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Invalidated concepts still show valid relationships

#1

I am looking to get the ‘Chemical Structure’ class’ tree hierarchy from both the RELATIONSHIP and CONCEPT table joined.

I’ve queried for the ‘Chemical Structure’ concept class and the ‘Is a’ relationships to get the child-parent relationships of the tree/graph. While doing so, I realized that some of the concepts in CONCEPT_ID_1 and CONCEPT_ID_2 are invalid (D), but the ‘Is a’ relationship still shows as valid. What is the reason for this?

I would think that if, a ‘Chemical Structure’ concept gets invalidated in the CONCEPT table, its ‘Is a’ and ‘subsumes’ relationships would get invalidated as well. At least the ‘subsumes’ relationship should get deleted. Given that this concept got deleted, its children would not exist anymore. Is this logic correct?

Examples:

4351452
4350603
4349704

4257524
40220356
4351934

Thank you for any clarification.

#2

@napanmo:

The hierarchical relationships within NDFRT are sourced from NDFRT. When the concepts are falling out they are deprecated, but their relationships continue. NDFRT is no longer supported anyway, and its presence there is a remnant from the past. I wouldn’t waste much time with it.

The hierarchical relationships we use in the OMOP Standardized Vocabularies are only between Standard Concepts (those that also can be used in the data), and they are represented in the CONCEPT_ANCESTOR table. For drugs, I would recommend using ATC. It contains chemical classes as part of the hierarchical structure.

#3

Hello Christian,

Thank you for the clarification. Yes, I am currently implementing ATC in my pipeline. I was just exploring the potential use of additional drug classes like NDFRT and SNOMED.

Thank you,
Pablo

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