Data File

DEPRECATED: Please see Data File entry for CSBC/PSON below with the rest of the portals.

This describes the 'Explore Data' table.

This is not a card, but an explore table.

Table driving this: https://www.synapse.org/#!Synapse:syn21346411/tables/

Previously used a file view to drive Explore Data: 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	facet	concept	example	GDC equivalent	faceted on GDC	facet on CSBC	GDC reference	comments
File Name	name	no	The name (or part of a name) of a file (of any type).		file_name	no	no
Title	Title	no
Species	species	yes			none		yes
Theme	Theme	yes		tumor-heterogeneity	none		yes
Data Category	NA	no	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	no	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	yes	Format of the data files.	CSV HDF5 TSV TXT SRA XML MAGE-TAB SDRF IDF ADF	data_format	yes	yes
Assay	experimentalStrategy	yes	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_size	NA	no	The size of the data file (object) in bytes.		file_size	no	no
md5sum	NA	no	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	NA	no			platform	yes	yes
Tumor Type	tumorType	yes	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	NA	no	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	NA	no	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	sex	yes	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	NA	no	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	tissue	yes	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
Grant	centerName	yes
Grant Type	grantType	yes		U54 or U01
Consortium	consortium	yes		CSBC or PSON
Age	NA	no			diagnosis/age_at_diagnosis	yes	??	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis
Primary Diagnosis	NA	no	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	NA	no	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	NA	no	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	NA	no	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	NA	no	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