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Standard but deprecated (by the source) “zombie” concepts

Maryia Khitrun edited this page Mar 31, 2023 · 4 revisions

Obsolete (by the source) concepts are usually represented in OMOP vocabularies as deprecated (invalid_reason = ‘D’) and non-standard (standard_concept = NULL. But there are cases when obsolete concepts that cannot be consistently mapped to Standard equivalents still widely persist in the clinical data tables. Since users may need to query them in their studies , there’s a workaround approach applied in OMOP vocabulary system: the concepts turned into Standard and valid, but with the validity end date defined in the past.

Properties of such concepts look like:

    standard_concept = ‘S’,


    valid_end_date < 2099-12-31,


    invalid_reason IS NULL.

In other words, they are so-called 'zombies', 'dead' but 'resurrected' in terms of validity because of the study needs.

Examples are provided below:

concept_id concept_code concept_name concept_class_id standard_concept valid_end_date domain_id vocabulary_id
42740582 0006F Statin therapy, prescribed (Deprecated) CPT4 Standard 2005-01-19 Procedure CPT4
40218366 C1059 Autologous cultrured chondrocytes, implantation, carticel HCPCS Standard 2001-06-30 Procedure HCPCS
42896034 037K0F6 Dilation of Right Internal Carotid Artery, Bifurcation, with Three Intraluminal Devices, Open Approach (Deprecated) ICD10PCS Standard 2020-09-30 Procedure ICD10PCS
2006317 84.58 Implantation of interspinous process decompression device Procedure Standard 2014-09-30 Procedure ICD9Proc

As at the v20220829_major release the number of standard but deprecated (by the source) concepts is following:

Vocabulary Count
CPT4 1862
Gemscript 7094
HCPCS 2905
ICD10PCS 4271
ICD9Proc 5
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