologyImage": {"$id": "/profiles/histology_image.json", "title": "Histology Image", "properties": {"submitted_id": {"pattern": "^[A-Z0-9]{3,}_HISTOLOGY-IMAGE_[A-Z0-9-_.]{4,}$", "title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "is_required": true}, "submitted_md5sum": {"title": "Submitted MD5", "description": "Submitted MD5 checksum of the file", "type": "string", "format": "hex"}, "external_quality_metrics": {"description": "Link to externally-generated QC metrics associated with file", "items": {"description": "Associated QC report", "linkTo": "ExternalQualityMetric", "title": "Quality Metric", "type": "string"}, "minItems": 1, "title": "External Quality Metrics", "type": "array", "uniqueItems": true}, "file_format": {"ff_flag": "filter:valid_item_types", "linkTo": "FileFormat", "title": "File Format", "type": "string", "description": "Format for the file", "is_required": true}, "filename": {"description": "The local file name used at time of submission. Must be alphanumeric, with the exception of the following special characters: '+=,.@-_'", "pattern": "^[\\w+=,.@-]*$", "title": "File Name", "type": "string", "is_required": true}, "analysis_details": {"title": "Analysis Details", "description": "Details of analysis performed on file", "type": "array", "items": {"type": "string", "enum": ["Aligned", "Filtered", "Sorted", "Phased", "Unphased"], "default": ["Unphased"]}}, "data_category": {"title": "Data Category", "description": "Category for information in the file", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "enum": ["Consensus Reads", "Genome Annotation", "Genome Region", "Germline Variant Calls", "Quality Control", "Genome Assembly", "Reference Genome", "Reference Conversion", "Reference Transcriptome", "RNA Quantification", "Sequencing Reads", "Sequencing Supplement", "Somatic Variant Calls", "Transcriptome Annotation"]}}, "data_type": {"title": "Data Type", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "enum": ["Aligned Reads", "Gene Expression", "Gene Model", "Image", "In Silico Generated", "Index", "Reference Sequence", "DSA", "Chain File", "Sequence Interval", "Statistics", "Transcript Expression", "Unaligned Reads", "CNV", "Indel", "MEI", "SNV", "SV", "Transcript Sequence", "Transcript Model", "Sequencing information"]}}, "description": {"title": "Description", "description": "Plain text description of the item", "type": "string", "formInput": "textarea"}, "pathology_reports": {"title": "Pathology Reports", "description": "Link to the pathology report for the section", "type": "array", "items": {"type": "string", "linkTo": "PathologyReport"}, "is_required": true}}}, "Library": {"$id": "/profiles/library.json", "title": "Library", "properties": {"submitted_id": {"title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "pattern": "^[A-Z0-9]{3,}_LIBRARY_[A-Z0-9-_.]{4,}$", "is_required": true}, "comments": {"title": "Comments", "comment": "General comments concerning an item. For internal use only.", "type": "array", "items": {"type": "string"}, "description": "Additional comments for library"}, "external_id": {"title": "External ID", "description": "External ID for the item provided by submitter", "type": "string", "pattern": "^[A-Za-z0-9-_]{3,}$"}, "description": {"title": "Description", "description": "Plain text description of the item", "type": "string", "formInput": "textarea"}, "a260_a280_ratio": {"title": "A260 A280 Ratio", "description": "Ratio of nucleic acid absorbance at 260 nm and 280 nm, used to determine a measure of DNA purity", "type": "number", "minimum": 0}, "adapter_name": {"title": "Adapter Name", "description": "Name of sequencing adapter", "type": "string"}, "adapter_sequence": {"title": "Adapter Sequence", "description": "Base sequence of sequencing adapter", "type": "string"}, "amplification_cycles": {"title": "Amplification Cycles", "description": "Number of PCR Cycles used for additional amplification", "type": "integer", "minimum": 0}, "analyte_weight": {"title": "Analyte Weight", "description": "Weight of analyte used to prepare library (mg)", "type": "number", "minimum": 0}, "antibody": {"title": "Antibody", "description": "Antibody used for affinity enrichment", "type": "array", "items": {"type": "string", "suggested_enum": ["H3K4me3", "RNAPII"]}}, "barcode_sequences": {"title": "Barcode Sequences", "description": "Barcode sequence for multiplexed sequencing", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string"}}, "concatenated_reads": {"title": "Concatenated Reads Included", "description": "Whether or not the library contains concatenated reads. Relevant for Kinnex", "type": "string", "enum": ["Yes", "No", "Not applicable", ""]}, "fragment_mean_length": {"title": "Fragment Mean Length", "description": "Mean length of the sequenced fragments, e.g. as predicted by Agilent Bioanalyzer (bp)", "type": "number", "minimum": 0}, "guide_sequence": {"title": "Guide Sequence", "description": "Guide sequence. Relevant for Cas9 capture experiments", "type": "array", "uniqueItems": true, "minItems": 1, "items": {"type": "string"}}, "insert_coefficient_of_variation": {"title": "Insert Coefficient of Variation", "description": "Coefficient of variation of the length of the sample molecule in the fragments to be sequenced", "type": "number", "minimum": 0}, "insert_maximum_length": {"title": "Insert Maximum Length", "description": "Maximum length of the sample molecule in the fragments to be sequenced (bp)", "type": "integer", "minimum": 0}, "insert_mean_length": {"title": "Insert Mean Length", "description": "Mean length of the sample molecule in the fragments to be sequenced (bp)", "type": "number", "minimum": 0}, "insert_minimum_length": {"title": "Insert Minimum Length", "description": "Minimum length of the sample molecule in the fragments to be sequenced (bp)", "type": "integer", "minimum": 0}, "preparation_date": {"title": "Preparation Date", "description": "Date of library preparation", "type": "string", "format": "date"}, "dna_target": {"title": "DNA Target", "description": "DNA target used in insert selection", "type": "array", "uniqueItems": true, "minItems": 1, "items": {"type": "string"}}, "target_fragment_size": {"title": "Target fragment size", "description": "Targeted fragment size for library (bp)", "type": "integer", "minimum": 0}, "target_insert_maximum_length": {"title": "Target Insert Maximum Length", "description": "Target maximum length of the insert (bp)", "type": "integer", "minimum": 0}, "target_insert_minimum_length": {"title": "Target Insert Minimum Length", "description": "Target minimum length of the insert (bp)", "type": "integer", "minimum": 0}, "target_monomer_size": {"title": "Target Monomer Size", "description": "For libraries with concatenated reads, the target monomer size (bp). Relevant for Kinnex", "type": "integer", "minimum": 0}, "analytes": {"title": "Analytes", "description": "Links to associated analytes", "type": "array", "uniqueItems": true, "minItems": 1, "items": {"type": "string", "linkTo": "Analyte"}, "is_required": true}, "assay": {"title": "Assay", "description": "Link to associated assay", "type": "string", "linkTo": "Assay", "is_required": true}, "library_preparation": {"title": "Library Preparation", "description": "Link to associated library preparation", "type": "string", "linkTo": "LibraryPreparation"}}}, "LibraryPreparation": {"$id": "/profiles/library_preparation.json", "title": "Library Preparation", "properties": {"submitted_id": {"pattern": "^[A-Z0-9]{3,}_LIBRARY-PREPARATION_[A-Z0-9-_.]{4,}$", "title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "is_required": true}, "preparation_kits": {"title": "Preparation Kits", "description": "Links to associated preparation kits", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "linkTo": "PreparationKit"}}, "treatments": {"title": "Treatments", "description": "Link to associated treatments performed during library preparation", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "linkTo": "Treatment"}}, "description": {"title": "Description", "description": "Plain text description of the item", "type": "string", "formInput": "textarea"}, "adapter_inclusion_method": {"title": "Adapter Inclusion Method", "description": "Method of library preparation from an analyte", "type": "array", "uniqueItems": true, "minItems": 1, "items": {"type": "string", "enum": ["Ligation", "Tagmentation", "Not Applicable"]}}, "amplification_method": {"title": "Amplification Method", "description": "Amplification method used to increase library products", "type": "array", "uniqueItems": true, "minItems": 1, "items": {"type": "string", "enum": ["PCR", "MALBAC", "PTA", "MDA", "Not Applicable"]}}, "fragmentation_method": {"title": "Fragmentation Method", "description": "Method used for nucleotide fragmentation", "type": "array", "uniqueItems": true, "minItems": 1, "items": {"type": "string", "enum": ["Mechanical", "Sonication", "Restriction Enzyme", "Transposase", "Not Applicable"]}}, "insert_selection_method": {"title": "Insert Selection Method", "description": "Method for selecting inserts included in library", "type": "array", "uniqueItems": true, "minItems": 1, "items": {"type": "string", "enum": ["Affinity Enrichment", "Hybrid Selection", "PCR", "PolyA Enrichment", "PolyT Enrichment", "rRNA Depletion", "Not applicable"]}}, "enzymes": {"title": "Enzymes", "description": "Enzymes used in fragmentation. Required if fragmentation_method contains Restriction Enzyme or Transposase", "type": "array", "uniqueItems": true, "minItems": 1, "items": {"type": "string", "suggested_enum": ["Mung Bean Nuclease", "HpyCH4V", "AluI", "Tn5"]}}, "rna_seq_protocol": {"title": "RNA-seq Protocol", "description": "Protocol used for RNA-seq assays. Required for RNA libraries", "type": "string", "enum": ["Watchmaker", "TruSeq"]}, "size_selection_method": {"title": "Size Selection Method", "description": "Method for selecting fragment sizes", "type": "array", "uniqueItems": true, "minItems": 1, "items": {"type": "string", "enum": ["Gel Electrophoresis", "Magnetic Beads", "Not Applicable"]}}, "strand": {"title": "Strand", "description": "Library stranded-ness of RNA-seq library prep. Required for RNA libraries", "type": "string", "enum": ["Unstranded", "First Stranded", "Second Stranded"]}, "trim_adapter_sequence": {"title": "Trim Adapter Sequence", "description": "Whether trimming adapter sequence is recommended", "type": "boolean"}}}, "MedicalHistory": {"$id": "/profiles/medical_history.json", "title": "Medical History", "properties": {"submitted_id": {"title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "pattern": "^[A-Z0-9]{3,}_MEDICAL-HISTORY_[A-Z0-9-_.]{4,}$", "is_required": true}, "alcohol_use": {"title": "Alcohol Use", "description": "Whether the donor had a history of alcohol use", "type": "string", "enum": ["No", "Unknown", "Yes"]}, "allergens": {"title": "Allergens", "description": "Substances to which the donor is allergic", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string"}}, "allergies": {"title": "Allergies", "description": "Whether the donor had any allergies", "type": "string", "enum": ["No", "Unknown", "Yes"]}, "autograft_transplantation": {"title": "Autograft Transplantation", "description": "Whether the donor had an autograft transplantation", "type": "string", "enum": ["No", "Unknown", "Yes"]}, "autograft_transplantation_details": {"title": "Autograft Transplantation Details", "description": "Details of the autograft transplantation", "type": "string"}, "body_mass_index": {"title": "Body Mass Index", "description": "Body mass index of the donor (m/kg^2)", "type": "number", "minimum": 0}, "cancer_chemotherapy": {"title": "Cancer Chemotherapy", "description": "Whether the donor had a history of cancer chemotherapy", "type": "string", "enum": ["No", "Unknown", "Yes"]}, "cancer_current": {"title": "Cancer Current", "description": "Whether the donor had a current diagnosis of cancer", "type": "string", "enum": ["No", "Unknown", "Yes"]}, "cancer_history": {"title": "Cancer History", "description": "Whether the donor had a history of cancer", "type": "string", "enum": ["No", "Unknown", "Yes"]}, "cancer_radiation_therapy": {"title": "Cancer Radiation Therapy", "description": "Whether the donor had a history of cancer radiation therapy", "type": "string", "enum": ["No", "Unknown", "Yes"]}, "cancer_type": {"title": "Cancer Type", "description": "Type(s) of cancer with which the donor has been diagnosed", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string"}}, "cmv_total_antibody": {"title": "CMV Total Antibody", "description": "Results of testing for CMV total antibody", "type": "string", "enum": ["Indeterminate", "Non-reactive", "Not Done", "Reactive"]}, "cmv_igg_antibody": {"title": "CMV IgG Antibody", "description": "Results of testing for CMV IgG antibody", "type": "string", "enum": ["Indeterminate", "Non-reactive", "Not Done", "Reactive"]}, "cmv_igm_antibody": {"title": "CMV IgM Antibody", "description": "Results of testing for CMV IgM antibody", "type": "string", "enum": ["Indeterminate", "Non-reactive", "Not Done", "Reactive"]}, "covid_19_pcr": {"title": "COVID-19 PCR", "description": "Results of testing for COVID-19 by PCR", "type": "string", "enum": ["Indeterminate", "Non-reactive", "Not Done", "Reactive"]}, "ebv_igg_antibody": {"title": "EBV IgG Antibody", "description": "Results of testing for EBV IgG antibody", "type": "string", "enum": ["Indeterminate", "Non-reactive", "Not Done", "Reactive"]}, "ebv_igm_antibody": {"title": "EBV IgM Antibody", "description": "Results of testing for EBV IgM antibody", "type": "string", "enum": ["Indeterminate", "Non-reactive", "Not Done", "Reactive"]}, "family_breast_cancer": {"title": "Family History Breast Cancer", "description": "Whether the donor had a family history of breast cancer", "type": "string", "enum": ["No", "Unknown", "Yes"]}, "family_cancer_under_50": {"title": "Family History Cancer Under 50", "description": "Whether the donor had a family history of cancer under the age of 50", "type": "string", "enum": ["No", "Unknown", "Yes"]}, "family_diabetes": {"title": "Family History Diabetes", "description": "Whether the donor had a family history of diabetes", "type": "string", "enum": ["No", "Unknown", "Yes"]}, "family_heart_disease": {"title": "Family History Heart Disease", "description": "Whether the donor had a family history of heart disease", "type": "string", "enum": ["No", "Unknown", "Yes"]}, "family_ovarian_pancreatic_prostate_cancer": {"title": "Family History Ovarian, Pancreatic, or Prostate Cancer", "description": "Whether the donor had a family history of ovarian, pancreatic, or prostate cancer", "type": "string", "enum": ["No", "Unknown", "Yes"]}, "height": {"title": "Height", "description": "Height of the donor (meters)", "type": "number", "minimum": 0}, "hepatitis_b_core_antibody": {"title": "Hepatitis B Core Antibody", "description": "Results of testing for hepatitis B core antibody", "type": "string", "enum": ["Indeterminate", "Non-reactive", "Not Done", "Reactive"]}, "hepatitis_b_surface_antibody": {"title": "Hepatitis B Surface Antibody", "description": "Results of testing for hepatitis B surface antibody", "type": "string", "enum": ["Indeterminate", "Non-reactive", "Not Done", "Reactive"]}, "hepatitis_b_surface_antigen": {"title": "Hepatitis B Surface Antigen", "description": "Results of testing for hepatitis B surface antigen", "type": "string", "enum": ["Indeterminate", "Non-reactive", "Not Done", "Reactive"]}, "hepatitis_c_antibody": {"title": "Hepatitis C Antibody", "description": "Results of testing for hepatitis C antibody", "type": "string", "enum": ["Indeterminate", "Non-reactive", "Not Done", "Reactive"]}, "hepatitis_c_nat": {"title": "Hepatitis C NAT", "description": "Results of testing for hepatitis C via NAT (nucleic acid testing)", "type": "string", "enum": ["Indeterminate", "Non-reactive", "Not Done", "Reactive"]}, "hiv_1_2_antibody": {"title": "HIV 1/2 Antibody", "description": "Results of testing for HIV 1/2 antibodies", "type": "string", "enum": ["Indeterminate", "Non-reactive", "Not Done", "Reactive"]}, "hiv_nat": {"title": "HIV NAT", "description": "Results of testing for HIV via NAT (nucleic acid testing)", "type": "string", "enum": ["Indeterminate", "Non-reactive", "Not Done", "Reactive"]}, "illicit_drug_use": {"title": "Illicit Drug Use", "description": "Whether the donor had a history of illicit drug use", "type": "string", "enum": ["No", "Unknown", "Yes"]}, "pregnancy_count": {"title": "Pregnancy Count", "description": "Number of pregnancies", "type": "integer", "minimum": 0}, "pregnancy_male_fetus": {"title": "Pregnancy Male Fetus", "description": "Whether the donor was ever pregnant with a male fetus", "type": "string", "enum": ["No", "Unknown", "Yes", "Not Applicable"]}, "syphilis_rpr": {"title": "Syphilis RPR", "description": "Results of testing for syphilis RPR (rapid plasma reagin)", "type": "string", "enum": ["Indeterminate", "Non-reactive", "Not Done", "Reactive"]}, "tobacco_use": {"title": "Tobacco Use", "description": "Whether the donor had a history of tobacco use", "type": "string", "enum": ["No", "Unknown", "Yes"]}, "toxic_exposure": {"title": "Toxic Exposure", "description": "Whether the donor had a history of toxic exposure", "type": "string", "enum": ["No", "Unknown", "Yes"]}, "twin_or_multiple_birth": {"title": "Twin or Multiple Birth", "description": "Whether the donor was part of a twin or multiple birth", "type": "string", "enum": ["No", "Unknown", "Yes"]}, "twin_or_multiple_birth_details": {"title": "Twin or Multiple Birth Details", "description": "Details of the twin or multiple birth the donor was a part of", "type": "string", "enum": ["Triplet, Fraternal", "Triplet, Identical", "Triplet, Unknown", "Twin, Fraternal", "Twin, Identical", "Twin, Unknown", ">3, Fraternal", ">3, Identical", ">3, Unknown"]}, "weight": {"title": "Weight", "description": "Weight of the donor (kg)", "type": "number", "minimum": 0}, "xenograft_transplantation": {"title": "Xenograft Transplantation", "description": "Whether the donor had a xenograft transplantation", "type": "string", "enum": ["No", "Unknown", "Yes"]}, "xenograft_transplantation_details": {"title": "Xenograft Transplantation Details", "description": "Details of the xenograft transplantation", "type": "string"}, "donor": {"title": "Donor", "description": "The donor to which this medical history applies", "type": "string", "linkTo": "AbstractDonor", "is_required": true}}}, "MedicalTreatment": {"$id": "/profiles/medical_treatment.json", "title": "Medical Treatment", "properties": {"title": {"title": "Title", "description": "Name of the treatment", "type": "string", "minLength": 3, "is_required": true}, "submitted_id": {"title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "pattern": "^[A-Z0-9]{3,}_MEDICAL-TREATMENT_[A-Z0-9-_.]{4,}$", "is_required": true}, "category": {"title": "Treatment Category", "description": "Type of treatment", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "enum": ["Chemotherapy", "Radiation", "Surgery"]}, "is_required": true}, "comments": {"title": "Comments", "description": "Additional information on the treatment", "type": "string"}, "counts": {"title": "Counts", "description": "Number of times the treatment was performed", "type": "integer", "minimum": 1}, "year_end": {"title": "Year Ended", "description": "Year in which the treatment was last administered", "type": "integer", "minimum": 1900, "maximum": 2100}, "year_start": {"title": "Year Started", "description": "Year in which the treatment was first administered", "type": "integer", "minimum": 1900, "maximum": 2100}, "diagnosis": {"title": "Diagnosis", "description": "Link to the associated diagnosis", "type": "string", "linkTo": "Diagnosis"}, "medical_history": {"title": "Medical History", "description": "Link to the associated medical history", "type": "string", "linkTo": "MedicalHistory", "is_required": true}}}, "NonBrainPathologyReport": {"$id": "/profiles/non_brain_pathology_report.json", "title": "Non Brain Pathology Report", "properties": {"submitted_id": {"pattern": "^[A-Z0-9]{3,}_NON-BRAIN-PATHOLOGY-REPORT_[A-Z0-9-_.]{4,}$", "title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "is_required": true}, "additional_notes": {"title": "Additional Notes", "description": "Additional notes or other findings related to the sample", "type": "string"}, "final_review_determination": {"title": "Final Review Determination", "description": "Whether a final review determination was made for the sample", "type": "string", "enum": ["Yes", "No"]}, "is_indeterminate": {"title": "Is Indeterminate", "description": "Whether the tissue sample is indeterminate", "type": "string", "enum": ["Yes", "No"]}, "outcome": {"title": "Outcome", "description": "Outcome of the pathology report", "type": "string", "enum": ["Acceptable", "Unacceptable"], "is_required": true}, "tissue_name": {"title": "Tissue Name", "description": "Name of the type of tissue the sample was taken from", "type": "string", "enum": ["Adrenal", "Aorta", "Ascending Colon", "Descending Colon", "Esophagus", "Heart Ventricle", "Liver", "Lung", "Muscle", "Ovary", "Skin", "Testis"], "is_required": true}, "unacceptable_description": {"title": "Unacceptable Description", "description": "Description of unacceptable review determination", "type": "string"}, "tissue_samples": {"title": "Tissue Samples", "description": "Link to associated tissue samples", "type": "array", "items": {"type": "string", "linkTo": "TissueSample"}, "is_required": true}, "version": {"title": "Version", "description": "Version for the item", "type": "string", "pattern": "^([0-9]+.)*[0-9]+$"}, "tissue_autolysis_score": {"title": "Tissue Autolysis Score", "description": "Tissue autolysis score of the sample or region. 0=None, 1=mild , 2=moderate, 3=severe", "type": "integer", "minimum": 0, "maximum": 3}, "description": {"title": "Description", "description": "Plain text description of the item", "type": "string", "formInput": "textarea"}, "anatomical_sample_location": {"title": "Anatomical Sample Location", "description": "Anatomical location from which the sample was taken", "type": "string", "enum": ["Left Adrenal", "Right Adrenal", "Skin Calf", "Skin Abdomen", "Left Ovary", "Right Ovary", "Left Testis", "Right Testis"]}, "target_tissues": {"title": "Target Tissues", "type": "array", "items": {"properties": {"target_tissue_subtype": {"title": "Target Tissue Subtype", "description": "Subtype of target tissue in sample", "type": "string", "enum": ["Cortex", "Dermis", "Endocardium", "Epicardium", "Epidermis", "Fallopian Tube", "Leydig Cells", "Liver", "Lung", "Medulla", "Mucosa", "Muscularis propria", "Myocardium", "Ovarian Follicles", "Ovarian Stroma", "Seminiferous Tubules", "Skeletal Muscle", "Vessel"]}, "target_tissue_present": {"title": "Target Tissue Present", "description": "Whether the target tissue subtype was present in the sample", "type": "string", "enum": ["Yes", "No"]}, "target_tissue_percentage": {"title": "Target Tissue Subtype Percentage", "description": "Percentage range of the sample that was the target tissue subtype (%)", "type": "string", "enum": ["0", "[0-10]", "[11-25]", "[26-49]", "[50-100]"]}, "target_tissue_autolysis_score": {"title": "Target Tissue Autolysis Score", "description": "Autolysis score of the target tissue in the sample. 0=None, 1=mild , 2=moderate, 3=severe", "type": "integer", "minimum": 0, "maximum": 3}}}}, "non_target_tissues": {"title": "Non-Target Tissues", "type": "array", "items": {"properties": {"non_target_tissue_subtype": {"title": "Non-Target Tissue Subtype", "description": "Subtype of non-target tissue in sample", "type": "string", "enum": ["Fibroadipose", "Lymphoid", "Other", "Epididymis", "Rete testes"]}, "non_target_tissue_present": {"title": "Non-Target Tissue Present", "description": "Whether the non-target tissue subtype was present in the sample", "type": "string", "enum": ["Yes", "No"]}, "non_target_tissue_percentage": {"title": "Non-Target Tissue Subtype Percentage", "description": "Percentage range of the sample that was the non-target tissue subtype (%)", "type": "string", "enum": ["[0-10]", "[11-25]", "[26-49]", "[50-100]"]}, "non_target_tissue_description": {"title": "Non-Target Tissue Description", "description": "Description of other non-target tissue present in the sample", "type": "string"}}}}, "pathologic_findings": {"title": "Pathologic Findings", "type": "array", "items": {"properties": {"finding_type": {"title": "Pathologic Finding Type", "description": "Type of pathologic/unexpected finding present in the sample", "type": "string", "enum": ["Inflammation", "Metaplasia", "Neoplasia/Tumor/Carcinoma", "Necrosis", "Other"]}, "finding_present": {"title": "Pathologic Finding Present", "description": "Whether pathologic/unexpected finding is present in the sample", "type": "string", "enum": ["Yes", "No"]}, "finding_description": {"title": "Pathologic Finding Description", "description": "Description of pathologic/unexpected finding", "type": "string"}, "finding_percentage": {"title": "Pathologic Finding Percentage", "description": "Percentage range of the sample that displayed the pathologic/unexpected finding (%)", "type": "string", "enum": ["[0-10]", "[11-25]", "[26-49]", "[50-100]"]}}}}}}, "PreparationKit": {"$id": "/profiles/preparation_kit.json", "title": "Preparation Kit", "properties": {"version": {"title": "Version", "description": "Version for the item", "type": "string", "pattern": "^([0-9]+.)*[0-9]+$"}, "title": {"title": "Title", "description": "Title for the item", "type": "string", "minLength": 3, "is_required": true}, "submitted_id": {"title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "pattern": "^[A-Z0-9]{3,}_PREPARATION-KIT_[A-Z0-9-_.]{4,}$", "is_required": true}, "catalog_number": {"title": "Catalog Number", "description": "Catalog number of preparation kit", "type": "string"}, "vendor": {"title": "Vendor", "description": "Vendor of preparation kit", "type": "string", "is_required": true}}}, "ProtectedDonor": {"$id": "/profiles/protected_donor.json", "title": "Protected Donor", "properties": {"external_id": {"submissionComment": "For donors from the TPC, this should be the TPC donor ID. Otherwise, the submitter's internal identifier can be used.", "type": "string", "pattern": "^[A-Za-z0-9-_]{2,}$", "is_required": true}, "submitted_id": {"pattern": "^[A-Z0-9]{3,}_PROTECTED-DONOR_[A-Z0-9-_.]{4,}$", "title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "is_required": true}, "age": {"title": "Age", "description": "Age of the donor (years). Note: donor age above 89 is represented as 89 to remove identifiable information.", "type": "integer", "minimum": 0, "maximum": 89, "is_required": true}, "eligibility": {"title": "Eligibility", "description": "Whether donor was deemed eligible for the study", "type": "string", "enum": ["Yes", "No", "Unknown"]}, "hardy_scale": {"title": "Hardy Scale", "description": "Death classification based on the 4-point Hardy Scale", "type": "integer", "minimum": 0, "maximum": 4}, "sex": {"title": "Sex", "description": "Sex of the donor", "type": "string", "enum": ["Male", "Female", "Unknown"], "is_required": true}, "tpc_submitted": {"title": "TPC Submitted", "description": "Whether the donor was submitted by the TPC", "type": "string", "enum": ["True", "False"], "is_required": true}}}, "Sequencing": {"$id": "/profiles/sequencing.json", "title": "Sequencing", "properties": {"submitted_id": {"title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "pattern": "^[A-Z0-9]{3,}_SEQUENCING_[A-Z0-9-_.]{4,}$", "is_required": true}, "additional_notes": {"title": "Additional Notes", "description": "Additional notes related to the sequencing", "type": "string"}, "flow_cell": {"title": "Flow Cell", "description": "Flow cell used for sequencing", "type": "string", "suggested_enum": ["R10.4.1", "R9.4.1", "25B", "10B"]}, "movie_length": {"title": "Movie Length", "description": "Length of movie used in sequencing (hours)", "type": "integer", "minimum": 0}, "read_type": {"title": "Read Type", "description": "Type of reads obtained from sequencing", "type": "string", "enum": ["Not Applicable", "Paired-end", "Single-end"], "is_required": true}, "on_target_rate": {"title": "On Target Rate", "description": " An expected ratio, the number of reads with enrichment signals for the targeted element versus the overall reads sequenced. Relevant for target capture sequencing", "type": "number", "minimum": 0, "required_if_not_one_of": ["target_coverage", "target_read_count"]}, "target_coverage": {"title": "Target Coverage", "description": "Expected coverage for the sequencing. For Duplex sequencing, this applies to the target duplex coverage for sequencing", "type": "number", "minimum": 0, "required_if_not_one_of": ["target_read_count", "on_target_rate"]}, "target_read_count": {"title": "Target Read Count", "description": "Expected read count for the sequencing, in read pairs if paired-end", "type": "integer", "minimum": 0, "required_if_not_one_of": ["target_coverage", "on_target_rate"]}, "target_read_length": {"title": "Target Read Length", "description": "Expected read length for the sequencing (bp)", "type": "integer", "minimum": 0, "allow_commas": true, "allow_multiplier_suffix": true, "is_required": true}, "target_monomer_length": {"title": "Target Monomer Length", "description": "Target monomer length for Kinnex/MAS-Seq (bp)", "type": "integer", "minimum": 0}, "sequencer": {"title": "Sequencer", "description": "Instrument used for sequencing", "type": "string", "linkTo": "Sequencer", "is_required": true}, "preparation_kits": {"title": "Preparation Kits", "description": "Links to sequencing preparation kits", "type": "array", "uniqueItems": true, "items": {"type": "string", "linkTo": "PreparationKit"}}}}, "Software": {"$id": "/profiles/software.json", "title": "Software", "properties": {"version": {"title": "Version", "description": "The version of the software", "type": "string", "pattern": "[A-Za-z0-9._-]+", "is_required": true}, "title": {"title": "Title", "description": "The name of the software", "type": "string", "minLength": 3, "is_required": true}, "submitted_id": {"title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "pattern": "^[A-Z0-9]{3,}_SOFTWARE_[A-Z0-9-_.]{4,}$", "submitterRequired": true, "is_required": true, "required_if_not_one_of": ["aliases", "aliases"], "prohibited_if_one_of": ["aliases", "aliases"]}, "description": {"title": "Description", "description": "Plain text description of the item", "type": "string", "formInput": "textarea"}, "category": {"title": "Category", "comment": "Intended for primary classification of an item, i.e. as a property to use instead of file_type for File", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "enum": ["Alignment", "Alignment Manipulation", "Assembly", "Basecaller", "Data Compression", "Feature Annotation", "Format Conversion", "Gene Quantification", "Quality Control", "Read Manipulation", "Transcript Quantification", "Variant Annotation", "Variant Calling", "Variant Manipulation"]}, "is_required": true}, "binary_url": {"title": "Binary URL", "description": "An external resource to a compiled download of the software.", "type": "string", "format": "uri"}, "commit": {"title": "Commit", "description": "The software commit hash.", "type": "string"}, "source_url": {"title": "Source URL", "description": "An external resource to the code base.", "type": "string", "format": "uri"}, "gpu_architecture": {"title": "GPU Architecture", "description": "GPU architecture used to run the basecalling software. Required for ONT Basecaller software", "type": "string", "suggested_enum": ["NVIDIA A100", "NVIDIA H100", "NVIDIA V100"]}, "model": {"title": "DNA Model", "description": "DNA model used for basecalling software. Required for ONT Basecaller software", "type": "string", "suggested_enum": ["dna_r10.4.1_e8.2_400bps_hac@v4.3.0", "dna_r10.4.1_e8.2_400bps_sup@v4.3.0", "dna_r10.4.1_e8.2_400bps_fast@v4.2.0", "dna_r10.4.1_e8.2_400bps_hac@v4.2.0", "dna_r10.4.1_e8.2_400bps_sup@v4.2.0", "dna_r10.4.1_e8.2_400bps_fast@v4.1.0", "dna_r10.4.1_e8.2_400bps_hac@v4.1.0", "dna_r10.4.1_e8.2_400bps_sup@v4.1.0", "dna_r10.4.1_e8.2_260bps_fast@v4.1.0", "dna_r10.4.1_e8.2_260bps_hac@v4.1.0", "dna_r10.4.1_e8.2_260bps_sup@v4.1.0", "dna_r10.4.1_e8.2_400bps_fast@v4.0.0", "dna_r10.4.1_e8.2_400bps_hac@v4.0.0", "dna_r10.4.1_e8.2_400bps_sup@v4.0.0", "dna_r10.4.1_e8.2_260bps_fast@v4.0.0", "dna_r10.4.1_e8.2_260bps_hac@v4.0.0", "dna_r10.4.1_e8.2_260bps_sup@v4.0.0", "dna_r10.4.1_e8.2_260bps_fast@v3.5.2", "dna_r10.4.1_e8.2_260bps_hac@v3.5.2", "dna_r10.4.1_e8.2_260bps_sup@v3.5.2", "dna_r10.4.1_e8.2_400bps_fast@v3.5.2", "dna_r10.4.1_e8.2_400bps_hac@v3.5.2", "dna_r10.4.1_e8.2_400bps_sup@v3.5.2", "dna_r9.4.1_e8_sup@v3.6", "dna_r9.4.1_e8_fast@v3.4", "dna_r9.4.1_e8_hac@v3.3", "dna_r9.4.1_e8_sup@v3.3", "rna004_130bps_fast@v5.0.0", "rna004_130bps_hac@v5.0.0", "rna004_130bps_sup@v5.0.0", "rna004_130bps_fast@v3.0.1", "rna004_130bps_hac@v3.0.1", "rna004_130bps_sup@v3.0.1", "rna002_70bps_fast@v3", "rna002_70bps_hac@v3"]}, "modification_tags": {"title": "Basecaller Modification Tags", "description": "Tags used to modify the basecaller software. Required for ONT Basecaller software", "type": "array", "uniqueItems": true, "minItems": 1, "items": {"type": "string", "enum": ["5mC", "5mCG", "5mC_5hmC", "5mCG_5hmCG", "6mA", "m6A_DRACH", "None"]}}}}, "SupplementaryFile": {"$id": "/profiles/supplementary_file.json", "title": "Supplementary File", "properties": {"submitted_id": {"pattern": "^[A-Z0-9]{3,}_SUPPLEMENTARY-FILE_[A-Z0-9-_.]{4,}$", "title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "is_required": true}, "submitted_md5sum": {"title": "Submitted MD5", "description": "Submitted MD5 checksum of the file", "type": "string", "format": "hex"}, "external_quality_metrics": {"description": "Link to externally-generated QC metrics associated with file", "items": {"description": "Associated QC report", "linkTo": "ExternalQualityMetric", "title": "Quality Metric", "type": "string"}, "minItems": 1, "title": "External Quality Metrics", "type": "array", "uniqueItems": true}, "file_format": {"ff_flag": "filter:valid_item_types", "linkTo": "FileFormat", "title": "File Format", "type": "string", "description": "Format for the file", "is_required": true}, "filename": {"description": "The local file name used at time of submission. Must be alphanumeric, with the exception of the following special characters: '+=,.@-_'", "pattern": "^[\\w+=,.@-]*$", "title": "File Name", "type": "string", "is_required": true}, "analysis_details": {"title": "Analysis Details", "description": "Details of analysis performed on file", "type": "array", "items": {"type": "string", "enum": ["Aligned", "Filtered", "Sorted", "Phased", "Unphased"], "default": ["Unphased"]}}, "data_category": {"title": "Data Category", "description": "Category for information in the file", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "enum": ["Consensus Reads", "Genome Annotation", "Genome Region", "Germline Variant Calls", "Quality Control", "Genome Assembly", "Reference Genome", "Reference Conversion", "Reference Transcriptome", "RNA Quantification", "Sequencing Reads", "Sequencing Supplement", "Somatic Variant Calls", "Transcriptome Annotation"]}, "is_required": true}, "data_type": {"title": "Data Type", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "enum": ["Aligned Reads", "Gene Expression", "Gene Model", "Image", "In Silico Generated", "Index", "Reference Sequence", "DSA", "Chain File", "Sequence Interval", "Statistics", "Transcript Expression", "Unaligned Reads", "CNV", "Indel", "MEI", "SNV", "SV", "Transcript Sequence", "Transcript Model", "Sequencing information"]}, "is_required": true}, "reference_genome": {"title": "Reference Genome", "description": "Reference genome used for alignment", "type": "string", "linkTo": "ReferenceGenome"}, "analysis_runs": {"title": "Analysis Runs", "description": "Link to analysis runs associated with this file", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "linkTo": "AnalysisRun"}}, "derived_from": {"title": "Derived From", "description": "Link to files used as input to create this file", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "linkTo": "File"}}, "file_sets": {"title": "File Sets", "description": "Link to file sets associated with this file", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "linkTo": "FileSet"}, "is_required": true}, "software": {"title": "Software", "description": "Link to software used to create this file", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "linkTo": "Software"}, "is_required": true}, "description": {"title": "Description", "description": "Plain text description of the item", "type": "string", "formInput": "textarea"}, "donor_specific_assembly": {"title": "Donor-Specific Assembly", "description": "Link to the associated Donor-Specific Assembly", "type": "string", "linkTo": "DonorSpecificAssembly"}, "haplotype": {"title": "Haplotype", "description": "Haplotype name for the file (for fasta files).", "type": "string", "suggested_enum": ["hapX", "hapY", "hap1", "hap2", "mt"]}, "target_assembly": {"title": "Target Assembly", "description": "The assembly to which the coordinates are being converted (required for chain files)", "type": "string"}, "source_assembly": {"title": "Source Assembly", "description": "The assembly from which the coordinates are being converted (required for chain files)", "type": "string"}}}, "Tissue": {"$id": "/profiles/tissue.json", "title": "Tissue", "properties": {"submitted_id": {"pattern": "^[A-Z0-9]{3,}_TISSUE_[A-Z0-9-_.]{4,}$", "title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "is_required": true}, "sample_count": {"title": "Sample Count", "description": "Number of samples produced from the tissue", "type": "integer", "minimum": 0}, "preservation_type": {"title": "Preservation Type", "description": "Method of preservation", "type": "string", "enum": ["Fixed", "Fresh", "Frozen", "Snap Frozen"]}, "preservation_medium": {"title": "Preservation Medium", "description": "Medium used for preservation", "type": "string"}, "external_id": {"title": "External ID", "description": "External ID for the item provided by submitter", "type": "string", "pattern": "^[A-Za-z0-9-_]{3,}$", "submissionExamples": ["ST001-1A", "PS0235"], "is_required": true}, "ischemic_time": {"title": "Ischemic Time", "description": "Time interval of ischemia (hours)", "type": "number", "minimum": 0}, "anatomical_location": {"title": "Anatomical Location", "description": "Anatomical location of the tissue in the donor", "type": "string"}, "pathology_notes": {"title": "Pathology Notes", "description": "Notes from pathologist report on the tissue", "type": "string"}, "ph": {"title": "pH", "description": "pH of the tissue", "type": "number", "minimum": 0, "maximum": 14}, "prosector_notes": {"title": "Prosector Notes", "description": "Notes from prosector report on the tissue recovery", "type": "string"}, "size": {"title": "Size", "description": "Size of the tissue", "type": "number", "minimum": 0, "also_requires": ["size_unit"]}, "size_unit": {"title": "Size Unit", "description": "Unit of measurement for size of the tissue", "type": "string", "enum": ["cm^2", "cm^3"], "also_requires": ["size"]}, "uberon_id": {"title": "Uberon Id", "description": "Uberon Ontology identifier for the tissue.", "type": "string", "linkTo": "OntologyTerm", "is_required": true}, "volume": {"title": "Volume", "description": "Volume of the tissue (mL)", "type": "number", "minimum": 0}, "weight": {"title": "Weight", "description": "Weight of the tissue (g)", "type": "number", "minimum": 0}, "donor": {"title": "Donor", "description": "Link to the associated donor", "type": "string", "linkTo": "Donor", "is_required": true}}}, "TissueCollection": {"$id": "/profiles/tissue_collection.json", "title": "Tissue Collection", "properties": {"submitted_id": {"title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "pattern": "^[A-Z0-9]{3,}_TISSUE-COLLECTION_[A-Z0-9-_.]{4,}$", "is_required": true}, "collection_site": {"title": "Collection Site", "description": "Site of tissue collection", "type": "string"}, "ischemic_time": {"title": "Ischemic Time", "description": "Time interval between death, presumed death, or cross-clamp application and beginning of tissue collection (hours)", "type": "number", "minimum": 0}, "organ_transplant": {"title": "Organ Transplant", "description": "Whether the donor had organs removed for transplant", "type": "string", "enum": ["Yes", "No", "Unknown"]}, "organs_transplanted": {"title": "Organs Transplanted", "description": "The organs of the donor that were transplanted", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "suggested_enum": ["Cornea", "Heart", "Intestine", "Kidney", "Liver", "Lung", "Pancreas", "Skin"]}}, "recovery_datetime": {"title": "Recovery Datetime", "description": "Date and time of tissue recovery", "type": "string", "anyOf": [{"format": "date-time"}, {"format": "date"}]}, "recovery_interval": {"title": "Recovery Interval", "description": "Total time interval of tissue collection (minutes)", "type": "integer", "minimum": 0}, "refrigeration_prior_to_procurement": {"title": "Refrigeration Prior To Procurement", "description": "Whether the donor was refrigerated prior to tissue collection", "type": "string", "enum": ["Yes", "No", "Unknown"]}, "refrigeration_prior_to_procurement_time": {"title": "Refrigeration Prior To Procurement Time", "description": "Interval of time the donor was refrigerated prior to tissue collection (hours)", "type": "number", "minimum": 0}, "donor": {"title": "Donor", "description": "Link to the associated donor", "type": "string", "linkTo": "AbstractDonor", "is_required": true}}}, "TissueSample": {"$id": "/profiles/tissue_sample.json", "title": "Tissue Sample", "properties": {"submitted_id": {"pattern": "^[A-Z0-9]{3,}_TISSUE-SAMPLE_[A-Z0-9-_.]{4,}$", "title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "is_required": true}, "sample_sources": {"title": "Sample Sources", "description": "Link to associated sample sources (e.g. tissue, cell culture, etc.)", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "linkTo": "SampleSource"}, "is_required": true}, "preservation_type": {"title": "Preservation Type", "description": "Method of preservation", "type": "string", "enum": ["Fixed", "Fresh", "Frozen", "Snap Frozen"]}, "preservation_medium": {"title": "Preservation Medium", "description": "Medium used for preservation", "type": "string"}, "parent_samples": {"title": "Parent Samples", "description": "Link to associated parent samples from which this sample was derived", "type": "array", "minItems": 1, "uniqueItems": true, "items": {"type": "string", "linkTo": "Sample"}}, "external_id": {"title": "External ID", "description": "External ID for the item provided by submitter", "type": "string", "pattern": "^[A-Za-z0-9-_]{3,}$", "is_required": true}, "description": {"title": "Description", "description": "Plain text description of the item", "type": "string", "formInput": "textarea"}, "category": {"title": "Category", "description": "Type of tissue sample", "type": "string", "enum": ["Tissue Aliquot", "Cells", "Core", "Homogenate", "Specimen", "Liquid"], "is_required": true}, "core_size": {"title": "Core Size", "description": "Size of core sample, if applicable (mm)", "type": "string", "enum": ["1.5", "3.0", "3.0 Donut"], "required_if_not_one_of": []}, "processing_date": {"title": "Processing Date", "description": "Date the sample was processed", "type": "string", "format": "date"}, "processing_notes": {"title": "Processing Notes", "description": "Notes on the processing of the sample", "type": "string"}, "weight": {"title": "Weight", "description": "Weight of the sample (mg)", "type": "number", "minimum": 0}}}, "Treatment": {"$id": "/profiles/treatment.json", "title": "Treatment", "properties": {"submitted_id": {"title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "pattern": "^[A-Z0-9]{3,}_TREATMENT_[A-Z0-9-_.]{4,}$", "is_required": true}, "description": {"title": "Description", "description": "Description of the treatment", "type": "string", "formInput": "textarea"}, "agent": {"title": "Agent", "description": "Agent applied in the treatment", "type": "string", "is_required": true}, "concentration": {"title": "Concentration", "description": "Concentration of the treatment", "type": "number", "minimum": 0, "also_requires": ["concentration_units"]}, "concentration_units": {"title": "Concentration Units", "description": "Units for the concentration of the treatment", "type": "string", "enum": ["ng/uL", "mg/mL", "units/uL", "pM", "nM", "\u03bcM", "\u03bcg/mL", "mM", "M", "percent", "units", "units/mL"], "also_requires": ["concentration"]}, "duration": {"title": "Duration", "description": "Duration of the treatment (minutes)", "type": "number", "minimum": 0}, "temperature": {"title": "Temperature", "description": "Temperature of the treatment (Celsius)", "type": "number"}}}, "UnalignedReads": {"$id": "/profiles/unaligned_reads.json", "title": "Unaligned Reads", "properties": {"submitted_id": {"pattern": "^[A-Z0-9]{3,}_UNALIGNED-READS_[A-Z0-9-_.]{4,}$", "title": "Submitted ID", "description": "Unique identifier for the item assigned by the submitter", "type": "string", "uniqueKey": "submitted_id", "submissionComment": "Starting characters must be the code of the submitter's submission center.", "is_required": true}, "submitted_md5sum": {"title": "Submitted MD5", "description": "Submitted MD5 checksum of the file", "type": "string", "format": "hex"}, "external_quality_metrics": {"description": "Link to externally-generated QC metrics associated with file", "items": {"description": "Associated QC report", "linkTo": "ExternalQualityMetric", "title": "Quality Metric", "type": "string"}, "minItems": 1, "title": "External Quality Metrics", "type": "array", "uniqueItems": true}, "file_format": {"ff_flag": "filter:valid_item_types", "linkTo": "FileFormat", "title": "File Format", "type": "string", "description": "Format for the file", "is_required": true}, "filename": {"description": "The local file name used at time of submission. 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