Data File

This describes the 'Explore Data' table.

This is not a card, but an explore table.

File view driving this table: https://www.synapse.org/#!Synapse:syn9630847/tables/

The following is a brief description of the relevant columns in the table below (by column header):

portal name: name as it should appear in data portal

synapse file view column: corresponding name (e.g., for SQL query) in Synapse table view

facet: true if column_name should be faceted in data portal.

desired for CSBC/PS-ON: should this column be included in the CSBC data portal

The following annotations do not exist on file: theme

The following annotations need to be "ported" to GDC: Data Category (currently use existing "assay", but eventually use "data_category");

The following have been added to the synapse table, but are blank. They need to be filled in:

portal name	synapse file view column	eventual synapse file view column	facet	card location	concept	example	GDC equivalent	faceted on GDC	facet on CSBC	GDC reference	comments
Grant Type			yes	NA		U54 or U01
Grant			yes	NA
Program			yes	NA		CSBC or PSON
Species	species	species	yes	secondary			none		yes
Scientific Theme	NA	theme	yes	secondary(or possibly pill directly beneath file name)		tumor-heterogeneity	none		yes
Data Category	assay	data_category	yes	secondary	Broad categorization of the contents of the data file.	Transcriptome Profiling	data_category	yes	yes		CSBC will need to add values to those in GDC (which only cover sequencing)
Data Type	NA	data_type	no?	NA	Specific content type of the data file.	Exon Expression Quantification Gene Expression Quantification Isoform Expression Quantification Splice Junction Quantification	data_type	yes	yes		CSBC will need to add values to those in GDC (which only cover sequencing)
Data Format	fileFormat	data_format	no?	NA	Format of the data files.	CSV HDF5 TSV TXT SRA XML MAGE-TAB SDRF IDF ADF	data_format	yes	yes
Experiment Strategy	assay	experimental_strategy	yes	secondary	The sequencing strategy used to generate the data file. REMOVE "sequencing" for CSBC.	RNA-Seq Total RNA-Seq	experimental_strategy	yes	yes		CSBC will need to add values to those in GDC (which only cover sequencing)
File Name			no	primary	The name (or part of a name) of a file (of any type).		file_name	no	no
file_size			no	NA	The size of the data file (object) in bytes.		file_size	no	no
md5sum			no	NA	The 128-bit hash value expressed as a 32 digit hexadecimal number (in lower case) used as a file's digital fingerprint.		md5sum	no	no
Platform			yes	NA			platform	yes	yes
Disease Type			yes	secondary	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	yes	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=case
Site			yes	secondary	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	yes	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=case
Ethnicity			no	NA	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	yes	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=demographic
Gender			no	NA	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	yes	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=demographic
Race			no	NA	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	yes	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=demographic
Tissue			yes	secondary	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	yes	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis
Age			yes (can we facet by range–i.e., between age 20 and 30?)	NA	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
Primary Diagnosis			no	NA	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	no	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis
Progression			no	NA	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	no	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis
Vital Status			no	NA	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			no	NA	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	yes	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=sample
Tissue Type			no	NA	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	yes	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

GDC submission process (and metadata templates) are described here: https://docs.gdc.cancer.gov/Data_Submission_Portal/Users_Guide/Data_Submission_Overview/

GDC Data Upload Walkthrough: https://docs.gdc.cancer.gov/Data_Submission_Portal/Users_Guide/Data_Submission_Walkthrough/#clinical-data-requirements