3. Documentation for the readme

[bhavikbhagat93]

Description

A readme file will be part of the zip file which that will include definition of each clinical exception.

File name: Exception manifest readme

File type : txt

File content:

• Program Exception -
• Entity Exception -
• Missing Entity Exception -
• Treatment Details Exception -

Acceptance criteria

[lindaxiang]

@bhavikbhagat93

• Program Exception: A Program Exception is granted when a specific data field is missing, unavailable, or not applicable across all donors in a program. Once a Program Exception is approved, the program is allowed to submit a non-permissible value (such as "unknown" or "not applicable") for these fields.
• Donor Exception: A Donor Exception is granted when a specific data field is missing, unavailable, or not applicable for only certain donors within a program. With a Donor Exception, the affected donors are permitted to submit a non-permissible value (such as "unknown" or "not applicable") for these fields.
• Missing Entity Exception: A Missing Entity Exception is granted when a donor, marked as "lost to follow-up," is missing core entities such as treatment or follow-up details. With this exception, donors can achieve clinical core completion and be eligible for release, even if they are missing some core entities.
• Treatment Details Exception: A Treatment Details Exception is granted when additional treatment details for a donor are missing, unavailable, or not applicable. With this exception, donors are not required to provide the missing treatment details.

[edsu7]

@bhavikbhagat93

Types of Program exceptions:

• Program Exception: A Program Exception is granted when a specific data field is missing, unavailable, or not applicable across all donors in a program. Once a Program Exception is approved, the program is allowed to submit a non-permissible value (such as "unknown" or "not applicable") for these fields.
• Entity Exception: An Entity Exception is granted when a specific data field is missing, unavailable, or not applicable for a donor, event, or specimen within a program. With an Entity Exception, the affected donors are permitted to submit a non-permissible value (such as "unknown" or "not applicable") for these fields.
• Missing Entity Exception: A Missing Entity Exception is granted when a donor, marked as "lost to follow-up," is missing core entities such as treatment or follow-up details. With this exception, donors can achieve clinical core completion and be eligible for release, even if they are missing some core entities.
• Treatment Details Exception: A Treatment Details Exception is granted when additional treatment details for a donor are missing, unavailable, or not applicable. With this exception, donors are not required to provide the missing treatment details.

Types of Program Examples:

Program Exception:

• Manifest table:
  • The validation rule is that a sample must provide a numeric value as specimen_acquisition_interval

programId	exceptionType	schemaName	propertyName	exceptionValue	donorId	submitterDonorId	submitterEntityId	entityId
DEMO-CA	ProgramProperty	specimen	specimen_acquisition_interval	Unknown

• Specimen table (Abbreviated - only a subset of columns shown):
  • With program exception in place, SP_A2 and SP_A3 can be submitted with specimen_acquisition_interval as Unknown value, displayed as blank value
  • An example is SP_A1 submitted with an appropriate specimen_acquisition_interval as comparison

donor_id	program_id	submitter_donor_id	submitter_specimen_id	submitter_primary_diagnosis_id	specimen_acquisition_interval	specimen_anatomic_location	percent_tumour_cells
00001	DEMO-CA	DO_A	SP_A1	PD_1	0	C15.5	0.825
00001	DEMO-CA	DO_A	SP_A2	PD_1		C15.9	0.97
00001	DEMO-CA	DO_A	SP_A3	PD_1		C15.9	0.50

Donor Exception:

• Manifest table:
  • The validation rule is that a sample must percent_tumour_cells and percent_tumour_cells_measurement_method for a given tumour sample

programId	exceptionType	schemaName	propertyName	exceptionValue	donorId	submitterDonorId	submitterEntityId	entityId
DEMO-CA	EntityProperty	specimen	percent_tumour_cells	Unknown	00001	DO_A	SP_A1	NNN9
DEMO-CA	EntityProperty	specimen	percent_tumour_cells_measurement_method	Unknown	00001	DO_A	SP_A1	NNN9

• Specimen table (Abbreviated - only a subset of columns shown):
  • With program exception in place, SP_A1 can be submitted with a blank percent_tumour_cells value and Unknown percent_tumour_cells_measurement_method.
  • Note that donor 00001 has multiple specimens but the exception only applies to one sample as per the manifest table, thus other samples must be submitted fully.

donor_id	program_id	submitter_donor_id	submitter_specimen_id	submitter_primary_diagnosis_id	percent_tumour_cells	percent_tumour_cells_measurement_method
00001	DEMO-CA	DO_A	SP_A1	PD_1		Unknown
00001	DEMO-CA	DO_A	SP_A2	PD_1	0.97	Genomics
00001	DEMO-CA	DO_A	SP_A3	PD_1	0.50	Pathology estimate by percent nuclei

Data when exceptions are inplace:

• While exceptions are in place, data can be submitted without adhering to exceptions. See program Exceptions example.
• In this events, metadata will be treated as normal and validated as well.