Data Dictionary

The ICGC ARGO Data Dictionary expresses the details of the ARGO data model, which adheres to specific formats and restrictions to ensure a standard of data quality. The Data Dictionary defines a set of files, each related to a clinical concept, that can be submitted to the ARGO Data Platform.

For recent updates, check the Dictionary Release Notes.

Understanding the Data Dictionary

The dictionary table view lists all of the clinical fields that the ARGO Data Platform accepts, separated by clinical TSV file.

Field listings can be filtered by Data Tier and Attribute, which can help identify which fields are necessary for clinical data completion.

You can explore previous dictionary versions using the dropdown at the top of the dictionary. Using the latest version of the dictionary is required during data submission.

Field Descriptors

Each field has a data tier and an attribute classification, which reflects the importance of the field in terms of clinical data completion.

ID classification indicates:

  • Field is a unique identifier that is used for cross file validation.
  • Field is a primary or foreign key.

Conditional classification indicates:

  • Field must meet certain conditions, depending on the value of another field.
  • Conditional rules are described in the data dictionary scripts & notes.

Required classification indicates:

  • Field must be provided in the submitted TSV file.

Core classification indicates:

  • Field is part of the mandatory minimum set of clinical data that must be submitted.
  • When paired with the Conditional attribute, this field is only required if conditional requirements are met.

The set of core clinical fields were defined by the Tissue & Clinical Annotations Working Group which involved regular discussions with members of the working group and ARGO Programs. Core clinical fields are commonly acquired in cohort-based studies and clinical trials and are required to address clinically relevant topics by cross entity analyses, and therefore constitute a critical element in the analysis of diverse ARGO Programs.

Extended classification indicates:

  • Field is not required for clinical data completion.
  • It is strongly encouraged to provide as many extended fields as possible.

Permissible Values

  • Some fields will only accept certain values from a list of controlled terminology that is provided in the permissible values column of the dictionary tables. Values must match the dictionary spelling exactly, but can be submitted case-insensitive.

  • Other fields must meet a regular expression for their value.

Dictionary Standards Used

The dictionary controlled terminology values were derived from external standards or common terminology used by ICGC ARGO programs. These include:

Tumour Staging Classifications

Revised International staging system (RISS)

StageDescription
Stage ISerum β2-microglobulin <3.5 mg/L and serum albumin ≥3.5 g/dL and no high-risk cytogenetics and Normal LDH
Stage IINot stage I or III
Stage IIISerum β2-microglobulin ≥5.5 mg/L and high-risk cytogenetics and/or high LDH

Reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4846284/

Lugano Staging System

StageDescription
Stage IInvolvement of a single lymphatic site (i.e., nodal region, Waldeyer’s ring, thymus, or spleen)
Stage IESingle extralymphatic site in the absence of nodal involvement (rare in Hodgkin lymphoma)
Stage IIInvolvement of two or more lymph node regions on the same side of the diaphragm
Stage IIEContiguous extralymphatic extension from a nodal site with or without involvement of other lymph node regions on the same side of the diaphragm
Stage IIIInvolvement of lymph node regions on both sides of the diaphragm; nodes above the diaphragm with spleen involvement
Stage IVDiffuse or disseminated involvement of one or more extralymphatic organs, with or without associated lymph node involvement; or noncontiguous extralymphatic organ involvement in conjunction with nodal Stage II disease or any extralymphatic organ involvement in nodal Stage III disease. Stage IV includes any involvement of the CSF, bone marrow, liver, or multiple lung lesions (other than by direct extension in Stage IIE disease).

Note: Hodgkin lymphoma uses A or B designation with stage group. A/B is no longer used in NHL

SuffixDescription
AAsymptomatic (No B symptoms)
BAny B symptom(s):
  • Fevers. Unexplained fever with temperature above 38°C.
  • Night sweats. Drenching sweats (e.g., those that require change of bed clothes).
  • Weight loss. Unexplained weight loss of more than 10% of the usual body weight in the 6 months prior to diagnosis

Reference: Amin, Mahul B.. AJCC Cancer Staging Manual, Eighth Edition (p. 981). American College of Surgeons.

St. Jude Children's Research Hospital Staging System

StageDescription
Stage IA single tumour (extranodal) or single anatomic area (nodal), with the exclusion of the mediastinum or abdomen
Stage IIA single tumour (extranodal) with regional node involvement Two or more nodal areas on the same side of the diaphragm Two single (extranodal) tumours with or without regional node involvement on the same side of the diaphragm A primary gastrointestinal tract tumour, usually in the ileocecal area, with or without involvement of associated mesenteric nodes only
Stage III
  • Two single tumours (extranodal) on opposite sides of the diaphragm.
  • Two or more nodal areas above and below the diaphragm.
  • All the primary intrathoracic tumours (mediastinal, pleural, and thymic).
  • All extensive primary intra-abdominal disease.
  • All paraspinal or epidural tumours, regardless of other tumour site(s)
Stage IVAny of the above with initial CNS and/or bone marrow involvement

Reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461808/

Ann Arbor Staging Classification for Hodgkin Lymphoma

StageDescription
Stage IInvolvement of a single lymphatic site (i.e., nodal region, Waldeyer's ring, thymus, or spleen) (I); or localized involvement of a single extralymphatic organ or site in the absence of any lymph node involvement (IE).
Stage IIInvolvement of two or more lymph node regions on the same side of the diaphragm (II); or localized involvement of a single extralymphatic organ or site in association with regional lymph node involvement with or without involvement of other lymph node regions on the same side of the diaphragm (IIE).
Stage IIIInvolvement of lymph node regions on both sides of the diaphragm (III), which also may be accompanied by extralymphatic extension in association with adjacent lymph node involvement (IIIE) or by involvement of the spleen (IIIS) or both (IIIE,S).
Stage IVDiffuse or disseminated involvement of one or more extralymphatic organs, with or without associated lymph node involvement; or isolated extralymphatic organ involvement in the absence of adjacent regional lymph node involvement, but in conjunction with disease in distant site(s). Stage IV includes any involvement of the liver or bone marrow, lungs (other than by direct extension from another site), or cerebrospinal fluid.
SuffixDescription
ANo symptoms.
BFever (temperature >38.0ºC), drenching night sweats, unexplained loss of >10% of body weight within the preceding 6 months.
EInvolvement of a single extranodal site that is contiguous or proximal to the known nodal site.
SSplenic involvement.

Reference: https://www.ncbi.nlm.nih.gov/books/NBK65726/table/CDR0000062933__557/

Rai Staging System

StageDescription
Stage 0Lymphocytosis (high blood count of lymphocytes) and no enlargement of the lymph nodes, spleen, or liver, and with near normal red blood cell and platelet counts.
Stage ILymphocytosis plus enlarged lymph nodes. The spleen and liver are not enlarged and the red blood cell and platelet counts are normal or only slightly low.
Stage IILymphocytosis plus an enlarged spleen (and possibly an enlarged liver), with or without enlarged lymph nodes. The red blood cell and platelet counts are normal or only slightly low
Stage IIILymphocytosis plus anemia (too few red blood cells), with or without enlarged lymph nodes, spleen, or liver. Platelet counts are near normal.
Stage IVLymphocytosis plus thrombocytopenia (too few platelets), with or without anemia, enlarged lymph nodes, spleen, or liver.

Reference: CLL Society, Inc. Rai Staging of CLL (chronic lymphocytic leukemia).

Durie-Salmon Staging System

StageDescription
Stage 1All of the following:
  • Hemoglobin value > 10 g/dl
  • Serum calcium value normal or <10.5 mg/dL
  • Bone X-ray, normal bone structure (scale 0), or solitary bone plasmactyoma only
  • Low M-component production rates IgG value < 5g/dL; IgA value < 3 g/dL
  • Urine light chain M-component on electrophoresis < 4 g/24h
Stage IIFitting neither Stage I nor Stage III
Stage IIIOne or more of the following:
  • Hemoglobin value < 8.5 g/dL
  • Serum calcium value > 12 mg/dL
  • Advanced lytic bone lesions (scale 3)
  • High M-component production rates IgG value > 7 g/dL; IgA value > 5 g/dL
  • Urine light chain M-component > 12 g/24h

Reference: https://www.myeloma.org/durie-salmon-staging

FIGO Staging of Cervical Carcinomas

StageDescription
Stage IAInvasive cancer identified only microscopically. Invasion is limited to measured stromal invasion with a maximum depth of 5 mm and no wider than 7 mm.
Stage IA1Measured invasion of the stroma no greater than 3 mm in depth and no wider than 7 mm diameter.
Stage IA2Measured invasion of stroma greater than 3 mm but no greater than 5 mm in depth and no wider than 7 mm in diameter.
Stage IBClinical lesions confined to the cervix or preclinical lesions greater than Stage IA. All gross lesions even with superficial invasion are Stage IB cancers.
Stage IB1Clinical lesions no greater than 4 cm in size.
Stage IB2Clinical lesions greater than 4 cm in size.
Stage IIANo obvious parametrial involvement. Involvement of up to the upper two-thirds of the vagina.
Stage IABObvious parametrial involvement, but not into the pelvic sidewall.
Stage IIIANo extension into the pelvic sidewall but involvement of the lower third of the vagina.
Stage IIIBExtension into the pelvic sidewall or hydronephrosis or non-functioning kidney.
Stage IVASpread of the tumour into adjacent pelvic organs.
Stage IVBSpread to distant organs.

Reference: https://screening.iarc.fr/viaviliappendix1.php

Binet Staging System

StageDescription
Stage AFewer than 3 groups of enlarged lymph nodes (lymphadenopathy) and a high white blood cell count
Stage BMore than 3 groups of enlarged lymph nodes and a high white blood cell count
Stage CEnlarged lymph nodes or spleen, a high white blood cell count, and low red blood cell or platelet counts

Reference: Amin, Mahul B.. AJCC Cancer Staging Manual, Eighth Edition (p. 975). American College of Surgeons.

Tumour Grading Classifications

Two-tier Grading System

Grade
Low grade
High grade

Reference: Reference: Amin, Mahul B.. AJCC Cancer Staging Manual, Eighth Edition

Three-tier Grading System

GradeDefinition
GXCannot be assessed
G1Well differentiated
G2Moderately differentiated
G3Poorly differentiated, undifferentiated

Reference: Reference: Amin, Mahul B.. AJCC Cancer Staging Manual, Eighth Edition

Four-tier Grading System

GradeDefinition
GXGrade cannot be assessed
G1Well differentiated
G2Moderately differentiated
G3Poorly differentiated
G4Undifferentiated

Reference: Reference: Amin, Mahul B.. AJCC Cancer Staging Manual, Eighth Edition

Grading for Gastrointestinal Stromal Tumours (GISTs)

Mitotic RateDefinition
Low5 or fewer mitoses per 5 mm2
HighOver 5 mitoses per 5 mm2

Reference: Amin, Mahul B.. AJCC Cancer Staging Manual, Eighth Edition (p. 546). American College of Surgeons.

Grading System for GNETs

GradeDefinition
GXGrade cannot be assessed
G1Mitotic count (per 10 HPF) < 2 and Ki-67 index (%) < 3
G2Mitotic count (per 10 HPF) = 2–20 or Ki-67 index (%) = 3–20
G3Mitotic count (per 10 HPF) > 20 or Ki-67 index (%) > 20

Reference: Amin, Mahul B.. AJCC Cancer Staging Manual, Eighth Edition (p. 374). American College of Surgeons.

ISUP Grading System

GradeDefinition
GXGrade cannot be assessed
G1Nucleoli absent or inconspicuous and basophilic at 400x magnification
G2Nucleoli conspicuous and eosinophilic at 400x magnification, visible but not prominent at 100x magnification
G3Nucleoli conspicuous and eosinophilic at 100x magnification
G4Marked nuclear pleomorphism and/or multinucleate giant cells and/or rhabdoid and/or sarcomatoid differentiation

Reference: Amin, Mahul B.. AJCC Cancer Staging Manual, Eighth Edition (p. 771). American College of Surgeons.

Nuclear Grading System for DCIS

GradeDefinition
GXGrade cannot be assessed
G1Low nuclear grade
G2Intermediate nuclear grade
G3High nuclear grade

Reference: Amin, Mahul B.. AJCC Cancer Staging Manual, Eighth Edition (p. 641). American College of Surgeons.

FNCLCC Grading System

GradeDefinition
GXGrade cannot be assessed
G1Total differentiation, mitotic count and necrosis score of 2 or 3
G2Total differentiation, mitotic count and necrosis score of 4 or 5
G3Total differentiation, mitotic count and necrosis score of 6, 7, or 8

References: https://academic.oup.com/jjco/article/49/2/103/5179391 Amin, Mahul B.. AJCC Cancer Staging Manual, Eighth Edition (p. 564). American College of Surgeons.

Scarff–Bloom–Richardson (SBR) Grading System

GradeDefinition
GXGrade cannot be assessed
G1Low combined histologic grade (favorable), SBR score of 3–5 points
G2Intermediate combined histologic grade (moderately favorable); SBR score of 6–7 points
G3High combined histologic grade (unfavorable); SBR score of 8–9 points

Reference: Amin, Mahul B.. AJCC Cancer Staging Manual, Eighth Edition (p. 652). American College of Surgeons.

WHO Grading System for CNS Tumours

GradeDefinition
Grade ICircumscribed tumours of low proliferative potential associated with the possibility of cure following resection
Grade IIInfiltrative tumours with low proliferative potential with increased risk of recurrence
Grade IIITumours with histologic evidence of malignancy, including nuclear atypia and mitotic activity, associated with an aggressive clinical course
Grade IVTumours that are cytologically malignant, mitotically active, and associated with rapid clinical progression and potential for dissemination

Reference: Amin, Mahul B.. AJCC Cancer Staging Manual, Eighth Edition (p. 894). American College of Surgeons.

Gleason Grade Group System

Grade GroupGleason score and pattern
Group 1≤6 (≤3+3)
Group 27 (3+4)
Group 37 (4+3)
Group 48 (4+4, 3+5 or 5+3)
Group 59 or 10 (4+5, 5+4, or 5+5)

References: Amin, Mahul B.. AJCC Cancer Staging Manual, Eighth Edition (p. 751). American College of Surgeons. http://pathology.jhu.edu/ProstateCancer/NewGradingSystem.pdf