Data File

column name	concept	example	GDC equivalent	faceted on GDC	GDC reference	comments
species			none
data_category	Broad categorization of the contents of the data file.	Transcriptome Profiling	data_category	yes		CSBC will need to add values to those in GDC (which only cover sequencing)
data_type	Specific content type of the data file.	Exon Expression Quantification Gene Expression Quantification Isoform Expression Quantification Splice Junction Quantification	data_type	yes		CSBC will need to add values to those in GDC (which only cover sequencing)
data_format	Format of the data files.	CSV HDF5 TSV TXT SRA XML MAGE-TAB SDRF IDF ADF	data_format	yes
experimental_strategy	The sequencing strategy used to generate the data file. REMOVE "sequencing" for CSBC.	RNA-Seq Total RNA-Seq	experimental_strategy	yes		CSBC will need to add values to those in GDC (which only cover sequencing)
file_name	The name (or part of a name) of a file (of any type).		file_name	no
file_size	The size of the data file (object) in bytes.		file_size	no
md5sum	The 128-bit hash value expressed as a 32 digit hexadecimal number (in lower case) used as a file's digital fingerprint.		md5sum	no
platform			platform	yes
workflow_type	Generic name for the workflow used to analyze a data set.	BWA BWA with BQSR BWA-aln BWA-mem BWA with Mark Duplicates and BQSR		yes
disease_type	The text term used to describe the type of malignant disease, as categorized by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).	Acinar Cell Neoplasms Adenomas and Adenocarcinomas Adnexal and Skin Appendage Neoplasms Basal Cell Neoplasms Blood Vessel Tumors	case/disease_type	yes	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=case
site	The text term used to describe the general location of the malignant disease, as categorized by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).	Accessory sinuses Adrenal gland Anus and anal canal Base of tongue Bladder	case/primary_site	yes	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=case
ethnicity	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.	hispanic or latino not hispanic or latino Unknown not reported not allowed to collect	demographic/ethnicity	yes	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=demographic
gender	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.]	female male unknown unspecified not reported	demographic/gender	yes	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=demographic
race	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.	white american indian or alaska native black or african american asian native hawaiian or other pacific	demographic/race	yes	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=demographic
tissue_or_organ_of_origin	The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).	Abdomen, NOS Abdominal esophagus Accessory sinus, NOS Acoustic nerve Adrenal gland, NOS	diagnosis/tissue_or_organ_of_origin	yes	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis
age_at_diagnosis	Age at the time of diagnosis expressed in number of days since birth.		diagnosis/age_at_diagnosis	yes	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis
days_to_last_follow_up	Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.		diagnosis/days_to_last_follow_up	no	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis
days_to_last_known_disease_status	Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.		diagnosis/days_to_last_known_disease_status	no	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis
days_to_recurrence	Number of days between the date used for index and the date the patient's disease recurred.		diagnosis/days_to_recurrence	no	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis
last_known_disease_status	Text term that describes the last known state or condition of an individual's neoplasm.	Distant met recurrence/progression Loco-regional recurrence/progression Biochemical evidence of disease without structural correlate Tumor free	diagnosis/last_known_disease_status	no	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis
morphology	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.		diagnosis/morphology	no	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis
primary_diagnosis	Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).	Abdominal desmoid Abdominal fibromatosis Achromic nevus Acidophil adenocarcinoma Acidophil adenoma	diagnosis/primary_diagnosis	no	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis
progression_or_recurrence	Yes/No/Unknown indicator to identify whether a patient has had a new tumor event after initial treatment.	yes no unknown not reported Not Allowed To Collect	diagnosis/progression_or_recurrence	no	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis
site_of_resection_or_biopsy	The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).	Abdomen, NOS Abdominal esophagus Accessory sinus, NOS Acoustic nerve Adrenal gland, NOS	diagnosis/site_of_resection_or_biopsy	no	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis
tumor_grade	Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.	G1 G2 G3 G4 GX	diagnosis/tumor_grade	no	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis
tumor_stage	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.		diagnosis/tumor_stage	no	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis
vital_status	The survival state of the person registered on the protocol.	alive dead lost to follow-up unknown not reported	diagnosis/vital_status	yes	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis
sample_type	Text term to describe the source of a biospecimen used for a laboratory test.	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	sample/sample_type	no	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=sample
tissue_type	Text term that represents a description of the kind of tissue collected with respect to disease status or proximity to tumor tissue.	Tumor Normal Abnormal Peritumoral Unknown	sample/tissue_type	no	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=sample

GDC Data Dictionary viewer: https://docs.gdc.cancer.gov/Data_Dictionary/viewer/

GDC Data Dictionary is implemented in YAML files: https://github.com/NCI-GDC/gdcdictionary