Dictionary Releases

A dictionary release happens when there has been an update to the clinical dataset in the ARGO Data Dictionary. Dictionary releases happen whenever needed.

Release 1.12

Release Date: September 02, 2021

Updates

  • According to AJCC Guidelines 8th Ed. if TX or NX categories are used, such cases usually cannot be assigned a stage group. In such a case, the data submitter will be allowed to submit "Cannot be assessed" for the stage_group field. However, there are exceptions according to the guidelines as follows:

    • Stage may be assigned when the TNM stage group results in Any T or Any N with M1, which includes TX or NX e.g. (TX NX M1, or TX N3 M1). These are classified as Stage IV.

    • Stage may be assigned when the TNM stage group results in Any T or Any N with M0, which includes TX or NX e.g. (TX N1 M0 Stage III in melanoma clinical stage or T4 NX M0 Stage III in pancreas).

  • Added pipe as a term to exposure.tobacco_type controlled terminology.

Bug Fixes

  • An incorrect abbreviation used in a field name in the Biomarker table. The biomarker is related to lactate dehydrogenase (LDH), not low-density lipoprotein (LDL), thus biomarker.ldl_level was adjusted to biomarker.ldh_level.

Release 1.11

Release Date: July 21, 2021

Updates

A new clinical table has been added to the dictionary along with the file template downloads for submission:

  1. Biomarker: The collection of data elements describing a donor's biomarker tests. A biomarker is a biological molecule found in blood, other body fluids, or tissues that is indicative of the presence of cancer in the body.

Bug Fixes

  • If survival_time field is submitted,then all other interval times should be less than that. The treatment.treatment_start_interval and folowup.interval_of_followup fields are now being validated correctly against this rule.

Release 1.10

Release Date: June 08, 2021

Updates

Two new clinical tables have been added to the dictionary along with the file template downloads for submission:

  1. Exposure: A donor's clinically relevant information not immediately resulting from genetic predispositions (e.g diet, drug use, smoking).

  2. Comorbidity: A donor's comorbidities are any medical condition that has existed or may occur during the clinical course of the donor who has the index disease under study (e.g diabetes, prior cancer malignancies).

Bug Fixes

  • immuotherapy.immunotherapy_type was not marked as a required field. It is now correctly identified.
  • follow_up.anatomic_site_progression_or_recurrences was misnamed as a plural field; it has been corrected to follow_up.anatomic_site_progression_or_recurrence.

Release 1.9

Release Date: May 10, 2021

Updates

  • Integer fields now all contain validation based on the acceptable ranges allowed for those fields.
  • primary_site now accepts multiple values.
  • Optional clinical fields detailing genetic disorders, hormone replacement therapy and contraception details have been added to the Donor file.
  • Validation was added to ensure that hematological_toxicity is only included for hematological toxicity types and non-hematological_toxicity is only included for non-hematological toxicity types:
toxicity_typehematological_toxicitynon-hematological_toxicity
HematologicalAllowed to be submittedShould not be submitted
Non-hematologicalShould not be submittedAllowed to be submitted
  • Validation was added to ensure that if a treatment has been marked as the primary_treatment, it is not assigned an advanced line of treatment:
is_primary_treatmentline_of_treatment
NoAllowed to have a value
Yes or UnknownShould be left empty

Bug Fixes

  • Some fields/permissible values in the treatment table containing the word hematological were misspelled hemotological. These have all been resolved.
  • height, weight and bmi can now be submitted as decimal values.

Release 1.8

Release Date: April 27, 2021

Updates

Two new clinical tables have been added to the dictionary and the file template downloads for submission:

  1. Immunotherapy: For treatment regimens that include immunotherapy, these details can now be submitted. Similar to the chemotherapy and hormone_therapy, immunotherapy drugs are recorded using the standardized vocabulary from the RxNorm database, provided by the NIH.

  2. Family History: A donor's familial relationships and familial cancer history.

The following updates are also included:

  • Validation has been added so that when the treatment_type = No Treatment, non-applicable core fields do not need to be submitted.

Bug Fixes

  • Previously missing stage groups Stage IVE and Stage IVS for Ann Arbor staging system has been added, as well as adding support for the Stage II bulky for the Lugano staging system.

  • In the primary_diagnosis table, there was a misleading combination of fields indicating the status/number of lymph nodes examined during clinical diagnosis. When the number_lymph_nodes_examined is left blank, a value of 0 for number_lymph_nodes_positive could be misinterpreted as several things:

    • an unknown number of lymph nodes were tested or
    • none were found to be positive for cancer or
    • no lymph nodes were examined.

    To make this more accurate to clinical use cases, a new field lymph_nodes_examined_status has been added to indicate if lymph nodes were examined. Depending on the status, the required number_of_lymph_nodes_examined and number_of_lymph_nodes_positive can now accurately reflect clinical use cases. For example:

lymph_nodes_examined_statusnumber_lymph_nodes_examinednumber_lymph_nodes_positive
YesOptional: If left blank, this means unknown/missing. If number is submitted, it must be greater than 0Required: If number_lymph_nodes_examined is > 0, then number_lymph_nodes_positive >= number_lymph_nodes_examined
No0 or left blankShould be left blank
Not applicable0 or left blankShould be left blank
No lymph nodes found in resected specimen0 or left blankShould be left blank
Cannot be determined0 or left blankShould be left blank

Release 1.5

Release Date: December 11, 2020

The following updates are included:

  • Removed ID prefix restriction and all notes referencing this restriction.

Release 1.3

Release Date: November 24, 2020

The following updates are included:

  • Changed Attribute for percent_proliferating_cells, percent_inflammatory_tissue, percent_stromal_cells and percent_necrosis fields from Required to Conditional.
  • Updated description for cumulative_drug_dosage field to indicate that the actual drug dose should be submitted.
  • Added two new terms ("Swelling in the Neck" and "Not Reported") to controlled terminology for presenting_symptoms field.

Initial Dictionary Release 1.0

Release Date: June 19, 2020

ICGC ARGO is excited to announce its initial data dictionary release, established as the minimum set of clinical data elements that the ARGO Data Platform requires. This includes:

  • Basic Donor, Specimen, and Sample data
  • Donor clinical record information including Primary Diagnosis, Follow Up and Treatment data

Future releases will extend clinical data concepts and integrations of standard clinical data elements.