Upcoming changes

2023 May Release

NAACCR

This release enriches the NAACCR vocabulary with mappings built and provided by the community contributors. Around 1.5k of codes from 'NAACCR Value' concept class are de-Standardized and mapped over to the Cancer Modifier vocabulary. Related NAACCR Variables with their standard concept and validity parameters remained intact.

Make sure that your ETL is ready to implement the changes:

• Retrieve the mappings from non-standard NAACCR Values to Cancer Modifier Measurement concepts (relationship_id = ‘Maps to’).
• Populate the measurement_concept_id with concept_id from the standard Cancer Modifier counterparts.
• Do not populate the value_as_concept_id field (even though it may be stored as the value in the source data).

Concept_id for event fields should be selected depending on the mapping of NAACCR Value solely.

Different ETL scenarios are described in following table:

Source data (NAACCR Variable-Value)							OMOP CDM target
Logical group	NAACCR Variable			NAACCR Value			concept code	concept name
	concept code	concept name	std concept	concept code	concept name	std concept
1	2860	CS Mets Eval	S	For cases when value is not mapped or not populated			2860	CS Mets Eval
	2860	CS Mets Eval	S	larynx_supraglottic@2860@3	Meets criteria for AJCC pathologic staging of distant metastasis:||Specimen from metastatic site microscopically positive WITHOUT pre-surgical systemic treatment or radiation |OR specimen from metastatic site microscopically positive, unknown if pre-surg	NULL	OMOP4998856	Metastasis
2.1	774	EOD Regional Nodes	S	For cases when value is not mapped or not populated			774	EOD Regional Nodes
	774	EOD Regional Nodes	S	melanoma_choroid_ciliary_body@774@999	Unknown; regional lymph node(s) not stated|Regional lymph node(s) cannot be assessed|Not documented in patient record||Death Certificate Only	NULL	NA	NA
2.2	774	EOD Regional Nodes	S	For cases when value is not mapped or not populated			NA	NA
	774	EOD Regional Nodes	S	net_jejunum_ileum@774@400	Large mesenteric masses (greater than 2 cm)|Lymph node metastasis greater than 2 cm	NULL	OMOP4998946	Regional spread to lymph node
2.3	774	EOD Regional Nodes	S	For cases when value is not mapped or not populated			774	EOD Regional Nodes
				liver@774@800	Regional lymph node(s), NOS|Lymph node(s), NOS	S	liver@774@800	Regional lymph node(s), NOS|Lymph node(s), NOS
3	merkel_cell_penis@2870	Size of Metastasis in Lymph Nodes	NULL	Irrespective of value			OMOP4998351	Dimension of Lymph Node
				merkel_cell_penis@2870@990	Metastasis or tumor nests in regional lymph nodes, size cannot be assessed	NULL	OMOP4998946	Regional spread to lymph node

*std - standard_concept

Smoking hierarchy

Our team continues remapping of smoking-related concepts to the OMOP Extension vocabulary. During our last major release, we created a set of OMOP Extension concepts to accompany the ETL Smoking convention. The progress can be tracked here on the OHDSI Forum.

During this release we will focus on remapping of SNOMED concepts: the smoking-related SNOMED terms will be mapped to new OMOP Extension concepts. These changes affect smoking-related concept sets and cohorts built on currently standard SNOMED concepts. The top concept of hierarchy is Findings of tobacco or its derivatives use or exposure. Tobacco users are now defined according to the type of the product they use (Smokeless, Electronic, Cigarettes, Cigars, etc.), while cigarette smokers are also classified according to the severity of smoking (Trivial, Light, Moderate, Heavy, Very heavy). Cigarette pack-years smoked during life concept is intended to capture the cumulative consumption of cigarettes.

Note 1: these changes do not concern the concepts that are adjacent to smoking (for example, Nicotine dependence). Identification of patients who smoke can be based on more broad terms (such as nicotine dependence or nicotine abuse), more granular terms (such as fact of smoking, number of pack-years, etc.) or combination of such. The hierarchy we created enables clean representation and retrieval of the granular concepts. Your concept set design should depend on code utilization in the data intended to be used and intended specificity/sensitivity of your phenotype.

Note 2: in some cases post-coordination in data modeling may be changed to pre-coordination and vice versa. These may significantly affect ETL process through the source_to_concept_map table.

Source data (various vocabularies*)				OMOP CDM target (OMOP Extension)
source_concept_id	source_concept_name	source_value_concept_id	source_value_concept_name	event_concept_id	concept_name	value_as_concept_id	concept_name
4310250	Ex-smoker	NA		1340204	History of event	903657	Cigarette smoker
				903651	Currently doesn't use tobacco or its derivatives	NA
4203874	Smoking monitoring status	For cases when value is not mapped or not populated		NA	NA	NA	NA
		4298794	Smoker	903657	Cigarette smoker

* - this might be relevant to custom mapping vocabularies also

Please make sure that upcoming changes will be addressed in your ETLs and studies.