TCGA Clinical XML file annotation

Property name	Description
kind	The resource type.
aliquots[]	List of barcodes of aliquots taken from this participant.
clinical_data	The clinical data about the participant.
clinical_data.ParticipantBarcode	Participant barcode.
clinical_data.Project	Project name, .eg. “TCGA”.
clinical_data.Study	Tumor type abbreviation, e.g. “BRCA”.
clinical_data.age_at_initial_pathologic_diagnosis	Age at which a condition or disease was first diagnosed in years.
clinical_data.anatomic_neoplasm_subdivision	Text term to describe the spatial location, subdivisions and/or anatomic site name of a tumor.
clinical_data.batch_number	Groups samples by the batch they were processed in.
clinical_data.bcr	Biospecimen core resource, e.g. “Nationwide Children’s Hospital”, “Washington University”.
clinical_data.clinical_M	Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.
clinical_data.clinical_N	Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.
clinical_data.clinical_T	Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.
clinical_data.clinical_stage	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.
clinical_data.colorectal_cancer	Text term to signify whether a patient has been diagnosed with colorectal cancer.
clinical_data.country	Text to identify the name of the state, province, or country in which the sample was procured.
clinical_data.days_to_birth	Time interval from a person’s date of birth to the date of initial pathologic diagnosis, represented as a calculated number of days.
clinical_data.days_to_initial_pathologic_diagnosis	Numeric value to represent the day of an individual’s initial pathologic diagnosis of cancer.
clinical_data.days_to_last_followup	Time interval from the date of last followup to the date of initial pathologic diagnosis, represented as a calculated number of days.
clinical_data.ethnicity	The text for reporting information about ethnicity based on the Office of Management and Budget (OMB) categories.
clinical_data.frozen_specimen_anatomic_site	Text description of the origin and the anatomic site regarding the frozen biospecimen tumor tissue sample.
clinical_data.gender	Text designations that identify gender.
clinical_data.histological_type	Text term for the structural pattern of cancer cells used to define a microscopic diagnosis.
clinical_data.history_of_colon_polyps	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).
clinical_data.history_of_neoadjuvant_treatment	Text term to describe the patient’s history of neoadjuvant treatment and the kind of treament given prior to resection of the tumor.
clinical_data.history_of_prior_malignancy	Text term to describe the patient’s history of prior cancer diagnosis and the spatial location of any previous cancer occurrence.
clinical_data.hpv_calls	Results of HPV tests.
clinical_data.hpv_status	Current HPV status.
clinical_data.icd_10	The tenth version of the International Classification of Disease (ICD).
clinical_data.icd_o_3_histology	The third edition of the International Classification of Diseases for Oncology.
clinical_data.icd_o_3_site	The third edition of the International Classification of Diseases for Oncology.
clinical_data.lymphatic_invasion	A yes/no indicator to ask if malignant cells are present in small or thin-walled vessels suggesting lymphatic involvement.
clinical_data.lymphnodes_examined	The yes/no/unknown indicator whether a lymph node assessment was performed at the primary presentation of disease.
clinical_data.lymphovascular_invasion_present	The yes/no indicator to ask if large vessel (vascular) invasion or small, thin-walled (lymphatic) invasion was detected in a tumor specimen.
clinical_data.menopause_status	Text term to signify the status of a woman’s menopause, the permanent cessation of menses, usually defined by 6 to 12 months of amenorrhea.
clinical_data.mononucleotide_and_dinucleotide_marker_panel_analysis_status	Text result of microsatellite instability (MSI) testing at using a mononucleotide and dinucleotide microsatellite panel.
clinical_data.mononucleotide_marker_panel_analysis_status	Text result of microsatellite instability (MSI) testing using a mononucleotide microsatellite panel.
clinical_data.neoplasm_histologic_grade	Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.
clinical_data.new_tumor_event_after_initial_treatment	Yes/No/Unknown indicator to identify whether a patient has had a new tumor event after initial treatment.
clinical_data.number_of_lymphnodes_examined	The total number of lymph nodes removed and pathologically assessed for disease.
clinical_data.number_of_lymphnodes_positive_by_he	Numeric value to signify the count of positive lymph nodes identified through hematoxylin and eosin (H&E) staining light microscopy.
clinical_data.pathologic_M	Code to represent the defined absence or presence of distant spread or metastases (M) to locations via vascular channels or lymphatics beyond the reg...
clinical_data.pathologic_N	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 Cance...
clinical_data.pathologic_stage	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.
clinical_data.pathologic_T	Code of pathological T (primary tumor) to define the size or contiguous extension of the primary tumor (T), using staging criteria from the American ...
clinical_data.person_neoplasm_cancer_status	The state or condition of an individual’s neoplasm at a particular point in time.
clinical_data.pregnancies	Value to describe the number of full-term pregnancies that a woman has experienced.
clinical_data.primary_neoplasm_melanoma_dx	Text indicator to signify whether a person had a primary diagnosis of melanoma.
clinical_data.primary_therapy_outcome_success	Measure of Success
clinical_data.prior_dx	Text term to describe the patient’s history of prior cancer diagnosis and the spatial location of any previous cancer occurrence.
clinical_data.race	The text for reporting information about race based on the Office of Management and Budget (OMB) categories.
clinical_data.residual_tumor	Text terms to describe the status of a tissue margin following surgical resection.
clinical_data.tobacco_smoking_history	Category describing current smoking status and smoking history as self-reported by a patient.
clinical_data.tumor_tissue_site	Text term that describes the anatomic site of the tumor or disease.
clinical_data.tumor_type	Text term to identify the morphologic subtype of papillary renal cell carcinoma.
clinical_data.vital_status	The survival state of the person registered on the protocol.
clinical_data.weiss_venous_invasion	The result of an assessment using the Weiss histopathologic criteria.
clinical_data.year_of_initial_pathologic_diagnosis	Numeric value to represent the year of an individual’s initial pathologic diagnosis of cancer.
samples[]	List of barcodes of samples taken from this participant.

Column Name	Description
CLINICAL_NO	Unique identifier for a clinical sample. Oracle sequence generated number.
PATIENT_NO	Link to patient table.
SAMPLE_SOURCE	Source of the sample (surgery, biopsy, etc.).
SAMPLE_STATE	State of the sample (fresh, frozen, etc.).
GRANULARITY	Granularity of the sample (grossly dissected, sorted cells, etc.).
TUMOR_TYPE	Type of the tumor.
MARGINS	Conditions of the margins (Coded: +=positive, -=negative, 0=not applicable, U=unknown).
ANGIO_INVASION	Whether there was angio invasion (Coded: Y=Yes, N=No, U=Unknown).
FOCAL	Focal (Coded: Uni, Multiple, Unknown).
POST_OP	Post operative.
RECURRENCE	Tumor recurrence (Coded: Distant, Local, Biochemical, Regional, None, Unknown).
NOTEBOOK_ID	Notebook identifier containing original data on the clinical sample.
NOTEBOOK_PAGE	Notebook page number.
DATE_CREATED	Date record was entered into the database (default=SYSDATE, YYYY-MM-DD).
CREATED_BY	Person who entered the record into the database.
DATE_MODIFIED	Date record was last updated (default=SYSDATE, YYYY-MM-DD).
MODIFIED_BY	Person who last modified the record.
CLINICAL_SAMPLE_ID	Identifier to another database.
SAMPLE_SIZE	Size of the sample.
SAMPLE_SIZE_UNITS	Units of the sample size (Coded: cc=cubic centimeters, cm=centimeters, grams, none).
TIME_PM	Time to post-mortem (hours) for sample removal.
ORGAN	Organ from which the sample came.
PRIOR_TREATMENT	Type of prior treatment (CHEMO, REDIO, HORMONAL, NONE, etc.).
CLINICAL_T	Clinical tumor.
CLINICAL_N	Clinical node.
CLINICAL_DM	Clinical distal metastasis.
TUMOR_GRADE	Tumor grade.
TUMOR_SIZE	Size of the tumor.
TUMOR_SIZE_UNITS	Units of tumor size (Coded: cc=cubic centimeters, cm=centimeters, grams, none).
TIME_DO	Time from diagnosis to the operation (days).
TOTAL_LN	Total number of lymph nodes.
POSITIVE_LN	Total number of positive lymph nodes.
PATH_T	Pathological tumor.
PATH_N	Pathological node.
PATH_DM	Pathological distal metastasis.
TIME_OR	Time from operation to recurrence (days).
NOTEBOOK_LOCATION	Notebook location.
SAMPLE_NOTES	Additional notes on the clinical sample.

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