Data Dictionary

The ICGC ARGO Data Dictionary expresses the details of the data model, which adheres to specific formats and restrictions to ensure a standard of data quality. The following list describes the attributes and permissible values for all of the fields within the clinical tsv files for the ARGO Data Platform.

Version 1.2

Last updated: August 5, 2020
9 files > 129 fields
Data Tier:

- Select an option -

Attribute:

- Select an option -

Sample Registration (sample_registration)

9 Fields
The collection of data elements required to register the required Donor-Specimen-Sample data to the ARGO Data Platform. Registration of samples is required before molecular and clinical data submission can proceed.
File Name Example: sample_registration[-optional-extension].tsv
Field & Description
Data Tier
Attributes
Type
Permissible Values
Notes & Scripts
program_id
Unique identifier of the ARGO program.
ID
Required
TEXT
This is the unique id that is assigned to your program. If you have logged into the platform, this is the Program Id that you see in the Program Services area. For example, TEST-CA is a Program ID.
submitter_donor_id
Unique identifier of the donor, assigned by the data provider.
ID
Required
TEXT
Values must meet the regular expression
To prevent data collisions, submitter_id cannot begin with any of the ARGO ID prefixes. The restricted prefixes include: `DO`, `SP`, `SA`,`TR`,`FU`, `PD`.
gender
Description of the donor self-reported gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles.
Core
Required
TEXT

Female

Male

Other

submitter_specimen_id
Unique identifier of the specimen, assigned by the data provider.
ID
Required
TEXT
Values must meet the regular expression
To prevent data collisions, submitter_id cannot begin with any of the ARGO ID prefixes. The restricted prefixes include: `DO`, `SP`, `SA`,`TR`,`FU`, `PD`.
specimen_tissue_source
Tissue source of the biospecimen.
Core
Required
TEXT

Blood derived - bone marrow

Blood derived - peripheral blood

Blood derived

Bone marrow

Bone

21 more
tumour_normal_designation
Description of specimens tumour/normal status for data processing.
Core
Required
TEXT

Normal

Tumour

specimen_type
Description of the kind of specimen that was collected with respect to tumour/normal tissue origin.
Core
Required
TEXT

Cell line - derived from normal

Cell line - derived from tumour

Cell line - derived from xenograft tumour

Metastatic tumour - additional metastatic

Metastatic tumour - metastasis local to lymph node

10 more
submitter_sample_id
Unique identifier of the sample, assigned by the data provider.
ID
Required
TEXT
Values must meet the regular expression
To prevent data collisions, submitter_id cannot begin with any of the ARGO ID prefixes. The restricted prefixes include: `DO`, `SP`, `SA`,`TR`,`FU`, `PD`.
sample_type
Description of the type of molecular sample used for testing.
Core
Required
TEXT

Amplified DNA

ctDNA

Other DNA enrichments

Other RNA fractions

polyA+ RNA

3 more

Donor (donor)

17 Fields
The collection of data elements related to a specific donor in an ARGO program.
File Name Example: donor[-optional-extension].tsv
Field & Description
Data Tier
Attributes
Type
Permissible Values
Notes & Scripts
program_id
Unique identifier of the ARGO program.
ID
Required
TEXT
submitter_donor_id
Unique identifier of the donor, assigned by the data provider.
ID
Required
TEXT
Values must meet the regular expression
To prevent data collisions, submitter_id cannot begin with any of the ARGO ID prefixes. The restricted prefixes include: `DO`, `SP`, `SA`,`TR`,`FU`, `PD`.
vital_status
Donor's last known state of living or deceased.
Core
Required
TEXT

Alive

Deceased

Unknown

cause_of_death
Indicate the cause of a donor's death.
Core
Conditional
TEXT

Died of cancer

Died of other reasons

Unknown

Cause of death is only required to be submitted if the donor's vital_status is Deceased.
survival_time
Interval of how long the donor has survived since primary diagnosis, in days.
Core
Conditional
INTEGER
Survival_time is only required to be submitted if the donor's vital_status is Deceased.
primary_site
The text term used to describe the primary site of disease, as categorized by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O). This categorization groups cases into general categories.
Core
Required
TEXT

Accessory sinuses

Adrenal gland

Anus and anal canal

Base of tongue

Bladder

66 more
prior_malignancy
Prior malignancy affecting donor.
Extended
TEXT

Yes

No

Unknown

cancer_type_prior_malignancy
The code to represent the cancer type of a prior malignancy using the WHO ICD-10 code (https://icd.who.int/browse10/2019/en) classification.
Extended
TEXT
Values must meet the regular expression
age_at_prior_malignancy
If donor has history of prior malignancy, indicate age at previous diagnosis, in years.
Extended
INTEGER
laterality_of_prior_malignancy
If donor has history of prior malignancy, indicate laterality of previous diagnosis. (Codelist reference: NCI CDE: 4122391)
Extended
TEXT

Bilateral

Left

Midline

Not applicable

Right

3 more
height
Indicate the donor's height, in centimeters (cm).
Extended
INTEGER
weight
Indicate the donor's weight, in kilograms (kg).
Extended
INTEGER
bmi
Indicate the donor's Body Mass Index (BMI) in kg/m².
Extended
INTEGER
menopause_status
Indicate the donor's menopause status at the time of primary diagnosis. (Codelist reference: NCI CDE ID: 2434914)
Extended
TEXT

Indeterminate or unknown

Not applicable

Perimenopausal

Postmenopausal

Premenopausal

age_at_menarche
Indicate the donor's age of menarche, the first occurrence of menstruation.
Extended
INTEGER
number_of_pregnancies
Indicate the number of pregnancies a donor has had.
Extended
INTEGER
number_of_children
Indicate the number of children the donor has birthed.
Extended
INTEGER

Specimen (specimen)

22 Fields
The collection of data elements related to a donor's specimen. A specimen is any material sample taken for testing, diagnostic or research purposes.
File Name Example: specimen[-optional-extension].tsv
Field & Description
Data Tier
Attributes
Type
Permissible Values
Notes & Scripts
program_id
Unique identifier of the ARGO program.
ID
Required
TEXT
submitter_donor_id
Unique identifier of the donor, assigned by the data provider.
ID
Required
TEXT
Values must meet the regular expression
To prevent data collisions, submitter_id cannot begin with any of the ARGO ID prefixes. The restricted prefixes include: `DO`, `SP`, `SA`,`TR`,`FU`, `PD`.
submitter_specimen_id
Unique identifier of the specimen, assigned by the data provider.
ID
Required
TEXT
Values must meet the regular expression
To prevent data collisions, submitter_id cannot begin with any of the ARGO ID prefixes. The restricted prefixes include: `DO`, `SP`, `SA`,`TR`,`FU`, `PD`.
submitter_primary_diagnosis_id
Indicate the primary diagnosis event in the clinical timeline that this specimen acquisition was related to.
ID
Required
TEXT
Values must meet the regular expression
To prevent data collisions, submitter_id cannot begin with any of the ARGO ID prefixes. The restricted prefixes include: `DO`, `SP`, `SA`,`TR`,`FU`, `PD`.
pathological_tumour_staging_system
Specify the tumour staging system used to assess the cancer at the time the tumour specimen was resected. Pathological classification is based on the clinical stage information (acquired before treatment) and supplemented/modified by operative findings and pathological evaluation of the resected specimen.
Core
Conditional
TEXT

AJCC 8th edition

AJCC 7th edition

Ann Arbor staging system

Binet staging system

Durie-Salmon staging system

5 more
This field is only required if the specimen is a tumour.
pathological_t_category
The code to represent the stage of cancer defined by the size or contiguous extension of the primary tumour (T), according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.
Core
Conditional
TEXT

T0

T1

T1a

T1a1

T1a2

35 more
This field is required only if the selected pathological_tumour_staging_system is any edition of the AJCC cancer staging system.
pathological_n_category
The code to represent the stage of cancer defined by whether or not the cancer has reached nearby lymph nodes (N), according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.
Core
Conditional
TEXT

N0

N0a

N0a (biopsy)

N0b

N0b (no biopsy)

21 more
This field is required only if the selected pathological_tumour_staging_system is any edition of the AJCC cancer staging system.
pathological_m_category
The code to represent the stage of cancer defined by whether there are distant metastases (M), meaning spread of cancer to other parts of the body, according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.
Core
Conditional
TEXT

M0

M0(i+)

M1

M1a

M1a(0)

11 more
This field is required only if the selected pathological_tumour_staging_system is any edition of the AJCC cancer staging system.
pathological_stage_group
Specify the tumour stage, based on pathological_tumour_staging_system, used to assess the cancer at the time the tumour specimen was resected.
Core
Conditional
TEXT

Stage 0

Stage 0a

Stage 0is

Stage I

Stage IA

60 more
This field depends on the selected pathological_tumour_staging_system, and is only required if the specimen is a tumour. Please refer to the documentation for Tumour Staging Classifications: http://docs.icgc-argo.org/docs/submission/dictionary-overview#tumour-staging-classifications
specimen_acquisition_interval
Interval between primary diagnosis and specimen acquisition, in days.
Core
Required
INTEGER
The associated primary diagnosis is used as the reference point for this interval. To calculate this, find the number of days since the date of primary diagnosis.
tumour_histological_type
The code to represent the histology (morphology) of neoplasms that is usually obtained from a pathology report, according to the International Classification of Diseases for Oncology, 3rd Edition (WHO ICD-O-3). Refer to the ICD-O-3 manual for guidelines at https://apps.who.int/iris/handle/10665/42344.
Core
Conditional
TEXT
Values must meet the regular expression
This field is only required if the specimen is a tumour.
specimen_anatomic_location
Indicate the ICD-O-3 topography code for the anatomic location of a specimen when it was collected. Refer to the guidelines provided in the ICD-O-3 manual at https://apps.who.int/iris/handle/10665/42344.
Core
Required
TEXT
Values must meet the regular expression

Examples:
specimen_processing
Indicate the technique used to process specimen.
Extended
TEXT

Cryopreservation in liquid nitrogen (dead tissue)

Cryopreservation in dry ice (dead tissue)

Cryopreservation of live cells in liquid nitrogen

Cryopreservation - other

Formalin fixed & paraffin embedded

4 more
specimen_storage
Indicate the method of specimen storage for specimens that were not extracted freshly or immediately cultured.
Extended
TEXT

Cut slide

Frozen in -70 freezer

Frozen in liquid nitrogen

Frozen in vapour phase

Not Applicable

3 more
For specimens that were freshly extracted or immediately cultured, select Not Applicable.
reference_pathology_confirmed
Indicate whether the pathological diagnosis was confirmed by a (central) reference pathologist.
Core
Conditional
TEXT

Yes

No

Unknown

This field is only required if the specimen is a tumour.
tumour_grading_system
Specify the tumour staging system used to assess the description of a tumour based on how abnormal the tumour cells and the tumour tissue look under a microscope. Tumour grade is an indicator of how quickly a tumour is likely to grow.
Core
Conditional
TEXT

FNCLCC grading system

Four-tier grading system

Gleason grade group system

Grading system for GISTs

Grading system for GNETs

6 more
This field is only required if the specimen is a tumour.
tumour_grade
Grade of the tumour as assigned by the reporting tumour_grading_system.
Core
Conditional
TEXT

Low grade

High grade

GX

G1

G2

13 more
This field depends on the selected tumour_grading_system, and is only required if the specimen is a tumour. Please refer to the documentation for Tumour Grading Classifications: http://docs.icgc-argo.org/docs/submission/dictionary-overview#tumour-grading-classifications
percent_tumour_cells
Indicate a value, in decimals, that represents the percentage of infiltration by tumour cells in a specimen.
Core
Conditional
NUMBER
This field is only required if the specimen is a tumour.
percent_proliferating_cells
Indicate a value, in decimals, that represents the count of proliferating cells determined during pathologic review of the specimen.
Core
Conditional
NUMBER
This field is only required if the specimen is a tumour.
percent_inflammatory_tissue
Indicate a value, in decimals, that represents local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by redness, heat, pain, swelling and loss of function, with the need to heal damaged tissue.
Core
Conditional
NUMBER
This field is only required if the specimen is a tumour.
percent_stromal_cells
Indicate a value, in decimals, that represents the percentage of reactive cells that are present in a malignant tumour specimen but are not malignant such as fibroblasts, vascular structures, etc.
Core
Conditional
NUMBER
This field is only required if the specimen is a tumour.
percent_necrosis
Indicate a value, in decimals, that represents the percentage of cell death in a malignant tumour specimen.
Core
Conditional
NUMBER
This field is only required if the specimen is a tumour.

Primary Diagnosis (primary_diagnosis)

16 Fields
The collection of data elements related to a donor's primary diagnosis. The primary diagnosis is the first diagnosed case of cancer in a donor. To submit multiple primary diagnoses for a single donor, submit multiple rows in the primary diagnosis file for this donor.
File Name Example: primary_diagnosis[-optional-extension].tsv
Field & Description
Data Tier
Attributes
Type
Permissible Values
Notes & Scripts
program_id
Unique identifier of the ARGO program.
ID
Required
TEXT
submitter_donor_id
Unique identifier of the donor, assigned by the data provider.
ID
Required
TEXT
Values must meet the regular expression
To prevent data collisions, submitter_id cannot begin with any of the ARGO ID prefixes. The restricted prefixes include: `DO`, `SP`, `SA`,`TR`,`FU`, `PD`.
submitter_primary_diagnosis_id
Unique identifier of the primary diagnosis event, assigned by the data provider.
ID
Required
TEXT
Values must meet the regular expression
To prevent data collisions, submitter_id cannot begin with any of the ARGO ID prefixes. The restricted prefixes include: `DO`, `SP`, `SA`,`TR`,`FU`, `PD`.
age_at_diagnosis
Age that the donor was first diagnosed with cancer, in years. This should be based on the earliest diagnosis of cancer.
Core
Required
INTEGER
cancer_type_code
The code to represent the cancer type using the WHO ICD-10 code (https://icd.who.int/browse10/2019/en) classification.
Core
Required
TEXT
Values must meet the regular expression
cancer_type_additional_information
Additional details related to the cancer type that are not covered by the ICD-10 code provided in the cancer_type field.
Extended
TEXT
basis_of_diagnosis
Indicate the most valid basis of how the primary diagnosis was identified. If more than one diagnosis technique was used, select the term that has the highest code number (see notes). (Reference: IACR Standard for Basis of Diagnosis http://www.iacr.com.fr/images/doc/basis.pdf)
Extended
TEXT

Clinical investigation

Clinical

Cytology

Death certificate only

Histology of a metastasis

3 more
0: Death certificate only: Information provided is from a death certificate. 1: Clinical: Diagnosis made before death. 2: Clinical investigation: All diagnostic techniques, including X-ray, endoscopy, imaging, ultrasound, exploratory surgery (such as laparotomy), and autopsy, without a tissue diagnosis. 4: Specific tumour markers: Including biochemical and/or immunologic markers that are specific for a tumour site. 5: Cytology: Examination of cells from a primary or secondary site, including fluids aspirated by endoscopy or needle; also includes the microscopic examination of peripheral blood and bone marrow aspirates. 6: Histology of a metastasis: Histologic examination of tissue from a metastasis, including autopsy specimens. 7: Histology of a primary tumour: Histologic examination of tissue from primary tumour, however obtained, including all cutting techniques and bone marrow biopsies; also includes autopsy specimens of primary tumour. 9: Unknown: No information on how the diagnosis has been made.
number_lymph_nodes_positive
The number of regional lymph nodes reported as being positive for tumour metastases. (Reference: NCI CDE ID: 6113694)
Core
Required
INTEGER
number_lymph_nodes_examined
The total number of lymph nodes tested for the presence of cancer. (Reference: NCI CDE ID: 3)
Extended
INTEGER
clinical_tumour_staging_system
Indicate the tumour staging system used to stage the cancer at the time of primary diagnosis (prior to treatment).
Core
Required
TEXT

AJCC 8th edition

AJCC 7th edition

Ann Arbor staging system

Binet staging system

Durie-Salmon staging system

5 more
clinical_stage_group
Stage group of the tumour, as assigned by the reporting clinical_tumour_staging_system, that indicates the overall prognostic tumour stage (ie. Stage I, Stage II, Stage III etc.).
Core
Required
Conditional
TEXT

Stage 0

Stage 0a

Stage 0is

Stage I

Stage IA

60 more
This field is dependent on the selected clinical_tumour_staging_system. Please refer to the documentation for Tumour Staging Classifications: http://docs.icgc-argo.org/docs/submission/dictionary-overview#tumour-staging-classifications
clinical_t_category
The code to represent the extent of the primary tumour (T) based on evidence obtained from clinical assessment parameters determined at time of primary diagnosis and prior to treatment, according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.
Core
Conditional
TEXT

T0

T1

T1a

T1a1

T1a2

35 more
This field is required only if the selected clinical_tumour_staging_system is any edition of the AJCC cancer staging system.
clinical_n_category
The code to represent the stage of cancer defined by the extent of the regional lymph node (N) involvement for the cancer based on evidence obtained from clinical assessment parameters determined at time of primary diagnosis and prior to treatment, according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.
Core
Conditional
TEXT

N0

N0a

N0a (biopsy)

N0b

N0b (no biopsy)

21 more
This field is required only if the selected clinical_tumour_staging_system is any edition of the AJCC cancer staging system.
clinical_m_category
The code to represent the stage of cancer defined by the extent of the distant metastasis (M) for the cancer based on evidence obtained from clinical assessment parameters determined at time of primary diagnosis and prior to treatment, according to criteria based on multiple editions of the AJCC's Cancer Staging Manual. MX is NOT a valid category and cannot be assigned.
Core
Conditional
TEXT

M0

M0(i+)

M1

M1a

M1a(0)

11 more
This field is required only if the selected clinical_tumour_staging_system is any edition of the AJCC cancer staging system.
presenting_symptoms
Indicate presenting symptoms at time of primary diagnosis.
Extended
TEXT

Abdominal Pain

Anemia

Back Pain

Bloating

Cholangitis

19 more
To include multiple values, separate values with a pipe delimiter '|' within your file.
performance_status
Indicate the donor's performance status grade at the time of primary diagnosis. (Reference source: ECOG performance score grades from https://ecog-acrin.org/resources/ecog-performance-status).
Extended
TEXT

Grade 0

Grade 1

Grade 2

Grade 3

Grade 4

Grade 0: Fully active, able to carry on all pre-disease performance without restriction. Grade 1: Restricted in physically strenuous activity but ambulatory and able to carry out work of a light or sedentary nature (ie. Light house work, office work). Grade 2: Ambulatory and capable of all selfcare but unable to carry out any work activities; up and about more than 50% of waking hours. Grade 3: Capable of only limited selfcare; confined to bed or chair more than 50% of waking hours. Grade 4: Completely disabled; cannot carry on any selfcare; totally confined to bed or chair

Treatment (treatment)

21 Fields
The collection of data elements related to a donor's treatment at a specific point in the clinical record. To submit multiple treatments for a single donor, please submit treatment rows in the treatment file for this donor.
File Name Example: treatment[-optional-extension].tsv
Field & Description
Data Tier
Attributes
Type
Permissible Values
Notes & Scripts
program_id
Unique identifier of the ARGO program.
ID
Required
TEXT
submitter_donor_id
Unique identifier of the donor, assigned by the data provider.
ID
Required
TEXT
Values must meet the regular expression
To prevent data collisions, submitter_id cannot begin with any of the ARGO ID prefixes. The restricted prefixes include: `DO`, `SP`, `SA`,`TR`,`FU`, `PD`.
submitter_treatment_id
Unique identifier of the treatment, assigned by the data provider.
ID
Required
TEXT
Values must meet the regular expression
To prevent data collisions, submitter_id cannot begin with any of the ARGO ID prefixes. The restricted prefixes include: `DO`, `SP`, `SA`,`TR`,`FU`, `PD`.
submitter_primary_diagnosis_id
Indicate the primary diagnosis event in the clinical timeline that this treatment was related to.
ID
Required
TEXT
Values must meet the regular expression
To prevent data collisions, submitter_id cannot begin with any of the ARGO ID prefixes. The restricted prefixes include: `DO`, `SP`, `SA`,`TR`,`FU`, `PD`.
treatment_type
Indicate the type of treatment regimen that the donor completed.
Core
Required
TEXT

Ablation

Bone marrow transplant

Chemotherapy

Endoscopic therapy

Hormonal therapy

7 more
Depending on the treatment_type(s) selected, additional treatment details may be required to be submitted. For example, if treatment_type includes 'Chemotherapy', the supplemental Chemotherapy treatment type file is required. To include multiple values, separate values with a pipe delimiter '|' within your file.
age_at_consent_for_treatment
Indicate the age of donor when consent was given for treatment.
Extended
INTEGER
is_primary_treatment
Indicate if the treatment was the primary treatment following the initial diagnosis.
Core
Required
TEXT

Yes

No

Unknown

line_of_treatment
Indicate the line of treatment if it is not the primary treatment.
Extended
INTEGER
treatment_start_interval
The interval between the primary diagnosis and initiation of treatment, in days.
Core
Required
INTEGER
The associated primary diagnosis is used as the reference point for this interval. To calculate this, find the number of days since the date of primary diagnosis.
treatment_duration
The duration of treatment regimen, in days.
Core
Required
INTEGER
days_per_cycle
Indicate the number of days in a treatment cycle.
Extended
INTEGER
number_of_cycles
Indicate the number of treatment cycles.
Extended
INTEGER
treatment_intent
Indicate the intended disease outcome for which the treatment is given. (Reference: CDISC [NCIt code: C124307])
Core
Required
TEXT

Curative

Palliative

Unknown

treatment_setting
Indicate the treatment setting, which describes the treatment's purpose in relation to the primary treatment. (Reference: CDISC [NCIt code: C124308])
Core
Required
TEXT

Adjuvant

Advanced/Metastatic

Neoadjuvant

Not applicable

response_to_treatment
The donor's response to the applied treatment regimen. (Source: RECIST)
Core
Required
TEXT

Complete response

Disease progression

NED

Partial response

Stable disease

outcome_of_treatment
Indicate the donor's outcome of the prescribed treatment.
Extended
TEXT

Treatment completed as prescribed

Treatment incomplete due to technical or organizational problems

Treatment incomplete because patient died

Patient choice (stopped or interrupted treatment)

Physician decision (stopped or interrupted treatment)

5 more
toxicity_type
If the treatment was terminated early due to acute toxicity, indicate whether it was due to hemotological toxicity or non-hemotological toxicity.
Extended
TEXT

Hemotological

Non-hemotological

hemotological_toxicity
Indicate the hemotological toxicities which caused early termination of the treatment. (Codelist reference: NCI-CTCAE (v5.0))
Extended
TEXT

Anemia - Grade 3

Anemia - Grade 4

Anemia - Grade 5

Neutropenia - Grade 3

Neutropenia - Grade 4

4 more
To include multiple values, separate values with a pipe delimiter '|' within your file.
adverse_events
Report any treatment related adverse events. (Codelist reference: NCI-CTCAE (v5.0))
Extended
TEXT

Abdominal distension

Abdominal infection

Abdominal pain

Abdominal soft tissue necrosis

Abducens nerve disorder

832 more
To include multiple values, separate values with a pipe delimiter '|' within your file.
clinical_trials_database
If the donor is a participant in a clinical trial, indicate the clinical trial database where the clinical trial is registered.
Extended
TEXT

NCI Clinical Trials

EU Clinical Trials Register

clinical_trial_number
Based on the clinical_trial_database, indicate the unique NCT or EudraCT clinical trial identifier of which the donor is a participant.
Extended
Conditional
TEXT

Chemotherapy (chemotherapy)

7 Fields
The collection of data elements describing the details of a chemotherapy treatment regimen completed by a donor. To submit multiple treatment drugs for a single regimen, submit multiple rows in the chemotherapy file.
File Name Example: chemotherapy[-optional-extension].tsv
Field & Description
Data Tier
Attributes
Type
Permissible Values
Notes & Scripts
program_id
Unique identifier of the ARGO program.
ID
Required
TEXT
submitter_donor_id
Unique identifier of the donor, assigned by the data provider.
ID
Required
TEXT
Values must meet the regular expression
To prevent data collisions, submitter_id cannot begin with any of the ARGO ID prefixes. The restricted prefixes include: `DO`, `SP`, `SA`,`TR`,`FU`, `PD`.
submitter_treatment_id
Unique identifier of the treatment, as assigned by the data provider.
ID
Required
TEXT
Values must meet the regular expression
To prevent data collisions, submitter_id cannot begin with any of the ARGO ID prefixes. The restricted prefixes include: `DO`, `SP`, `SA`,`TR`,`FU`, `PD`.
drug_rxnormcui
The unique RxNormID assigned to the treatment regimen drug.
Core
Required
TEXT
This field uses standardized vocabulary from the RxNorm database (https://www.nlm.nih.gov/research/umls/rxnorm), provided by the NIH. You can search for RX Norm values through the web interface (https://mor.nlm.nih.gov/RxNav/) or API (https://mor.nlm.nih.gov/download/rxnav/RxNormAPIs.html). For example, to find the rxnormcui based on drug name, you can use: https://rxnav.nlm.nih.gov/REST/rxcui.json?name=leucovorin or https://mor.nlm.nih.gov/RxNav/search?searchBy=String&searchTerm=leucovorin
drug_name
Name of agent or drug administered to patient as part of the treatment regimen.
Core
Required
TEXT
This field uses standardized vocabulary from the RxNorm database (https://www.nlm.nih.gov/research/umls/rxnorm), provided by the NIH. You can search for RX Norm values through the web interface (https://mor.nlm.nih.gov/RxNav/) or API (https://mor.nlm.nih.gov/download/rxnav/RxNormAPIs.html). For example, to find the rxnormcui based on drug name, you can use: https://rxnav.nlm.nih.gov/REST/rxcui.json?name=leucovorin or https://mor.nlm.nih.gov/RxNav/search?searchBy=String&searchTerm=leucovorin
chemotherapy_dosage_units
Indicate units used to record chemotherapy drug dosage.
Core
Required
TEXT

mg/m2

IU/m2

ug/m2

g/m2

mg/kg

cumulative_drug_dosage
Indicate the total drug dose in the same units specified in chemotherapy_dosage_units.
Core
Required
NUMBER

Hormone Therapy (hormone_therapy)

7 Fields
The collection of data elements describing the details of a hormone treatment therapy completed by a donor. To submit multiple treatment drugs for a single regimen, submit multiple rows in the hormone_therapy file.
File Name Example: hormone_therapy[-optional-extension].tsv
Field & Description
Data Tier
Attributes
Type
Permissible Values
Notes & Scripts
program_id
Unique identifier of the ARGO program.
ID
Required
TEXT
submitter_donor_id
Unique identifier of the donor, assigned by the data provider.
ID
Required
TEXT
Values must meet the regular expression
To prevent data collisions, submitter_id cannot begin with any of the ARGO ID prefixes. The restricted prefixes include: `DO`, `SP`, `SA`,`TR`,`FU`, `PD`.
submitter_treatment_id
Unique identifier of the treatment, assigned by the data provider.
ID
Required
TEXT
Values must meet the regular expression
To prevent data collisions, submitter_id cannot begin with any of the ARGO ID prefixes. The restricted prefixes include: `DO`, `SP`, `SA`,`TR`,`FU`, `PD`.
drug_rxnormcui
The unique RxNormID assigned to the treatment regimen drug.
Core
Required
TEXT
This field uses standardized vocabulary from the RxNorm database (https://www.nlm.nih.gov/research/umls/rxnorm), provided by the NIH. You can search for RX Norm values through the web interface (https://mor.nlm.nih.gov/RxNav/) or API (https://mor.nlm.nih.gov/download/rxnav/RxNormAPIs.html). For example, to find the rxnormcui based on drug name, you can use: https://rxnav.nlm.nih.gov/REST/rxcui.json?name=leucovorin or https://mor.nlm.nih.gov/RxNav/search?searchBy=String&searchTerm=leucovorin
drug_name
Name of agent or drug administered to patient as part of the treatment regimen.
Core
Required
TEXT
This field uses standardized vocabulary from the RxNorm database (https://www.nlm.nih.gov/research/umls/rxnorm), provided by the NIH. You can search for RX Norm values through the web interface (https://mor.nlm.nih.gov/RxNav/) or API (https://mor.nlm.nih.gov/download/rxnav/RxNormAPIs.html). For example, to find the rxnormcui based on drug name, you can use: https://rxnav.nlm.nih.gov/REST/rxcui.json?name=leucovorin or https://mor.nlm.nih.gov/RxNav/search?searchBy=String&searchTerm=leucovorin
hormone_drug_dosage_units
Indicate the units used to record hormone drug dosage.
Core
Required
TEXT

mg/m2

IU/m2

ug/m2

g/m2

mg/kg

cumulative_drug_dosage
Indicate total drug dose in units specified in hormone_drug_dosage_units.
Core
Required
NUMBER

Radiation (radiation)

8 Fields
The collection of data elements describing the details of a radiation treatment completed by a donor.
File Name Example: radiation[-optional-extension].tsv
Field & Description
Data Tier
Attributes
Type
Permissible Values
Notes & Scripts
program_id
Unique identifier of the ARGO program.
ID
Required
TEXT
submitter_donor_id
Unique identifier of the donor, assigned by the data provider.
ID
Required
TEXT
Values must meet the regular expression
To prevent data collisions, submitter_id cannot begin with any of the ARGO ID prefixes. The restricted prefixes include: `DO`, `SP`, `SA`,`TR`,`FU`, `PD`.
submitter_treatment_id
Unique identifier of the treatment, assigned by the data provider.
ID
Required
TEXT
Values must meet the regular expression
To prevent data collisions, submitter_id cannot begin with any of the ARGO ID prefixes. The restricted prefixes include: `DO`, `SP`, `SA`,`TR`,`FU`, `PD`.
radiation_therapy_modality
Indicate the method of radiation treatment or modality.
Core
Required
TEXT

Electron

Heavy Ions

Photon

Proton

radiation_therapy_type
Indicate type of radiation therapy administered.
Core
Required
TEXT

External

Internal

Internal application includes Brachytherapy.
radiation_therapy_fractions
Indicate the total number of fractions delivered as part of treatment.
Core
Required
INTEGER
radiation_therapy_dosage
Indicate the total dose given in units of Gray (Gy).
Core
Required
INTEGER
anatomical_site_irradiated
Indicate localization site where radiation therapy was administered.
Core
Required
TEXT

Abdomen

Bone

Brain

Extremities

Head

7 more

Follow Up (follow_up)

22 Fields
The collection of data elements related to a specific follow-up visit to a donor. A follow-up is defined as any point of contact with a patient after primary diagnosis. To submit multiple follow-ups for a single donor, please submit multiple rows in the follow-up file for this donor.
File Name Example: follow_up[-optional-extension].tsv
Field & Description
Data Tier
Attributes
Type
Permissible Values
Notes & Scripts
program_id
Unique identifier of the ARGO program.
ID
Required
TEXT
submitter_donor_id
Unique identifier of the donor, assigned by the data provider.
ID
Required
TEXT
Values must meet the regular expression
To prevent data collisions, submitter_id cannot begin with any of the ARGO ID prefixes. The restricted prefixes include: `DO`, `SP`, `SA`,`TR`,`FU`, `PD`.
submitter_follow_up_id
Unique identifier for a follow-up event in a donor's clinical record, assigned by the data provider.
ID
Required
TEXT
Values must meet the regular expression
To prevent data collisions, submitter_id cannot begin with any of the ARGO ID prefixes. The restricted prefixes include: `DO`, `SP`, `SA`,`TR`,`FU`, `PD`.
interval_of_followup
Interval from the primary diagnosis date to the follow-up date, in days.
Core
Required
INTEGER
The associated primary diagnosis is used as the reference point for this interval. To calculate this, find the number of days since the date of primary diagnosis.
disease_status_at_followup
Indicate the donor's disease status at time of follow-up. (Reference: RECIST)
Core
Required
TEXT

Complete remission

Distant progression

Loco-regional progression

No evidence of disease

Partial remission

3 more
submitter_primary_diagnosis_id
Indicate if the follow-up is related to a specific primary diagnosis event in the clinical timeline.
ID
TEXT
Values must meet the regular expression
To prevent data collisions, submitter_id cannot begin with any of the ARGO ID prefixes. The restricted prefixes include: `DO`, `SP`, `SA`,`TR`,`FU`, `PD`.
submitter_treatment_id
Indicate if the follow-up is related to a specific treatment event in the clinical timeline.
ID
TEXT
Values must meet the regular expression
To prevent data collisions, submitter_id cannot begin with any of the ARGO ID prefixes. The restricted prefixes include: `DO`, `SP`, `SA`,`TR`,`FU`, `PD`.
weight_at_followup
Indicate the donor's weight, in kilograms (kg), at the time of follow-up.
Extended
INTEGER
relapse_type
Indicate the donor's relapse type.
Core
Conditional
TEXT

Distant recurrence/metastasis

Local recurrence

Local recurrence and distant metastasis

Progression (liquid tumours)

This field is required to be submitted if disease_status_at_followup indicates a state of progression, relapse, or recurrence.
relapse_interval
If the donor was clinically disease free following primary treatment and then relapse or recurrence or progression (for liquid tumours) occurred afterwards, then this field will indicate the length of disease free interval, in days.
Core
Conditional
INTEGER
This field is required to be submitted if disease_status_at_followup indicates a state of progression, relapse, or recurrence.
method_of_progression_status
Indicate the method(s) used to confirm the donor's progression or relapse or recurrence disease status. (Codelist reference: NCI CDE ID: 6161031)
Core
Conditional
TEXT

Biomarker in liquid biopsy (e.g. tumour marker in blood or urine)

Biopsy

Blood draw

Bone marrow aspirate

Core biopsy

19 more
This field is required to be submitted if disease_status_at_followup indicates a state of progression, relapse, or recurrence. To include multiple values, separate values with a pipe delimiter '|' within your file.
anatomic_site_progression_or_recurrences
Indicate the ICD-O-3 topography code for the anatomic site where disease progression, relapse or recurrence occurred, according to the International Classification of Diseases for Oncology, 3rd Edition (WHO ICD-O-3). Refer to the ICD-O-3 manual for guidelines at https://apps.who.int/iris/handle/10665/42344.
Core
Conditional
TEXT
Values must meet the regular expression

Examples:
This field is required to be submitted if disease_status_at_followup indicates a state of progression, relapse, or recurrence.
recurrence_tumour_staging_system
Specify the tumour staging system used to stage the cancer at time of retreatment for recurrence or disease progression. This may be represented as rTNM in the medical report.
Core
Conditional
TEXT

AJCC 8th edition

AJCC 7th edition

Ann Arbor staging system

Binet staging system

Durie-Salmon staging system

5 more
This field is required to be submitted if disease_status_at_followup indicates a state of progression, relapse, or recurrence.
recurrence_t_category
The code to represent the extent of the primary tumour (T) based on evidence obtained from clinical assessment parameters determined at the time of retreatment for a recurrence or disease progression, according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.
Core
Conditional
TEXT

T0

T1

T1a

T1a1

T1a2

35 more
This field is required only if the selected recurrence_tumour_staging_system is any edition of the AJCC cancer staging system.
recurrence_n_category
The code to represent the stage of cancer defined by the extent of the regional lymph node (N) involvement for the cancer based on evidence obtained from clinical assessment parameters determined at the time of retreatment for a recurrence or disease progression, according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.
Core
Conditional
TEXT

N0

N0a

N0a (biopsy)

N0b

N0b (no biopsy)

21 more
This field is required only if the selected recurrence_tumour_staging_system is any edition of the AJCC cancer staging system.
recurrence_m_category
The code to represent the stage of cancer defined by the extent of the distant metastasis (M) for the cancer based on evidence obtained from clinical assessment parameters determined at the time of retreatment for a recurrence or disease progression, according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.
Core
Conditional
TEXT

M0

M0(i+)

M1

M1a

M1a(0)

11 more
This field is required only if the selected recurrence_tumour_staging_system is any edition of the AJCC cancer staging system.
recurrence_stage_group
The code to represent the stage group of the tumour, as assigned by the reporting recurrence_tumour_staging_system, that indicates the overall prognostic tumour stage (ie. Stage I, Stage II, Stage III etc.) at the time of retreatment for a recurrence or disease progression.
Core
Conditional
TEXT

Stage 0

Stage 0a

Stage 0is

Stage I

Stage IA

60 more
This field is dependent on the selected recurrence_tumour_staging_system. Please refer to the documentation for Tumour Staging Classifications: http://docs.icgc-argo.org/docs/submission/dictionary-overview#tumour-staging-classifications
posttherapy_tumour_staging_system
Specify the tumour staging system used to stage the cancer after treatment for patients receiving systemic and/or radiation therapy alone or as a component of their initial treatment, or as neoadjuvant therapy before planned surgery. This may be represented as ypTNM or ycTNM in the medical report.
Extended
TEXT

AJCC 8th edition

AJCC 7th edition

Ann Arbor staging system

Binet staging system

Durie-Salmon staging system

5 more
posttherapy_t_category
The code to represent the extent of the primary tumour (T) based on evidence obtained from clinical assessment parameters determined after treatment for patients receiving systemic and/or radiation therapy alone or as a component of their initial treatment, or as neoadjuvant therapy before planned surgery, according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.
Extended
Conditional
TEXT

T0

T1

T1a

T1a1

T1a2

35 more
This field is required only if the selected posttherapy_tumour_staging_system is any edition of the AJCC cancer staging system.
posttherapy_n_category
The code to represent the stage of cancer defined by the extent of the regional lymph node (N) involvement for the cancer based on evidence obtained from clinical assessment parameters determined determined after treatment for patients receiving systemic and/or radiation therapy alone or as a component of their initial treatment, or as neoadjuvant therapy before planned surgery, according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.
Extended
Conditional
TEXT

N0

N0a

N0a (biopsy)

N0b

N0b (no biopsy)

21 more
This field is required only if the selected posttherapy_tumour_staging_system is any edition of the AJCC cancer staging system.
posttherapy_m_category
The code to represent the stage of cancer defined by the extent of the distant metastasis (M) for the cancer based on evidence obtained from clinical assessment parameters determined after treatment for patients receiving systemic and/or radiation therapy alone or as a component of their initial treatment, or as neoadjuvant therapy before planned surgery, according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.
Extended
Conditional
TEXT

M0

M0(i+)

M1

M1a

M1a(0)

11 more
This field is required only if the selected posttherapy_tumour_staging_system is any edition of the AJCC cancer staging system.
posttherapy_stage_group
The code to represent the stage group of the tumour, as assigned by the reporting posttherapy_tumour_staging_system, that indicates the overall prognostic tumour stage (ie. Stage I, Stage II, Stage III etc.) after treatment for patients receiving systemic and/or radiation therapy alone or as a component of their initial treatment, or as neoadjuvant therapy before planned surgery.
Extended
Conditional
TEXT

Stage 0

Stage 0a

Stage 0is

Stage I

Stage IA

60 more
This field is dependent on the selected posttherapy_tumour_staging_system. Please refer to the documentation for Tumour Staging Classifications: http://docs.icgc-argo.org/docs/submission/dictionary-overview#tumour-staging-classifications
  • sample_registration
    9 fields
    • specimen
      22 fields
      • donor
        17 fields
        • primary_diagnosis
          16 fields
        • treatment
          21 fields
          • chemotherapy
            7 fields
          • hormone_therapy
            7 fields
          • radiation
            8 fields
        • follow_up
          22 fields

Filter by Data Tier