Complete Donor Scripts Based Validations

Currently all scripts listed in the dictionary are placeholders. We need to update these to include real script based validation.

An example script is here: https://wiki.oicr.on.ca/display/icgcargotech/Validation+Script+Template

For the sample_registration file (https://github.com/icgc-argo/argo-dictionary/blob/master/schemas/donor.json), please implement the following script based validations in the dictionary:

1) Add script validation to cause_of_death
This field should be filled in if vital_status=deceased
2) Add the correct tags to the dictionary schema so they will appear in the Dictionary viewer. A guide for tags can be found here: https://wiki.oicr.on.ca/pages/viewpage.action?pageId=134938807

Feature Request: Assiciate treatments to samples/followup/primary_diagnoses

We need to be able to answer the questions like this:
Which tumour was this treatment related to?
Which sample was associated with this primary diagnosis?
Which diagnosis was this follow_up related to?

Implementation

add submitter_primary_diagnosis_id on primary_diagnosis file
add submitter_primary_diagnosis_id on specimen file
add submitter_primary_diagnosis_id on treatment file
add submitter_primary_diagnosis_id on follow_up file
add submitter_treatment_id on follow_up file (optional)

Noted for clinical

For this dictionary change we will have some dependencies on clinical:

Make sure there can be multiple primary_diagnosis entities

Feature Request: Create codelist for staging groups and stage systems

Will generate a codelist containing list of all possible stage groups.This codelist will be used in the following fields:

clinical_stage_group
pathological_stage_group
recurrence_stage_group

Will update codelist used in clinical_staging_system, pathological_staging_system and recurrence_staging_system to make sure they contain all the staging systems recommended by AJCC.

Will also add a script validation check (similar to the one we use for tumour grading) to check the stage group value against the staging system specified.

Work in progress: https://docs.google.com/spreadsheets/d/1RCUqJ2DeK5vynGrYzhLOu-UAs9Kvxx_4L_5sWo_TtHc/edit?usp=sharing

Complete AJCC Script Based Validation across all examples

Currently all scripts listed in the dictionary are placeholders. We need to update these to include real script based validation.

An example script is here: https://wiki.oicr.on.ca/display/icgcargotech/Validation+Script+Template

There is one field that will use the same script across multiple files. This is the clinical staging system and its associated fields.

(https://github.com/icgc-argo/argo-dictionary/blob/master/schemas/donor.json), please implement the following script based validations in the dictionary:

1) Create the tumor staging script that can be used across multiple files
For the staging_system field, when any AJCC value is selected, then the t_category, n_category, and m_category, stage_group, stage_suffix fields are required to be filled in.
NOTE: not all file schema staging_system groupings contain stage_group &clinical_stage_suffix fields.
2) Assign the script to the correct fields in follow_up, primary_diagnosis, and specimen schemas
3) Add the correct tags to the dictionary schemas so they will appear in the Dictionary viewer. A guide for tags can be found here: https://wiki.oicr.on.ca/pages/viewpage.action?pageId=134938807

Feature Request: Change "relapse" to "relapse or recurrence" in disease_status_at_followup codelist

Detailed Description

Beta-testers from the PACA-CA project were confused as to how to submit the disease_status_at_followup since apparently the term "relapse" is not used in pancreatic cancer (they use recurrence).

Based on discussions with the working group, it was confirmed that the terms "relapse" and "recurrence" are actually synonymous, so it's been proposed we allow both terms.

change the term "relapse" to "relapse or recurrence" in the disease_status_at_followup codelist.

🐛 Script failing when t,n,m headers aren't even provided

Describe the bug

script was complaining about wrongly provided fields when the headers weren't defined, in the case of non ajcc values

Steps To Reproduce

Steps to reproduce the behaviour:

Submit a primary diagnosis file with clinical tumour staging system set to 'murphy'
Don't provide headers ( thus values) for t, n , m categories
Get an error stating you wrongly provided values for those categories

Expected behaviour

A clear and concise description of what you expected to happen.

🐛 Remove specal character

Drug dosage units has a special character:

In chemotherapy and hormone therapy

Create Unit Testing System

Create a system within argo dictionary to run unit tests on the validation functions.

Before npm run compile can proceed, all unit tests should pass first.

Look into different testing frameworks.

--

test that the scripts themselves are formatted correctly as javascript inside the dictionary
model framework and implement first tests

Add note about comma with array

I think we should mention somewhere that data submitters can submit an array of values here and how to do so.

Something like:

Feature Request: Create new treatment table for Immunotherapy

As discussed with working group:

In our dictionary, we use the term “Monoclonal antibodies (for liquid tumours)”. However, monoclonal antibodies are not always associated with liquid tumours. For example, in breast cancer HER+, patients get treated with monoclonal antibodies (sometimes called immunotherapy). Proposed the following changes:

Instead of the two current categories “Immunotherapy” and “Monoclonal antibodies” use:
Immunotherapy, monoclonal antibodies other than immune checkpoint inhibitors
Immunotherapy, immune checkpoint inhibitors
Immunotherapy, cell-based
Immunotherapy, other immunomodulatory substances

Detailed Description

Will remove the term Monoclonal antibodies (for liquid tumours) from the treatment_type codelist and leave just Immunotherapy
Will create a separate treatment table called Immunotherapy with the following fields (to begin with):

program_id
submitter_donor_id
submitter_treatment_id
immunotherapy_type which will include a codelist with the following terms:

Immunotherapy, monoclonal antibodies other than immune checkpoint inhibitors
Immunotherapy, immune checkpoint inhibitors
Immunotherapy, cell-based
Immunotherapy, other immunomodulatory substances

immunotherapy_drug_name (similar to how we plan to have RxNorm drug name fields set up in the hormone and chemotherapy tables)

Will most likely add a few more fields to this table after gathering more information from working group.

Show an error on data update that has dependencies

When a user makes updates to data they have already submitted, and that data has dependencies, check that the dependent fields are filled out correctly.

For example:

I submitted a primary diagnosis file with clinical_tumour_staging_system:AJCC 8th Edition, and also filled the required T, N, M values.
Then I went to that file and changed the clinical_tumour_staging_system to Lugano (which does not require T, N, M values). I did not erase the T, N, M values from before though.
I submitted for DCC approval and the submission went through and was locked for approval.

The submitter should be prompted to remove the dependent values too.

From Christina:
We should check that the dependent fields are left empty in this case during initial submission and subsequent update. And give error if they are filled out in the wrong context

Create system where more than one validation function can be assigned to a field

Detailed Description

Dictionary repo is only able to reference one validation function per field
It's currently not possible to have a field validated in two ways.

Need to make a system where any number of validation functions can be referenced, and they get combined, and return one comprehensive result.

Possible Implementation

-reference to a script whose sole purpose is to combine n number of functions
-import the required functions in the field

somehow (???????), said script will need to both piece together the results of each function into one major returned object, while still being able to merge them as individual strings, also making sure there's no explicit return statement (clinical's sandbox will automatically return the last statement executed)

🐛 Remove commas in controlled vocabulary lists

Description

There are currently values in dictionary that has commas in them, that will conflict with the new array of values feature.

Remove commas for terms. Affected controlled vocabulary lists:
https://github.com/icgc-argo/argo-dictionary/blob/master/references/list.json#L243
https://github.com/icgc-argo/argo-dictionary/blob/master/schemas/specimen.json#L178-L182 https://github.com/icgc-argo/argo-dictionary/blob/master/schemas/specimen.json#L199-L201

🐛 Prevent data submitters from submitting ARGO IDs

Issue

The current regex for submitter_donor_id, submitter_specimen_id and submitter_sample_id do not prevent a data submitter from submitting an identifier that has the same prefix as ARGO reserved prefixes (ie. DO*, SP* and SA*).

In ICGC, we had a script validation to prevent data submitters from using ICGC reserved prefixes. We can do the same, or modify the existing regex.

Exclude following prefixes:
submitter_donor_id: exclude DO prefix
submitter_specimen_id: exclude SP prefix
submitter_sample_id: exclude SA prefix
submitter_treatment_id: exclude TR prefix
submitter_primary_diagnosis_id: exclude PD prefix
submitter_follow_up_id: exclude FU prefix

Rename central_pathology_confirmed and application_form fields

Based on user feedback, there are two clinical fields that will require re-naming. The current clinical field names are confusing some data submitters. After discussions with working group, it was agreed to update the following:

central_pathology_confirmed -> reference_pathology_confirmed. Will also update description so it is more clear.
application_form -> radiation_therapy_type

🐛 Correct dosage units used for children < 10kg

Describe the bug

For children under 10kg, the dosing of chemotherapeutic drugs is dosed according to body weight instead of body surface area.

Fix

Need to update codelist to mg/kg here and here

🐛 Add examples for donor.cancer_type_prior_malignancy

🐛 The word "or" in the codelist values for tumour_grade make it appear as though there are 2 options

Example of bug:

The codelist for "tumour_grade" when tumour_grading_system is "lymphoid neoplasms" looks like this:

low grade or indolent nhl
high grade or aggressive nhl

A data submitter may confuse the "or" as an option to submit either "low grade" or "indolent nhl". But they need to submit the whole phrase (ie. "low grade or indolent nhl"). If they submit just "low grade", the validation fails like this:

Expected behaviour

Format the newline response to show this:

- `low grade or indolent nhl`
- `high grade or aggressive nhl`

🐛 When a field is invalid by script, the script error message doesn't appear on the UI

Describe the bug

The error message from validation scripts doesn't show up on the UI.

I uploaded a sample registration file, with invalid field data, on Platform UI (Dev).

   Specimen Type: 'Cell line - derived from normal'
   Tumour_Normal_Designation: 'Tumour'

The error outputted should have been:
"Invalid specimen_type. Specimen_type cannot be set to normal type value (Normal or Cell line - derived from normal) when tumour_normal_designation is set to Tumour."

Instead, the error was the following:
The value is not permissible for this field (see image below).

Steps To Reproduce

Steps to reproduce the behaviour:

Go to Platform UI (Dev)
Click on the Z5480984-CA program
Click on 'register samples'
Upload the following tsv file
Error report appears

Expected behaviour

The error outputted should have been:
"Invalid specimen_type. Specimen_type cannot be set to normal type value (Normal or Cell line - derived from normal) when tumour_normal_designation is set to Tumour."

Add an extended field for weight in Follow up table

Description:

We currently ask for the patient's "weight" in the Donor level. This would be baseline weight, but it would also be good to have the patient's weight at followup since it can change:

Use case from data submitter for PACA-CA project:

Email from Rajshree:

The weight of patients may vary substantially from diagnosis till resection. Neoadjuvant chemotherapy, if given prior to surgery, can result in significant appetite changes; biliary obstruction due to a pancreatic mass can alter eating habits as can cause nausea and vomiting. So the weight can drop significantly and is monitored at each clinic visit

Implementation

Will add a new optional field called "weight_at_followup" in the Followup table

Feature Request: Drugbank names for Chemotherapy

Detailed Description

We should use the drug names from DrugBank for chemotherapy_drug_name, but this will obviously make the codelist really long. Can we store the DrugBank information in a database and then have a script validation here to cross-check the submitted drug name?

https://wiki.oicr.on.ca/pages/viewpage.action?spaceKey=icgcargotech&title=Drug+Name+Specification

🐛 Fix codelist for tumour grades and add update tumour grading systems

Describe the bug

The existing codelist for Gleason values (ie. when tumour_grading_system is gleason) contains dashes (ie. gleason 2–6). When a data submitter copies and pastes a gleason value from the browser to an excel file, the dash renders as a special character.

Error during clinical validation:

Solution

Consider replacing existing codelist with gleason grade groups which don't contain dashes. Can provide mapping information between grade groups and scores in "Notes" section:

fix `internal` in radiation_therapy.application_form

Need regex example on Cancer Type Code

Feature Request: Add non-malignant neoplasms to cancer_type_code.

After discussions with working group, decided we should accept non-malignant neoplasms as well. Comment from working group:

"I see no problem in listing non-malignant neoplasms as well. For some longitudinal cancer studies an early diagnosis of a precursor lesion and its genetic information might be highly relevant."

Will update regex for following fields:
cancer_type_code
cancer_type_prior_malignancy

Add dictionary tests

regexes are valid
dictionary can compile (JSON valid)
individual schemas conform to file metaschema for lectern

🐛 Dictionary label: tumour dependencies in specimen file

Describe the bug

Some fields in the specimen file are dependent on if tumour_normal_designation = tumour
(in sample-registration file). This is not reflected in the dictionary labels.

Expected behaviour

The following tumour-related fields should only need to be completed only if tumour_normal_designation is Tumour. these should have dependency tags.

pathological_tumour_staging_system
pathological_T_category
pathological_N_category
pathological_M_category
pathological_stage_group
tumour_grading_system
tumour_grade
percent_tumour_cells
percent_proliferating_cells
percent_stromal_cells
percent_necrosis

@hknahal these
pathological_T_category
pathological_N_category
pathological_M_category are dependent on pathological_tumour_staging_system already...so not sure if those need to be dependent on tumour_normal_designation too.

🐛 post therapy tumour staging system is not dependent on disease_status_at_followup

Description of bug:

Post-therapy tumour staging system should not be dependent on whether the disease status is relapse or progression.

Solution

We can remove the following script validations for posttherapy_tumour_staging_system:

https://github.com/icgc-argo/argo-dictionary/blob/master/references/validationFunctions/follow_up/posttherapy_tumour_staging_system.js#L2
https://github.com/icgc-argo/argo-dictionary/blob/master/references/validationFunctions/follow_up/posttherapy_tumour_staging_system.js#L3

Complete Specimen Script Based Validation

Currently all scripts listed in the dictionary are placeholders. We need to update these to include real script based validation. An example script is here: https://wiki.oicr.on.ca/display/icgcargotech/Validation+Script+Template

For the follow_up schema (https://github.com/icgc-argo/argo-dictionary/blob/master/schemas/specimen.json), please implement the following script based validations in the dictionary:

1) For the field tumour_grade, select a value based on tumor_grading_system according to this matrix:

Default	Gleason	Nottingham	Brain cancer	ISUP for renal cell carcinoma	Lymphoid neoplasms
Gx - cannot be assessed	Gleason X: Gleason score cannot be determined	G1 (Low grade or well differentiated)	Grade I	Grade 1: Tumor cell nucleoli invisible or small and basophilic at 400 x magnification	Low grade or indolent NHL
G1 well differentiated/low grade	Gleason 2–6: The tumor tissue is well differentiated	G2 (Intermediate grade or moderately differentiated)	Grade II	Grade 2: Tumor cell nucleoli conspicuous at 400 x magnification but inconspicuous at 100 x magnification	High grade or aggressive NHL
G2 moderately differentiated/intermediated grade	Gleason 7: The tumor tissue is moderately differentiated	G3 (High grade or poorly differentiated)	Grade III	Grade 3: Tumor cell nucleoli eosinophilic and clearly visible at 100 x magnification
G3 poorly differentiated/high grade	Gleason 8–10: The tumor tissue is poorly differentiated or undifferentiated		Grade IV	Grade 4: Tumors showing extreme nuclear pleomorphism and/or containing tumor giant cells and/or the presence of any proportion of tumor showing sarcomatoid and/or rhabdoid dedifferentiation
G4 undifferentiated/high grade

2) Add the correct tags to the dictionary schemas so they will appear in the Dictionary viewer. A guide for tags can be found here: https://wiki.oicr.on.ca/pages/viewpage.action?pageId=134938807

🐛 Data validation: error needed for T, N, M values

Describe the bug

In many files, I shouldn't be able to put in T, N, M values when staging system is NOT any edition of the AJCC cancer staging system.

This occurs in the following files:
specimen file: pathological_tumour_staging_system
Primary Diagnosis file: clinical_tumour_staging_system
Follow up file: recurrence_tumour_staging_system and posttherapy_tumour_staging_system

So only when the values of these files are any edition of AJCC, then the T, N, M field values should be filled out.

For example:

Steps To Reproduce

Steps to reproduce the behaviour:

Register this sample file: https://drive.google.com/open?id=1LupVPP-a-zdXkcG1R7gSFRomXbgLeMPe
In clinical submission, upload these files:
https://drive.google.com/open?id=1mFKTvo-AGcVaieE4YlH09uCY8zBAhef_
https://drive.google.com/open?id=18475-neMEddf1xLNK3UD8Dm8vRFtWq_Z
You will see that you can upload and validate without error - but I have T, N, M values filled in:

Expected behaviour

I should get an error that the T, N, M values shouldn't be filled in if the staging system field is not any edition of AJCC

Sequencing Experiment Schema Analysis

🐛 Incorrect regex for tumour_histological_type.

Issue

The regular expression for tumour_histological_type is incorrect. For example: 8140/3 will fail valdiation.

I need to fix this regex at: https://github.com/icgc-argo/argo-dictionary/blob/master/schemas/specimen.json#L141

Add new meta field for Display Name

Complete Follow Up Scripts Based Validations

Currently all scripts listed in the dictionary are placeholders. We need to update these to include real script based validation. An example script is here: https://wiki.oicr.on.ca/display/icgcargotech/Validation+Script+Template

For the follow_up schema (https://github.com/icgc-argo/argo-dictionary/blob/master/schemas/follow_up.json), please implement the following script based validations in the dictionary:

1) For the field relapse_interval , if disease_status_at_followup =relapse then this field must have a value.
2) For the field method_of_progression_status, if disease_status_at_followup =progression or relapse, then this field must have a value.
3) For the field anatomic_site_progression_or_recurrences, if disease_status_at_followup =progression or relapse, then this field must have a value
4) For the field, recurrence_tumour_staging_system, if disease_status_at_followup =progression or relapse, then this field must have a value.
For the field, posttherapy_tumour_staging_system, if disease_status_at_followup =progression or relapse, then this field can have a value, otherwise it should not have a value.
3) Add the correct tags to the dictionary schemas so they will appear in the Dictionary viewer. A guide for tags can be found here: https://wiki.oicr.on.ca/pages/viewpage.action?pageId=134938807

Need codelist for T, N and M values

Detailed Description

We need a codelist for all the T, N and M values when the cancer staging system is AJCC. Some cancer types only allow certain values for T. For example, breast cancer allows Tis but other cancer types do not.

🐛 treatment.age_at_consent_for_treatment has no units.

treatment.age_at_consent_for_treatment has no units.

Should this be, in years?

Complete Sample_Registration Scripts

Currently all scripts listed in the dictionary are placeholders. We need to update these to include real script based validation.

An example script is here: https://wiki.oicr.on.ca/display/icgcargotech/Validation+Script+Template

For the sample_registration file (https://github.com/icgc-argo/argo-dictionary/blob/master/schemas/sample_registration.json ), please implement the following script based validations in the dictionary:

Add a script based validation on the field specimen_type. The logic should be:
If tumor_normal_designation = Normal then specimen_type can be equal to one of:
Normal,
Normal - tissue adjacent to primary tumour
Cell line - derived from normal

Other wise, tumor_normal_designation = Tumour
If tumor_normal_designation = Tumour then specimen_type can be equal to any values EXCEPT:

Normal,
Cell line - derived from normal
Add the correct tags to the dictionary schema so they will appear in the Dictionary viewer. A guide for tags can be found here: https://wiki.oicr.on.ca/pages/viewpage.action?pageId=134938807

Exit Criteria

A script is written
Script is added to the dictionary file schema
A version of dictionary with script is in Argo QA
A file uploaded with the data that matches the script logic passes

Beta Feedback: Alphabetize permissible values

Beta feedback: would be easier to read the values if they were in alphabetic order.

Alphabetize permissible values for all value lists in the dictionary

Dictionary Scripts

Add new extended field in Primary Diagnosis table "basis_of_diagnosis"

Description

A few projects have asked what the primary diagnosis should be since they use different methods to determine the diagnosis. In reality, the primary diagnosis can be made on the basis of different methods and each project/cancer type may use different ways to determine the diagnosis (ie. imaging or biopsy or clinical only etc.).

Implementation

Propose adding a new extended (optional) field called "basis_of_diagnosis" in the Primary Diagnosis table which will let data submitters specify the method of primary diagnosis. This field will consist of a controlled vocabulary recommended by the IARC and WHO:

Both WHO (see see https://apps.who.int/iris/bitstream/handle/10665/96612/9789241548496_eng.pdf page 27, Table 26) and the ENCR (European Network of Cancer Registries) recommend this codelist (see here). Only the most valid basis of diagnosis is required (ie. only need to submit one value for this clinical field). The "Notes" section will contain details and a link to WHO/IARC for reference.

🐛 tumour related fields in Specimen should only be required if specimen is tumour

Describe the bug

Currently, the data submitter is expected to submit clinical data for the tumour-related specific fields when the tumour_normal_designation is Normal which is incorrect.

Expected behaviour

The following tumour-related fields should only need to be completed only if tumour_normal_designation is Tumour. If tumour_normal_designation is Normal, then these fields should not be filled in:

pathological_tumour_staging_system
pathological_T_category
pathological_N_category
pathological_M_category
pathological_stage_group
tumour_grading_system
tumour_grade
percent_tumour_cells
percent_proliferating_cells
percent_stromal_cells
percent_necrosis

Beta Feedback: Note for each program_id

Beta testers are confused as to where they find their program_id.

For each program_id entry in the dictionary, please add the following note:

This is the unique id that is assigned to your program. When you are logged in, the program_id can be found in the top title bar of your Submission Dashboard. PACA-AU is an example of a program_id.

update readme with reges instruciotns

\b should be escaped \\b in the regex, see submitter_id for exmaple because it's a JS white space character

Error suggestion for specimen requiring donor file

I was confused at what the last two errors meant

Suggestion to change:
[specimen_acquisition_interval] requires [donor.vital_status], [donor.survival_time] in order to complete validation. Please upload data for all fields in this clinical data submission.

to
specimen_acquisition_interval requires vital_status for this donor in order to complete validation. Please upload donor data for this specimen using the donor.tsv file.

Wondering if we say "and survival_time" in this error as for donors that are alive, they don't require survival time

if so we can write:
specimen_acquisition_interval requires vital_status and survival_time (for deceased donors) in order to complete validation. Please upload donor data for this specimen using the donor.tsv file.

🐛 Remove autopsy from method_of_progression_status

Autopsy should be removed from this codelist.

Feature Request: Add optional fields for clinical trial information

Add two optional fields in Treatment table for clinical trial information

clinical_trials_database: Will consist of a codelist which will contain (will add more if requested):
"NCI Clinical Trials"
"EU Clinical Trials Register"
clinical_trial_number: This will contain a script validation that will use a regex to ensure the format of the clinical trial number matches that clinical_trial_database.

🐛 Drug Dosage units should be NUMBER not Integer

I cannot submit decimals for drug dosages:

expected behaviour

these values should allow integers

solution

change from type integer to number
dictionary locations

argo-dictionary/schemas/hormone_therapy.json

Line 92 in 69f864d

"name": "cumulative_drug_dosage",

argo-dictionary/schemas/chemotherapy.json

Line 81 in 69f864d

"name": "chemotherapy_dosage_units",

Add primary_site at donor level

There are programs with multiple primary sites or "pancancer"

Thus, we need to identify primary_site at a donor level so that each donor can be associated with the correct primary site.

Suggest adding this at the _primary_diagnosis level as a donor may have >1 instances of cancer
Suggesy making this core & required

GDC Reference:
https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=case&anchor=primary_site

Possible Implementation

    {
    	"name": "primary_site",
    	"valueType": "string",
    	"description": "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.",
    	"meta": {
    		"displayName": "Primary Site"
    		"core": true,
    	},
    	"restrictions": {
    		"required": true,
    		"enum": [
    			"Accessory sinuses",
    			"Adrenal gland",
    			"Anus and anal canal",
    			"Base of tongue",
    			"Bladder",
    			"Bones, joints and articular cartilage of limbs",
    			"Bones, joints and articular cartilage of other and unspecified sites",
    			"Brain",
    			"Breast",
    			"Bronchus and lung",
    			"Cervix uteri",
    			"Colon",
    			"Connective, subcutaneous and other soft tissues",
    			"Corpus uteri",
    			"Esophagus",
    			"Eye and adnexa",
    			"Floor of mouth",
    			"Gallbladder",
    			"Gum",
    			"Heart, mediastinum, and pleura",
    			"Hematopoietic and reticuloendothelial systems",
    			"Hypopharynx",
    			"Kidney",
    			"Larynx",
    			"Lip",
    			"Liver and intrahepatic bile ducts",
    			"Lymph nodes",
    			"Meninges",
    			"Nasal cavity and middle ear",
    			"Nasopharynx",
    			"Oropharynx",
    			"Other and ill-defined digestive organs",
    			"Other and ill-defined sites",
    			"Other and ill-defined sites in lip, oral cavity and pharynx",
    			"Other and ill-defined sites within respiratory system and intrathoracic organs",
    			"Other and unspecified female genital organs",
    			"Other and unspecified major salivary glands",
    			"Other and unspecified male genital organs",
    			"Other and unspecified parts of biliary tract",
    			"Other and unspecified parts of mouth",
    			"Other and unspecified parts of tongue",
    			"Other and unspecified urinary organs",
    			"Other endocrine glands and related structures",
    			"Ovary",
    			"Palate",
    			"Pancreas",
    			"Parotid gland",
    			"Penis",
    			"Peripheral nerves and autonomic nervous system",
    			"Placenta",
    			"Prostate gland",
    			"Pyriform sinus",
    			"Rectosigmoid junction",
    			"Rectum",
    			"Renal pelvis",
    			"Retroperitoneum and peritoneum",
    			"Skin",
    			"Small intestine",
    			"Spinal cord, cranial nerves, and other parts of central nervous system",
    			"Stomach",
    			"Testis",
    			"Thymus",
    			"Thyroid gland",
    			"Tonsil",
    			"Trachea",
    			"Ureter",
    			"Uterus, NOS",
    			"Vagina",
    			"Vulva",
    			"Unknown",
    			"Not Reported"
    		]
    	}
    }

Include references to external standards in Description field where applicable

Many of the codelists used in the dictionary are from external standards (ie. NCI, ICD-10, ICD-O-3, RECIST etc.) Include a reference to these external standards so users know where the codelist was derived from.

🐛 Cancer Type Code Regex is too Restricive

Describe the bug

There are some ICD codes with NO content in the second half .<123>.
Example C61:

The regex prevents the submitter from submitting this valid code.

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Noted for clinical

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Error during clinical validation:

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expected behaviour

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