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 1.21

Release Date: Feburary 07, 2024

Updates

• New permissible term End of life care added to treatment_type field in Treatment table.
• Updated validation scripts for conditional fields percent_tumour_cell and percent_tumour_cells_measurement_method fields to take into account clinical exception values.

Release 1.20

Release Date: October 30, 2023

Updates

• Updated validation scripts for required field treatment_type in treatment table to take into account clinical exception value Unknown.

Release 1.19

Release Date: October 18, 2023

Updates

• New optional field called lost_to_followup_after_clinical_event_id added to Donor table to allow data submitters to indicate whether donor was lost to follow up after a clinical event.
• New permissible terms (Cell line – derived from metastatic tumour and Xenograft – derived from metastatic tumour) added to specimen_type field in Sample Registration table.
• Updated regular expression condition for all identifier fields to prevent invalid characters from being submitted.
• New permissible term Physician assessed progressive disease added to response_to_treatment field in Treatment table.

Release 1.18

Release Date: August 25, 2023

Updates

• Updated validation scripts for conditional fields tumour_grade, lymph_nodes_examined_method and prescribed_cumulative_drug_dose and actual_cumulative_drug_dose fields to take into account clinical exception values.

Release 1.17

Release Date: May 11, 2023

Updates

• Updated anatomic_site_progression_or_recurrence field in Follow Up table to accept multiple values.
• Added new permissible term (Tumour - unknown if derived from primary or metastatic) to specimen_type field in Sample Registration table.
• Added new required core field percent_tumour_cells_measurement_method in Specimen table.
• Fixed minor bug in validation script for existing lymph_nodes_examined_method field in Primary Diagnosis table.

Release 1.16

Release Date: January 5, 2023

Updates

• Added new term Unknown primary site to the controlled terminology for the primary_site field in the Donor table.
• Added 6 new terms (Supportive, Diagnostic, Preventative, Guidance, Screening, Forensic) to the controlled terminology for the treatment_intent field in the Treatment table.
• Added 8 new terms (Conditioning, Induction, Locally advanced, Maintenance, Mobilization, Preventative, Radiosensitization, Salvage) to the controlled terminology for the treatment_setting field in the Treatment table. The term Not applicable was removed. If required, programs will need to apply for a clinical exception.
• Removed Unknown from is_primary_treatment field. If required, programs will need to apply for a clinical exception.
• Added a new required response_to_treatment_criteria_method field in the Treatment table. This field consists of a list of response criteria methods, in addition to RECIST.
• Added new terms for response criteria in the response_to_treatment field in the Treatment table. The value submitted in this field will be validated against the response_to_treatment_criteria_method field to ensure the correct response criteria term is submitted.
• Added a new required lymph_nodes_examined_method field in the Primary Diagnosis table.
• Updated validation to permit the pathological_m_category field in the Specimen table to be submitted as "Not applicable" if AJCC 7th or 8th editions used.
• Changed data tier for the recurrence_tumour_staging_system field in the Follow Up table so it is no longer a core field.
• Updated foreignKey attribute for ID fields in the Specimen, Treatment, Follow up and Biomarker tables.
• Added new prescribed_cumulative_drug_dose field and renamed existing cumulative_drug_dose field to actual_cumulative_drug_dose in the Chemotherapy and Hormone Therapy tables. Added new fields for prescribed_cumulative_drug_dose and actual_cumulative_drug_dose in the Immunotherapy table. Either field can be submitted. Replaced dosage with dose for consistency purposes.
• Corrected term Revised International staging system (RISS) in the tumour_staging_system fields to R-ISS instead of RISS.

Release 1.15

Release Date: September 23, 2022

Updates

• Added four new terms ('Hemithyroidectomy', 'Near-total thyroidectomy', 'Subtotal thyroidectomy' and 'Total thyroidectomy') to the controlled terminology for the surgery_type field in the Surgery table.

Release 1.14

Release Date: June 16, 2022

Updates

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

1. Surgery: The collection of data elements related to a donor's surgical treatment at a specific point in the clinical record. For treatment regimens that include surgery, these details can now be submitted in this table. Refer to Submitting data in Surgery file documentation for guidelines on how to submit clinical data in this table.

The following updates are also included:

• Addition of 'Unknown' and 'Not applicable' terms to controlled terminology for extended clinical fields. Refer to Submitting Missing Values for Extended Clinical Fields documentation on how to submit these values.
• Added new term ("Oral contraceptive pill") to controlled terminology for contraception_type field.
• Corrected Data Tier for family_relative_id to 'ID'.

Release 1.13

Release Date: November 17, 2021

Updates

• The "AJCC 6th Edition" has been added to the controlled terminology for tumour staging systems. This will allow data submitters to submit TNM categories and stage groups for the AJCC 6th Edition.
• Optional clinical fields related to dose intensity reduction have been added to the Chemotherapy table. These include dose_intensity_reduction, dose_intensity_reduction_event and dose_intensity_reduction_amount.
• Optional clinical fields related to laterality have been added. These include the laterality field in the Primary Diagnosis table and the specimen_laterality field in the Specimen table.
• Removed the term "Unknown" from the controlled terminology of the core vital_status clinical field so it is consistent with other core clinical fields.
• Updated notes to clarify requirements for certain fields:
  • Added clarification about why the comorbidity_type_code field is "Conditional".
  • Updated description of age_at_menarche field to indicate it should be submitted in years.
  • Updated notes for number_lymph_nodes_examined field to indicate it is only required if lymph_nodes_examined_status is 'Yes'.
  • Updated notes for percent_proliferating_cells, percent_inflammatory_tissue, percent_stromal_cells and percent_necrosis fields in the Specimen table to indicate that they should only be submitted if the specimen is tumour.
  • Added clarification on how to submit fields in Biomarker table.
• Changed radiation_therapy_dosage to accept number instead of integer.
• Updated controlled terminology for anatomical_site_irradiated.

Bug fixes:

• Added sample_registration file to download templates from Dictionary Viewer page

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_type	hematological_toxicity	non-hematological_toxicity
Hematological	Allowed to be submitted	Should not be submitted
Non-hematological	Should not be submitted	Allowed 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_treatment	line_of_treatment
No	Allowed to have a value
Yes or Unknown	Should 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_status	number_lymph_nodes_examined	number_lymph_nodes_positive
Yes	Optional: If left blank, this means unknown/missing. If number is submitted, it must be greater than 0	Required: If number_lymph_nodes_examined is > 0, then number_lymph_nodes_positive >= number_lymph_nodes_examined
No	0 or left blank	Should be left blank
Not applicable	0 or left blank	Should be left blank
No lymph nodes found in resected specimen	0 or left blank	Should be left blank
Cannot be determined	0 or left blank	Should 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.