MIDRC-478 Fix type conversion in TSV array submission #409
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The style in this PR agrees with This formatting comment was generated automatically by a script in uc-cdis/wool. |
paulineribeyre
commented
Apr 22, 2024
| @@ -1 +1 @@ | |||
| {"treatment.yaml": {"description": "Record of the administration and intention of therapeutic agents provided to a patient to alter the course of a pathologic process.\n", "links": [{"backref": "treatments", "name": "diagnoses", "multiplicity": "many_to_one", "required": true, "target_type": "diagnosis", "label": "describes"}], "uniqueKeys": [["id"], ["project_id", "submitter_id"]], "validators": null, "id": "treatment", "$schema": "http://json-schema.org/draft-04/schema#", "properties": {"updated_datetime": {"$ref": "_definitions.yaml#/datetime"}, "submitter_id": {"type": ["string", "null"]}, "therapeutic_agents": {"term": {"$ref": "_terms.yaml#/therapeutic_agents"}, "type": "string"}, "treatment_anatomic_site": {"term": {"$ref": "_terms.yaml#/treatment_anatomic_site"}, "enum": ["Abdomen, total", "Arm", "Ascites", "Axillary", "Body, total", "Bone", "Bone, non-spine", "Brain, focal", "Brain, whole", "Brain-C2", "Breast", "Cervical", "Chest Wall", "Effusion", "Epitrochlear", "Eye", "Femoral", "Gastrointestinal, Colon", "Gastrointestinal, Gallbladder", "Gastrointestinal, Intestine", "Gastrointestinal, Liver", "Gastrointestinal, NOS", "Gastrointestinal, Pancreas", "Gastrointestinal, Rectum", "Gastrointestinal, Stomach", "Genitourinary, Bladder", "Genitourinary, Kidney", "Genitourinary, NOS", "Genitourinary, Prostate", "Genitourinary, Prostate and Seminal Vesicles", "Head", "Head, Face, or Neck", "Hilar", "Iliac-common", "Iliac-external", "Inguinal", "Internal Mammary Nodes", "Leg", "Lung", "Lymph Nodes", "Lymph node, distant (specify site)", "Lymph node, locoregional (specify site)", "Mantle", "Mediastinal", "Mediastinum", "Mesenteric", "Occipital", "Other", "Paraaortic", "Parametrium", "Parotid", "Pelvis", "Popliteal", "Primary tumor site", "Prostate", "Prostate Bed", "Prostate, Seminal Vesicles and Lymph Nodes", "Rectum", "Retroperitoneal", "Sacrum", "Seminal vesicles", "Shoulder", "Skin, lower extremity, local", "Skin, total", "Skin, trunk, local", "Skin, upper extremity, local", "Spine", "Spine, whole", "Splenic", "Submandibular", "Supraclavicular", "Supraclavicular/Axillary Level 3", "Thorax", "Trunk", "Unknown", "Not Reported", "Not Allowed To Collect"]}, "treatment_outcome": {"term": {"$ref": "_terms.yaml#/treatment_outcome"}, "enum": ["Complete Response", "Partial Response", "Treatment Ongoing", "Treatment Stopped Due to Toxicity", "Unknown"]}, "days_to_treatment_end": {"term": {"$ref": "_terms.yaml#/days_to_treatment_end"}, "type": "number"}, "diagnoses": {"$ref": "_definitions.yaml#/to_one"}, "days_to_treatment_start": {"term": {"$ref": "_terms.yaml#/days_to_treatment_start"}, "type": "number"}, "created_datetime": {"$ref": "_definitions.yaml#/datetime"}, "treatment_type": {"term": {"$ref": "_terms.yaml#/treatment_type"}, "enum": ["Ablation", "Chemotherapy", "Concurrent Chemoradiation", "Cryoablation", "Embolization", "Hormone Therapy", "Internal Radiation", "Immunotherapy (Including Vaccines)", "Other", "Pharmaceutical Therapy", "Radiation Therapy", "Stem Cell Treatment", "Surgery", "Targeted Molecular Therapy", "Unknown", "Not Reported", "Not Allowed To Collect"]}, "id": {"systemAlias": "node_id", "$ref": "_definitions.yaml#/UUID"}, "state": {"$ref": "_definitions.yaml#/state"}, "days_to_treatment": {"term": {"$ref": "_terms.yaml#/days_to_treatment"}, "type": "number"}, "project_id": {"$ref": "_definitions.yaml#/project_id"}, "type": {"enum": ["treatment"]}, "treatment_intent_type": {"term": {"$ref": "_terms.yaml#/treatment_intent_type"}, "type": "string"}, "treatment_or_therapy": {"term": {"$ref": "_terms.yaml#/treatment_or_therapy"}, "enum": ["yes", "no", "unknown", "not reported"]}}, "category": "clinical", "title": "Treatment", "systemProperties": ["id", "project_id", "state", "created_datetime", "updated_datetime"], "namespace": "http://gdc.nci.nih.gov", "submittable": true, "project": "*", "program": "*", "additionalProperties": false, "type": "object"}, "submitted_unaligned_reads.yaml": {"description": "Data file containing unaligned reads that have not been GDC Harmonized.", "links": [{"backref": "submitted_unaligned_reads_files", "name": "read_groups", "multiplicity": "many_to_one", "required": true, "target_type": "read_group", "label": "data_from"}], "uniqueKeys": [["id"], ["project_id", "submitter_id"]], "validators": null, "id": "submitted_unaligned_reads", "$schema": "http://json-schema.org/draft-04/schema#", "properties": {"read_groups": {"$ref": "_definitions.yaml#/to_one"}, "data_category": {"term": {"$ref": "_terms.yaml#/data_category"}, "enum": ["Sequencing Data", "Sequencing Reads", "Raw Sequencing Data"]}, "data_type": {"term": {"$ref": "_terms.yaml#/data_type"}, "enum": ["Unaligned Reads"]}, "experimental_strategy": {"term": {"$ref": "_terms.yaml#/experimental_strategy"}, "enum": ["WGS", "WXS", "Low Pass WGS", "Validation", "RNA-Seq", "miRNA-Seq", "Total RNA-Seq", "DNA Panel"]}, "type": {"enum": ["submitted_unaligned_reads"]}, "data_format": {"term": {"$ref": "_terms.yaml#/data_format"}, "enum": ["BAM", "FASTQ"]}, "$ref": "_definitions.yaml#/data_file_properties"}, "category": "data_file", "title": "Submitted Unaligned Reads", "systemProperties": ["id", "project_id", "created_datetime", "updated_datetime", "state", "file_state", "error_type"], "required": ["submitter_id", "file_name", "file_size", "md5sum", "data_category", "data_type", "data_format", "experimental_strategy", "read_groups"], "namespace": "http://gdc.nci.nih.gov", "submittable": true, "project": "*", "program": "*", "additionalProperties": false, "type": "object"}, "submitted_aligned_reads.yaml": {"description": "Data file containing aligned reads that are used as input to GDC workflows.\n", "links": [{"backref": "submitted_aligned_reads_files", "name": "read_groups", "multiplicity": "one_to_many", "required": true, "target_type": "read_group", "label": "data_from"}], "uniqueKeys": [["id"], ["project_id", "submitter_id"]], "validators": null, "id": "submitted_aligned_reads", "$schema": "http://json-schema.org/draft-04/schema#", "properties": {"read_groups": {"$ref": "_definitions.yaml#/to_many"}, "data_category": {"term": {"$ref": "_terms.yaml#/data_category"}, "enum": ["Sequencing Data", "Sequencing Reads", "Raw Sequencing Data"]}, "data_type": {"term": {"$ref": "_terms.yaml#/data_type"}, "enum": ["Aligned Reads", "Alignment Coordinates"]}, "experimental_strategy": {"term": {"$ref": "_terms.yaml#/experimental_strategy"}, "enum": ["WGS", "WXS", "Low Pass WGS", "Validation", "RNA-Seq", "miRNA-Seq", "Total RNA-Seq", "DNA Panel"]}, "type": {"enum": ["submitted_aligned_reads"]}, "data_format": {"term": {"$ref": "_terms.yaml#/data_format"}, "enum": ["BAM", "BED"]}, "$ref": "_definitions.yaml#/data_file_properties"}, "category": "data_file", "title": "Submitted Aligned Reads", "systemProperties": ["id", "project_id", "created_datetime", "updated_datetime", "state", "file_state", "error_type"], "required": ["submitter_id", "file_name", "file_size", "data_format", "md5sum", "data_category", "data_type", "experimental_strategy", "read_groups"], "namespace": "http://gdc.nci.nih.gov", "submittable": true, "project": "*", "program": "*", "additionalProperties": false, "type": "object"}, "demographic.yaml": {"description": "Data for the characterization of the patient by means of segementing the population (e.g., characterization by age, sex, or race).\n", "links": [{"backref": "demographics", "name": "cases", "multiplicity": "one_to_one", "required": true, "target_type": "case", "label": "describes"}], "uniqueKeys": [["id"], ["project_id", "submitter_id"]], "preferred": ["year_of_death"], "validators": null, "id": "demographic", "$schema": "http://json-schema.org/draft-04/schema#", "properties": {"updated_datetime": {"$ref": "_definitions.yaml#/datetime"}, "created_datetime": {"$ref": "_definitions.yaml#/datetime"}, "gender": {"term": {"$ref": "_terms.yaml#/gender"}, "enum": ["female", "male", "unknown", "unspecified", "not reported"]}, "state": {"$ref": "_definitions.yaml#/state"}, "submitter_id": {"type": ["string", "null"]}, "year_of_birth": {"term": {"$ref": "_terms.yaml#/year_of_birth"}, "type": ["number", "null"]}, "race": {"term": {"$ref": "_terms.yaml#/race"}, "enum": ["white", "american indian or alaska native", "black or african american", "asian", "native hawaiian or other pacific islander", "other", "Unknown", "not reported", "not allowed to collect"]}, "cases": {"$ref": "_definitions.yaml#/to_one"}, "project_id": {"$ref": "_definitions.yaml#/project_id"}, "type": {"type": "string"}, "id": {"systemAlias": "node_id", "$ref": "_definitions.yaml#/UUID"}, "ethnicity": {"term": {"$ref": "_terms.yaml#/ethnicity"}, "enum": ["hispanic or latino", "not hispanic or latino", "Unknown", "not reported", "not allowed to collect"]}, "year_of_death": {"term": {"$ref": "_terms.yaml#/year_of_death"}, "type": "number"}}, "category": "clinical", "title": "Demographic", "systemProperties": ["id", "project_id", "state", "created_datetime", "updated_datetime"], "required": ["submitter_id", "cases"], "namespace": "http://gdc.nci.nih.gov", "submittable": true, "project": "*", "program": "*", "additionalProperties": false, "type": "object"}, "experiment.yaml": {"description": "A coordinated set of actions and observations designed to generate data, with the ultimate goal of discovery or hypothesis testing.\n", "links": [{"backref": "experiments", "name": "projects", "multiplicity": "many_to_one", "required": true, "target_type": "project", "label": "performed_for"}], "uniqueKeys": [["id"], ["project_id", "submitter_id"]], "validators": null, "id": "experiment", "$schema": "http://json-schema.org/draft-04/schema#", "properties": {"associated_experiment": {"type": ["string"], "description": "The submitter_id for any experiment with which this experiment is associated, paired, or matched."}, "updated_datetime": {"$ref": "_definitions.yaml#/datetime"}, "marker_panel_description": {"type": "string", "description": "Brief description of the marker panel used in this experiment."}, "submitter_id": {"type": ["string", "null"]}, "experimental_intent": {"type": ["string"], "description": "Summary of the goals the experiment is designed to discover."}, "copy_numbers_identified": {"type": "boolean", "description": "Are copy number variations identified in this experiment?"}, "somatic_mutations_identified": {"type": "boolean", "description": "Are somatic mutations identified for this experiment?"}, "type_of_specimen": {"type": ["string"], "description": "Broad description of the specimens used in the experiment."}, "type_of_data": {"enum": ["Raw", "Processed"], "description": "Is the data raw or processed?"}, "id": {"systemAlias": "node_id", "$ref": "_definitions.yaml#/UUID"}, "projects": {"$ref": "_definitions.yaml#/to_one"}, "number_samples_per_experimental_group": {"type": ["integer"], "description": "The number of samples contained within this experimental group."}, "type_of_sample": {"type": ["string"], "description": "String indicator identifying the types of samples as contrived or clinical."}, "created_datetime": {"$ref": "_definitions.yaml#/datetime"}, "indels_identified": {"type": "boolean", "description": "Are indels identified in this experiment?"}, "number_experimental_group": {"type": ["integer"], "description": "The number denoting this experiment's place within the group within the whole."}, "state": {"$ref": "_definitions.yaml#/state"}, "project_id": {"$ref": "_definitions.yaml#/project_id"}, "type": {"enum": ["experiment"]}, "experimental_description": {"type": ["string"], "description": "A brief description of the experiment being performed."}, "data_description": {"type": "string", "description": "Brief description of the data being provided for this experiment."}}, "category": "administrative", "title": "Experiment", "systemProperties": ["id", "project_id", "created_datetime", "updated_datetime", "state"], "required": ["submitter_id", "projects"], "namespace": "http://bloodprofilingatlas.org/bpa/", "submittable": true, "project": "*", "program": "*", "additionalProperties": false, "type": "object"}, "_definitions.yaml": {"data_file_properties": {"md5sum": {"$ref": "#/md5sum"}, "updated_datetime": {"$ref": "#/datetime"}, "created_datetime": {"$ref": "#/datetime"}, "file_name": {"$ref": "#/file_name"}, "error_type": {"$ref": "#/data_file_error_type"}, "object_id": {"$ref": "#/object_id"}, "submitter_id": {"type": ["string", "null"], "description": "The file ID assigned by the submitter."}, "state": {"$ref": "#/state"}, "file_size": {"$ref": "#/file_size"}, "project_id": {"$ref": "#/project_id"}, "state_comment": {"type": "string", "description": "Optional comment about why the file is in the current state, mainly for invalid state.\n"}, "id": {"systemAlias": "node_id", "$ref": "#/UUID"}, "file_state": {"$ref": "#/file_state"}}, "data_file_error_type": {"term": {"$ref": "_terms.yaml#/data_file_error_type"}, "enum": ["file_size", "file_format", "md5sum"]}, "file_name": {"term": {"$ref": "_terms.yaml#/file_name"}, "type": "string"}, "foreign_key": {"additionalProperties": true, "type": "object", "properties": {"id": {"$ref": "#/UUID"}, "submitter_id": {"type": "string"}}}, "data_bundle_state": {"default": "submitted", "enum": ["submitted", "validated", "error", "released", "suppressed", "redacted"], "description": "State of a data bundle."}, "workflow_properties": {"updated_datetime": {"$ref": "#/datetime"}, "created_datetime": {"$ref": "#/datetime"}, "workflow_start_datetime": {"$ref": "#/datetime"}, "submitter_id": {"type": ["string", "null"], "description": "The file ID assigned by the submitter."}, "state": {"$ref": "#/state"}, "workflow_end_datetime": {"$ref": "#/datetime"}, "workflow_link": {"type": "string", "description": "Link to Github hash for the CWL workflow used."}, "project_id": {"$ref": "#/project_id"}, "id": {"systemAlias": "node_id", "$ref": "#/UUID"}, "workflow_version": {"type": "string", "description": "Major version for a GDC workflow."}}, "parent_uuids": {"minItems": 1, "items": {"$ref": "#/UUID"}, "uniqueItems": true, "type": "array"}, "file_size": {"term": {"$ref": "_terms.yaml#/file_size"}, "type": "integer"}, "datetime": {"oneOf": [{"type": "string", "format": "date-time"}, {"type": "null"}], "term": {"$ref": "_terms.yaml#/datetime"}}, "id": "_definitions", "to_many": {"anyOf": [{"items": {"minItems": 1, "$ref": "#/foreign_key"}, "type": "array"}, {"$ref": "#/foreign_key"}]}, "UUID": {"pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": {"$ref": "_terms.yaml#/UUID"}, "type": "string"}, "file_format": {"term": {"$ref": "_terms.yaml#/file_format"}, "type": "string"}, "to_one": {"anyOf": [{"items": {"minItems": 1, "maxItems": 1, "$ref": "#/foreign_key"}, "type": "array"}, {"$ref": "#/foreign_key"}]}, "md5sum": {"pattern": "^[a-f0-9]{32}$", "term": {"$ref": "_terms.yaml#/md5sum"}, "type": "string"}, "object_id": {"type": "string", "description": "The GUID of the object in the index service."}, "state": {"default": "validated", "term": {"$ref": "_terms.yaml#/state"}, "downloadable": ["uploaded", "md5summed", "validating", "validated", "error", "invalid", "released"], "oneOf": [{"enum": ["uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live"]}, {"enum": ["validated", "submitted", "released"]}], "public": ["live"]}, "release_state": {"default": "unreleased", "enum": ["unreleased", "released", "redacted"], "description": "Release state of an entity."}, "project_id": {"term": {"$ref": "_terms.yaml#/project_id"}, "type": "string"}, "qc_metrics_state": {"term": {"$ref": "_terms.yaml#/qc_metric_state"}, "enum": ["FAIL", "PASS", "WARN"]}, "file_state": {"default": "registered", "term": {"$ref": "_terms.yaml#/file_state"}, "enum": ["registered", "uploading", "uploaded", "validating", "validated", "submitted", "processing", "processed", "released", "error"]}}, "_terms.yaml": {"her2_erbb2_result_ihc": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2957563&version=2.0", "source": "caDSR", "term": "Laboratory Procedure HER2/neu Immunohistochemistry Receptor Status", "cde_version": 2.0, "cde_id": 2957563}, "description": "Text term to signify the result of the medical procedure that involves testing a sample of blood or tissue for HER2 by histochemical localization of immunoreactive substances using labeled antibodies as reagents.\n"}, "method_of_diagnosis": {"termDef": {"term_url": null, "source": null, "term": "Method of Diagnosis", "cde_version": null, "cde_id": null}, "description": "The method used to initially the patient's diagnosis.\n"}, "laterality": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=827&version=3.0", "source": "caDSR", "term": "Primary Tumor Laterality", "cde_version": 3.0, "cde_id": 827}, "description": "For tumors in paired organs, designates the side on which the cancer originates.\n"}, "ann_arbor_pathologic_stage": {"termDef": {"term_url": null, "source": null, "term": "Ann Arbor Pathologic Stage", "cde_version": null, "cde_id": null}, "description": "The classification of the pathologically confirmed anatomic disease extent of lymphoma (Hodgkin's and Non-Hodgkins) based on the Ann Arbor Staging System.\n"}, "analyte_type": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2513915&version=2.0", "source": "caDSR", "term": "Molecular Specimen Type Text Name", "cde_version": 2.0, "cde_id": 2513915}, "description": "Text term that represents the kind of molecular specimen analyte.\n"}, "datetime": {"description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n"}, "library_preparation_kit_name": {"description": "Name of Library Preparation Kit\n"}, "intermediate_dimension": {"description": "Intermediate dimension of the sample, in millimeters.\n"}, "to_trim_adapter_sequence": {"description": "Does the user suggest adapter trimming?\n"}, "target_capture_kit_name": {"description": "Name of Target Capture Kit.\n"}, "vital_status": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5&version=5.0", "source": "caDSR", "term": "Patient Vital Status", "cde_version": 5.0, "cde_id": 5}, "description": "The survival state of the person registered on the protocol.\n"}, "morphology": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3226275&version=1.0", "source": "caDSR", "term": "International Classification of Diseases for Oncology, Third Edition ICD-O-3 Histology Code", "cde_version": 1.0, "cde_id": 3226275}, "description": "The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.\n"}, "days_to_death": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3165475&version=1.0", "source": "caDSR", "term": "Death Less Initial Pathologic Diagnosis Date Calculated Day Value", "cde_version": 1.0, "cde_id": 3165475}, "description": "Time interval from a person's date of death to the date of initial pathologic diagnosis, represented as a calculated number of days.\n"}, "percent_inflam_infiltration": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897695&version=1.0", "source": "caDSR", "term": "Specimen Inflammation Change Percentage Value", "cde_version": 1.0, "cde_id": 2897695}, "description": "Numeric value to represent local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by reddness, heat, pain, swelling and loss of function, with the need to heal damaged tissue.\n"}, "fev1_fvc_post_bronch_percent": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302956&version=1.0", "source": "caDSR", "term": "Post Bronchodilator FEV1/FVC Percent Value", "cde_version": 1.0, "cde_id": 3302956}, "description": "Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) post-bronchodilator.\n"}, "days_to_last_known_disease_status": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008273&version=1.0", "source": "caDSR", "term": "Last Communication Contact Less Initial Pathologic Diagnosis Date Calculated Day Value", "cde_version": 1.0, "cde_id": 3008273}, "description": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.\n"}, "days_to_hiv_diagnosis": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4618491&version=1.0", "source": "caDSR", "term": "Human Immunodeficiency Virus Diagnosis Subtract Initial Pathologic Diagnosis Time Duration Day Calculation Value", "cde_version": 1.0, "cde_id": 4618491}, "description": "Time interval from the date of the initial pathologic diagnosis to the date of human immunodeficiency diagnosis, represented as a calculated number of days.\n"}, "ajcc_pathologic_t": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3045435&version=1.0", "source": "caDSR", "term": "American Joint Committee on Cancer Tumor Stage Code", "cde_version": 1.0, "cde_id": 3045435}, "description": "Code of pathological T (primary tumor) to define the size or contiguous extension of the primary tumor (T), using staging criteria from the American Joint Committee on Cancer (AJCC).\n"}, "prior_treatment": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4231463&version=1.0", "source": "caDSR", "term": "Therapeutic Procedure Prior Specimen Collection Administered Yes No Unknown Not Applicable Indicator", "cde_version": 1.0, "cde_id": 4231463}, "description": "A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.\n"}, "encoding": {"termDef": {"term_url": "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/1%20Basic%20Statistics.html", "source": "FastQC", "term": "Encoding", "cde_version": null, "cde_id": null}, "description": "Version of ASCII encoding of quality values found in the file.\n"}, "RIN": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5278775&version=1.0", "source": "caDSR", "term": "Biospecimen RNA Integrity Number Value", "cde_version": 1.0, "cde_id": 5278775}, "description": "A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products.\n"}, "ajcc_pathologic_m": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3045439&version=1.0", "source": "caDSR", "term": "American Joint Committee on Cancer Metastasis Stage Code", "cde_version": 1.0, "cde_id": 3045439}, "description": "Code to represent the defined absence or presence of distant spread or metastases (M) to locations via vascular channels or lymphatics beyond the regional lymph nodes, using criteria established by the American Joint Committee on Cancer (AJCC).\n"}, "ajcc_pathologic_n": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3203106&version=1.0", "source": "caDSR", "term": "Neoplasm Disease Lymph Node Stage American Joint Committee on Cancer Code", "cde_version": 1.0, "cde_id": 3203106}, "description": "The codes that represent the stage of cancer based on the nodes present (N stage) according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.\n"}, "ldh_level_at_diagnosis": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2798766&version=1.0", "source": "caDSR", "term": "Laboratory Procedure Lactate Dehydrogenase Result Integer::2 Decimal Place Value", "cde_version": 1.0, "cde_id": 2798766}, "description": "The 2 decimal place numeric laboratory value measured, assigned or computed related to the assessment of lactate dehydrogenase in a specimen.\n"}, "percent_normal_cells": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841233&version=1.0", "source": "caDSR", "term": "Malignant Neoplasm Normal Cell Percentage Value", "cde_version": 1.0, "cde_id": 2841233}, "description": "Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.\n"}, "number_proliferating_cells": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432636&version=1.0", "source": "caDSR", "term": "Pathology Review Slide Proliferating Cell Count", "cde_version": 1.0, "cde_id": 5432636}, "description": "Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).\n"}, "project_id": {"description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n"}, "library_strand": {"description": "Library stranded-ness.\n"}, "file_state": {"description": "The current state of the data file object.\n"}, "time_between_clamping_and_freezing": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432611&version=1.0", "source": "caDSR", "term": "Tissue Sample Clamping and Freezing Elapsed Minute Time", "cde_version": 1.0, "cde_id": 5432611}, "description": "Numeric representation of the elapsed time between the surgical clamping of blood supply and freezing of the sample, measured in minutes.\n"}, "alcohol_history": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2201918&version=1.0", "source": "caDSR", "term": "Alcohol Lifetime History Indicator", "cde_version": 1.0, "cde_id": 2201918}, "description": "A response to a question that asks whether the participant has consumed at least 12 drinks of any kind of alcoholic beverage in their lifetime.\n"}, "percent_monocyte_infiltration": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5455535&version=1.0", "source": "caDSR", "term": "Specimen Monocyte Infiltration Percentage Value", "cde_version": 1.0, "cde_id": 5455535}, "description": "Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.\n"}, "fastq_name": {"description": "Names of FASTQs.\n"}, "portion_weight": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432593&version=1.0", "source": "caDSR", "term": "Biospecimen Portion Weight Milligram Value", "cde_version": 1.0, "cde_id": 5432593}, "description": "Numeric value that represents the sample portion weight, measured in milligrams.\n"}, "lymphatic_invasion_present": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64171&version=3.0", "source": "caDSR", "term": "Lymphatic/Small vessel Invasion Ind", "cde_version": 3.0, "cde_id": 64171}, "description": "A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement\n"}, "smoking_history": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2181650&version=1.0", "source": "caDSR", "term": "Smoking History", "cde_version": 1.0, "cde_id": 2181650}, "description": "Category describing current smoking status and smoking history as self-reported by a patient.\n"}, "biomarker_result": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3234680&version=1.0", "source": "caDSR", "term": "Laboratory Procedure Genetic Abnormality Test Result Type", "cde_version": 1.0, "cde_id": 3234680}, "description": "Text term to define the results of genetic testing.\n"}, "days_to_sample_procurement": {"description": "The number of days from the date the patient was diagnosed to the date of the procedure that produced the sample.\n"}, "freezing_method": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432607&version=1.0", "source": "caDSR", "term": "Tissue Sample Freezing Method Type", "cde_version": 1.0, "cde_id": 5432607}, "description": "Text term that represents the method used for freezing the sample.\n"}, "UUID": {"termDef": {"term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100", "source": "NCIt", "term": "Universally Unique Identifier", "cde_version": null, "cde_id": "C54100"}, "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n"}, "cause_of_death": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2554674&version=3.0", "source": "caDSR", "term": "Patient Death Reason", "cde_version": 3.0, "cde_id": 2554674}, "description": "Text term to identify the cause of death for a patient.\n"}, "aliquot_quantity": {"termDef": {"term_url": null, "source": null, "term": "Biospecimen Aliquot Quantity", "cde_version": null, "cde_id": null}, "description": "The quantity in micrograms (ug) of the aliquot(s) derived from the analyte(s) shipped for sequencing and characterization.\n"}, "gender": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2200604&version=3.0", "source": "caDSR", "term": "Person Gender Text Type", "cde_version": 3.0, "cde_id": 2200604}, "description": "Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Explanatory Comment 1: Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]\n"}, "percent_eosinophil_infiltration": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897700&version=2.0", "source": "caDSR", "term": "Specimen Eosinophilia Percentage Value", "cde_version": 2.0, "cde_id": 2897700}, "description": "Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.\n"}, "preservation_method": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432521&version=1.0", "source": "caDSR", "term": "Tissue Sample Preservation Method Type", "cde_version": 1.0, "cde_id": 5432521}, "description": "Text term that represents the method used to preserve the sample.\n"}, "base_caller_name": {"description": "Name of the base caller.\n"}, "her2_erbb2_result_fish": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2854089&version=1.0", "source": "caDSR", "term": "Laboratory Procedure HER2/neu in situ Hybridization Outcome Type", "cde_version": 1.0, "cde_id": 2854089}, "description": "the type of outcome for HER2 as determined by an in situ hybridization (ISH) assay.\n"}, "flow_cell_barcode": {"description": "Flow Cell Barcode.\n"}, "alcohol_intensity": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3457767&version=1.0", "source": "caDSR", "term": "Person Self-Report Alcoholic Beverage Exposure Category", "cde_version": 1.0, "cde_id": 3457767}, "description": "Category to describe the patient's current level of alcohol use as self-reported by the patient.\n"}, "ajcc_clinical_stage": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440332&version=1.0", "source": "caDSR", "term": "Neoplasm American Joint Committee on Cancer Clinical Group Stage", "cde_version": 1.0, "cde_id": 3440332}, "description": "Stage group determined from clinical information on the tumor (T), regional node (N) and metastases (M) and by grouping cases with similar prognosis for cancer.\n"}, "experimental_strategy": {"description": "The sequencing strategy used to generate the data file.\n"}, "source_center": {"description": "Name of the center that provided the item.\n"}, "hiv_positive": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4030799&version=1.0", "source": "caDSR", "term": "Physician Diagnosed HIV Infection Personal Medical History Yes No Not Applicable Indicator", "cde_version": 1.0, "cde_id": 4030799}, "description": "Text term to signify whether a physician has diagnosed HIV infection in a patient.\n"}, "percent_tumor_cells": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432686&version=1.0", "source": "caDSR", "term": "Specimen Tumor Cell Percentage Value", "cde_version": 1.0, "cde_id": 5432686}, "description": "Numeric value that represents the percentage of infiltration by granulocytes in a sample.\n"}, "ann_arbor_extranodal_involvement": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3364582&version=1.0", "source": "caDSR", "term": "Lymphomatous Extranodal Site Involvement Indicator", "cde_version": 1.0, "cde_id": 3364582}, "description": "Indicator that identifies whether a patient with malignant lymphoma has lymphomatous involvement of an extranodal site.\n"}, "ann_arbor_b_symptoms": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2902402&version=1.0", "source": "caDSR", "term": "Lymphoma B-Symptoms Medical Record Documented Indicator", "cde_version": 1.0, "cde_id": 2902402}, "description": "Text term to signify whether lymphoma B-symptoms are present as noted in the patient's medical record.\n"}, "sample_type_id": {"description": "The accompanying sample type id for the sample type.\n"}, "cigarettes_per_day": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2001716&version=4.0", "source": "caDSR", "term": "Smoking Use Average Number", "cde_version": 4.0, "cde_id": 2001716}, "description": "The average number of cigarettes smoked per day.\n"}, "is_paired_end": {"description": "Are the reads paired end?\n"}, "weight": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=651&version=4.0", "source": "caDSR", "term": "Patient Weight Measurement", "cde_version": 4.0, "cde_id": 651}, "description": "The weight of the patient measured in kilograms.\n"}, "adapter_sequence": {"description": "Base sequence of the sequencing adapter.\n"}, "oct_embedded": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432538&version=1.0", "source": "caDSR", "term": "Tissue Sample Optimal Cutting Temperature Compound Embedding Indicator", "cde_version": 1.0, "cde_id": 5432538}, "description": "Indicator of whether or not the sample was embedded in Optimal Cutting Temperature (OCT) compound.\n"}, "relationship_type": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2690165&version=2.0", "source": "caDSR", "term": "Family Member Relationship Type", "cde_version": 2.0, "cde_id": 2690165}, "description": "The subgroup that describes the state of connectedness between members of the unit of society organized around kinship ties.\n"}, "days_to_treatment": {"termDef": {"term_url": null, "source": null, "term": "Days to Treatment Start", "cde_version": null, "cde_id": null}, "description": "Number of days from date of initial pathologic diagnosis that treatment began.\n"}, "fev1_fvc_pre_bronch_percent": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302955&version=1.0", "source": "caDSR", "term": "Pre Bronchodilator FEV1/FVC Percent Value", "cde_version": 1.0, "cde_id": 3302955}, "description": "Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) pre-bronchodilator.\n"}, "age_at_diagnosis": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3225640&version=2.0", "source": "caDSR", "term": "Patient Diagnosis Age Day Value", "cde_version": 2.0, "cde_id": 3225640}, "description": "Age at the time of diagnosis expressed in number of days since birth.\n"}, "hpv_positive_type": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2922649&version=1.0", "source": "caDSR", "term": "Human Papillomavirus Type", "cde_version": 1.0, "cde_id": 2922649}, "description": "Text classification to represent the strain or type of human papillomavirus identified in an individual.\n"}, "tobacco_smoking_status": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2181650&version=1.0", "source": "caDSR", "term": "Patient Smoking History Category", "cde_version": 1.0, "cde_id": 2181650}, "description": "Category describing current smoking status and smoking history as self-reported by a patient.\n"}, "percent_gc_content": {"termDef": {"term_url": "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/1%20Basic%20Statistics.html", "source": "FastQC", "term": "%GC", "cde_version": null, "cde_id": null}, "description": "The overall %GC of all bases in all sequences.\n"}, "percent_granulocyte_infiltration": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897705&version=2.0", "source": "caDSR", "term": "Specimen Granulocyte Infiltration Percentage Value", "cde_version": 2.0, "cde_id": 2897705}, "description": "Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.\n"}, "analyte_type_id": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432508&version=1.0", "source": "caDSR", "term": "Molecular Analyte Identification Code", "cde_version": 1.0, "cde_id": 5432508}, "description": "A single letter code used to identify a type of molecular analyte.\n"}, "pack_years_smoked": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2955385&version=1.0", "source": "caDSR", "term": "Person Cigarette Smoking History Pack Year Value", "cde_version": 1.0, "cde_id": 2955385}, "description": "Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.\n"}, "her2_erbb2_percent_positive_ihc": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3086980&version=1.0", "source": "caDSR", "term": "HER2 ERBB Positive Finding Cell Percentage Category", "cde_version": 1.0, "cde_id": 3086980}, "description": "Classification to represent the number of positive HER2/ERBB2 cells in a specimen or sample.\n"}, "treatment_type": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102381&version=1.0", "source": "caDSR", "term": "Treatment Method Type", "cde_version": 1.0, "cde_id": 5102381}, "description": "Text term that describes the kind of treatment administered.\n"}, "spike_ins_fasta": {"description": "Name of the FASTA file that contains the spike-in sequences.\n"}, "biomarker_test_method": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3121575&version=1.0", "source": "caDSR", "term": "Disease Detection Molecular Analysis Method Type", "cde_version": 1.0, "cde_id": 3121575}, "description": "Text descriptor of a molecular analysis method used for an individual.\n"}, "state": {"description": "The current state of the object.\n"}, "race": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2192199&version=1.0", "source": "caDSR", "term": "Race Category Text", "cde_version": 1.0, "cde_id": 2192199}, "description": "An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation within a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.\n"}, "spike_ins_concentration": {"description": "Spike in concentration.\n"}, "library_strategy": {"description": "Library strategy.\n"}, "current_weight": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432606&version=1.0", "source": "caDSR", "term": "Tissue Sample Current Weight Milligram Value", "cde_version": 1.0, "cde_id": 5432606}, "description": "Numeric value that represents the current weight of the sample, measured in milligrams.\n"}, "relationship_age_at_diagnosis": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5300571&version=1.0", "source": "caDSR", "term": "Relative Diagnosis Age Value", "cde_version": 1.0, "cde_id": 5300571}, "description": "The age (in years) when the patient's relative was first diagnosed.\n"}, "days_to_recurrence": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3392464&version=1.0", "source": "caDSR", "term": "New Tumor Event Less Initial Pathologic Diagnosis Date Calculated Day Value", "cde_version": 1.0, "cde_id": 3392464}, "description": "Time interval from the date of new tumor event including progression, recurrence and new primary malignancies to the date of initial pathologic diagnosis, represented as a calculated number of days.\n"}, "data_type": {"description": "Specific content type of the data file.\n"}, "figo_stage": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3225684&version=1.0", "source": "caDSR", "term": "Gynecologic Tumor Grouping Cervical Endometrial FIGO 2009 Stage", "cde_version": 1.0, "cde_id": 3225684}, "description": "The extent of a cervical or endometrial cancer within the body, especially whether the disease has spread from the original site to other parts of the body, as described by the International Federation of Gynecology and Obstetrics (FIGO) stages.\n"}, "tumor_code": {"description": "Diagnostic tumor code of the tissue sample source.\n"}, "target_capture_kit_version": {"description": "Version of Target Capture Kit.\n"}, "percent_lymphocyte_infiltration": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897710&version=2.0", "source": "caDSR", "term": "Specimen Lymphocyte Infiltration Percentage Value", "cde_version": 2.0, "cde_id": 2897710}, "description": "Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.\n"}, "tissue_or_organ_of_origin": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3427536&version=3.0", "source": "caDSR", "term": "Tumor Disease Anatomic Site", "cde_version": 3.0, "cde_id": 3427536}, "description": "Text term that describes the anatomic site of the tumor or disease.\n"}, "base_caller_version": {"description": "Version of the base caller.\n"}, "tobacco_smoking_quit_year": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2228610&version=1.0", "source": "caDSR", "term": "Stopped Smoking Year", "cde_version": 1.0, "cde_id": 2228610}, "description": "The year in which the participant quit smoking.\n"}, "prior_malignancy": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3382736&version=2.0", "source": "caDSR", "term": "Prior Cancer Diagnosis Occurrence Description Text", "cde_version": 2.0, "cde_id": 3382736}, "description": "Text term to describe the patient's history of prior cancer diagnosis and the spatial location of any previous cancer occurrence.\n"}, "estrogen_receptor_percent_positive_ihc": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3128341&version=1.0", "source": "caDSR", "term": "ER Level Cell Percentage Category", "cde_version": 1.0, "cde_id": 3128341}, "description": "Classification to represent ER Positive results expressed as a percentage value.\n"}, "library_preparation_kit_vendor": {"description": "Vendor of Library Preparation Kit\n"}, "days_to_treatment_start": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102411&version=1.0", "source": "caDSR", "term": "Treatment Start Subtract First Pathologic Diagnosis Time Day Calculation Value", "cde_version": 1.0, "cde_id": 5102411}, "description": "Time interval from the date of the initial pathologic diagnosis to the start of treatment, represented as a calculated number of days.\n"}, "circumferential_resection_margin": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64202&version=3.0", "source": "caDSR", "term": "Colorectal Surgical Margin Circumferential Distance Measurement", "cde_version": 3.0, "cde_id": 64202}, "description": "A value in millimeters indicating the measured length between a malignant lesion of the colon or rectum and the nearest radial (or circumferential) border of tissue removed during cancer surgery.\n"}, "28s_16s_ribosomal_rna_ratio": {"termDef": {"term_url": null, "source": null, "term": "28s/18s Ribosomal RNA Ratio", "cde_version": null, "cde_id": null}, "description": "The 28S/18S ribosomal RNA band ratio used to assess the quality of total RNA.\n"}, "lymph_nodes_positive": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=89&version=3.0", "source": "caDSR", "term": "Lymph Node(s) Positive Number", "cde_version": 3.0, "cde_id": 89}, "description": "The number of lymph nodes involved with disease as determined by pathologic examination.\n"}, "estrogen_receptor_result_ihc": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2957359&version=2.0", "source": "caDSR", "term": "Breast Carcinoma Estrogen Receptor Status", "cde_version": 2.0, "cde_id": 2957359}, "description": "Text term to represent the overall result of Estrogen Receptor (ER) testing.\n"}, "data_format": {"description": "Format of the data files.\n"}, "ann_arbor_tumor_stage": {"termDef": {"term_url": null, "source": null, "term": "Ann Arbor Tumor Stage", "cde_version": null, "cde_id": null}, "description": "The classification of the anatomic disease extent of lymphoma (Hodgkin's and Non-Hodgkins) based on the Ann Arbor Staging System.\n"}, "days_to_last_follow_up": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008273&version=1.0", "source": "caDSR", "term": "Last Communication Contact Less Initial Pathologic Diagnosis Date Calculated Day Value", "cde_version": 1.0, "cde_id": 3008273}, "description": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.\n"}, "amount": {"description": "Weight in grams or volume in mL.\n"}, "therapeutic_agents": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2975232&version=1.0", "source": "caDSR", "term": "Prior Therapy Regimen Text", "cde_version": 1.0, "cde_id": 2975232}, "description": "Text identification of the individual agent(s) used as part of a prior treatment regimen.\n"}, "initial_weight": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432605&version=1.0", "source": "caDSR", "term": "Tissue Sample Initial Weight Milligram Value", "cde_version": 1.0, "cde_id": 5432605}, "description": "Numeric value that represents the initial weight of the sample, measured in milligrams.\n"}, "sequencing_center": {"description": "Name of the center that provided the sequence files.\n"}, "year_of_diagnosis": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2896960&version=1.0", "source": "caDSR", "term": "Year of initial pathologic diagnosis", "cde_version": 1.0, "cde_id": 2896960}, "description": "Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer.\n"}, "size_selection_range": {"description": "Range of size selection.\n"}, "library_name": {"description": "Name of the library.\n"}, "residual_disease": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2608702&version=1.0", "source": "caDSR", "term": "Surgical Margin Resection Status", "cde_version": 1.0, "cde_id": 2608702}, "description": "Text terms to describe the status of a tissue margin following surgical resection.\n"}, "tumor_code_id": {"description": "BCR-defined id code for the tumor sample.\n"}, "height": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=649&version=4.1", "source": "caDSR", "term": "Patient Height Measurement", "cde_version": 4.1, "cde_id": 649}, "description": "The height of the patient in centimeters.\n"}, "qc_metric_state": {"termDef": {"term_url": "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/", "source": "FastQC", "term": "QC Metric State", "cde_version": null, "cde_id": null}, "description": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.\n"}, "smoking_intensity": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2955385&version=1.0", "source": "caDSR", "term": "Person Cigarette Smoking History Pack Year Value", "cde_version": 1.0, "cde_id": 2955385}, "description": "Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20\n"}, "percent_necrosis": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841237&version=1.0", "source": "caDSR", "term": "Malignant Neoplasm Necrosis Percentage Value", "cde_version": 1.0, "cde_id": 2841237}, "description": "Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.\n"}, "ann_arbor_clinical_stage": {"termDef": {"term_url": null, "source": null, "term": "Ann Arbor Clinical Stage", "cde_version": null, "cde_id": null}, "description": "The classification of the clinically confirmed anatomic disease extent of lymphoma (Hodgkin's and Non-Hodgkins) based on the Ann Arbor Staging System.\n"}, "treatment_outcome": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102383&version=1.0", "source": "caDSR", "term": "Treatment Outcome Type", "cde_version": 1.0, "cde_id": 5102383}, "description": "Text term that describes the patient\u00bfs final outcome after the treatment was administered.\n"}, "perineural_invasion_present": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64181&version=3.0", "source": "caDSR", "term": "Tumor Perineural Invasion Ind", "cde_version": 3.0, "cde_id": 64181}, "description": "a yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.\n"}, "platform": {"description": "Name of the platform used to obtain data.\n"}, "ajcc_clinical_t": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440328&version=1.0", "source": "caDSR", "term": "Neoplasm American Joint Committee on Cancer Clinical Primary Tumor T Stage", "cde_version": 1.0, "cde_id": 3440328}, "description": "Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.\n"}, "colon_polyps_history": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3107197&version=1.0", "source": "caDSR", "term": "Colon Carcinoma Polyp Occurrence Indicator", "cde_version": 1.0, "cde_id": 3107197}, "description": "Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).\n"}, "ajcc_clinical_m": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440331&version=1.0", "source": "caDSR", "term": "Neoplasm American Joint Committee on Cancer Clinical Distant Metastasis M Stage", "cde_version": 1.0, "cde_id": 3440331}, "description": "Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.\n"}, "ajcc_clinical_n": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440330&version=1.0", "source": "caDSR", "term": "Neoplasm American Joint Committee on Cancer Clinical Regional Lymph Node N Stage", "cde_version": 1.0, "cde_id": 3440330}, "description": "Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.\n"}, "progesterone_receptor_result_ihc": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2957357&version=2.0", "source": "caDSR", "term": "Breast Carcinoma Progesterone Receptor Status", "cde_version": 2.0, "cde_id": 2957357}, "description": "Text term to represent the overall result of Progresterone Receptor (PR) testing.\n"}, "library_selection": {"description": "Library Selection Method\n"}, "a260_a280_ratio": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432595&version=1.0", "source": "caDSR", "term": "Nucleic Acid Absorbance at 260 And Absorbance at 280 DNA Purity Ratio Value", "cde_version": 1.0, "cde_id": 5432595}, "description": "Numeric value that represents the sample ratio of nucleic acid absorbance at 260 nm and 280 nm, used to determine a measure of DNA purity.\n"}, "diagnosis_pathologically_confirmed": {"termDef": {"term_url": null, "source": null, "term": "Post-Diagnostic Pathology Review Confirmation", "cde_version": null, "cde_id": null}, "description": "The histologic description of tissue or cells confirmed by a pathology review of frozen or formalin fixed slide(s) completed after the diagnostic pathology review of the tumor sample used to extract analyte(s).\n"}, "treatment_intent_type": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2793511&version=1.0", "source": "caDSR", "term": "Treatment Regimen Intent Type", "cde_version": 1.0, "cde_id": 2793511}, "description": "Text term to identify the reason for the administration of a treatment regimen. [Manually-curated]\n"}, "cea_level_preoperative": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2716510&version=1.0", "source": "caDSR", "term": "Preoperative Carcinoembryonic Antigen Result Value", "cde_version": 1.0, "cde_id": 2716510}, "description": "Numeric value of the Carcinoembryonic antigen or CEA at the time before surgery. [Manually- curated]\n"}, "aliquot_volume": {"termDef": {"term_url": null, "source": null, "term": "Biospecimen Aliquot Volume", "cde_version": null, "cde_id": null}, "description": "The volume in microliters (ml) of the aliquot(s) derived from the analyte(s) shipped for sequencing and characterization.\n"}, "shortest_dimension": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432603&version=1.0", "source": "caDSR", "term": "Tissue Sample Short Dimension Millimeter Measurement", "cde_version": 1.0, "cde_id": 5432603}, "description": "Numeric value that represents the shortest dimension of the sample, measured in millimeters.\n"}, "biomarker_name": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5473&version=2.31", "source": "caDSR", "term": "Biomarker Name", "cde_version": 11.0, "cde_id": 5473}, "description": "The name of the biomarker being tested for this specimen and set of test results.\n"}, "bmi": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4973892&version=1.0", "source": "caDSR", "term": "Body Mass Index (BMI)", "cde_version": 1.0, "cde_id": 4973892}, "description": "The body mass divided by the square of the body height expressed in units of kg/m^2.\n"}, "tobacco_smoking_onset_year": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2228604&version=1.0", "source": "caDSR", "term": "Started Smoking Year", "cde_version": 1.0, "cde_id": 2228604}, "description": "The year in which the participant began smoking.\n"}, "progression_or_recurrence": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3121376&version=1.0", "source": "caDSR", "term": "New Neoplasm Event Post Initial Therapy Indicator", "cde_version": 1.0, "cde_id": 3121376}, "description": "Yes/No/Unknown indicator to identify whether a patient has had a new tumor event after initial treatment.\n"}, "days_to_new_event": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3392464&version=1.0", "source": "caDSR", "term": "New Tumor Event Less Initial Pathologic Diagnosis Date Calculated Day Value", "cde_version": 1.0, "cde_id": 3392464}, "description": "Time interval from the date of new tumor event including progression, recurrence and new primary malignacies to the date of initial pathologic diagnosis, represented as a calculated number of days.\n"}, "total_sequences": {"termDef": {"term_url": "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/1%20Basic%20Statistics.html", "source": "FastQC", "term": "Total Sequences", "cde_version": null, "cde_id": null}, "description": "A count of the total number of sequences processed.\n"}, "days_to_treatment_end": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102431&version=1.0", "source": "caDSR", "term": "Treatment End Subtract First Pathologic Diagnosis Day Calculation Value", "cde_version": 1.0, "cde_id": 5102431}, "description": "Time interval from the date of the initial pathologic diagnosis to the date of treatment end, represented as a calculated number of days.\n"}, "data_file_error_type": {"description": "Type of error for the data file object.\n"}, "ajcc_pathologic_stage": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3203222&version=1.0", "source": "caDSR", "term": "Neoplasm Disease Stage American Joint Committee on Cancer Code", "cde_version": 1.0, "cde_id": 3203222}, "description": "The extent of a cancer, especially whether the disease has spread from the original site to other parts of the body based on AJCC staging criteria.\n"}, "spectrophotometer_method": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008378&version=1.0", "source": "caDSR", "term": "Purification Nucleic Acid Solution Concentration Determination Method Type", "cde_version": 1.0, "cde_id": 3008378}, "description": "Name of the method used to determine the concentration of purified nucleic acid within a solution.\n"}, "burkitt_lymphoma_clinical_variant": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3770421&version=1.0", "source": "caDSR", "term": "Burkitt Lymphoma Clinical Variant Type", "cde_version": 1.0, "cde_id": 3770421}, "description": "Burkitt's lymphoma categorization based on clinical features that differ from other forms of the same disease.\n"}, "tumor_stage": {"termDef": {"term_url": "https://ncit.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=NCI%20Thesaurus&code=C16899", "source": "NCIt", "term": "Tumor Stage", "cde_version": null, "cde_id": "C16899"}, "description": "The extent of a cancer in the body. Staging is usually based on the size of the tumor, whether lymph nodes contain cancer, and whether the cancer has spread from the original site to other parts of the body. The accepted values for tumor_stage depend on the tumor site, type, and accepted staging system. These items should accompany the tumor_stage value as associated metadata.\n"}, "analyte_volume": {"termDef": {"term_url": null, "source": null, "term": "Biospecimen Analyte Volume", "cde_version": null, "cde_id": null}, "description": "The volume in microliters (ml) of the analyte(s) derived from the analyte(s) shipped for sequencing and characterization.\n"}, "md5sum": {"description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint.\n"}, "fev1_ref_pre_bronch_percent": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302947&version=1.0", "source": "caDSR", "term": "Pre Bronchodilator Lung Forced Expiratory Volume 1 Test Lab Percentage Value", "cde_version": 1.0, "cde_id": 3302947}, "description": "The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second pre-bronchodilator.\n"}, "includes_spike_ins": {"description": "Spike-in included?\n"}, "days_to_collection": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008340&version=1.0", "source": "caDSR", "term": "Biospecimen Collection Date Less Initial Pathologic Diagnosis Date Calculated Day Value", "cde_version": 1.0, "cde_id": 3008340}, "description": "Time interval from the date of biospecimen collection to the date of initial pathologic diagnosis, represented as a calculated number of days.\n"}, "library_preparation_kit_catalog_number": {"description": "Catalog of Library Preparation Kit\n"}, "experiment_name": {"description": "Submitter-defined name for the experiment.\n"}, "data_category": {"description": "Broad categorization of the contents of the data file.\n"}, "target_capture_kit_catalog_number": {"description": "Catalog of Target Capture Kit.\n"}, "year_of_death": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897030&version=1.0", "source": "caDSR", "term": "Year Death Number", "cde_version": 1.0, "cde_id": 2897030}, "description": "Numeric value to represent the year of the death of an individual.\n"}, "percent_tumor_nuclei": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841225&version=1.0", "source": "caDSR", "term": "Malignant Neoplasm Neoplasm Nucleus Percentage Cell Value", "cde_version": 1.0, "cde_id": 2841225}, "description": "Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.\n"}, "classification_of_tumor": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3288124&version=1.0", "source": "caDSR", "term": "Tumor Tissue Disease Description Type", "cde_version": 1.0, "cde_id": 3288124}, "description": "Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.\n"}, "last_known_disease_status": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2759550&version=1.0", "source": "caDSR", "term": "Person Last Known Neoplasm Status", "cde_version": 1.0, "cde_id": 5424231}, "description": "Text term that describes the last known state or condition of an individual's neoplasm.\n"}, "time_between_excision_and_freezing": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432612&version=1.0", "source": "caDSR", "term": "Tissue Sample Excision and Freezing Elapsed Minute Time", "cde_version": 1.0, "cde_id": 5432612}, "description": "Numeric representation of the elapsed time between the excision and freezing of the sample, measured in minutes.\n"}, "biospecimen_anatomic_site": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4742851&version=1.0", "source": "caDSR", "term": "Submitted Tumor Sample Primary Anatomic Site", "cde_version": 1.0, "cde_id": 4742851}, "description": "Text term that represents the name of the primary disease site of the submitted tumor sample.\n"}, "file_name": {"description": "The name (or part of a name) of a file (of any type).\n"}, "years_smoked": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3137957&version=1.0", "source": "caDSR", "term": "Person Smoking Duration Year Count", "cde_version": 1.0, "cde_id": 3137957}, "description": "Numeric value (or unknown) to represent the number of years a person has been smoking.\n"}, "primary_diagnosis": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3081934&version=3.0", "source": "caDSR", "term": "Neoplasm Histologic Type Name", "cde_version": 3.0, "cde_id": 3081934}, "description": "Text term for the structural pattern of cancer cells used to define a microscopic diagnosis.\n"}, "microsatellite_instability_abnormal": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3123142&version=1.0", "source": "caDSR", "term": "Microsatellite Instability Occurrence Indicator", "cde_version": 1.0, "cde_id": 3123142}, "description": "The yes/no indicator to signify the status of a tumor for microsatellite instability.\n"}, "adapter_name": {"description": "Name of the sequencing adapter.\n"}, "fev1_ref_post_bronch_percent": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302948&version=1.0", "source": "caDSR", "term": "Post Bronchodilator Lung Forced Expiratory Volume 1 Test Lab Percentage Value", "cde_version": 1.0, "cde_id": 3302948}, "description": "The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second post-bronchodilator.\n"}, "file_size": {"description": "The size of the data file (object) in bytes.\n"}, "concentration": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432594&version=1.0", "source": "caDSR", "term": "Biospecimen Analyte or Aliquot Extracted Concentration Milligram per Milliliter Value", "cde_version": 1.0, "cde_id": 5432594}, "description": "Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter.\n"}, "library_preparation_kit_version": {"description": "Version of Library Preparation Kit\n"}, "id": "_terms", "ethnicity": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2192217&version=2.0", "source": "caDSR", "term": "Ethnic Group Category Text", "cde_version": 2.0, "cde_id": 2192217}, "description": "An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.\n"}, "is_ffpe": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4170557&version=1.0", "source": "caDSR", "term": "Specimen Processing Formalin Fixed Paraffin Embedded Tissue Indicator", "cde_version": 1.0, "cde_id": 4170557}, "description": "Indicator to signify whether or not the tissue sample was fixed in formalin and embedded in paraffin (FFPE).\n"}, "dlco_ref_predictive_percent": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2180255&version=1.0", "source": "caDSR", "term": "Lung Carbon Monoxide Diffusing Capability Test Assessment Predictive Value Percentage Value", "cde_version": 1.0, "cde_id": 2180255}, "description": "The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide detected in a patient's lungs.\n"}, "read_length": {"description": "The length of the reads.\n"}, "vascular_invasion_present": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64358&version=3.0", "source": "caDSR", "term": "Tumor Vascular Invasion Ind-3", "cde_version": 3.0, "cde_id": 64358}, "description": "The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.\n"}, "tumor_descriptor": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3288124&version=1.0", "source": "caDSR", "term": "Tumor Tissue Disease Description Type", "cde_version": 1.0, "cde_id": 3288124}, "description": "Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.\n"}, "analyte_quantity": {"termDef": {"term_url": null, "source": null, "term": "Biospecimen Analyte Quantity", "cde_version": null, "cde_id": null}, "description": "The quantity in micrograms (ug) of the analyte(s) derived from the analyte(s) shipped for sequencing and characterization.\n"}, "new_event_anatomic_site": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3108271&version=2.0", "source": "caDSR", "term": "New Neoplasm Event Occurrence Anatomic Site", "cde_version": 2.0, "cde_id": 3108271}, "description": "Text term to specify the anatomic location of the return of tumor after treatment.\n"}, "relative_with_cancer_history": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3901752&version=1.0", "source": "caDSR", "term": "Other Cancer Biological Relative History Indicator", "cde_version": 1.0, "cde_id": 3901752}, "description": "Indicator to signify whether or not an individual's biological relative has been diagnosed with another type of cancer.\n"}, "section_location": {"description": "Tissue source of the slide.\n"}, "portion_number": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432711&version=1.0", "source": "caDSR", "term": "Biospecimen Portion Sequence Number", "cde_version": 1.0, "cde_id": 5432711}, "description": "Numeric value that represents the sequential number assigned to a portion of the sample.\n"}, "composition": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432591&version=1.0", "source": "caDSR", "term": "Biospecimen Cellular Composition Type", "cde_version": 1.0, "cde_id": 5432591}, "description": "Text term that represents the cellular composition of the sample.\n"}, "treatment_or_therapy": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4231463&version=1.0", "source": "caDSR", "term": "Therapeutic Procedure Prior Specimen Collection Administered Yes No Unknown Not Applicable Indicator", "cde_version": 1.0, "cde_id": 4231463}, "description": "A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.\n"}, "progesterone_receptor_percent_positive_ihc": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3128342&version=1.0", "source": "caDSR", "term": "Progesterone Receptor Level Cell Percentage Category", "cde_version": 1.0, "cde_id": 3128342}, "description": "Classification to represent Progesterone Receptor Positive results expressed as a percentage value.\n"}, "creation_datetime": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432592&version=1.0", "source": "caDSR", "term": "Biospecimen Portion Creation Seconds Date/Time", "cde_version": 1.0, "cde_id": 5432592}, "description": "The datetime of portion creation encoded as seconds from epoch.\n"}, "tumor_grade": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2785839&version=2.0", "source": "caDSR", "term": "Neoplasm Histologic Grade", "cde_version": 2.0, "cde_id": 2785839}, "description": "Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.\n"}, "target_capture_kit_target_region": {"description": "Target Capture Kit BED file.\n"}, "method_of_sample_procurement": {"termDef": {"term_url": null, "source": null, "term": "Method of Sample Procurement", "cde_version": null, "cde_id": null}, "description": "The method used to procure the sample used to extract analyte(s).\n"}, "percent_stromal_cells": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841241&version=1.0", "source": "caDSR", "term": "Malignant Neoplasm Stromal Cell Percentage Value", "cde_version": 1.0, "cde_id": 2841241}, "description": "Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc.\n"}, "normal_tumor_genotype_snp_match": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4588156&version=1.0", "source": "caDSR", "term": "Normal Tumor Genotype Match Indicator", "cde_version": 1.0, "cde_id": 4588156}, "description": "Text term that represents whether or not the genotype of the normal tumor matches or if the data is not available.\n"}, "year_of_birth": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2896954&version=1.0", "source": "caDSR", "term": "Year Birth Date Number", "cde_version": 1.0, "cde_id": 2896954}, "description": "Numeric value to represent the calendar year in which an individual was born.\n"}, "tissue_type": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432687&version=1.0", "source": "caDSR", "term": "Tissue Sample Description Type", "cde_version": 1.0, "cde_id": 5432687}, "description": "Text term that represents a description of the kind of tissue collected with respect to disease status or proximity to tumor tissue.\n"}, "days_to_birth": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008233&version=1.0", "source": "caDSR", "term": "Person Birth Date Less Initial Pathologic Diagnosis Date Calculated Day Value", "cde_version": 1.0, "cde_id": 3008233}, "description": "Time interval from a person's date of birth to the date of initial pathologic diagnosis, represented as a calculated negative number of days.\n"}, "hpv_status": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2230033&version=1.0", "source": "caDSR", "term": "Oncogenic Human Papillomavirus Result Type", "cde_version": 1.0, "cde_id": 2230033}, "description": "The findings of the oncogenic HPV.\n"}, "treatment_anatomic_site": {"termDef": {"term_url": null, "source": null, "term": "Treatment Anatomic Site", "cde_version": null, "cde_id": null}, "description": "The anatomic site or field targeted by a treatment regimen or single agent therapy.\n"}, "percent_neutrophil_infiltration": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841267&version=1.0", "source": "caDSR", "term": "Malignant Neoplasm Neutrophil Infiltration Percentage Cell Value", "cde_version": 1.0, "cde_id": 2841267}, "description": "Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.\n"}, "read_group_name": {"description": "The name of the read group.\n"}, "sample_type": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3111302&version=2.0", "source": "caDSR", "term": "Specimen Type Collection Biospecimen Type", "cde_version": 2.0, "cde_id": 3111302}, "description": "Text term to describe the source of a biospecimen used for a laboratory test.\n"}, "new_event_type": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3119721&version=1.0", "source": "caDSR", "term": "New Neoplasm Event Type", "cde_version": 1.0, "cde_id": 3119721}, "description": "Text term to identify a new tumor event.\n"}, "target_capture_kit_vendor": {"description": "Vendor of Target Capture Kit.\n"}, "ldh_normal_range_upper": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2597015&version=1.0", "source": "caDSR", "term": "Laboratory Procedure Lactate Dehydrogenase Result Upper Limit of Normal Value", "cde_version": 1.0, "cde_id": 2597015}, "description": "The top value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for lactate dehydrogenase (units not specified).\n"}, "well_number": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432613&version=1.0", "source": "caDSR", "term": "Biospecimen Analyte or Aliquot Plate Well Number", "cde_version": 1.0, "cde_id": 5432613}, "description": "Numeric value that represents the the well location within a plate for the analyte or aliquot from the sample.\n"}, "instrument_model": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432604&version=1.0", "source": "caDSR", "term": "Tissue Sample Intermediate Dimension Millimeter Measurement", "cde_version": 1.0, "cde_id": 5432604}, "description": "Numeric value that represents the sample dimension that is greater than the shortest dimension and less than the longest dimension, measured in millimeters.\n"}, "workflow_type": {"description": "Generic name for the workflow used to analyze a data set.\n"}, "site_of_resection_or_biopsy": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3226281&version=1.0", "source": "caDSR", "term": "International Classification of Diseases for Oncology, Third Edition ICD-O-3 Site Code", "cde_version": 1.0, "cde_id": 3226281}, "description": "The third edition of the International Classification of Diseases for Oncology, published in 2000, used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The description of an anatomical region or of a body part. Named locations of, or within, the body. A system of numbered categories for representation of data.\n"}, "longest_dimension": {"termDef": {"term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432602&version=1.0", "source": "caDSR", "term": "Tissue Sample Longest Dimension Millimeter Measurement", "cde_version": 1.0, "cde_id": 5432602}, "description": "Numeric value that represents the longest dimension of the sample, measured in millimeters.\n"}}, "experimental_metadata.yaml": {"description": "Data file containing the metadata for the experiment performed.\n", "links": [{"backref": "experiment_metadata_files", "name": "experiments", "multiplicity": "many_to_many", "required": false, "target_type": "experiment", "label": "derived_from"}], "uniqueKeys": [["id"], ["project_id", "submitter_id"]], "validators": null, "id": "experimental_metadata", "$schema": "http://json-schema.org/draft-04/schema#", "properties": {"experiments": {"$ref": "_definitions.yaml#/to_one"}, "data_category": {"term": {"$ref": "_terms.yaml#/data_category"}, "type": ["string"]}, "data_type": {"term": {"$ref": "_terms.yaml#/data_type"}, "enum": ["Experimental Metadata"]}, "type": {"enum": ["experimental_metadata"]}, "data_format": {"term": {"$ref": "_terms.yaml#/data_format"}, "type": ["string"]}, "$ref": "_definitions.yaml#/data_file_properties"}, "category": "metadata_file", "title": "Experimental Metadata", "systemProperties": ["id", "project_id", "created_datetime", "updated_datetime", "state", "file_state", "error_type"], "required": ["submitter_id", "file_name", "file_size", "md5sum", "data_category", "data_type", "data_format"], "namespace": "http://gdc.nci.nih.gov", "submittable": true, "project": "*", "program": "*", "additionalProperties": false, "type": "object"}, "publication.yaml": {"description": "Publication for a project.", "links": [{"backref": "publications", "name": "projects", "multiplicity": "many_to_many", "required": true, "target_type": "project", "label": "refers_to"}], "uniqueKeys": [["id"], ["project_id", "submitter_id"]], "validators": null, "id": "publication", "$schema": "http://json-schema.org/draft-04/schema#", "properties": {"doi": {"type": "string"}, "updated_datetime": {"$ref": "_definitions.yaml#/datetime"}, "created_datetime": {"$ref": "_definitions.yaml#/datetime"}, "submitter_id": {"type": ["string", "null"]}, "state": {"$ref": "_definitions.yaml#/state"}, "pmid": {"type": "string"}, "project_id": {"type": "string"}, "type": {"enum": ["publication"]}, "id": {"systemAlias": "node_id", "$ref": "_definitions.yaml#/UUID"}, "projects": {"$ref": "_definitions.yaml#/to_many"}}, "category": "administrative", "title": "Publication", "systemProperties": ["id", "project_id", "state", "created_datetime", "updated_datetime"], "required": ["submitter_id", "projects"], "namespace": "http://gdc.nci.nih.gov", "submittable": true, "project": "*", "program": "*", "additionalProperties": false, "type": "object"}, "aliquot.yaml": {"description": "Pertaining to a portion of the whole; any one of two or more samples of something, of the same volume or weight.\n", "links": [{"backref": "aliquots", "name": "samples", "multiplicity": "many_to_many", "required": true, "target_type": "sample", "label": "derived_from"}], "uniqueKeys": [["id"], ["project_id", "submitter_id"]], "validators": [], "id": "aliquot", "$schema": "http://json-schema.org/draft-04/schema#", "properties": {"aliquot_quantity": {"term": {"$ref": "_terms.yaml#/aliquot_quantity"}, "type": "number"}, "aliquot_volume": {"term": {"$ref": "_terms.yaml#/aliquot_volume"}, "type": "number"}, "updated_datetime": {"$ref": "_definitions.yaml#/datetime"}, "created_datetime": {"$ref": "_definitions.yaml#/datetime"}, "analyte_type_id": {"term": {"$ref": "_terms.yaml#/analyte_type_id"}, "enum": ["D", "E", "G", "H", "R", "S", "T", "W", "X", "Y"]}, "analyte_type": {"term": {"$ref": "_terms.yaml#/analyte_type"}, "type": "string"}, "submitter_id": {"type": ["string", "null"], "description": "The legacy barcode used before prior to the use UUIDs. For TCGA this is bcraliquotbarcode.\n"}, "amount": {"term": {"$ref": "_terms.yaml#/amount"}, "type": "number"}, "state": {"$ref": "_definitions.yaml#/state"}, "samples": {"$ref": "_definitions.yaml#/to_one"}, "type": {"type": "string"}, "concentration": {"term": {"$ref": "_terms.yaml#/concentration"}, "type": "number"}, "project_id": {"$ref": "_definitions.yaml#/project_id"}, "source_center": {"term": {"$ref": "_terms.yaml#/source_center"}, "type": "string"}, "id": {"systemAlias": "node_id", "$ref": "_definitions.yaml#/UUID"}}, "category": "biospecimen", "title": "Aliquot", "systemProperties": ["id", "project_id", "state", "created_datetime", "updated_datetime"], "required": ["submitter_id", "samples"], "submittable": true, "project": "*", "program": "*", "additionalProperties": false, "type": "object", "constraints": null}, "sample.yaml": {"description": "Any material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes, including a sample obtained from a living organism or taken from the biological object after halting of all its life functions. Biospecimen can contain one or more components including but not limited to cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory products.\n", "links": [{"backref": "samples", "name": "cases", "multiplicity": "many_to_one", "required": true, "target_type": "case", "label": "derived_from"}, {"backref": "samples", "name": "diagnoses", "multiplicity": "many_to_one", "required": false, "target_type": "diagnosis", "label": "related_to"}], "uniqueKeys": [["id"], ["project_id", "submitter_id"]], "validators": null, "id": "sample", "$schema": "http://json-schema.org/draft-04/schema#", "properties": {"sample_type_id": {"term": {"$ref": "_terms.yaml#/sample_type_id"}, "enum": ["01", "02", "03", "04", "05", "06", "07", "08", "09", "10", "11", "12", "13", "14", "15", "16", "20", "40", "41", "42", "50", "60", "61", "99"]}, "updated_datetime": {"$ref": "_definitions.yaml#/datetime"}, "biospecimen_anatomic_site": {"term": {"$ref": "_terms.yaml#/biospecimen_anatomic_site"}, "enum": ["Abdomen", "Abdominal Wall", "Acetabulum", "Adenoid", "Adipose", "Adrenal", "Alveolar Ridge", "Amniotic Fluid", "Ampulla Of Vater", "Anal Sphincter", "Ankle", "Anorectum", "Antecubital Fossa", "Antrum", "Anus", "Aorta", "Aortic Body", "Appendix", "Aqueous Fluid", "Arm", "Artery", "Ascending Colon", "Ascending Colon Hepatic Flexure", "Auditory Canal", "Autonomic Nervous System", "Axilla", "Back", "Bile Duct", "Bladder", "Blood", "Blood Vessel", "Bone", "Bone Marrow", "Bowel", "Brain", "Brain Stem", "Breast", "Broad Ligament", "Bronchiole", "Bronchus", "Brow", "Buccal Cavity", "Buccal Mucosa", "Buttock", "Calf", "Capillary", "Cardia", "Carina", "Carotid Artery", "Carotid Body", "Cartilage", "Cecum", "Cell-Line", "Central Nervous System", "Cerebellum", "Cerebral Cortex", "Cerebrospinal Fluid", "Cerebrum", "Cervical Spine", "Cervix", "Chest", "Chest Wall", "Chin", "Clavicle", "Clitoris", "Colon", "Colon - Mucosa Only", "Common Duct", "Conjunctiva", "Connective Tissue", "Dermal", "Descending Colon", "Diaphragm", "Duodenum", "Ear", "Ear Canal", "Ear, Pinna (External)", "Effusion", "Elbow", "Endocrine Gland", "Epididymis", "Epidural Space", "Esophagogastric Junction", "Esophagus", "Esophagus - Mucosa Only", "Eye", "Fallopian Tube", "Femoral Artery", "Femoral Vein", "Femur", "Fibroblasts", "Fibula", "Finger", "Floor Of Mouth", "Fluid", "Foot", "Forearm", "Forehead", "Foreskin", "Frontal Cortex", "Frontal Lobe", "Fundus Of Stomach", "Gallbladder", "Ganglia", "Gastroesophageal Junction", "Gastrointestinal Tract", "Groin", "Gum", "Hand", "Hard Palate", "Head & Neck", "Head - Face Or Neck, Nos", "Heart", "Hepatic", "Hepatic Duct", "Hepatic Vein", "Hip", "Hippocampus", "Humerus", "Hypopharynx", "Ileum", "Ilium", "Index Finger", "Ischium", "Islet Cells", "Jaw", "Jejunum", "Joint", "Kidney", "Knee", "Lacrimal Gland", "Large Bowel", "Laryngopharynx", "Larynx", "Leg", "Leptomeninges", "Ligament", "Lip", "Liver", "Lumbar Spine", "Lung", "Lymph Node", "Lymph Node(s) Axilla", "Lymph Node(s) Cervical", "Lymph Node(s) Distant", "Lymph Node(s) Epitrochlear", "Lymph Node(s) Femoral", "Lymph Node(s) Hilar", "Lymph Node(s) Iliac-Common", "Lymph Node(s) Iliac-External", "Lymph Node(s) Inguinal", "Lymph Node(s) Internal Mammary", "Lymph Node(s) Mammary", "Lymph Node(s) Mesenteric", "Lymph Node(s) Occipital", "Lymph Node(s) Paraaortic", "Lymph Node(s) Parotid", "Lymph Node(s) Pelvic", "Lymph Node(s) Popliteal", "Lymph Node(s) Regional", "Lymph Node(s) Retroperitoneal", "Lymph Node(s) Scalene", "Lymph Node(s) Splenic", "Lymph Node(s) Subclavicular", "Lymph Node(s) Submandibular", "Lymph Node(s) Supraclavicular", "Lymph Nodes(s) Mediastinal", "Mandible", "Maxilla", "Mediastinal Soft Tissue", "Mediastinum", "Mesentery", "Mesothelium", "Middle Finger", "Mitochondria", "Muscle", "Nails", "Nasal Cavity", "Nasal Soft Tissue", "Nasopharynx", "Neck", "Nerve", "Nerve(s) Cranial", "Occipital Cortex", "Ocular Orbits", "Omentum", "Oral Cavity", "Oral Cavity - Mucosa Only", "Oropharynx", "Other", "Ovary", "Palate", "Pancreas", "Paraspinal Ganglion", "Parathyroid", "Parotid Gland", "Patella", "Pelvis", "Penis", "Pericardium", "Periorbital Soft Tissue", "Peritoneal Cavity", "Peritoneum", "Pharynx", "Pineal", "Pineal Gland", "Pituitary Gland", "Placenta", "Pleura", "Popliteal Fossa", "Prostate", "Pylorus", "Rectosigmoid Junction", "Rectum", "Retina", "Retro-Orbital Region", "Retroperitoneum", "Rib", "Ring Finger", "Round Ligament", "Sacrum", "Salivary Gland", "Scalp", "Scapula", "Sciatic Nerve", "Scrotum", "Seminal Vesicle", "Shoulder", "Sigmoid Colon", "Sinus", "Sinus(es), Maxillary", "Skeletal Muscle", "Skin", "Skull", "Small Bowel", "Small Bowel - Mucosa Only", "Small Finger", "Soft Tissue", "Spinal Column", "Spinal Cord", "Spleen", "Splenic Flexure", "Sternum", "Stomach", "Stomach - Mucosa Only", "Subcutaneous Tissue", "Synovium", "Temporal Cortex", "Tendon", "Testis", "Thigh", "Thoracic Spine", "Thorax", "Throat", "Thumb", "Thymus", "Thyroid", "Tibia", "Tongue", "Tonsil", "Tonsil (Pharyngeal)", "Trachea / Major Bronchi", "Transverse Colon", "Trunk", "Umbilical Cord", "Ureter", "Urethra", "Urinary Tract", "Uterus", "Uvula", "Vagina", "Vas Deferens", "Vein", "Venous", "Vertebra", "Vulva", "White Blood Cells", "Wrist", "Unknown", "Not Reported", "Not Allowed To Collect"]}, "oct_embedded": {"term": {"$ref": "_terms.yaml#/oct_embedded"}, "type": "string"}, "tumor_code_id": {"term": {"$ref": "_terms.yaml#/tumor_code_id"}, "enum": ["00", "01", "02", "03", "04", "10", "20", "21", "30", "40", "41", "50", "51", "52", "60", "61", "62", "63", "64", "65", "70", "71", "80", "81"]}, "submitter_id": {"type": ["string", "null"], "description": "The legacy barcode used before prior to the use UUIDs, varies by project. For TCGA this is bcrsamplebarcode.\n"}, "intermediate_dimension": {"terms": {"$ref": "_terms.yaml#/intermediate_dimension"}, "type": "string"}, "sample_volume": {"type": "number", "description": "The volume of the sample in mL."}, "id": {"systemAlias": "node_id", "$ref": "_definitions.yaml#/UUID"}, "is_ffpe": {"term": {"$ref": "_terms.yaml#/is_ffpe"}, "type": "boolean"}, "created_datetime": {"$ref": "_definitions.yaml#/datetime"}, "tumor_descriptor": {"term": {"$ref": "_terms.yaml#/tumor_descriptor"}, "enum": ["Metastatic", "Not Applicable", "Primary", "Recurrence", "Xenograft", "NOS", "Unknown", "Not Reported", "Not Allowed To Collect"], "description": "A description of the tumor from which the sample was derived."}, "sample_type": {"enum": ["Additional Metastatic", "Additional - New Primary", "Blood Derived Cancer - Bone Marrow, Post-treatment", "Blood Derived Cancer - Peripheral Blood, Post-treatment", "Blood Derived Normal", "Bone Marrow Normal", "Buccal Cell Normal", "Cell Line Derived Xenograft Tissue", "Cell Lines", "cfDNA", "Circulating Tumor Cell (CTC)", "Control Analyte", "Clinical", "Contrived", "ctDNA", "DNA", "EBV Immortalized Normal", "FFPE Recurrent", "FFPE Scrolls", "Fibroblasts from Bone Marrow Normal", "GenomePlex (Rubicon) Amplified DNA", "Granulocytes", "Human Tumor Original Cells", "Metastatic", "Mononuclear Cells from Bone Marrow Normal", "Primary Blood Derived Cancer - Peripheral Blood", "Recurrent Blood Derived Cancer - Peripheral Blood", "Pleural Effusion", "Primary Blood Derived Cancer - Bone Marrow", "Primary Tumor", "Primary Xenograft Tissue", "Post neo-adjuvant therapy", "Recurrent Blood Derived Cancer - Bone Marrow", "Recurrent Tumor", "Repli-G (Qiagen) DNA", "Repli-G X (Qiagen) DNA", "RNA", "Slides", "Solid Tissue Normal", "Total RNA", "Xenograft Tissue", "Unknown", "Not Reported", "Not Allowed To Collect"], "description": "Characterization of the sample as either clinical or contrived."}, "time_between_excision_and_freezing": {"term": {"$ref": "_terms.yaml#/time_between_excision_and_freezing"}, "type": "string"}, "state": {"$ref": "_definitions.yaml#/state"}, "diagnosis_pathologically_confirmed": {"term": {"ref": "_terms.yaml#/diagnosis_pathologically_confirmed"}, "enum": ["Yes", "No", "Unknown"]}, "project_id": {"type": "string"}, "current_weight": {"term": {"$ref": "_terms.yaml#/current_weight"}, "type": "number"}, "composition": {"term": {"$ref": "_terms.yaml#/composition"}, "enum": ["Buccal Cells", "Buffy Coat", "Bone Marrow Components", "Bone Marrow Components NOS", "Control Analyte", "Cell", "Circulating Tumor Cell (CTC)", "Derived Cell Line", "EBV Immortalized", "Fibroblasts from Bone Marrow Normal", "Granulocytes", "Human Original Cells", "Lymphocytes", "Mononuclear Cells from Bone Marrow Normal", "Peripheral Blood Components NOS", "Peripheral Blood Nucleated Cells", "Pleural Effusion", "Plasma", "Peripheral Whole Blood", "Serum", "Saliva", "Sputum", "Solid Tissue", "Whole Bone Marrow", "Unknown", "Not Reported", "Not Allowed To Collect"]}, "time_between_clamping_and_freezing": {"term": {"$ref": "_terms.yaml#/time_between_clamping_and_freezing"}, "type": "string"}, "shortest_dimension": {"term": {"$ref": "_terms.yaml#/shortest_dimension"}, "type": "string"}, "method_of_sample_procurement": {"term": {"$ref": "_terms.yaml#/method_of_sample_procurement"}, "enum": ["Abdomino-perineal Resection of Rectum", "Anterior Resection of Rectum", "Aspirate", "Biopsy", "Blood Draw", "Bone Marrow Aspirate", "Core Biopsy", "Cystectomy", "Endo Rectal Tumor Resection", "Endoscopic Biopsy", "Endoscopic Mucosal Resection (EMR)", "Enucleation", "Excisional Biopsy", "Fine Needle Aspiration", "Full Hysterectomy", "Gross Total Resection", "Hand Assisted Laparoscopic Radical Nephrectomy", "Hysterectomy NOS", "Incisional Biopsy", "Indeterminant", "Laparoscopic Biopsy", "Laparoscopic Partial Nephrectomy", "Laparoscopic Radical Nephrectomy", "Laparoscopic Radical Prostatectomy with Robotics", "Laparoscopic Radical Prostatectomy without Robotics", "Left Hemicolectomy", "Lobectomy", "Local Resection (Exoresection; wall resection)", "Lumpectomy", "Modified Radical Mastectomy", "Needle Biopsy", "Open Craniotomy", "Open Partial Nephrectomy", "Open Radical Nephrectomy", "Open Radical Prostatectomy", "Orchiectomy", "Other", "Other Surgical Resection", "Pan-Procto Colectomy", "Pneumonectomy", "Right Hemicolectomy", "Sigmoid Colectomy", "Simple Mastectomy", "Subtotal Resection", "Surgical Resection", "Thoracoscopic Biopsy", "Total Colectomy", "Total Mastectomy", "Transplant", "Transurethral resection (TURBT)", "Transverse Colectomy", "Tumor Resection", "Wedge Resection", "Unknown", "Not Reported", "Not Allowed To Collect"]}, "tumor_code": {"term": {"$ref": "_terms.yaml#/tumor_code"}, "enum": ["Non cancerous tissue", "Diffuse Large B-Cell Lymphoma (DLBCL)", "Lung Cancer (all types)", "Lung Adenocarcinoma", "Non-small Cell Lung Carcinoma (NSCLC)", "Colon Cancer (all types)", "Breast Cancer (all types)", "Cervical Cancer (all types)", "Anal Cancer (all types)", "Acute lymphoblastic leukemia (ALL)", "Acute myeloid leukemia (AML)", "Induction Failure AML (AML-IF)", "Neuroblastoma (NBL)", "Osteosarcoma (OS)", "Ewing sarcoma", "Wilms tumor (WT)", "Clear cell sarcoma of the kidney (CCSK)", "Rhabdoid tumor (kidney) (RT)", "CNS, ependymoma", "CNS, glioblastoma (GBM)", "CNS, rhabdoid tumor", "CNS, low grade glioma (LGG)", "CNS, medulloblastoma", "CNS, other", "NHL, anaplastic large cell lymphoma", "NHL, Burkitt lymphoma (BL)", "Rhabdomyosarcoma", "Soft tissue sarcoma, non-rhabdomyosarcoma", "Castration-Resistant Prostate Cancer (CRPC)", "Prostate Cancer", "Hepatocellular Carcinoma (HCC)"]}, "tissue_type": {"term": {"$ref": "_terms.yaml#/tissue_type"}, "enum": ["Tumor", "Normal", "Abnormal", "Peritumoral", "Contrived", "Unknown", "Not Reported", "Not Allowed To Collect"]}, "days_to_sample_procurement": {"term": {"$ref": "_terms.yaml#/days_to_sample_procurement"}, "type": "integer"}, "cases": {"$ref": "_definitions.yaml#/to_one"}, "freezing_method": {"term": {"$ref": "_terms.yaml#/freezing_method"}, "type": "string"}, "diagnoses": {"$ref": "_definitions.yaml#/to_one"}, "type": {"type": "string"}, "preservation_method": {"term": {"$ref": "_terms.yaml#/preservation_method"}, "enum": ["Cryopreserved", "FFPE", "Fresh", "OCT", "Snap Frozen", "Frozen", "Unknown", "Not Reported", "Not Allowed To Collect"]}, "days_to_collection": {"term": {"$ref": "_terms.yaml#/days_to_collection"}, "type": "integer"}, "initial_weight": {"term": {"$ref": "_terms.yaml#/initial_weight"}, "type": "number"}, "longest_dimension": {"terms": {"$ref": "_terms.yaml#/longest_dimension"}, "type": "string"}}, "category": "biospecimen", "title": "Sample", "systemProperties": ["id", "project_id", "state", "created_datetime", "updated_datetime"], "required": ["submitter_id", "cases"], "namespace": "http://gdc.nci.nih.gov", "submittable": true, "project": "*", "program": "*", "additionalProperties": false, "type": "object"}, "acknowledgement.yaml": {"description": "Acknowledgement of an individual involved in a project.", "links": [{"backref": "acknowledgements", "name": "projects", "multiplicity": "many_to_many", "required": true, "target_type": "project", "label": "contribute_to"}], "uniqueKeys": [["id"], ["project_id", "submitter_id"]], "validators": null, "id": "acknowledgement", "$schema": "http://json-schema.org/draft-04/schema#", "properties": {"updated_datetime": {"$ref": "_definitions.yaml#/datetime"}, "created_datetime": {"$ref": "_definitions.yaml#/datetime"}, "acknowledgee": {"type": "string", "description": "The indvidiual or group being acknowledged by the project."}, "submitter_id": {"type": ["string", "null"]}, "state": {"$ref": "_definitions.yaml#/state"}, "project_id": {"type": "string"}, "type": {"enum": ["acknowledgement"]}, "id": {"systemAlias": "node_id", "$ref": "_definitions.yaml#/UUID"}, "projects": {"$ref": "_definitions.yaml#/to_many"}}, "category": "administrative", "title": "Acknowledgement", "systemProperties": ["id", "project_id", "state", "created_datetime", "updated_datetime"], "required": ["submitter_id", "projects"], "namespace": "http://gdc.nci.nih.gov", "submittable": true, "project": "*", "program": "*", "additionalProperties": false, "type": "object"}, "submitted_copy_number.yaml": {"description": "Data file containing normalized copy number information from an aliquot.\n", "links": [{"exclusive": true, "required": true, "subgroup": [{"backref": "submitted_copy_number_files", "name": "aliquots", "multiplicity": "one_to_one", "required": false, "target_type": "aliquot", "label": "derived_from"}, {"backref": "submitted_copy_number_files", "name": "read_groups", "multiplicity": "many_to_many", "required": false, "target_type": "read_group", "label": "derived_from"}]}], "uniqueKeys": [["id"], ["project_id", "submitter_id"]], "validators": null, "id": "submitted_copy_number", "$schema": "http://json-schema.org/draft-04/schema#", "properties": {"read_groups": {"$ref": "_definitions.yaml#/to_many"}, "data_category": {"term": {"$ref": "_terms.yaml#/data_category"}, "type": "string"}, "data_type": {"term": {"$ref": "_terms.yaml#/data_type"}, "type": "string"}, "data_format": {"term": {"$ref": "_terms.yaml#/data_format"}, "type": "string"}, "aliquots": {"$ref": "_definitions.yaml#/to_one"}, "experimental_strategy": {"term": {"$ref": "_terms.yaml#/experimental_strategy"}, "type": "string"}, "type": {"enum": ["submitted_copy_number"]}, "$ref": "_definitions.yaml#/data_file_properties"}, "category": "data_file", "title": "Submitted Copy Number", "systemProperties": ["id", "project_id", "created_datetime", "updated_datetime", "state", "file_state", "error_type"], "required": ["submitter_id", "file_name", "file_size", "data_format", "md5sum", "data_category", "data_type", "experimental_strategy"], "namespace": "http://gdc.nci.nih.gov", "submittable": true, "project": "*", "program": "*", "additionalProperties": false, "type": "object"}, "family_history.yaml": {"description": "Record of a patient's background regarding cancer events of blood relatives.\n", "links": [{"backref": "family_histories", "name": "cases", "multiplicity": "many_to_one", "required": true, "target_type": "case", "label": "describes"}], "uniqueKeys": [["id"], ["project_id", "submitter_id"]], "validators": null, "id": "family_history", "$schema": "http://json-schema.org/draft-04/schema#", "properties": {"project_id": {"$ref": "_definitions.yaml#/project_id"}, "relative_with_cancer_history": {"term": {"$ref": "_terms.yaml#/relative_with_cancer_history"}, "enum": ["yes", "no", "unknown", "not reported"]}, "created_datetime": {"$ref": "_definitions.yaml#/datetime"}, "relationship_primary_diagnosis": {"term": {"$ref": "_terms.yaml#/primary_diagnosis"}, "type": "string"}, "updated_datetime": {"$ref": "_definitions.yaml#/datetime"}, "relationship_gender": {"term": {"$ref": "_terms.yaml#/gender"}, "enum": ["female", "male", "unknown", "unspecified", "not reported"]}, "state": {"$ref": "_definitions.yaml#/state"}, "id": {"systemAlias": "node_id", "$ref": "_definitions.yaml#/UUID"}, "relationship_type": {"term": {"$ref": "_terms.yaml#/relationship_type"}, "type": "string"}, "cases": {"$ref": "_definitions.yaml#/to_one"}, "submitter_id": {"type": ["string", "null"]}, "type": {"enum": ["family_history"]}, "relationship_age_at_diagnosis": {"term": {"$ref": "_terms.yaml#/relationship_age_at_diagnosis"}, "type": "number"}}, "category": "clinical", "title": "Family History", "systemProperties": ["id", "project_id", "state", "created_datetime", "updated_datetime"], "namespace": "http://gdc.nci.nih.gov", "submittable": true, "project": "*", "program": "*", "additionalProperties": false, "type": "object"}, "slide_image.yaml": {"description": "Data file containing image of a slide.\n", "links": [{"backref": "slide_images", "name": "slides", "multiplicity": "many_to_one", "required": true, "target_type": "slide", "label": "data_from"}], "uniqueKeys": [["id"], ["project_id", "submitter_id"]], "validators": null, "id": "slide_image", "$schema": "http://json-schema.org/draft-04/schema#", "properties": {"protocol_used": {"type": "string", "description": "Name or other identifier given to the protocol used during an IMC run."}, "cell_type": {"type": "string", "description": "The type of cell being imaged or otherwised analysed."}, "type": {"enum": ["slide_image"]}, "data_type": {"term": {"$ref": "_terms.yaml#/data_type"}, "enum": ["image", "Single Cell Image", "Raw IMC Data", "Single Channel IMC Image", "Antibody Panel Added"]}, "frame_identifier": {"type": "string", "description": "Name, number, or other identifier given to the frame of the slide from which this image was taken."}, "cell_identifier": {"type": "string", "description": "An alternative identifier for a given cell type."}, "cell_count": {"type": "integer", "description": "Count of the cell type being imaged or otherwise analysed."}, "data_format": {"term": {"$ref": "_terms.yaml#/data_format"}, "type": "string"}, "slides": {"$ref": "_definitions.yaml#/to_one"}, "data_category": {"term": {"$ref": "_terms.yaml#/data_category"}, "enum": ["Biospecimen", "Slide Image", "Mass Cytometry"]}, "run_name": {"type": "string", "description": "Name, number, or other identifier given to the run that generated this slide image."}, "experimental_strategy": {"enum": ["Diagnostic Slide", "Tissue Slide"], "description": "Classification of the slide type with respect to its experimental use."}, "panel_used": {"type": "string", "description": "Name or other identifier given to the panel used during an IMC run."}, "$ref": "_definitions.yaml#/data_file_properties"}, "category": "data_file", "title": "Slide Image", "systemProperties": ["id", "project_id", "created_datetime", "updated_datetime", "state", "file_state", "error_type"], "required": ["submitter_id", "file_name", "file_size", "md5sum", "data_category", "data_type", "data_format", "slides"], "namespace": "http://gdc.nci.nih.gov", "submittable": true, "project": "*", "program": "*", "additionalProperties": false, "type": "object"}, "read_group.yaml": {"description": "Sequencing reads from one lane of an NGS experiment.", "links": [{"backref": "read_groups", "name": "aliquots", "multiplicity": "many_to_one", "required": true, "target_type": "aliquot", "label": "derived_from"}], "uniqueKeys": [["id"], ["project_id", "submitter_id"]], "validators": null, "id": "read_group", "$schema": "http://json-schema.org/draft-04/schema#", "properties": {"library_name": {"term": {"$ref": "_terms.yaml#/library_name"}, "type": "string"}, "is_paired_end": {"term": {"$ref": "_terms.yaml#/is_paired_end"}, "type": "boolean"}, "size_selection_range": {"term": {"$ref": "_terms.yaml#/size_selection_range"}, "type": "string"}, "adapter_sequence": {"term": {"$ref": "_terms.yaml#/adapter_sequence"}, "type": "string"}, "library_strand": {"term": {"$ref": "_terms.yaml#/library_strand"}, "enum": ["Unstranded", "First_Stranded", "Second_Stranded"]}, "submitter_id": {"type": "string"}, "library_preparation_kit_name": {"term": {"$ref": "_terms.yaml#/library_preparation_kit_name"}, "type": "string"}, "adapter_name": {"term": {"$ref": "_terms.yaml#/adapter_name"}, "type": "string"}, "target_capture_kit_name": {"term": {"$ref": "_terms.yaml#/target_capture_kit_name"}, "type": "string"}, "includes_spike_ins": {"term": {"$ref": "_terms.yaml#/includes_spike_ins"}, "type": "boolean"}, "library_preparation_kit_version": {"term": {"$ref": "_terms.yaml#/library_preparation_kit_version"}, "type": "string"}, "id": {"$ref": "_definitions.yaml#/UUID"}, "spike_ins_concentration": {"term": {"$ref": "_terms.yaml#/spike_ins_concentration"}, "type": "string"}, "read_length": {"type": "integer"}, "sequencing_date": {"$ref": "_definitions.yaml#/datetime"}, "updated_datetime": {"$ref": "_definitions.yaml#/datetime"}, "spike_ins_fasta": {"term": {"$ref": "_terms.yaml#/spike_ins_fasta"}, "type": "string"}, "to_trim_adapter_sequence": {"term": {"$ref": "_terms.yaml#/to_trim_adapter_sequence"}, "type": "boolean"}, "RIN": {"term": {"$ref": "_terms.yaml#/RIN"}, "type": "number"}, "platform": {"term": {"$ref": "_terms.yaml#/platform"}, "enum": ["Illumina", "SOLiD", "LS454", "Ion Torrent", "Complete Genomics", "PacBio", "Other"]}, "state": {"$ref": "_definitions.yaml#/state"}, "barcoding_applied": {"type": "boolean", "description": "True/False: was barcoding applied?"}, "library_selection": {"term": {"$ref": "_terms.yaml#/library_selection"}, "enum": ["Hybrid_Selection", "PCR", "Affinity_Enrichment", "Poly-T_Enrichment", "RNA_Depletion", "Other"]}, "library_strategy": {"term": {"$ref": "_terms.yaml#/library_strategy"}, "enum": ["WGS", "WXS", "RNA-Seq", "ChIP-Seq", "miRNA-Seq", "Bisulfite-Seq", "Validation", "Amplicon", "Other"]}, "library_preparation_kit_catalog_number": {"term": {"$ref": "_terms.yaml#/library_preparation_kit_catalog_number"}, "type": "string"}, "sequencing_center": {"term": {"$ref": "_terms.yaml#/sequencing_center"}, "type": "string"}, "target_capture_kit_target_region": {"term": {"$ref": "_terms.yaml#/target_capture_kit_target_region"}, "type": "string"}, "target_capture_kit_version": {"term": {"$ref": "_terms.yaml#/target_capture_kit_version"}, "type": "string"}, "aliquots": {"$ref": "_definitions.yaml#/to_one"}, "read_group_name": {"type": "string", "description": "Read Group Name"}, "library_preparation_kit_vendor": {"term": {"$ref": "_terms.yaml#/library_preparation_kit_vendor"}, "type": "string"}, "project_id": {"$ref": "_definitions.yaml#/project_id"}, "type": {"enum": ["read_group"]}, "target_capture_kit_catalog_number": {"term": {"$ref": "_terms.yaml#/target_capture_kit_catalog_number"}, "type": "string"}, "instrument_model": {"enum": ["454 GS FLX Titanium", "AB SOLiD 4", "AB SOLiD 2", "AB SOLiD 3", "Complete Genomics", "Illumina HiSeq X Ten", "Illumina HiSeq X Five", "Illumina Genome Analyzer II", "Illumina Genome Analyzer IIx", "Illumina HiSeq 2000", "Illumina HiSeq 2500", "Illumina HiSeq 4000", "Illumina MiSeq", "Illumina NextSeq", "Ion Torrent PGM", "Ion Torrent Proton", "PacBio RS", "Ion S5 XL System, Ion 530 Chip", "Other"], "terms": {"$ref": "_terms.yaml#/instrument_model"}}, "base_caller_name": {"term": {"$ref": "_terms.yaml#/base_caller_name"}, "type": "string"}, "created_datetime": {"$ref": "_definitions.yaml#/datetime"}, "experiment_name": {"term": {"$ref": "_terms.yaml#/experiment_name"}, "type": "string"}, "flow_cell_barcode": {"term": {"$ref": "_terms.yaml#/flow_cell_barcode"}, "type": "string"}, "target_capture_kit_vendor": {"term": {"$ref": "_terms.yaml#/target_capture_kit_vendor"}, "type": "string"}, "base_caller_version": {"term": {"$ref": "_terms.yaml#/base_caller_version"}, "type": "string"}}, "category": "biospecimen", "title": "Read Group", "systemProperties": ["id", "project_id", "created_datetime", "updated_datetime", "state"], "required": ["type", "submitter_id", "aliquots"], "namespace": "http://gdc.nci.nih.gov", "submittable": true, "project": "*", "program": "*", "additionalProperties": false, "type": "object"}, "exposure.yaml": {"description": "Clinically relevant patient information not immediately resulting from genetic predispositions.\n", "links": [{"backref": "exposures", "name": "cases", "multiplicity": "many_to_one", "required": true, "target_type": "case", "label": "describes"}], "uniqueKeys": [["id"], ["project_id", "submitter_id"]], "preferred": ["cigarettes_per_day", "years_smoked"], "validators": null, "id": "exposure", "$schema": "http://json-schema.org/draft-04/schema#", "properties": {"cigarettes_per_day": {"term": {"$ref": "_terms.yaml#/cigarettes_per_day"}, "type": "number"}, "weight": {"term": {"$ref": "_terms.yaml#/weight"}, "type": "number"}, "updated_datetime": {"$ref": "_definitions.yaml#/datetime"}, "alcohol_history": {"term": {"$ref": "_terms.yaml#/alcohol_history"}, "type": "string"}, "bmi": {"term": {"$ref": "_terms.yaml#/bmi"}, "type": "number"}, "years_smoked": {"term": {"$ref": "_terms.yaml#/years_smoked"}, "type": "number"}, "submitter_id": {"type": ["string", "null"]}, "tobacco_smoking_status": {"term": {"$ref": "_terms.yaml#/tobacco_smoking_status"}, "enum": [1, 2, 3, 4, 5, 6, 7, "Unknown", "Not Reported", "Not Allowed To Collect"]}, "cases": {"$ref": "_definitions.yaml#/to_one"}, "height": {"term": {"$ref": "_terms.yaml#/height"}, "type": "number"}, "id": {"systemAlias": "node_id", "$ref": "_definitions.yaml#/UUID"}, "pack_years_smoked": {"term": {"$ref": "_terms.yaml#/pack_years_smoked"}, "type": "number"}, "created_datetime": {"$ref": "_definitions.yaml#/datetime"}, "alcohol_intensity": {"term": {"$ref": "_terms.yaml#/alcohol_intensity"}, "type": "string"}, "state": {"$ref": "_definitions.yaml#/state"}, "tobacco_smoking_onset_year": {"term": {"$ref": "_terms.yaml#/tobacco_smoking_onset_year"}, "type": 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"her2_erbb2_percent_positive_ihc": {"term": {"$ref": "_terms.yaml#/her2_erbb2_percent_positive_ihc"}, "enum": ["<1%", "1-10%", "11-20%", "21-30%", "31-40%", "41-50%", "51-60%", "61-70%", "71-80%", "81-90%", "91-100%"]}, "created_datetime": {"$ref": "_definitions.yaml#/datetime"}, "ldh_normal_range_upper": {"term": {"$ref": "_terms.yaml#/ldh_normal_range_upper"}, "type": "number"}, "fev1_ref_pre_bronch_percent": {"term": {"$ref": "_terms.yaml#/fev1_ref_pre_bronch_percent"}, "type": "number"}, "her2_erbb2_result_fish": {"term": {"$ref": "_terms.yaml#/her2_erbb2_result_fish"}, "enum": ["Negative", "Not Performed", "Positive", "Unknown"]}, "estrogen_receptor_percent_positive_ihc": {"term": {"$ref": "_terms.yaml#/estrogen_receptor_percent_positive_ihc"}, "enum": ["<1%", "1-10%", "11-20%", "21-30%", "31-40%", "41-50%", "51-60%", "61-70%", "71-80%", "81-90%", "91-100%"]}, "biomarker_name": {"term": {"$ref": "_terms.yaml#/biomarker_name"}, "type": "string"}, "state": {"$ref": "_definitions.yaml#/state"}, "ldh_level_at_diagnosis": {"term": {"$ref": "_terms.yaml#/ldh_level_at_diagnosis"}, "type": "number"}, "microsatellite_instability_abnormal": {"term": {"$ref": "_terms.yaml#/microsatellite_instability_abnormal"}, "enum": ["Yes", "No", "Unknown"]}, "project_id": {"$ref": "_definitions.yaml#/project_id"}, "type": {"enum": ["clinical_test"]}, "progesterone_receptor_percent_positive_ihc": {"term": {"$ref": "_terms.yaml#/progesterone_receptor_percent_positive_ihc"}, "enum": ["<1%", "1-10%", "11-20%", "21-30%", "31-40%", "41-50%", "51-60%", "61-70%", "71-80%", "81-90%", "91-100%"]}}, "category": "clinical", "title": "Clinical Test", "systemProperties": ["id", "project_id", "created_datetime", "updated_datetime", "state"], "required": ["biomarker_name", "biomarker_result", "biomarker_test_method", "cases"], "namespace": "http://gdc.nci.nih.gov", "submittable": true, "project": "*", "program": "*", "additionalProperties": false, "type": "object"}, "_settings.yaml": {"enable_case_cache": false}, "case.yaml": {"description": "The collection of all data related to a specific subject in the context of a specific experiment. \n", "links": [{"backref": "cases", "name": "experiments", "multiplicity": "many_to_one", "required": true, "target_type": "experiment", "label": "member_of"}], "uniqueKeys": [["id"], ["project_id", "submitter_id"]], "validators": null, "id": "case", "$schema": "http://json-schema.org/draft-04/schema#", "properties": {"consent_codes": {"type": "array", "description": "", "items": {"type": "string"}}, "disease_type": {"type": "string", "description": "Name of the disease for the case."}, "updated_datetime": {"$ref": "_definitions.yaml#/datetime"}, "created_datetime": {"$ref": "_definitions.yaml#/datetime"}, "submitter_id": {"type": ["string", "null"]}, "state": {"$ref": "_definitions.yaml#/state"}, "experiments": {"$ref": "_definitions.yaml#/to_one"}, "primary_site": {"type": "string", "description": "Primary site for the case."}, "project_id": {"$ref": "_definitions.yaml#/project_id"}, "type": {"type": "string"}, "id": {"systemAlias": "node_id", "$ref": "_definitions.yaml#/UUID"}}, "category": "administrative", "title": "Case", "systemProperties": ["id", "project_id", "created_datetime", "updated_datetime", "state"], "required": ["submitter_id", "experiments"], "namespace": "http://gdc.nci.nih.gov", "submittable": true, "project": "*", "program": "*", "additionalProperties": false, "type": "object"}, "submitted_methylation.yaml": {"description": "DNA methylation data files contain information on raw and normalized signal intensities, detection confidence and calculated beta values for methylated and unmethylated probes. DNA methylation is an epigenetic mark which can be associated with transcriptional inactivity when located in promoter regions.", "links": [{"backref": "submitted_methylation_files", "name": "aliquots", "multiplicity": "many_to_one", "required": true, "target_type": "aliquot", "label": "data_from"}], "uniqueKeys": [["id"], ["project_id", "submitter_id"]], "validators": null, "id": "submitted_methylation", "$schema": "http://json-schema.org/draft-04/schema#", "properties": {"assay_method": {"enum": ["Methylation Array"]}, "data_category": {"term": {"$ref": "_terms.yaml#/data_category"}, "enum": ["Methylation Data"]}, "data_type": {"term": {"$ref": "_terms.yaml#/data_type"}, "enum": ["Methylation Intensity Values"]}, "assay_instrument_model": {"enum": ["Illumina Infinium HumanMethylation450", "Illumina Infinium HumanMethylation450K"]}, "data_format": {"term": {"$ref": "_terms.yaml#/data_format"}, "enum": ["IDAT"]}, "aliquots": {"$ref": "_definitions.yaml#/to_one"}, "$ref": "_definitions.yaml#/data_file_properties", "type": {"enum": ["submitted_methylation"]}, "assay_instrument": {"enum": ["Illumina"]}}, "category": "data_file", "title": "Submitted Methylation", "systemProperties": ["id", "project_id", "created_datetime", "updated_datetime", "state", "file_state", "error_type"], "required": ["submitter_id", "file_name", "file_size", "md5sum", "data_category", "data_type", "data_format", "aliquots"], "namespace": "https://www.bloodpac.org/", "submittable": true, "project": "*", "program": "*", "additionalProperties": false, "type": "object"}, "slide.yaml": {"description": "A digital image, microscopic or otherwise, of any sample, portion, or sub-part thereof. (GDC)\n", "links": [{"backref": "slides", "name": "samples", "multiplicity": "many_to_many", "required": true, "target_type": "sample", "label": "derived_from"}], "uniqueKeys": [["id"], ["project_id", "submitter_id"]], "validators": null, "id": "slide", "$schema": "http://json-schema.org/draft-04/schema#", "properties": {"percent_tumor_nuclei": {"term": {"$ref": "_terms.yaml#/percent_tumor_nuclei"}, "type": "number"}, "updated_datetime": {"$ref": "_definitions.yaml#/datetime"}, "percent_monocyte_infiltration": {"term": {"$ref": "_terms.yaml#/percent_monocyte_infiltration"}, "type": "number"}, "percent_lymphocyte_infiltration": {"term": {"$ref": "_terms.yaml#/percent_lymphocyte_infiltration"}, "type": "number"}, "submitter_id": {"type": ["string", "null"]}, "run_datetime": {"$ref": "_definitions.yaml#/datetime"}, "run_name": {"type": "string", "description": "Name, number, or other identifier given to this slide's run."}, "percent_necrosis": {"term": {"$ref": "_terms.yaml#/percent_necrosis"}, "type": "number"}, "percent_granulocyte_infiltration": {"term": {"$ref": "_terms.yaml#/percent_granulocyte_infiltration"}, "type": "number"}, "percent_inflam_infiltration": {"term": {"$ref": "_terms.yaml#/percent_inflam_infiltration"}, "type": "number"}, "percent_neutrophil_infiltration": {"term": {"$ref": "_terms.yaml#/percent_neutrophil_infiltration"}, "type": "number"}, "id": {"systemAlias": "node_id", "$ref": "_definitions.yaml#/UUID"}, "apoptotic_concentration": {"type": "number", "description": "The concentration, in cells/mL, of apoptotic cells in the slide blood."}, "percent_normal_cells": {"term": {"$ref": "_terms.yaml#/percent_normal_cells"}, "type": "number"}, "percent_stromal_cells": {"term": {"$ref": "_terms.yaml#/percent_stromal_cells"}, "type": "number"}, "ctc_concentration": {"type": "number", "description": "The concentration, in cells/mL, of traditional CTC cells (intact and enlarged cell and nucleus, cytokeratin positive, and CD45 negative) in the slide blood."}, "created_datetime": {"$ref": "_definitions.yaml#/datetime"}, "number_nucleated_cells": {"type": "integer", "description": "The total number of nucleated cells identified on the slide."}, "percent_eosinophil_infiltration": {"term": {"$ref": "_terms.yaml#/percent_eosinophil_infiltration"}, "type": "number"}, "slide_identifier": {"type": "string", "description": "Unique identifier given to the this slide."}, "state": {"$ref": "_definitions.yaml#/state"}, "methanol_added": {"type": "boolean", "description": "True/False indicator for if methanol was used in the slide preparation process."}, "section_location": {"term": {"$ref": "_terms.yaml#/section_location"}, "type": "string"}, "samples": {"$ref": "_definitions.yaml#/to_many"}, "ctc_low_concentration": {"type": "number", "description": "The concentration, in cells/mL, of CTC-low cells (those with low cytokeratin levels compared to traditional CTCs) in the slide blood."}, "number_proliferating_cells": {"term": {"$ref": "_terms.yaml#/number_proliferating_cells"}, "type": "integer"}, "project_id": {"$ref": "_definitions.yaml#/project_id"}, "type": {"type": "string"}, "ctc_small_concentration": {"type": "number", "description": "The concentration, in cells/mL, of CTC-small cells (those with a small nuclear and cellular size relative to traditional CTCs) in the slide blood."}, "percent_tumor_cells": {"term": {"$ref": "_terms.yaml#/percent_tumor_cells"}, "type": "number"}}, "category": "biospecimen", "title": "Slide", "systemProperties": ["id", "project_id", "state", "created_datetime", "updated_datetime"], "required": ["submitter_id", "samples"], "namespace": "http://gdc.nci.nih.gov", "submittable": true, "project": "*", "program": "*", "additionalProperties": false, "type": "object"}, "aligned_reads_index.yaml": {"description": "Data file containing the index for a set of aligned reads.", "links": [{"backref": "aligned_reads_indexes", "name": "submitted_aligned_reads_files", "multiplicity": "one_to_one", "required": true, "target_type": "submitted_aligned_reads", "label": "derived_from"}], "uniqueKeys": [["id"], ["project_id", "submitter_id"]], "validators": null, "id": "aligned_reads_index", "$schema": "http://json-schema.org/draft-04/schema#", "properties": {"submitted_aligned_reads_files": {"$ref": "_definitions.yaml#/to_one"}, "data_category": {"term": {"$ref": "_terms.yaml#/data_category"}, "enum": ["Sequencing Data", "Sequencing Reads", "Raw Sequencing Data"]}, "data_type": {"term": {"$ref": "_terms.yaml#/data_type"}, "enum": ["Aligned Reads Index"]}, "type": {"enum": ["aligned_reads_index"]}, "data_format": {"term": {"$ref": "_terms.yaml#/data_format"}, "enum": ["BAI"]}, "$ref": "_definitions.yaml#/data_file_properties"}, "category": "index_file", "title": "Aligned Reads Index", "systemProperties": ["id", "project_id", "created_datetime", "updated_datetime", "state", "file_state", "error_type"], "required": ["submitter_id", "file_name", "file_size", "md5sum", "data_category", "data_type", "data_format", "submitted_aligned_reads_files"], "namespace": "http://gdc.nci.nih.gov", "submittable": true, "project": "*", "program": "*", "additionalProperties": false, "type": "object"}, "program.yaml": {"description": "A broad framework of goals to be achieved. (NCIt C52647)\n", "links": [], "uniqueKeys": [["id"], ["name"]], "validators": null, "id": "program", "$schema": "http://json-schema.org/draft-04/schema#", "properties": {"dbgap_accession_number": {"type": "string", "description": "The dbgap accession number provided for the program."}, "type": {"type": "string"}, "id": {"systemAlias": "node_id", "$ref": "_definitions.yaml#/UUID"}, "name": {"type": "string", "description": "Full name/title of the program."}}, "category": "administrative", "title": "Program", "systemProperties": ["id"], "required": ["name", "dbgap_accession_number"], "submittable": false, "project": "*", "program": "*", "additionalProperties": false, "type": "object"}, "project.yaml": {"description": "Any specifically defined piece of work that is undertaken or attempted to meet a single requirement. (NCIt C47885)\n", "links": [{"backref": "projects", "name": "programs", "multiplicity": "many_to_one", "required": true, "target_type": "program", "label": "member_of"}], "uniqueKeys": [["id"], ["code"]], "validators": null, "id": "project", "$schema": "http://json-schema.org/draft-04/schema#", "properties": {"date_collected": {"type": "string", "description": "The date or date range in which the project data was collected."}, "code": {"type": "string", "description": "Unique identifier for the project."}, "intended_release_date": {"type": "string", "description": "Tracks a Project's intended release date.", "format": "date-time"}, "support_id": {"type": "string", "description": "The ID of the source providing support/grant resources."}, "releasable": {"default": false, "type": "boolean", "description": "A project can only be released by the user when `releasable` is true.\n"}, "released": {"default": false, "type": "boolean", "description": "To release a project is to tell the GDC to include all submitted\nentities in the next GDC index.\n"}, "availability_type": {"enum": ["Open", "Restricted"], "description": "Is the project open or restricted?"}, "dbgap_accession_number": {"type": "string", "description": "The dbgap accession number provided for the project."}, "id": {"systemAlias": "node_id", "description": "UUID for the project.", "$ref": "_definitions.yaml#/UUID"}, "name": {"type": "string", "description": "Display name/brief description for the project."}, "programs": {"description": "Indicates that the project is logically part of the indicated project.\n", "$ref": "_definitions.yaml#/to_one"}, "investigator_affiliation": {"type": "string", "description": "The investigator's affiliation with respect to a research institution."}, "availability_mechanism": {"type": "string", "description": "Mechanism by which the project will be made avilable."}, "support_source": {"type": "string", "description": "The name of source providing support/grant resources."}, "state": {"default": "open", "enum": ["open", "review", "submitted", "processing", "closed", "legacy"], "description": "The possible states a project can be in. All but `open` are\nequivalent to some type of locked state.\n"}, "investigator_name": {"type": "string", "description": "Name of the principal investigator for the project."}, "type": {"type": "string"}}, "category": "administrative", "title": "Project", "systemProperties": ["id", "state", "released", "releasable", "intended_release_date"], "required": ["code", "name", "programs"], "submittable": true, "project": "*", "program": "*", "additionalProperties": false, "type": "object", "constraints": null}, "read_group_qc.yaml": {"description": "GDC QC run metadata.", "links": [{"exclusive": true, "required": true, "subgroup": [{"backref": "read_group_qcs", "name": "submitted_aligned_reads_files", "multiplicity": "one_to_one", "required": false, "target_type": "submitted_aligned_reads", "label": "data_from"}, {"backref": "read_group_qcs", "name": "submitted_unaligned_reads_files", "multiplicity": "one_to_many", "required": false, "target_type": "submitted_unaligned_reads", "label": "data_from"}]}, {"backref": "read_group_qcs", "name": "read_groups", "multiplicity": "many_to_one", "required": true, "target_type": "read_group", "label": "generated_from"}], "uniqueKeys": [["id"], ["project_id", "submitter_id"]], "validators": null, "id": "read_group_qc", "$schema": "http://json-schema.org/draft-04/schema#", "properties": {"read_groups": {"$ref": "_definitions.yaml#/to_one"}, "percent_aligned": {"minimum": 0, "type": "integer", "description": "The percent of reads with at least one reported alignment.", "maximum": 100}, "adapter_content": {"$ref": "_definitions.yaml#/qc_metrics_state"}, "encoding": {"term": {"$ref": "_terms.yaml#/encoding"}, "type": "string"}, "per_base_sequence_quality": {"$ref": "_definitions.yaml#/qc_metrics_state"}, "sequence_duplication_levels": {"$ref": "_definitions.yaml#/qc_metrics_state"}, "submitted_aligned_reads_files": {"$ref": "_definitions.yaml#/to_one"}, "fastq_name": {"term": {"$ref": "_terms.yaml#/file_name"}, "type": "string"}, "basic_statistics": {"$ref": "_definitions.yaml#/qc_metrics_state"}, "per_base_sequence_content": {"$ref": "_definitions.yaml#/qc_metrics_state"}, "kmer_content": {"$ref": "_definitions.yaml#/qc_metrics_state"}, "percent_gc_content": {"term": {"$ref": "_terms.yaml#/percent_gc_content"}, "minimum": 0, "type": "integer", "maximum": 100}, "total_sequences": {"term": {"$ref": "_terms.yaml#/total_sequences"}, "type": "integer"}, "workflow_type": {"term": {"$ref": "_terms.yaml#/workflow_type"}, "enum": ["Read Group Quality Control"]}, "$ref": "_definitions.yaml#/workflow_properties", "total_aligned_reads": {"type": "integer", "description": "The total number of reads with at least one reported alignment."}, "sequence_length_distribution": {"$ref": "_definitions.yaml#/qc_metrics_state"}, "per_sequence_quality_score": {"$ref": "_definitions.yaml#/qc_metrics_state"}, "submitted_unaligned_reads_files": {"$ref": "_definitions.yaml#/to_many"}, "per_tile_sequence_quality": {"$ref": "_definitions.yaml#/qc_metrics_state"}, "per_sequence_gc_content": {"$ref": "_definitions.yaml#/qc_metrics_state"}, "per_base_n_content": {"$ref": "_definitions.yaml#/qc_metrics_state"}, "overrepresented_sequences": {"$ref": "_definitions.yaml#/qc_metrics_state"}, "type": {"enum": ["read_group_qc"]}}, "category": "notation", "title": "Read Group QC", "systemProperties": ["id", "project_id", "created_datetime", "updated_datetime", "state"], "required": ["submitter_id", "workflow_link", "type", "percent_gc_content", "encoding", "total_sequences", "basic_statistics", "per_base_sequence_quality", "per_tile_sequence_quality", "per_sequence_quality_score", "per_base_sequence_content", "per_sequence_gc_content", "per_base_n_content", "sequence_length_distribution", "sequence_duplication_levels", "overrepresented_sequences", "adapter_content", "kmer_content", "read_groups"], "namespace": "http://gdc.nci.nih.gov", "submittable": false, "project": "*", "program": "*", "additionalProperties": false, "type": "object"}, "keyword.yaml": {"description": "A keyword for a project.", "links": [{"backref": "keywords", "name": "projects", "multiplicity": "many_to_many", "required": true, "target_type": "project", "label": "describe"}], "uniqueKeys": [["id"], ["project_id", "submitter_id"]], "validators": null, "id": "keyword", "$schema": "http://json-schema.org/draft-04/schema#", "properties": {"updated_datetime": {"$ref": "_definitions.yaml#/datetime"}, "created_datetime": {"$ref": "_definitions.yaml#/datetime"}, "keyword_name": {"type": "string", "description": "The name of the keyword."}, "submitter_id": {"type": ["string", "null"]}, "state": {"$ref": "_definitions.yaml#/state"}, "project_id": {"type": "string"}, "type": {"enum": ["keyword"]}, "id": {"systemAlias": "node_id", "$ref": "_definitions.yaml#/UUID"}, "projects": {"$ref": "_definitions.yaml#/to_many"}}, "category": "administrative", "title": "Keyword", "systemProperties": ["id", "project_id", "state", "created_datetime", "updated_datetime"], "required": ["submitter_id", "projects"], "namespace": "http://gdc.nci.nih.gov", "submittable": true, "project": "*", "program": "*", "additionalProperties": false, "type": "object"}, "submitted_somatic_mutation.yaml": {"description": "Data file containing somatic mutation calls from a read group.\n", "links": [{"backref": "submitted_somatic_mutations", "name": "read_groups", "multiplicity": "many_to_many", "required": true, "target_type": "read_group", "label": "derived_from"}], "uniqueKeys": [["id"], ["project_id", "submitter_id"]], "validators": null, "id": "submitted_somatic_mutation", "$schema": "http://json-schema.org/draft-04/schema#", "properties": {"read_groups": {"$ref": "_definitions.yaml#/to_many"}, "data_type": {"term": {"$ref": "_terms.yaml#/data_type"}, "type": "string"}, "data_format": {"term": {"$ref": "_terms.yaml#/data_format"}, "type": "string"}, "data_category": {"term": {"$ref": "_terms.yaml#/data_category"}, "type": "string"}, "experimental_strategy": {"term": {"$ref": "_terms.yaml#/experimental_strategy"}, "type": "string"}, "type": {"enum": ["submitted_somatic_mutation"]}, "total_variants": {"type": "integer", "description": "The total number of variants detected carrying a base change difference from the reference genome."}, "$ref": "_definitions.yaml#/data_file_properties"}, "category": "data_file", "title": "Submitted Somatic Mutation", "systemProperties": ["id", "project_id", "created_datetime", "updated_datetime", "state", "file_state", "error_type"], "required": ["submitter_id", "file_name", "file_size", "data_format", "md5sum", "data_category", "data_type", "experimental_strategy", "read_groups"], "namespace": "http://gdc.nci.nih.gov", "submittable": true, "project": "*", "program": "*", "additionalProperties": false, "type": "object"}} | |||
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Describing the change since the file is minimized: in the Case node, in addition to the existing consent_codes property, i added properties consent_codes_ints, consent_codes_floats and consent_codes_bools
"properties": {
"consent_codes": {
"type": "array",
"items": {
"type": "string"
}
},
"consent_codes_ints": {
"type": "array",
"items": {
"type": "integer"
}
},
"consent_codes_floats": {
"type": "array",
"items": {
"type": "number"
}
},
"consent_codes_bools": {
"type": "array",
"items": {
"type": "boolean"
}
},
Pull Request Test Coverage Report for Build 8790316054Details
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I have looked over the code, and run tests locally and it looks great. However really the only thing I can't find is where the transform is actually called when sheepdog receives a submission? |
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@SpencerAxelrod |
Aha, I was searching the codebase for only DelimitedConverter and not TSVToJSONConverter, and now I am seeing it's use. I am approving |
SpencerAxelrod
approved these changes
Apr 23, 2024
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Link to JIRA ticket if there is one: https://ctds-planx.atlassian.net/browse/MIDRC-478
Addressing #371
New Features
Breaking Changes
Bug Fixes
Improvements
Dependency updates
Deployment changes