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An assumption is made that all concept synonyms and ancestor information will be input in an aggregated format with each aggregated concept separated by a | delimiter. That's a brittle assumption that should be improved. Examples of specs for input data can be found here: resources/clinical_data/README.md
EXAMPLE: Input Data
The CONCEPT_SYNONYM column below displays data in the expected input format
CONCEPT_ID
CONCEPT_SOURCE_CODE
CONCEPT_LABEL
CONCEPT_SOURCE_LABEL
CONCEPT_SYNONYM
37018594
snomed:80251000119104
Complement level below reference range
Complement level below reference range
Complement level below reference range | Complement level below reference range (finding)
Example of Data that Breaks Assumptions:
The CONCEPT_SYNONYM column below displays data in an unexpected input format (i.e. two types of delimiters | and ;)
CONCEPT_ID
CONCEPT_SOURCE_CODE
CONCEPT_LABEL
CONCEPT_SYNONYM
40771573
loinc:69052-9
Flow cytometry specialist review of results
Flow cytometry specialist review of results | Flow cytometry specialist review | Dynamic; Impression; Impression/interpretation of study; Impressions; Interp; Interpretation; Misc; Miscellaneous; Narrative; Other; Point in time; Random; Report; To be specified in another part of the message; Unspecified
Impact Level
LOW - the string similarity mapping pipeline correctly handles all types of pipings allowing the recovery of missed mappings in the exact match part of the pipeline.
Describe the Bug
An assumption is made that all concept synonyms and ancestor information will be input in an aggregated format with each aggregated concept separated by a
|
delimiter. That's a brittle assumption that should be improved. Examples of specs for input data can be found here:resources/clinical_data/README.md
EXAMPLE:
Input Data
The
CONCEPT_SYNONYM
column below displays data in the expected input formatExample of Data that Breaks Assumptions:
The
CONCEPT_SYNONYM
column below displays data in an unexpected input format (i.e. two types of delimiters|
and;
)Impact Level
LOW - the string similarity mapping pipeline correctly handles all types of pipings allowing the recovery of missed mappings in the exact match part of the pipeline.
Impacted Scripts
omop2obo/clinical_concept_annotator.py
Solution
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