pathologic_N
N0 (i-)
Bone
c34.9
Controlled
CONTROLLED
c25.9
The longest dimension of sample/specimen (in centimeters).
has Longest dimension
samples.longest_dimension
Stomach, Intestinal Adenocarcinoma, Papillary Type
British Columbia Cancer Agency
Bladder Urothelial Carcinoma
BLCA
c76.0
5
drug
has Drug therapy
A pharmaceutical product that contains one or more active and/or inactive ingredients. It is intended to treat, prevent or alleviate the symptoms of disease. A Case can have more them one drug treatment that can be identified by a UUID.NCI Thesaurus Code: C15986.
T3b
clinical_T
Additional - New Primary
sample_type
UVM
Uveal Melanoma
Glioblastoma Multiforme
has Per tile sequence quality
The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
read_group_qcs.per_tile_sequence_quality
Stanford University
ESCA
Esophageal Carcinoma
Analysis workflows used for processing data, and it can be identified by a UUID.
analysis.analysis_id
has Analysis
c67.2
Tissue or organ of origin
The text term that describes the anatomic site of the tumor or disease. See CDE (Common Data Element) Public ID: 3226281.
Primary Tumor Field
Read group QC
read_group_qcs.read_group_qc_id
false
Read group quality control which can be identified with a UUID.
c34.8
c06.2
has Read group name
The name of the read group.
read_groups.read_group_name
c06.9
Glioblastoma Multiforme
GBM
c47.1
c74.1
8145/3
samples.sample_type_id
has Sample type ID
A code that determines type of material taken from a biological entity for testing, diagnosis, propagation, treatment, or research purposes. This includes tissues, body fluids, cells, organs, embryos, body excretory products, etc. See NCI Thesaurus Code: C70713.
c10.3
The name of the center that provided the item.
has Source center
aliquots.source_center
c77.3
primary_therapy_outcome_success
Stable Disease
Endometrioid endometrial adenocarcinoma
8691/1
c45.0
8583/1
new_tumor_event_after_initial_treatment
has New tumor event after initial treatment
A Boolean value which denotes whether a neoplasm developed after the initial treatment has finished.
New Primary Tumor
Not available
Lung
c25.9
has Sequencing center
portions.read_groups.sequencing_center
The name of the center that provided the sequence files.
Regional site
has Gender
demographic.gender
The collection of behaviors and attitudes that distinguish people on the basis of the societal roles expected for the two sexes. See NCI Thesaurus Code: C17357.
Genotyping Array
N2c
pathologic_N
Brigham and Women's Hospital Division of Thoracic Surgery
20
WXS
Larynx
8071/3
c18.0
c67.2
stage is
9041/3
Spindle Cell
Asbestos Diseases Research Institute
read_groups.read_group_id
Sequencing reads from one lane of an NGS experiment. This can be identified by a UUID.
true
Read group
stage iiic
The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
read_group_qcs.sequence_length_distribution
has Sequence length distribution
Type of newly developed neoplasm after initial treatment has finished.
has New tumor event type
new_neoplasm_event_type
Epithelioid Cell
Endocervical Type of Adenocarcinoma
The unique identifier for a file, such as a Universally Unique Identifier (UUID).
has GDC file UUID
gdc_file_uuid
project.dbgap_accession_number
has dbGaP accession number
The dbGaP accession number provided for each study. See NCI Thesaurus Code: C25402.
Head & Neck Squamous Cell Carcinoma Basaloid Type
slides.slide_id
Slide
true
A tissue slide is a thin slice of a snap-frozen OCT embedded block of tissue sent for imaging. It can be identified by a UUID. The same tissue used for this imaging provides DNA and RNA for the analysis.
The time interval from the date of the last follow up to the date of the initial pathologic diagnosis, represented as a calculated number of days. See CDE (Common Data Element) Public ID: 3008273.
has Days to last follow up
days_to_last_followup
clinical_T
T4d
performance_status_scale_timing
has Performance status score: timing
A time reference for the Karnofsky score and/or the ECOG score using the defined categories.
c17.1
clinical_T
T1c
6
c49.3
The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
Per sequence GC content
8052/3
has Radiation therapy site
The location to which radiation therapy was administered.
anatomic_treatment_site
Thymoma; Type B2
read_group_qcs.read_group_qc_id
has Read group QC
Read group quality control which can be identified with a UUID.
c09.9
bcr_drug_uuid
A pharmaceutical product that contains one or more active and/or inactive ingredients. It is intended to treat, prevent or alleviate the symptoms of disease. A Case can have more them one drug treatment that can be identified by a UUID.NCI Thesaurus Code: C15986.
true
Drug therapy
c77.4
has Primary therapy outcome success
primary_therapy_outcome_success
A value denoting the result of therapy for a given disease or condition in a patient or group of patients. See NCI Thesaurus Code: C18919.
c49.1
M1c
clinical_M
c67.0
has Percent inflam infiltration
percent_inflam_infiltration
The ratio of inflammatory cells to the gross cell population seen on a slide.
Uterine Carcinosarcoma
Read Group Quality Control
c38.0
c34.8
c72.0
Maine Medical Center
3
demographic.demographic_id
The statistical characterization of human populations or segments of human populations (e.g., characterization by age, sex, race, or income), and can be identified by a UUID. See NCI Thesaurus Code: C16495.
has Demographic
has Library selection
read_groups.library_selection
The method used to select and/or enrich the material being sequenced.
c44.6
c40.3
The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
Per base sequence content
female
gender
pathologic_M
MX
c15.5
New primary melanoma
T4e
pathologic_T
read_group_qcs.encoding
has Encoding
The version of ASCII encoding of quality values found in the file.
c25.2
Washington University St. Louis
clinical_M
Clinical M (TNM)
The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The M category tells whether there are distant metastases (spread of cancer to other parts of the body). NCI Thesaurus Code: C48881 and C25385.
c71.8
Ohio State University
8211/3
Prince Charles Hospital
c41.0
PROCURE Biobank
Primary therapy outcome success
primary_therapy_outcome_success
A value denoting the result of therapy for a given disease or condition in a patient or group of patients. See NCI Thesaurus Code: C18919.
Workflow version
The version of the workflow used to analyze data.
21
Cholangiocarcinoma
Molecular Response
c18.4
has Per sequence quality score
The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
read_group_qcs.per_sequence_quality_score
2
eastern_cancer_oncology_group
samples.preservation_method
The primary preservation method used to store the sample.
has Preservation method
Cedars Sinai
bcgsc.ca
94
c77.5
Christiana Care
Clinical
9040/3
treatments.treatment_id
Treatment
A record of the administration and intention of therapeutic agents provided to a patient to alter the course of a pathologic process, and can be identified by a UUID. See NCI Thesaurus Code: C15368.
true
8461/3
9071/3
Cholangiocarcinoma
CHOL
c48.0
St Joseph's Medical Center (MD)
read_groups.RIN
The RNA integrity number.
has RIN
hms.harvard.edu
clinical_M
M1b
21
D
has Well number
The number of wells on the plate in which an analyte has been stored for shipment and for the analysis.
well_number
Chemotherapy
therapy_type
c67.4
Pelvis
Medical College of Wisconsin
c06.0
Pancreas-Adenocarcinoma Ductal Type
c44.3
Stage IIB
clinical_stage
stage i
has Years smoked
exposures.years_smoked
The numeric value (or unknown) to represent the number of years a person has been smoking. See CDE (Common Data Element) Public ID: 3137957.
Raw Simple Somatic Mutation
The dbGaP accession number provided for each study. See NCI Thesaurus Code: C25402.
dbGaP accession number
pathologic_N
N0 (i+)
c34.1
Induction Failure AML (AML-IF)
Analyte type
This defines the type of an analyte on molecular bases.
MD Anderson - Pathology/Lab Medicine Hamilton
8805/3
Country where the specimen/sample has been procured.
has Country of sample procurement
country_of_procurement
Pathologic N (TNM)
pathologic_N
The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The N category describes whether or not the cancer has reached nearby lymph nodes NCI Thesaurus Code: C48881 and C48740.
karnofsky_performance_score
30
Methylation Array
Oral Cavity
Johns Hopkins / University of Southern California
The fraction of the granulocyte component to the gross inflammatory cells seen on a slide.
has Percent granulocyte infiltration
percent_granulocyte_infiltration
8560/3
8050/3
8344/3
samples.composition
has Composition
The cellular composition of the sample.
exposures.cigarettes_per_day
has Cigarettes per day
The average number of cigarettes smoked per day. See CDE (Common Data Element) Public ID: 2001716.
c00.9
Mucinous Adenocarcinoma of Endocervical Type
primary_therapy_outcome_success
Progressive Disease
c50.4
Follow ups which monitor a person's health over time after treatment. Members of the follow up entity can be identified by a UUID. A case can have multiple follow ups generated at different time. See NCI Thesaurus Code: C16033.
Follow up
bcr_followup_uuid
true
Lung Basaloid Squamous Cell Carcinoma
BRCA
Breast Invasive Carcinoma
Erasmus MC
8010/3
v1
has Analyte
analytes.analyte_id
A molecular specimen extracted for analysis from a portion using a specific extraction protocol. This can be identified by a UUID.
ABS IUPUI
has Ethnicity
A socially defined category of people based on common ancestral, cultural, biological, and social factors. See NCI Thesaurus Code: C29933.
demographic.ethnicity
c44.5
Paraganglioma
The fraction of eosinophil cells to the gross granulocyte component of inflammatory cells seen on a slide.
percent_eosinophil_infiltration
has Percent eosinophil infiltration
c74.0
c44.31
Primary DLBCL of the CNS
8585/3
Bone Marrow Normal
sample_type
A description of the tumor from which the sample was derived.
samples.tumor_descriptor
has Tumor descriptor
Barretos Cancer Hospital
8350/3
c24.0
Targeted Molecular therapy
therapy_type
current_weight
Current sample/specimen weight (in grams).
has Current weight
portions.portion_id
has Portion
A portion of the sample or specimen (in the scope of TCGA), which is one of several sequential 100-120 mg sections. It can be identified by a Universally Unique Identifier (UUID).
5
University of Pittsburgh
has Center namespace
aliquots.center.namespace,portions.center.namespace
The domain name of the center (e.g. borad.mit.edu).
c53.0
diagnoses.diagnosis_id
true
The investigation, analysis, and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms. This also refers to a scientific determination of any kind or the concise results of such an investigation. A diagnosis can be identified by a UUID. See NCI Thesaurus Code: C15220.
Diagnosis
Kidney Renal Papillary Cell Carcinoma
The version of the sequencing library preparation kit.
has Library preparation kit version
read_groups.library_preparation_kit_version
Uterine Carcinosarcoma/ MMMT: Heterologous Type
8013/3
BCGSC
Persistent Disease
primary_therapy_outcome_success
University Of Michigan
Rectal Adenocarcinoma
8830/3
NX
pathologic_N
A molecular specimen extracted for analysis from a portion using a specific extraction protocol. This can be identified by a Universally Unique Identifier (UUID).
Analyte
analytes.analyte_id
true
A further, more specific classification of the data category, based on the information that it contains.
Data type
8771/3
c15.4
c77.4
Total RNA
true
bcr_radiation_uuid
The treatment of a disease by means of exposure of the target or the whole body to radiation. A Case can have more then one radiation treatment that can be identified by a UUID. NCI Thesaurus Code: C15986.
Radiation therapy
The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The M category tells whether there are distant metastases (spread of cancer to other parts of the body). NCI Thesaurus Code: C48881 and C48741.
has Pathologic M (TNM)
pathologic_M
Greenville Health System
The type of treatment of the disease through the use of drugs. NCI Thesaurus Code: C15986.
therapy_type
has Pharmaceutical therapy type
Data category
The classification of data used in (or produced by) the analysis, based on its form and content. See NCI Thesaurus Code: C42645.
read_groups.flow_cell_barcode
has Flow cell barcode
The barcode assigned to flow cell.
Genome build
The reference genome or assembly (such as HG19/GRCh37 or GRCh38) to which the nucleotide sequence of a case/subject/sample can be aligned.
Infiltrating Ductal Carcinoma
28
WARN
8171/3
c76.2
University of Ulm
c44.7
The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The M category tells whether there are distant metastases (spread of cancer to other parts of the body). NCI Thesaurus Code: C48881 and C25385.
clinical_M
has Clinical M (TNM)
T1b2
pathologic_T
c67.3
c49.5
c15.5
c04.9
Per base N content
The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
ethnicity
hispanic or latino
Tis
pathologic_T
A classification of humans characterized by certain heritable traits, common history, nationality, or geographic distribution. See NCI Thesaurus Code: C17049.
demographic.race
has Race
c16.0
T3a
clinical_T
8317/3
Intrapleural Progression
MSKCC
Giant cell 'MFH' / Undifferentiated pleomorphic sarcoma with giant cells
Performance status score: Karnofsky score
karnofsky_performance_score
An index designed for classifying patients 16 years of age or older by their functional impairment. A standard way of measuring the ability of cancer patients to perform ordinary tasks. NCI Thesaurus Code: C28013.
Harvard
University of Iowa
c48.1
c71.1
clinical_stage
Stage IVB
not reported
clinical_M
M0
has Total sequences
read_group_qcs.total_sequences
The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
has Time between clamping and freezing
time_between_clamping_and_freezing
Time elapsed (in minutes) between clamping (supplying vessel) and freezing a sample.
Stage IC
clinical_stage
c13.9
Emory University - Winship Cancer Inst.
radiation
The treatment of a disease by means of exposure of the target or the whole body to radiation. A Case can have more then one radiation treatment that can be identified by a UUID. NCI Thesaurus Code: C15986.
has Radiation therapy
Roswell
Other
performance_status_scale_timing
treatments.treatment_id
A record of the administration and intention of therapeutic agents provided to a patient to alter the course of a pathologic process, and can be identified by a UUID. See NCI Thesaurus Code: C15368.
has Treatment
c64.9
Mixed Histology (please specify)
Essen
white
race
Stomach, Intestinal Adenocarcinoma, Not Otherwise Specified (NOS)
read_groups.is_paired_end
Is paired end
A Boolean value which denotes whether sequence reads are paired end or not.
Biphasic mesothelioma
sample_type_id
6
has Prior malignancy
Text term to describe the patient's history of prior cancer diagnosis and the spatial location of any previous cancer occurrence. See CDE (Common Data Element) Public ID: 3081934.
diagnoses.prior_malignancy
8858/3
Stage IB2
clinical_stage
Metastatic
sample_type
Fondazione-Besta
clinical_stage
Stage IB
has Site of resection or biopsy
diagnoses.site_of_resection_or_biopsy
The topography code which describes the anatomical site of origin of the neoplasm according to the third edition of the International Classification of Diseases for Oncology (ICD-O). See NCI Thesaurus Code: C37978. See CDE (Common Data Element) Public ID: 3226281.
8401/3
not reported
c71.0
READ
Rectum Adenocarcinoma
c38.4
diagnoses.tissue_or_organ_of_origin
The text term that describes the anatomic site of the tumor or disease. See CDE (Common Data Element) Public ID: 3226281.
has Tissue or organ of origin
Tumor status
The condition or state of the tumor at a particular time. See NCI Thesaurus Code: C96643.
Thymoma
THYM
University of Hawaii
not reported
c67.0
8480/3
Clear cell sarcoma of the kidney (CCSK)
c67.1
c40.2
Prostate Adenocarcinoma
c10.9
8550/3
8980/3
8460/3
vital_status
has Vital status
The state of being living or deceased for Cases that are part of the investigation. See NCI Thesaurus Code: C25717.
c32.1
9052/3
has Library name
The name of the sequencing library preparation.
read_groups.library_name
Alberta Health Services
has Analyte type
This defines the type of an analyte on molecular bases.
analytes.analyte_type
Mayo Clinic - Rochester
Locoregional (Urothelial tumor event)
c54.2
MuTect2
has Target capture kit vendor
read_groups.target_capture_kit_vendor
The vendor of target capture kit.
Entity
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. NCI Thesaurus Code: C16899; also see NCI Thesaurus Code: C28257 for Pathological stage.
T1c
pathologic_T
The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
Per sequnce quality score
c76.3
c69.40
8384/3
YES
The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
has Sequence duplication levels
read_group_qcs.sequence_duplication_levels
8743/3
0.3
c44.4
tissue_source_site.code
The alphanumeric code for clinical site that collects and provides patient samples and clinical metadata for research use. See NCI Thesaurus Code: C103264.
has Tissue source site code
Hartford
Clinical Supplement
0.7
c20.9
Per base sequence quality
The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
DLBC
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma
clinical_T
T1b
30
A classification of humans characterized by certain heritable traits, common history, nationality, or geographic distribution. See NCI Thesaurus Code: C17049.
Race
c48.0
OTHER
radiation_type
unc.edu
Adrenocortical Carcinoma
ACC
N1
clinical_N
New tumor anatomic site
Anatomic site of newly developed neoplasm.
Testis
c41.1
8144/3
Providence Portland Medical Center
c19.9
has Freezing method
Method used to freeze the sample/specimen.
freezing_method
9080/0
c22.0
Harvard Medical School
has Aliquot
aliquots.aliquot_id
The aliquot is a product or unit extracted from a sample or specimen 's portion and prepared for analysis. It can be identified by a UUID. See NCI Thesaurus Code: C25414.
radiation_type
Systemic
IDI-IRCCS
c77.9
c19.9
c71.2
c02.2
c40.2
Mesothelioma
has Genome name
The reference genome or assembly that also contains decoy viral sequnce to which the nucleotide sequence of a case/subject/sample can be aligned.
race
black or african american
c71.6
c56.9
Mucinous Carcinoma
Colon Adenocarcinoma
has Per base sequence quality
The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
read_group_qcs.per_base_sequence_quality
read_groups.adapter_name
has Adapter name
The name of the sequencing adapter.
Blader Urothelial Carcinoma
has Base caller version
The version of the base caller.
read_groups.base_caller_version
analytes.analyte_type_id
has Analyte type ID
An ID that determines the type of an analyte on molecular bases. A single letter BCR code for the analyte type.
c14.8
VarScan2 Annotation
c49.4
The shortest dimension of sample/specimen (in centimeters).
samples.shortest_dimension
has Shortest dimension
Kidney Chromophobe
WARN
National Cancer Center Korea
BLN - Cleveland Clinic
The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
Overrepresented sequences
batch_number
A set of related analytes prepared for further analysis, numbered sequentially, from the same disease. Once a Case has been assigned to a batch, subsequent shipments from that case are assigned the same batch number as the original. Seven Bridges only field.
has Batch number
Capital Biosciences
Ontario Institute for Cancer Research (OICR)
performance_status_scale_timing
Post Secondary Therapy
Lung Acinar Adenocarcinoma
14
c67.1
A code that determines type of material taken from a biological entity for testing, diagnosis, propagation, treatment, or research purposes. This includes tissues, body fluids, cells, organs, embryos, body excretory products, etc. See NCI Thesaurus Code: C70713.
Sample type ID
M1c
pathologic_M
Center name
The name of the center (e.g. Broad Institute of MIT and Harvard).
UNC
c50.919
Stage IS
clinical_stage
7
Colorectal
c15.3
has Performance status score: Karnofsky score
karnofsky_performance_score
An index designed for classifying patients 16 years of age or older by their functional impairment. A standard way of measuring the ability of cancer patients to perform ordinary tasks. NCI Thesaurus Code: C28013.
24
The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The T category describes the original (primary) tumor. NCI Thesaurus Code: C48881 and C253840.1321.
has Clinical T (TNM)
clinical_T
Exposure
true
Clinically relevant patient information not immediately resulting from genetic predispositions which and can be identified by a UUID.
exposures.exposure_id
section_location
TOP
The name of the target capture kit.
has Target capture kit name
read_groups.target_capture_kit_name
c71.4
8575/3
pathologic_N
has Pathologic N (TNM)
The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The N category describes whether or not the cancer has reached nearby lymph nodes NCI Thesaurus Code: C48881 and C48740.
N2a
clinical_N
c76.1
St. Joseph's Hospital AZ
c19
8584/1
COAD
Colon Adenocarcinoma
The height of the patient in centimeters. See CDE (Common Data Element) Public ID: 649.
exposures.height
has Height
c38.1
pathologic_T
T4
files.file_id
This value is denoted by a list of file names associated with the File node.
has File
Rhabdoid tumor (kidney) (RT)
Vaccine
therapy_type
Pre-Adjuvant Therapy
performance_status_scale_timing
8770/3
The numerical value that represents the order of a portion in the series.
portions.portion_number
has Portion number
Institute of Human Virology Nigeria
pathologic_M
M1a
Thyroid Papillary Carcinoma - Classical/usual
Washington University
https://github.com/NCI-GDC/varscan-cwl
c00.9
c55
Pheochromocytoma and Paraganglioma
Cervical Squamous Cell Carcinoma
aliquots.created_datetime,analysis.created_datetime,downstream_analysis.created_datetime,cases.created_datetime,demographic.created_datetime,diagnoses.created_datetime,exposures.created_datetime,files.created_datetime,read_groups.created_datetime,read_group_qcs.created_datetime,samples.created_datetime,treatments.created_datetime,analyte.created_datetime,slide.created_datetime
Created datetime
Created datetime.
University of Hawaii - Normal Study
Ipsilateral Pleura
PASS
FAIL
stage iv
https://github.com/NCI-GDC/somaticsniper-cwl
Paraganglioma; Extra-adrenal Pheochromocytoma
c16.3
c38.3
A shortened name of the center (e.g. BI).
has Center short name
aliquots.center.short_name,portions.center.short_name
SomaticSniper Annotation
Stomach Adenocarcinoma
has Platform
read_groups.platform,files.platform
The version (for instance, manufacturer or model) of the technology that was used for sequencing or assaying. See NCI Thesaurus Code: C45378.
8382/3
Technical University of Munich
Pancreas-Colloid (mucinous non-cystic) Carcinoma
c67.6
Stomach
A molecular specimen extracted for analysis from a portion using a specific extraction protocol. This can be identified by a UUID.
Section location
Testes
Star 2-Pass
has Workflow end datetime
The end of the analysis workflow in datatime format.
analysis.workflow_end_datetime,read_group_qcs.workflow_end_datetime
c54.9
St. Joseph's Medical Center (MD)
Lymph Node(s)
c49.1
T4d
pathologic_T
c01.9
8253/3
Boston Medical Center
c62.9
The version of ASCII encoding of quality values found in the file.
Encoding
c41.1
SomaticSniper Variant Aggregation and Masking
c16.1
has Library preparation kit name
The name of the sequencing library preparation kit.
read_groups.library_preparation_kit_name
c14.8
c64.9
Lung Papillary Adenocarcinoma
c75.5
c53.0
pathologic_M
cM0 (i+)
mskcc.org
has 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. NCI Thesaurus Code: C16899; also see NCI Thesaurus Code: C28257 for Pathological stage.
diagnoses.tumor_stage
exposures.bmi
The body mass divided by the square of the body height expressed in units of kg/m2. See CDE (Common Data Element) Public ID: 4973892.
has BMI
The method or protocol used to perform the laboratory analysis. See NCI Thesaurus Code: C43622.
Experimental strategy
8073/3
The base sequence of the sequencing adapter.
has Adapter sequence
read_groups.adapter_sequence
Case Western - St Joes
c51.9
has Progression or recurrence
diagnoses.progression_or_recurrence
Yes/No/Unknown indicator to identify whether a patient has had a new tumor event after initial treatment. See CDE (Common Data Element) Public ID: 3121376.
T
has Center
c34.30
c63.1
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. See CDE (Common Data Element) Public ID: 5243162.
clinical_stage
Clinical stage
Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)
TUMOR FREE
person_neoplasm_cancer_status
c64.9
pathologic_N
N0 (mol+)
c34.9
c09.9
clinical_N
N2b
c15.3
A specific model of sequencing instrument used.
read_groups.instrument_model
has Instrument model
has Fastq name
read_group_qcs.fastq_name
The names of FASTQs.
clinical_T
T4e
c71.9
c49.4
100
karnofsky_performance_score
8310/3
Case
The subject who has taken part in the investigation/program, and can be identified by a Universally Unique Identifier (UUID). See NCI Thesaurus Code: C15362.
true
cases.case_id,patient
Papworth Hospital
Myxofibrosarcoma
Mayo
T3c
pathologic_T
c49.2
24
slides.percent_tumor_cells
has Percent tumor cells
The percent of identified tumor cells based on the tissue image.
eastern_cancer_oncology_group
4
Head & Neck Squamous Cell Carcinoma
1.0
c69.90
c16.9
NCI HRE Branch
Varscan2 Variant Aggregation and Masking
c72.9
c02.1
Rectal Mucinous Adenocarcinoma
c25.1
The name of the base caller.
has Base caller name
read_groups.base_caller_name
Uterine Carcinosarcoma/ Malignant Mixed Mullerian Tumor (MMMT): NOS
Diagnosis of a disease based on the type of tissue, where type is determined based on the microscopic examination of tissue. See NCI Thesaurus Code: C61478.
Histological diagnosis
c52
Northwestern University
MuSE Variant Aggregation and Masking
c71.3
c44.3
M1
pathologic_M
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma
jhu.edu
c18.2
c67.3
Urethra
c71.1
c71.7
34
Retroperitoneal lymph nodes
c49.20
race
american indian or alaska native
has Per sequence GC content
The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
read_group_qcs.per_sequence_gc_content
diagnoses.classification_of_tumor
Text that describes the kind of disease present in the tumor specimen as related to a specific point in time. See CDE (Common Data Element) Public ID: 3288124
has Classification of tumor
Toronto Western Hospital
4
The type of format that determines data content.
Data format
c44.601
c15.5
Esophagus Squamous Cell Carcinoma
vanderbilt.edu
Additional options for histologics diagnosis (see Histologic diagnosis), which have not been pre-determined in the listed values for histologic diagnosis.
histological_type_other
has Other histological diagnosis
UNC
Liftover
8
c03.1
c48.0
c54.3
University of California San Francisco
c17.1
c77.2
UNC
Breast Invasive Carcinoma
c34.2
NCH
c04.0
Rectum Adenocarcinoma
c30.0
Tissue source site
A clinical site that collects and provides patient samples and clinical metadata for research use. See NCI Thesaurus Code: C103264.
Local Recurrence
c49.9
Washington University - CHUV
Isoform Expression Quantification
c16.1
International Genomics Conosrtium
sample_type_id
14
DNA
slides.slide_id
A tissue slide is a thin slice of a snap-frozen OCT embedded block of tissue sent for imaging. It can be identified by a UUID. The same tissue used for this imaging provides DNA and RNA for the analysis.
has Slide
has Alcohol intensity
exposures.alcohol_intensity
A category to describe the patient's current level of alcohol use as self-reported by the patient. See CDE (Common Data Element) Public ID: 3457767.
8260/3
University Health Network, Toronto
c50.8
Aggregated Somatic Mutation
sample_type_id
1
has File size
The size of a file measured in bytes (B), kilobytes (KB), megabytes (MB), gigabytes (GB), terabytes (TB), and larger values.
files.file_size
c73.9
year_of_initial_pathologic_diagnosis
The numeric value to represent the year of an individual's initial pathologic diagnosis of cancer. See CDE (Common Data Element) Public ID: 2896960.
has Year of diagnosis
SingHealth
c77.2
has Sample
samples.sample_id
A sample or specimen is material taken from a biological entity for testing, diagnosis, propagation,treatment, or research purposes, including but not limited to tissues, body fluids, cells, organs, embryos, body excretory products, etc. It can be identified by a UUID. See NCI Thesaurus Code: C19157.
Stage IIC
clinical_stage
8822/1
Progression or recurrence
Yes/No/Unknown indicator to identify whether a patient has had a new tumor event after initial treatment. See CDE (Common Data Element) Public ID: 3121376.
Norfolk and Norwich Hospital
University of California, Davis
Yale University
A Boolean value which denotes adapter trimming or not.
read_groups.to_trim_adapter_sequence
has To trim adapter sequence
clinical_stage
Stage IA
FAIL
c04.9
University of North Carolina
DNAcopy
TXT
The domain name of the center (e.g. borad.mit.edu).
Center namespace
has Days to birth
diagnoses.days_to_birth
The time interval from a person's date of birth to the date of initial pathologic diagnosis, represented as a calculated negative number of days. See CDE (Common Data Element) Public ID: 3008233.
Bladder
c69.9
c18.7
c34.1
PASS
Christiana Healthcare
c14.8
has Tissue source site ID
tissue_source_site.tissue_source_site_id
A clinical site that collects and provides patient samples and clinical metadata for research use. This is identified with UUID. See NCI Thesaurus Code: C103264.
26
exposures.weight
The weight of the patient measured in kilograms. See CDE (Common Data Element) Public ID: 651.
has Weight
has Code
Method used to freeze the sample/specimen.
Freezing method
The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The T category describes the original (primary) tumor. NCI Thesaurus Code: C48881 and C253840.
Clinical T (TNM)
clinical_T
dead
vital_status
9080/3
An analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
Basic statistics
c17.9
c77.0
8312/3
has Submitter ID
files.submitter_id,aliquots.submitter_id,analytes.submitter_id,analysis.submitter_id,cases.submitter_id,demographic.submitter_id,diagnoses.submitter_id,exposures.submitter_id,portions.submitter_id,read_groups.submitter_id,read_group_qcs.submitter_id,samples.submitter_id,slides.submitter_id,treatments.submitter_id,bcr_followup_barcode,bcr_drug_barcode,bcr_radiation_barcode
Usually a human-readable identifier, such as a number or a string that may contain metadata information. In some instances, this can also be a UUID.
Huntsman Cancer Institute
https://github.com/NCI-GDC/mirna-profiler
exposures.exposure_id
Clinically relevant patient information not immediately resulting from genetic predispositions which and can be identified by a UUID.
has Exposure
Masked Copy Number Segment
not reported
race
clinical_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. See CDE (Common Data Element) Public ID: 5243162.
has Clinical stage
Ovarian Serous Cystadenocarcinoma
WXS
Repli-G (Qiagen) DNA
Hospital Louis Pradel
Genome name
The reference genome or assembly that also contains decoy viral sequnce to which the nucleotide sequence of a case/subject/sample can be aligned.
Aliquot
true
aliquots.aliquot_id
The aliquot is a product or unit extracted from a sample or specimen 's portion and prepared for analysis. It can be identified by a UUID. See NCI Thesaurus Code: C25414.
The type of format that determines data content.
files.data_format
has Data format
c16.0
Lung Small Cell Squamous Cell Carcinoma
University of Michigan
diagnoses.age_at_diagnosis
has Age at diagnosis
The age in years of the case at the initial pathological diagnosis of disease or cancer. See NCI Thesaurus Code: C15220.
c20
2
sample_type_id
c21.8
8201/3
pathologic_N
N0
c18.5
The percent of identified tumor cell necrosis based on the tissue image.
slides.percent_necrosis
has Percent necrosis
c49.1
c17.9
LBL
Lung Papillary Squamous Cell Caricnoma
PASS
8774/3
Hypopharynx
Synovial Sarcoma - Biphasic
54
0.025
Anchor Of
has Therapeutic agents
The text identification of the individual agent(s) used as part of a prior treatment regimen. See CDE (Common Data Element) Public ID: 2975232
treatments.therapeutic_agents
miRNA Expression Quantification
9043/3
project.primary_site
The anatomical site where the primary tumor is located in the organism. See NCI Thesaurus Code: C43761.
has Primary site
8070/3
c49.6
Mount Sinai School of Medicine
c74.1
c04.9
c18.5
has Performance status score: ECOG
A performance status scale designed to assess disease progression and its effect on the daily living abilities of the patient. NCI Thesaurus Code: C105721.
eastern_cancer_oncology_group
Kidney Papillary Renal Cell Carcinoma
c37.9
clinical_T
T4a
c37.9
N1a
pathologic_N
University of North Carolina
At Recurrence/Progression Of Disease
performance_status_scale_timing
c77.9
performance_status_scale_timing
Post-Adjuvant Therapy
The value denotes the type of high-energy radiation used to kill cancer cells and shrink tumors. NCI Thesaurus Code: C15986.
has Radiation type
radiation_type
8680/1
Fox Chase
broad.mit.edu
9061/3
Kidney Renal Clear Cell Carcinoma
has Year of birth
demographic.year_of_birth
A numeric value to represent the calendar year in which an individual was born. See CDE (Common Data Element) Public ID: 2896954.
6
8263/3
c50.4
The concentration of a product (in molarity) prepared for an analysis.
has Concentration
aliquots.concentration,analytes.concentration
Non-Seminoma; Embryonal Carcinoma
M1b
pathologic_M
c18.4
c01.9
WUGSC
c18.0
c76.2
Proteogenex, Inc.
Wellcome Trust Sanger Institute
VCF
eastern_cancer_oncology_group
Performance status score: ECOG
A performance status scale designed to assess disease progression and its effect on the daily living abilities of the patient. NCI Thesaurus Code: C105721.
Thoraxklinik
Holy Cross
Non-Seminoma; Choriocarcinoma
Global Bioclinical-Moldova
Pleomorphic 'MFH' / Undifferentiated pleomorphic sarcoma
has Center name
aliquots.center.name,portions.center.name
The name of the center (e.g. Broad Institute of MIT and Harvard).
Ovarian Serous Cystadenocarcinoma
OV
pathologic_T
T1b1
Library strategy
The sequencing technique intended for the library.
T1a1
pathologic_T
T3
clinical_T
N3
clinical_N
c44.50
Portion
portions.portion_id
true
A portion of the sample or specimen (in the scope of TCGA), which is one of several sequential 100-120 mg sections. It can be identified by a UUID.
karnofsky_performance_score
90
11
sample_type_id
9050/3
PASS
Colon
ILSbio
c64.1
Non-regional / Distant Lymph Nodes
Adrenocortical Carcinoma- Oncocytic Type
hgsc.bcm.edu
9081/3
Montefiore Medical Center
has Case
The subject who has taken part in the investigation/program, and can be identified by a Universally Unique Identifier (UUID). See NCI Thesaurus Code: C15362.
cases.case_id,patient
c25.2
The percent of identified tumor nuclei based on the tissue image.
has Percent tumor nuclei
slides.percent_tumor_nuclei
c63.1
clinical_stage
Stage IA1
c61
Not available
read_groups.experiment_name
A submitter-defined name for the experiment.
has Experiment name
Washington University - Cleveland Clinic
Thyroid Carcinoma
THCA
stage iib
c50.4
c07.9
has Center
Not available
person_neoplasm_cancer_status
has Kmer content
The number of times the kmer occurs in the sequence. Analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
read_group_qcs.kmer_content
NCI Urologic Oncology Branch
University of Minnesota
c34.1
0.9
not reported
Memorial Sloan-Kettering Cancer Center
Utility
10
sample_type_id
8802/3
FAIL
The section of a tissue that has been imaged. The value denotes top, middle, or bottom.
has Section location
slides.section_location
0.05
c38.4
The time interval from a person's date of death to the date of initial pathologic diagnosis, represented as a calculated number of days. See CDE (Common Data Element) Public ID: 3165475.
days_to_death
has Days to death
c05.0
samples.tumor_code
The diagnostic tumor code of the tissue sample source.
has Tumor code
clinical_stage
Stage IA2
slides.percent_neutrophil_infiltration
has Percent neutrophile infiltration
The fraction of neutrophile cells to the gross granulocyte component of inflammatory cells seen on a slide.
TGCT
Testicular Germ Cell Tumors
c34.3
true
demographic.demographic_id
Demographic
The statistical characterization of human populations or segments of human populations (e.g., characterization by age, sex, race, or income), and can be identified by a UUID. See NCI Thesaurus Code: C16495.
Thymoma; Type B1
Copy Number Variation
BCR XML
clinical_T
T2a
SomaticSniper
c76.0
W
has Library preparation kit vendor
The vendor of the sequencing library preparation kit.
read_groups.library_preparation_kit_vendor
c34.0
23
Kidney
sanger.ac.uk
Illumina
Pleura
aliquots.center.code,portions.center.code
The code that determins center that has submitted data.
has Center code
The ratio of identified stromal cells present on the tissue slide.
has Percent stromal cells
slides.percent_stromal_cells
Thymoma
Undifferentiated Pleomorphic Sarcoma (UPS)
ABS - Lahey Clinic
Supraclavicular lymph nodes
Eye
Synovial Sarcoma - Monophasic
University of Southern California
An analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
read_group_qcs.adapter_content
has Adapter content
c22.0
Adenosquamous
University of Miami
c49.0
The time interval from the date of biospecimen collection to the date of initial pathologic diagnosis, represented as a calculated number of days. Sample can be collected prospectively or retrospectively. This can be a negative value for samples taken retrospectively. See CDE (Common Data Element) Public ID: 3008340.
days_to_collection
has Days to collection
WARN
NX
clinical_N
c22.1
Head & Neck
c70.1
WARN
c06.0
c49.3
c67.1
c49.8
Stomach Adenocarcinoma, Signet Ring Type
Ontario Institute for Cancer Research
Sample
true
A sample or specimen is material taken from a biological entity for testing, diagnosis, propagation,treatment, or research purposes, including but not limited to tissues, body fluids, cells, organs, embryos, body excretory products, etc. It can be identified by a UUID. See NCI Thesaurus Code: C19157.
samples.sample_id
samples.oct_embedded
has OCT embedded
A Boolean value indicating whether the Optimal Cutting Temperature compound (OCT) is used to embed tissue samples prior to frozen sectioning on a microtome-cryostat.
primary_therapy_outcome_success
No Measureable Tumor or Tumor Markers
NCH
8120/3
has Tumor status
The condition or state of the tumor at a particular time. See NCI Thesaurus Code: C96643.
person_neoplasm_cancer_status
8255/3
The number of proliferating cells identified in the slide sample.
number_proliferating_cells
has Number proliferating cells
histological_type
Diagnosis of a disease based on the type of tissue, where type is determined based on the microscopic examination of tissue. See NCI Thesaurus Code: C61478.
has Histological diagnosis
The start of the analysis workflow in datetime format.
analysis.workflow_start_datetime,read_group_qcs.workflow_start_datetime
has Workflow start datetime
c03.1
8246/3
c44.2
has Percent normal cells
slides.percent_normal_cells
The percent of normal cell based on the tissue image.
c49.3
BI
c49.2
8700/0
read_groups.target_capture_kit_catalog_number
has Target capture kit catalog number
The catalog number of target capture kit.
pathologic_T
T3b
Raw Sequencing Data
c07
BLN - University Of Chicago
c75.5
Astrocytoma
Pancreas
clinical_T
T2b
Distant Metastasis
The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
Per tile sequence quality
John Wayne Cancer Center
Peritoneal Surfaces
Cervix
pathologic_T
T3
N2
clinical_N
0.0
has Library strand
read_groups.library_strand
This determines whether the 'first strand' or 'second strand' of cDNA was used to prepare the library.
4
13
c44.6
c71.4
Renal Pelvis
Leiomyosarcoma (LMS)
Thymoma; Type B3
T4a
pathologic_T
Glioblastoma Multiforme (GBM)
c08.0
8772/0
c77.3
9450/3
Extrahepatic Recurrence
c05.0
c54.2
hudsonalpha.org
WARN
c71.0
stage ia
Princess Margaret Hospital (Canada)
has Tumor grade
The numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness. See CDE (Common Data Element) Public ID: 2785839.
diagnoses.tumor_grade
c67.9
FAIL
1.1
c71.9
c50.3
c70.1
clinical_N
The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The N category describes whether or not the cancer has reached nearby lymph nodes NCI Thesaurus Code: C48881 and C25384.
has Clinical N (TNM)
The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The M category tells whether there are distant metastases (spread of cancer to other parts of the body). NCI Thesaurus Code: C48881 and C48741.
pathologic_M
Pathologic M (TNM)
c72.9
c53.0
Walter Reed
T1
pathologic_T
has Basic statistics
An analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
read_group_qcs.basic_statistics
Melbourne Health
Lung
Kidney Chromophobe
KICH
c18.2
A description of the tissue type with respect its tumor/normal source.
has Tissue type
c15.9
Endometrioid Adenocarcinoma of Endocervix
c73.9
Brain
PAAD
Pancreatic Adenocarcinoma
The time interval from the date of new tumor event, including progression, recurrence and new primary malignancies, to the date of the initial pathologic diagnosis, represented as a calculated number of days. See CDE (Common Data Element) Public ID: 3392464.
has Days to recurrence
diagnoses.days_to_recurrence
29
stage ii
The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
Sequence duplication levels
c74.0
eastern_cancer_oncology_group
3
c34.8
has Genome build
The reference genome or assembly (such as HG19/GRCh37 or GRCh38) to which the nucleotide sequence of a case/subject/sample can be aligned.
has Overrepresented sequences
The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
read_group_qcs.overrepresented_sequences
c03.0
MDA
1
radiation_type
Internal
Stage IIA
clinical_stage
c71.3
c62.9
Investigation
false
project.project_id
A value denoting the project or study that generated the data. See NCI Thesaurus Code: C41198.
The numerical value that represents the order of a portion in the series.
Portion number
Prostate Adenocarcinoma
PRAD
pathologic_T
T2
A generic name for the workflow used to analyze data.
read_group_qcs.workflow_type,analysis.workflow_type
has Workflow type
not reported
8721/3
Washington University - St. Louis
https://github.com/NCI-GDC/star-2pass-tool
new_tumor_event
has New tumor event
Newly developed neoplasm after initial treatment has finished.
samples.tumor_code_id
has Tumor code ID
A BCR-defined ID code for the tumor sample.
Thymus
8
Complete Remission/Response
primary_therapy_outcome_success
The type of the disease or condition studied. See NCI Thesaurus Code: C2991.
Disease type
c13.9
true
This value is denoted by a list of file names associated with the File node.
files.file_id
File
Tumor code
samples.tumor_code
c34.2
c18.9
Intrahepatic Recurrence
Annotated Somatic Mutation
Partial Remission/Response
primary_therapy_outcome_success
0.6
GRCh38.d1.vd1
Illumina Human Methylation 450
exposures.alcohol_history
has Alcohol history
A response to the question that asks whether the participant has consumed at least 12 drinks of any kind of alcoholic beverage in their lifetime. See CDE (Common Data Element) Public ID: 2201918. Also: A description of an individual's current and past experience with alcoholic beverage consumption. See NCI Thesaurus Code: C81229.
Nationwide Children's Hospital BCR
72
The morphology code which describes the characteristics of the tumor itself, including its cell type and biologic activity, according to the third edition of the International Classification of Diseases for Oncology (ICD-O). See CDE (Common Data Element) Public ID: 3226275.
Morphology
Lung Clear Cell Adenocarcinoma
Pharmaceutical therapy type
The type of treatment of the disease through the use of drugs. NCI Thesaurus Code: C15986.
20
karnofsky_performance_score
WARN
Canada's Michael Smith Genome Sciences Centre
c83.3
The full name of the project or study that generated the data. See NCI Thesaurus Code: C41198.
Investigation name
c02.9
Harvard Beth Israel
c18.6
N1b
pathologic_N
genome.wustl.edu
Sample type
The type of material taken from a biological entity for testing, diagnosis, propagation, treatment, or research purposes. This includes tissues, body fluids, cells, organs, embryos, body excretory products, etc. See NCI Thesaurus Code: C70713.
Mesothelioma
MESO
University of Sydney
T1b
pathologic_T
8503/3
Hepatocholangiocarcinoma (Mixed)
8500/3
Ovary
clinical_T
T4c
not reported
c06.9
Gundersen Lutheran
c44.9
Pancreas-Undifferentiated Carcinoma
pathologic_T
T3a
Imperial College
Lung Signet Ring Adenocarcinoma
Muscle invasive urothelial carcinoma (pT2 or above)
Hormone Therapy
therapy_type
c50.5
c34.9
treatments.treatment_or_therapy
A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected. See CDE (Common Data Element) Public ID: 4231463.
has Treatment or therapy
8742/3
Kidney Clear Cell Renal Carcinoma
Oligodendroglioma
T2a1
pathologic_T
St. Joseph's Hospital (AZ)
Other, specify
MD Anderson
Simple Nucleotide Variation
Thyroid Papillary Carcinoma - Tall Cell (>= 50% tall cell features)
read_group_qcs.workflow_link,analysis.workflow_link
The link to Github hash for the CWL workflow used (GDC related).
has Workflow link
8290/3
Cervical Lymph Nodes
https://github.com/NCI-GDC/vep-cwl
performance_status_scale_timing
Preoperative
N1mi
pathologic_N
spectrophotometer_method
PicoGreen
University of Utah
clinical_T
T4b
race
native hawaiian or other pacific islander
Ethnicity
A socially defined category of people based on common ancestral, cultural, biological, and social factors. See NCI Thesaurus Code: C29933.
c05.0
Hartford Hospital
A Boolean value that denotes whether tissue samples used in the analysis were formalin-fixed paraffin-embedded (FFPE)
samples.is_ffpe,portions.is_ffpe
Is FFPE
has Tissue source site name
tissue_source_site.name
The full name of a clinical site that collects and provides patient samples and clinical metadata for research use. See NCI Thesaurus Code: C103264.
c49.8
HTSeq - FPKM
Center type
The type classification of the center (e.g. CGCC).
Stage IIIC2
clinical_stage
c02.1
Prior malignancy
Text term to describe the patient's history of prior cancer diagnosis and the spatial location of any previous cancer occurrence. See CDE (Common Data Element) Public ID: 3081934.
c21.8
Mary Bird Perkins Cancer Center - Our Lady of the Lake
WITH TUMOR
person_neoplasm_cancer_status
project.disease_type
The type of the disease or condition studied. See NCI Thesaurus Code: C2991.
has Disease type
BWA with Mark Duplicates and Cocleaning
MD Anderson Cancer Center
karnofsky_performance_score
40
c16.5
c25.0
41
c71.7
Biochemical evidence of disease
c15.4
Greenville Health Systems
new_neoplasm_event_occurrence_anatomic_site
Anatomic site of newly developed neoplasm.
has New tumor anatomic site
A Boolean value which denotes whether a spike-in is included or not.
read_groups.includes_spike_ins
has Includes spike ins
8730/3
8582/1
c77.2
BCM
c50.9
FAIL
8811/3
c67.9
Emory University
NO
not reported
ethnicity
8173/3
Regina Elena National Cancer Institute
has Percent GC content
The overall %GC of all bases in all sequences.
read_group_qcs.percent_gc_content
c13.9
https://github.com/NCI-GDC/mutect-cwl
c15.3
MuSE Annotation
The full name of the project or study that generated the data. See NCI Thesaurus Code: C41198.
project.name
has Investigation name
JHU
BCGSC miRNA Profiling
Untreated primary (de novo) GBM
read_groups.size_selection_range
has Size selection range
The range of size selection.
8380/3
c06.2
8582/3
The investigation, analysis, and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms. This also refers to a scientific determination of any kind or the concise results of such an investigation. A diagnosis can be identified by a UUID. See NCI Thesaurus Code: C15220.
diagnoses.diagnosis_id
has Diagnosis
Classification of tumor
Text that describes the kind of disease present in the tumor specimen as related to a specific point in time. See CDE (Common Data Element) Public ID: 3288124
c69.4
22
University of Kansas
Acute Myeloid Leukemia
stage iia
8074/3
c77.9
FAIL
pathologic_N
N1
X
samples.initial_weight
has Initial weight
Initial sample/specimen weight (in grams).
IMPLANTS
radiation_type
c03.9
Oropharynx
8772/3
c74.9
has Drug name
The most recognizable term associated with a pharmaceutical product used to prevent, diagnose, treat or relieve symptoms of a disease or abnormal condition. NCI Thesaurus Code: C97104.
drug_name
Lymph Node Only
PCPG
Pheochromocytoma and Paraganglioma
Proteogenex, Inc
Bile Duct
Head & Neck Squamous Cell Carcinoma, Spindle Cell Variant
9540/3
c18.2
c54.0
Malignant Peripheral Nerve Sheath Tumors (MPNST)
has Follow up
Follow ups which monitor a person's health over time after treatment. Members of the follow up entity can be identified by a UUID. A case can have multiple follow ups generated at different time. See NCI Thesaurus Code: C16033.
follow_up
Cornell Medical College
61
The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The T category describes the original (primary) tumor. NCI Thesaurus Code: C48881 and C48739.
pathologic_T
has Pathologic T (TNM)
c00.9
c44.7
12
sample_type_id
University of Kansas Medical Center
c54.3
has Pathology report UUID
UUID of the related pathology report.
samples.pathology_report_uuid
3
sample_type_id
section_location
BOTTOM
Stage IIIC
clinical_stage
c74.9
BAM
9401/3
University of Chicago
Liver Hepatocellular Carcinoma
LIHC
The version of the workflow used to analyze data.
read_group_qcs.workflow_version,analysis.workflow_version
has Workflow version
c67.5
Thymoma; Type AB
c56.9
Wake Forest University
8890/3
primary_therapy_outcome_success
Normalization of Tumor Markers, but Residual Tumor Mass
University of Mannheim
Trunk
c16.2
Garvan Institute of Medical Research
c54.9
8370/3
WARN
clinical_stage
Stage IIA2
Washington University - Mayo Clinic
Brain Lower Grade Glioma
Ontario Institute for Cancer Research (OICR)/Ottawa
International Genomics Consortium
has Amount
analytes.amount,aliquots.amount
The amount of a product (in g or volume in mL) prepared for an analysis.
Sequencing center
The name of the center that provided the sequence files.
c77.5
8584/3
c18.9
has Spike ins concentration
The concentration of a spike-in.
read_groups.spike_ins_concetration
University of Pennsylvania
c03.0
Adrenocortical Carcinoma- Myxoid Type
Neuroblastoma (NBL)
c04.0
c77.1
miRNA-Seq
Buccal Cell Normal
sample_type
Kidney Renal Papillary Cell Carcinoma
KIRP
8720/3
Aligned Reads
Not available
c61.9
c54.0
other
race
RNA-Seq
Henry Ford Hospital
62
Soft Tissue
c69.8
not reported
new_neoplasm_occurrence_anatomic_site_text
Alternative anatomic site of a newly developed neoplasm which has not been listed under 'New tumor anatomic site'.
has Other new tumor anatomic site
stage iic
c77.3
PASS
c24.0
N2c
clinical_N
has Spectrophotometer method
A method of quantifying the content of nucleic acids in any sample, used to measure sample purity (e.g. UV spec.)
analytes.spectrophotometer_method
c49.6
https://github.com/NCI-GDC/somatic-maf-cwl
Translational Genomics Research Institute
c38.1
c34.3
has Portion weight
portions.weight
Weight of a portion prepared for the analysis (in mg).
c67.3
c52.9
c76.3
SKCM
Skin Cutaneous Melanoma
Tayside Tissue Bank
c15.9
8821/1
T1a
pathologic_T
c25.9
c48.1
c16.5
8541/3
c67.5
pathologic_M
M0
c17.9
clinical_T
T2
Lung Bronchioloalveolar Carcinoma Nonmucinous
c53.1
c18.7
c50.2
c80.9
has Per base N content
read_group_qcs.per_base_n_content
The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
Global BioClinical - Georgia
Candler
32
c54.9
pathologic_T
T0
33
c74.9
Wilms tumor (WT)
i/ii nos
Regional lymph node
RNA
73
A shortened name of the center (e.g. BI).
Center short name
c25.1
WARN
23
Pheochromocytoma
Not available
8851/3
53
T1
clinical_T
OPEN
Open
TX
clinical_T
c25.0
Masked Somatic Mutation
c77.1
clinical_stage
Stage III
Non cancerous tissue
8850/3
Not available
Prostate
Greater Poland Cancer Center
Recurrent Tumor
sample_type
Paraaortic lymph nodes
Distant Recurrence
c67.5
Broad Institute of MIT and Harvard
diagnoses.primary_diagnosis
has Primary diagnosis
Text term for the structural pattern of cancer cells used to define a microscopic diagnosis. See CDE (Common Data Element) Public ID: 3081934.
Colon Mucinous Adenocarcinoma
Institute for Medical Research
Adrenal Gland
GSC
8581/3
c71.7
https://github.com/NCI-GDC/htseq-cwl
c44.7
Thyroid
Serous Cystadenocarcinoma
42
Skin
has Experimental strategy
files.experimental_strategy
The method or protocol used to perform the laboratory analysis. See NCI Thesaurus Code: C43622.
pathologic_T
T4c
c16.5
c44.2
Head and Neck Squamous Cell Carcinoma
HNSC
71
8170/3
c62.90
PASS
sample_type_id
7
SANGER
c44.3
c71.9
9020/3
9053/3
PNNL
Sequence length distribution
The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
therapy_type
Ancillary
Adrenocortical Carcinoma
stage iiib
c18.0
c34.0
Medical College of Georgia
new_tumor_event
New tumor event
Newly developed neoplasm after initial treatment has finished.
false
Cholangiocarcinoma; intrahepatic
Hepatocellular Carcinoma
Immunotherapy
therapy_type
Not available
vital_status
The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The T category describes the original (primary) tumor. NCI Thesaurus Code: C48881 and C48739.
Pathologic T (TNM)
pathologic_T
TX
pathologic_T
8502/3
The number of times the kmer occurs in the sequence. Analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
Kmer content
has Target capture kit target region
read_groups.target_capture_kit_target_region
The target region for target capture kit.
c69.9
Performance status score: timing
performance_status_scale_timing
A time reference for the Karnofsky score and/or the ECOG score using the defined categories.
8744/3
c04.0
31
c50.5
c53.9
c76.1
WARN
c50.2
c48.2
stage 0
Stage I
clinical_stage
Cholangiocarcinoma; distal
University Medical Center Hamburg-Eppendorf
Medullary Carcinoma
Institut Curie
Lung Adenocarcinoma- Not Otherwise Specified (NOS)
c69.80
2
gender
male
Lung Solid Pattern Predominant Adenocarcinoma
8140/3
The sequencing technique intended for the library.
read_groups.library_strategy
has Library strategy
Lawrence Berkeley National Laboratory
T2b
pathologic_T
8252/3
8693/3
c08.0
Primary site
The anatomical site where the primary tumor is located in the organism. See NCI Thesaurus Code: C43761.
has Percent lymphocyte infiltration
The fraction of lymphocyte cells to the gross inflammatory cells seen on a slide.
slides.percent_lymphocyte_infiltration
43
University of Florida
BWA-aln
c49.5
has Last known disease status
diagnoses.last_known_disease_status
The state or condition of an individual's neoplasm at a particular point in time. See CDE (Common Data Element) Public ID: 3392464.
clinical_stage
Stage IIIA
Testicular Germ Cell Tumors
Skin
8583/3
has Tissue source site
c54.1
aliquots.center.center_id,portions.center.center_id
has Center ID
A professional organization or group which has or is able to submit data. It can be identified by a UUID.
not reported
8370/1
c38.0
University of Sao Paulo
Washington University School of Medicine Proteomics
c18.3
8335/3
c02.2
c16.1
9680/3
Desmoid Tumor
8230/3
stage iiia
Liver
c77.0
c18.6
Not available
c41.0
c16.3
sample_type
Additional Metastatic
Mayo Clinic Rochester
radiation_type
EXTERNAL BEAM
https://github.com/NCI-GDC/cocleaning-cwl
vital_status
alive
HudsonAlpha Institute for Biotechnology
samples.sample_type
has Sample type
The type of material taken from a biological entity for testing, diagnosis, propagation, treatment, or research purposes. This includes tissues, body fluids, cells, organs, embryos, body excretory products, etc. See NCI Thesaurus Code: C70713.
Tufts Medical Center
Locoregional Disease
WUSM
Kidney Chromophobe
52
Head and Neck Squamous Cell Carcinoma
performance_status_scale_timing
Post Adjuvant Therapy
c18.4
therapy_type
Not available
c44.9
c41.1
The Johns Hopkins University Proteomics
8330/3
Adapter content
An analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
The name of the center that provided the item.
Source center
27
c76.0
c34.90
Esophagus
Washington University - NYU
Washington University - Rush University
Thoraxklinik at University Hospital Heidelberg
c44.5
c25.2
Ovary
c06.2
COMBINATION
radiation_type
read_groups.read_length
has Read length
The length of the reads.
Lung Squamous Cell Carcinoma
Retroperitoneum
MD Anderson - Institute for Applied Cancer Science
clinical_T
T1a
c15.1
c38.0
70
karnofsky_performance_score
9051/3
Mayo Clinic
Mucinous (Colloid) Carcinoma
has Access level
A Boolean value indicating Controlled Data or Open Data. Controlled Data is data from public datasets that has limitations on use and requires approval by dbGaP. Open Data is data from public datasets that doesn't have limitations on its use.
files.access
A further, more specific classification of the data category, based on the information that it contains.
files.data_type
has Data type
c67.0
Leptomeninges
Gender
The collection of behaviors and attitudes that distinguish people on the basis of the societal roles expected for the two sexes. See NCI Thesaurus Code: C17357.
c71.6
Contralateral Pleura
MAF
ABS - Research Metrics Pakistan
Lung Squamous Cell Carcinoma
LUSC
Lung Adenocarcinoma Mixed Subtype
c71.0
Radiation therapy site
The location to which radiation therapy was administered.
The fraction of monocyte cells to the gross inflammatory cells seen on a slide.
has Percent monocyte infiltration
slides.percent_monocyte_infiltration
N0
clinical_N
8854/3
c18.7
Milan - Italy, Fondazione IRCCS Instituto Neuroligico C. Besta
Vital status
The state of being living or deceased for Cases that are part of the investigation. See NCI Thesaurus Code: C25717.
Liver Hepatocellular Carcinoma
c49.0
Ipsilateral Chest Cavity
c50.9
8083/3
c15.9
Metaplastic Carcinoma
10
karnofsky_performance_score
Tumor grade
The numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness. See CDE (Common Data Element) Public ID: 2785839.
RNA-Seq
Copy Number Segment
Warm ischemia time, elapsed between clamping and freezing a sample, as denoted in minutes.
has Time between excision and freezing
time_between_excision_and_freezing
c25.0
31
c30.0
Text term for the structural pattern of cancer cells used to define a microscopic diagnosis. See CDE (Common Data Element) Public ID: 3081934.
Primary diagnosis
Kidney Renal Clear Cell Carcinoma
KIRC
R
Stage IB1
clinical_stage
has Center type
aliquots.center.center_type,portions.center.center_type
The type classification of the center (e.g. CGCC).
c22.1
has Intermediate dimension
samples.intermediate_dimension
The intermediate dimension of sample/specimen (in centimeters).
8160/3
c71.6
https://github.com/NCI-GDC/dnacopy-tool
BLN - University of Miami
c55.9
Memorial Sloan Kettering Cancer Center
10
c69.30
Infiltrating Lobular Carcinoma
Skin Cutaneous Melanoma
SANGER
DNA Methylation
Uterine Corpus Endometrial Carcinoma
Transcriptome Profiling
8521/1
Saint Mary's Health Care
Washington University - Emory
A Boolean value indicating Controlled Data or Open Data. Controlled Data is data from public datasets that has limitations on use and requires approval by dbGaP. Open Data is data from public datasets that doesn't have limitations on its use.
Access level
9
clinical_stage
Stage IIIB
University of Nebraska Medical Center (UNMC)
Lung Bronchioloalveolar Carcinoma Mucinous
2
has Target capture kit version
The version of a target capture kit.
read_groups.target_capture_kit_version
Uveal Melanoma
Stage IVC
clinical_stage
Diffuse malignant mesothelioma - NOS
Biospecimen Supplement
St. Joseph's Medical Center-(MD)
Baylor College of Medicine
SBG cancer ontology
The shortest dimension of sample/specimen (in centimeters).
Shortest dimension
Stomach, Adenocarcinoma, Diffuse Type
HMS
stage ivb
PASS
Gene Expression Quantification
Epithelioid mesothelioma
sample_type
Primary Blood Derived Cancer - Peripheral Blood
Indivumed
clinical_stage
Stage IIIC1
c69.3
c44.4
Pleura/Pleural effusion
stage iii
c67.9
c37
The time interval from the date of the last follow up to the date of the initial pathologic diagnosis, represented as a calculated number of days. See CDE (Common Data Element) Public ID: 3008273.
diagnoses.days_to_last_known_disease_status
has Days to last known disease status
c10.9
c67.4
c71.3
N2a
pathologic_N
pathologic_T
T2c
60
karnofsky_performance_score
mdanderson.org
ILSBio
can start query
CESC
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma
St. University of Colorado Denver
c22.0
MX
clinical_M
stage ib
MuTect2 Variant Aggregation and Masking
MuSE
c25.1
Adrenocortical carcinoma- Usual Type
c49.8
Clinical N (TNM)
The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The N category describes whether or not the cancer has reached nearby lymph nodes NCI Thesaurus Code: C48881 and C25384.
clinical_N
c18.3
Lung Micropapillary Adenocarcinoma
c49.6
The catalog number of the sequencing library preparation kit.
read_groups.library_preparation_kit_catalog_number
has Library preparation kit catalog number
1.5
clinical_stage
Stage IIA2
8896/3
8174/3
University of New Mexico
Spectrophotometer method
A method of quantifying the content of nucleic acids in any sample, used to measure sample purity (e.g. UV spec.)
has Year of death
demographic.year_of_death
A numeric value to represent the year of the death of an individual. See CDE (Common Data Element) Public ID: 2897030.
8700/3
treatments.treatment_intent_type
The text term to identify the reason for the administration of a treatment regimen. [Manually-curated]. See CDE (Common Data Element) Public ID: 2793511.
has Treatment intent type
Dedifferentiated liposarcoma
c43.51
c10.9
HTSeq - Counts
The classification of data used in (or produced by) the analysis, based on its form and content. See NCI Thesaurus Code: C42645.
files.data_category
has Data category
Uterus
VarScan2
8950/3
Brain
c47.1
BC Cancer Agency
ABS - IUPUI
8020/3
c67.2
3
Primary mediastinal (thymic) DLBCL
c16.3
c50.3
Not available
project.project_id
A value denoting the project or study that generated the data. See NCI Thesaurus Code: C41198.
has Investigation
CGCC
Metastatic
c63.1
Abdomen
Seminoma; NOS
1
eastern_cancer_oncology_group
Michigan University
Center
Head and Neck
c34.0
Sarcoma; synovial; poorly differentiated
clinical_T
T4
BLN - UT Southwestern Medical Center at Dallas
c49.2
BLN Baylor
Washington University School of Medicine
91
8524/3
read_groups.spike_ins_fasta
has Spike ins fasta
The name of the FASTA file that contains the spike-in sequences.
Locoregional Recurrence
Soft Tissue
University of Sheffield
analytes.a260_a280_ratio
A purity measurement that weighs the absorbance at 260nm (DNA concentration) against the absorbance at 280nm (protein concentration/contamination).
has A260_A280 ratio
c73
BLN UT Southwestern Medical Center at Dallas
Ipsilateral Chest Wall
c47.1
8022/3
University of Western Australia
PASS
c16.0
Swedish Neurosciences
VUMC
Vanderbilt
Oligoastrocytoma
clinical_T
T2c
Uterine Carcinosarcoma
UCS
c01
c07.9
No New Tumor Event
Sapienza University of Rome
karnofsky_performance_score
50
8574/3
University of Puerto Rico
Esophagus Adenocarcinoma, NOS
c40.2
1.2
University of Texas MD Anderson Cancer Center
c72.0
Liver
pathologic_N
N2
radiation_type
RADIOISOTOPE
Vulva
Acute myeloid leukemia (AML)
Thomas Jefferson University
7
8581/1
MD Anderson - RPPA Core Facility (Proteomics)
c48.2
c32.9
c74.0
8072/3
c34.10
c16.9
GRCh38.p0
Both Locoregional and Distant Metastasis
Pulmonary
University of Colorado Denver
c10.3
c32.1
Cleveland Clinic Foundation
JHU_USC
Non-Seminoma; Teratoma (Mature)
c49.5
Sequencing reads from one lane of an NGS experiment. This can be identified by a UUID.
read_groups.read_group_id
has Read group
c22.1
stage ivc
SARC
Sarcoma
Lymph Nodes
Fibrolamellar Carcinoma
c55.9
Stomach Adenocarcinoma
STAD
MSKCC
G
Pancreas-Adenocarcinoma-Other Subtype
13
Bone Marrow
5
sample_type_id
Not available
c15.4
LAML
Acute Myeloid Leukemia
c67.6
Colon Adenocarcinoma
https://github.com/NCI-GDC/muse-cwl
Fundacio Clinic per a la Recerca Biomedica
NCH
Methylation Beta Value
Mayo Clinic Arizona
Breast
BCGSC
Asterand
The version (for instance, manufacturer or model) of the technology that was used for sequencing or assaying. See NCI Thesaurus Code: C45378.
Platform
c05.9
8523/3
c03.9
c49.9
c77.0
8680/3
Baylor College of Medicine
UCEC
Uterine Corpus Endometrial Carcinoma
c03.0
c50.3
nationwidechildrens.org
days_to_sample_procurement
has Days to sample procurement
The time interval from the date of sample collection to the date of sample procurement, expressed in days.
tissue_source_site.bcr_id
The BCR (Biospecimen Core Resource) provided ID for a tissue source site. See NCI Thesaurus Code: C103264.
has Tissue source site bcr ID
N2b
pathologic_N
pathologic_N
N3a
Primary Tumor
sample_type
10
Biospecimen
The full name of a clinical site that collects and provides patient samples and clinical metadata for research use. See NCI Thesaurus Code: C103264.
Tissue source site name
0
karnofsky_performance_score
Spectrum Health
Sarcoma
clinical_stage
Stage IVA
IGC
Serous endometrial adenocarcinoma
Yale
c16.2
1.3
UV Spec
spectrophotometer_method
Valley Hospital
analysis.analysis_id,downstream_analyses.analysis_id
Analysis workflows used for processing data, and it can be identified by a UUID.
true
Analysis
University Health Network
PASS
c18.3
Updated datetime
demographic.updated_datetime,treatments.updated_datetime,diagnoses.updated_datetime,exposures.updated_datetime,aliquots.updated_datetime,analytes.updated_datetime,samples.updated_datetime,cases.updated_datetime,slides.updated_datetime,portions.updated_datetime,read_group_qcs.updated_datetime,read_groups.updated_datetime,analysis.updated_datetime,files.updated_datetime,downstream_analysis.updated_datetime
Updated datetime.
Type of newly developed neoplasm after initial treatment has finished.
New tumor event type
c71.8
c44.5
pathologic_N
N1c
University of Schleswig-Holstein
T4b
pathologic_T
9400/3
Columbia University
The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
read_group_qcs.per_base_sequence_content
has Per base sequence content
University of Oklahoma HSC
51
Albert Einstein Medical Center
c38.1
c54.0
c02.1
Analyte type ID
An ID that determines the type of an analyte on molecular bases. A single letter BCR code for the analyte type.
c50.5
radiation_type
External
c18.6
N3
pathologic_N
Affymetrix SNP 6.0
c15.1
Repli-G X (Qiagen) DNA
c67.6
Adjuvant Therapy
performance_status_scale_timing
Pacific Northwest National Lab
0
eastern_cancer_oncology_group
c32.9
c44.2
c44.6
c71.4
12
Cureline
c77.4
Thyroid Carcinoma
BI
c08.0
c54.1
c18.5
c80.1
c69.8
Tumor Bed
0.2
0.1
The BCR (Biospecimen Core Resource) provided ID for a tissue source site. See NCI Thesaurus Code: C103264.
Tissue source site bcr ID
c71.2
8250/3
stage x
0.4
University Hospital Erlangen
The date of sequencing.
read_groups.sequencing_date
has Sequencing date
c71.2
c48.2
Sanger / Illumina 1.9
36
FAIL
MuTect2 Annotation
8200/3
c16.9
c41.0
HAIB
pathologic_N
N3b
8507/3
c72.9
c76.3
not reported
c24.0
9382/3
Thymoma; Type C
Solid Tissue Normal
sample_type
A generic name for the workflow used to analyze data.
Workflow type
Case Western
Vanderbilt University Proteomics
Diffuse large B-cell lymphoma (DLBCL) NOS (any anatomic site nodal or extranodal)
PASS
c50.2
c49.4
8693/1
Duke
c02.9
Peter MacCallum Cancer Center
Kidney
c74.1
8586/3
c16.2
9070/3
race
asian
Stomach, Intestinal Adenocarcinoma, Tubular Type
has Tissue source site
Non-Seminoma; Teratoma (Immature)
Extremities
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma
8482/3
Treated primary GBM
Vanderbilt University
Blood Derived Normal
sample_type
Mixed serous and endometrioid
8441/3
c20.9
c25.8
H
miRNA-Seq
pathologic_T
T2a2
c44.9
Gynecologic Oncology Group
Progression of Disease
BCR
c09.9
Lung Adenocarcinoma
LUAD
PASS
National Institutes of Health
c10.3
University Hospital Motol
c32.1
diagnoses.morphology
The morphology code which describes the characteristics of the tumor itself, including its cell type and biologic activity, according to the third edition of the International Classification of Diseases for Oncology (ICD-O). See CDE (Common Data Element) Public ID: 3226275.
has Morphology
c03.1
not hispanic or latino
ethnicity
9440/3
81
Last known disease status
The state or condition of an individual's neoplasm at a particular point in time. See CDE (Common Data Element) Public ID: 3392464.
0.8
c54.2
Illumina Human Methylation 27
Brain Lower Grade Glioma
LGG
University of Alabama
44
c53.1
jhu-usc.edu
FAIL
Uterine Carcinosarcoma/MMMT: Homologous Type
8522/3
c32.9
c61.9
HTSeq - FPKM-UQ
FAIL
8130/3
8800/3
c40.3
c25.8
Illumina 1.5
c51.9
Cholangiocarcinoma; hilar/perihilar
c38.3
Wills Eye Institute
c70.1
32
The link to Github hash for the CWL workflow used (GDC related).
Workflow link
Osteosarcoma (OS)
University of Washington
Prostate Adenocarcinoma Acinar Type
80
karnofsky_performance_score
BCM
Stomach, Adenocarcinoma, Not Otherwise Specified (NOS)
8340/3
c75.5
8520/3
Distant site
University of Arizona
Roswell Park
M1a
clinical_M
Endocervical Adenocarcinoma of the Usual Type
Brigham and Women's Hospital
lbl.gov
Esophageal Carcinoma
N3c
pathologic_N
c50.8
Not available
c44.4
c06.0
ILSBIO
c03.9
9085/3
NCH BCR
c40.3
The topography code which describes the anatomical site of origin of the neoplasm according to the third edition of the International Classification of Diseases for Oncology (ICD-O). See NCI Thesaurus Code: C37978. See CDE (Common Data Element) Public ID: 3226281.
Site of resection or biopsy
c02.9
Recurrence
FAIL
c53.9
c02.2
Bladder
12
Thymoma; Type A
c18.9
8951/3
Not available
pnl.gov
c49.0
FFPE Scrolls
sample_type
WARN
8510/3
stage iva
11
c71.8
c05.9
The value denotes the type of high-energy radiation used to kill cancer cells and shrink tumors. NCI Thesaurus Code: C15986.
Radiation type
c25.8
Fred Hutchinson
c77.1
pathologic_T
T2a
University of California San Diego
Moffitt Cancer Center
c49.9
BLN - Baylor
c38.3
treatments.days_to_treatment
The number of days from the date of the initial pathologic diagnosis that treatment began.
has Days to treatment
c50.9
The code that determins center that has submitted data.
Center code
c76.2
c69.4
c76.1
Lung Adenocarcinoma
Gundersen Lutheran Health System
A response to the question that asks whether the participant has consumed at least 12 drinks of any kind of alcoholic beverage in their lifetime. See CDE (Common Data Element) Public ID: 2201918. Also: A description of an individual's current and past experience with alcoholic beverage consumption. See NCI Thesaurus Code: C81229.
Alcohol history
TSV
https://github.com/NCI-GDC/met-liftover-tool
c77.5
c72.0
c34.2
GenomePlex (Rubicon) Amplified DNA
c56.9
8090/3
c71.1
Non-Seminoma; Yolk Sac Tumor
8342/3
22
University of Liverpool
St. Joseph's Hospital Arizona
UCSF
Thyroid Papillary Carcinoma - Follicular (>= 99% follicular patterned)
8440/3
c54.3
8490/3
c80.9
Stage IV
clinical_stage
0.5
9451/3
Other, specify
phs000178
8180/3
clinical_stage
Stage II
Sarcomatoid mesothelioma
Distant Metastasis
Infiltrating Carcinoma NOS
Fox Chase Cancer Center
c44.701
Dept of Neurosurgery at University of Heidelberg
Johns Hopkins
Lung Mucinous Adenocarcinoma
1
23
not reported
Prostate
c62.9
c06.9
c53.1
c38.4
c53.9
WARN
c05.9
Other, specify in notes
therapy_type
Duke University
clinical_M
M1
The University of New South Wales
c61.9
c67.4
Cleveland Clinic
Cervix
c51.9
Pancreatic Adenocarcinoma
c34.3
c52.9
c49.10
Memorial Sloan Kettering
c48.1
Washington University - Alabama
c50.8
c54.1
CHI-Penrose Colorado
Stomach, Intestinal Adenocarcinoma, Mucinous Type
c69.3
The Ohio State University
Prostate Adenocarcinoma, Other Subtype
Washington University - CALGB
PASS