I have completed a review of the recent updates to the oncology-related terminology within the OMOP vocabulary (DeltaVocab). This message is not to highlight a problem per se, but rather to enhance our understanding of the variations between different versions of the vocabulary. I recommend this issue be closed after it has been evaluated by the working group.
Findings:
1) Ambiguous Source Concept Names:
The concept table shows 89 instances where different concept_ids share identical names despite having different semantic meanings. This overlap can lead to confusion and mismatches when these names are used to link source data with non-standard terms. A possible solution is to revise the concept names to include more descriptive, distinguishing details and move the current identical names to the concept_synonym table.
Snippet 1:
Source Concept ID
Source Name
Relationship ID
Target Concept ID
Target Concept Name
Concept Label
Category
Type
35919047
0
Maps to
1634502
c-AJCC/UICC-Stage-0
AJCC/UICC clinical Stage 0
Staging/Grading
Measurement
35919331
0
Maps to
1633542
p-AJCC/UICC-Stage-0
AJCC/UICC pathological Stage 0
Staging/Grading
Measurement
35919511
0a
Maps to
1635865
p-AJCC/UICC-Stage-0A
AJCC/UICC pathological Stage 0a
Staging/Grading
Measurement
35919890
0a
Maps to
1635434
c-AJCC/UICC-Stage-0A
AJCC/UICC clinical Stage 0a
Staging/Grading
Measurement
2) Potentially Misaligned Stage Mappings:
I have identified 21 mappings that potentially incorrectly align pathological stages with clinical stages. To rectify this, a review and realignment of these mappings in OMOP Vocabulary are suggested, ensuring each term accurately reflects its designated stage category, either clinical or pathological.
Snippet 2:
Source Concept ID
Source Name
Relationship ID
Target Concept ID
Target Concept Name
Additional Relationship ID
Concept ID
Concept Name
45876314
Stage IVC
Maps to
1635567
AJCC/UICC pathological Stage 4C
Answer of
3022698
Stage group.clinical Cancer
45876315
Stage IVB
Maps to
1633577
AJCC/UICC pathological Stage 4B
Answer of
3022698
Stage group.clinical Cancer
45876316
Stage IIA
Maps to
1634960
AJCC/UICC pathological Stage 2A
Answer of
3022698
Stage group.clinical Cancer
45878382
Stage IIC
Maps to
1633859
AJCC/UICC pathological Stage 2C
Answer of
3022698
Stage group.clinical Cancer
Please find the attached XLSX file for a detailed review. I have used the SSSOM approach for the "IdenticalSourceNames_DiffMeaning" spreadsheet and modified the typical OMOP mapping representation in the "StageConflict_PathVsClinical" spreadsheet (just for your reference).
Hello everyone,
I have completed a review of the recent updates to the oncology-related terminology within the OMOP vocabulary (DeltaVocab). This message is not to highlight a problem per se, but rather to enhance our understanding of the variations between different versions of the vocabulary. I recommend this issue be closed after it has been evaluated by the working group.
Findings: 1) Ambiguous Source Concept Names: The concept table shows 89 instances where different concept_ids share identical names despite having different semantic meanings. This overlap can lead to confusion and mismatches when these names are used to link source data with non-standard terms. A possible solution is to revise the concept names to include more descriptive, distinguishing details and move the current identical names to the concept_synonym table.
Snippet 1:
2) Potentially Misaligned Stage Mappings: I have identified 21 mappings that potentially incorrectly align pathological stages with clinical stages. To rectify this, a review and realignment of these mappings in OMOP Vocabulary are suggested, ensuring each term accurately reflects its designated stage category, either clinical or pathological.
Snippet 2:
Please find the attached XLSX file for a detailed review. I have used the SSSOM approach for the "IdenticalSourceNames_DiffMeaning" spreadsheet and modified the typical OMOP mapping representation in the "StageConflict_PathVsClinical" spreadsheet (just for your reference).
Looking forward to further discussion.
OncologyWG-VocabDeltaReview.xlsx .