Baseline mapping with value as number AND value as concept

[MaximMoinat]

Currently, it is not possible to map to both a value_as_number (+unit) AND value_as_concept. The baseline field mapper is divides all codes into discrete fields (has mappings for values) OR numeric fields (if no mapping for values).

In the case of e.g. Age Glaucoma Diagnosed, the Athena to standard mapping has a maps to unit AND a maps to value.

This results in a mapping like given below. We do not support the mapping to value_as_concept_id and only number and unit are captured. To allow also a value_as_concept_id, the Field Mapper should be updated.

field	value
concept_id	History of clinical finding in subject - 4214956
value_as_concept_id	Glaucoma - 437541 <--- currently not supported
value_as_number	67
unit_concept_id	year - 9448

Still, also this mapping is not ideal:

• It is implicit that the 67 is the age of diagnosis. Could also be number of years ago.
• The history of clinical finding of Glaucoma will also be captured by mapping of field 6148

[MaximMoinat]

Another enhancement is to integrate all the new baseline field mappings that were included by the OHDSI vocabulary team. All the Maps to relations in the vocab files can be transformed in our mapping table format.

[MaximMoinat]

There are just 17 UKB codes mapped to a unit and value in the Athena vocabulary. All about past events with a mapping like Maps to 'History of clinical finding / Past history of procedure', Maps to unit 'year' and Maps to value condition/procedure concept.

concept_id	concept_code	concept_name	relationship_id	target_concept_name	relationship_id	target_concept_name	relationship_id	target_concept_name
35810062	2355	Most recent bowel cancer screening	Maps to	Past history of procedure	Maps to unit	year	Maps to value	Screening for malignant neoplasm of large intestine
35810063	3809	Time since last prostate specific antigen (PSA) test	Maps to	Past history of procedure	Maps to unit	year	Maps to value	Prostate specific antigen measurement
35810333	2966	Age high blood pressure diagnosed	Maps to	History of clinical finding in subject	Maps to unit	year	Maps to value	Hypertensive disorder
35810334	2976	Age diabetes diagnosed	Maps to	History of clinical finding in subject	Maps to unit	year	Maps to value	Diabetes mellitus
35810386	3627	Age angina diagnosed	Maps to	History of clinical finding in subject	Maps to unit	year	Maps to value	Angina pectoris
35810400	3786	Age asthma diagnosed	Maps to	History of clinical finding in subject	Maps to unit	year	Maps to value	Asthma
35810408	3894	Age heart attack diagnosed	Maps to	History of clinical finding in subject	Maps to unit	year	Maps to value	Myocardial infarction
35810413	3992	Age emphysema/chronic bronchitis diagnosed	Maps to	History of clinical finding in subject	Maps to unit	year	Maps to value	Chronic obstructive lung disease
35810414	4012	Age deep-vein thrombosis (DVT, blood clot in leg) diagnosed	Maps to	History of clinical finding in subject	Maps to unit	year	Maps to value	Deep venous thrombosis of lower extremity
35810415	4022	Age pulmonary embolism (blood clot in lung) diagnosed	Maps to	History of clinical finding in subject	Maps to unit	year	Maps to value	Pulmonary thrombosis
35810417	4056	Age stroke diagnosed	Maps to	History of clinical finding in subject	Maps to unit	year	Maps to value	Cerebrovascular accident
35810533	4689	Age glaucoma diagnosed	Maps to	History of clinical finding in subject	Maps to unit	year	Maps to value	Glaucoma
35810534	4700	Age cataract diagnosed	Maps to	History of clinical finding in subject	Maps to unit	year	Maps to value	Cataract
35810685	5430	Age when loss of vision due to injury or trauma diagnosed	Maps to	History of clinical finding in subject	Maps to unit	year	Maps to value	Injury of globe of eye
35810709	5901	Age when diabetes-related eye disease diagnosed	Maps to	History of clinical finding in subject	Maps to unit	year	Maps to value	Disorder of eye due to diabetes mellitus
35810711	5923	Age macular degeneration diagnosed	Maps to	History of clinical finding in subject	Maps to unit	year	Maps to value	Degenerative disorder of macula
35810713	5945	Age other serious eye condition diagnosed	Maps to	History of clinical finding in subject	Maps to unit	year	Maps to value	Disorder of eye