Known Issues in Vocabularies

Vocabualary machinery

1. In deStandardization/mapping of historical and vaccine administration concepts we faced unexpected results and lots of different patterns of script behavior in SNOMED and ICDs. This is due to a complex (and probably stale) logic of vocabulary machinery that does not cope well with adjustments and requires lots of manual curation. In the long run, the entire machinery has to be revised / refactored. At the moment it may result in inconsistent mapping in a small number of concepts, e.g. missing or excessive mapping to value, duplicative mapping to pre-coordinated and post-coordinated expressions.

ICD family vocabulary

1. Mapping reuse logic among different ICD family vocabularies is corrupted. It leads to occasional different mapping of the same codes among different vocabularies. This will be fixed with an implementation of the CDE (common data environment) for ICD vocabulary family.

SNOMED

1. For a substantial part of SNOMED concepts the validity dates in the concept table do not correspond to them in the sources. The possible reason is generally poor logic of date assignment in the SNOMED load_stage.

2. A substantial part of concepts with replacement relationships ("Concept replaced by", "Concept same_as to", "Concept alt_to to", "Concept was_a to") do not have valid "Maps to" relationships. A possible reason is a wrong location of the "AddFreshMapsTo" function in the load_stages or conflicting function vs load_stage logic.

3. In the v20220829_major release, we revoked the "Concept poss_eq to" (Inactive possibly equivalent to active) from the list of replacement relationships. It means that "Maps to" relationships will no longer be automatically constructed based on "Concept poss_eq to". This decision was taken based on multiple erroneous "Maps to" relationships, previously built from "Concept poss_eq to" (because in many cases one from many was chosen randomly). Also, we allowed 1-to-many linkage for the "Concept poss_eq to" relationship so that multiple relationships that are provided by the source will be included to the concept_relationship table, e.g. "Integument anomalies: [ichthyosis congenita] or [Darier's] or [keratosis follicularis] or [Meige's] or [Milroy's] or [Mongolian spots] or [pseudoxanthoma elasticum] or [congenital NOS]" concept has 7 such links. All historical "Maps to" relationships that were build based on "Concept poss_eq to" are preserved for now but will be tagged for removal in a later clean-up job.

4. In deStandardization/mapping of historical and vaccine administration concepts (and probably some other groups) we've missed a small part of them. It mostly happens due to discrepancies in hierarchy (most of the concepts derive from a single ancestor within a group, but a small portion of them are floating in SNOMED without a good hierarchy and should be pulled out manually, which inevitably results in missing concepts).

HCPCS

1. Since the vocabulary release v20230123 28 HCPCS codes appear to be reused:

concept_id	HCPCS code	Old HCPCS name	New HCPCS name
44782058	G0030	PET IMAGING PREV PET SINGLE	Patient screened for tobacco use and received tobacco cessation intervention on the date of the encounter or within the previous 12 months (counseling, pharmacotherapy, or both), if identified as a tobacco user
44782059	G0031	PET IMAGING PREV PET MULTPLE	Palliative care services given to patient any time during the measurement period
44782060	G0032	PET FOLLOW SPECT 78464 SINGL	Two or more antipsychotic prescriptions ordered for patients who had a diagnosis of schizophrenia, schizoaffective disorder, or bipolar disorder on or between january 1 of the year prior to the measurement period and the index prescription start date (ipsd) for antipsychotics
44782061	G0033	PET FOLLOW SPECT 78464 MULT	Two or more benzodiazepine prescriptions ordered for patients who had a diagnosis of seizure disorders, rapid eye movement sleep behavior disorder, benzodiazepine withdrawal, ethanol withdrawal, or severe generalized anxiety disorder on or between january 1 of the year prior to the measurement period and the ipsd for benzodiazepines
44782062	G0034	PET FOLLOW SPECT 76865 SINGL	Patients receiving palliative care during the measurement period
44782063	G0035	PET FOLLOW SPECT 78465 MULT	Patient has any emergency department encounter during the performance period with place of service indicator 23
44782064	G0036	PET FOLLOW CORNRY ANGIO SING	Patient or care partner decline assessment
44782065	G0037	PET FOLLOW CORNRY ANGIO MULT	On date of encounter, patient is not able to participate in assessment or screening, including non-verbal patients, delirious, severely aphasic, severely developmentally delayed, severe visual or hearing impairment and for those patients, no knowledgeable informant available
44782066	G0038	PET FOLLOW MYOCARD PERF SING	Clinician determines patient does not require referral
44782067	G0039	PET FOLLOW MYOCARD PERF MULT	Patient not referred, reason not otherwise specified
44782068	G0040	PET FOLLOW STRESS ECHO SINGL	Patient already receiving physical/occupational/speech/recreational therapy during the measurement period
44782069	G0041	PET FOLLOW STRESS ECHO MULT	Patient and/or care partner decline referral
44782070	G0042	PET FOLLOW VENTRICULOGM SING	Referral to physical, occupational, speech, or recreational therapy
44782071	G0043	PET FOLLOW VENTRICULOGM MULT	Patients with mechanical prosthetic heart valve
44782072	G0044	PET FOLLOWING REST ECG SINGL	Patients with moderate or severe mitral stenosis
44782073	G0045	PET FOLLOWING REST ECG MULT	Clinical follow-up and mrs score assessed at 90 days following endovascular stroke intervention
44782074	G0046	PET FOLLOW STRESS ECG SINGL	Clinical follow-up and mrs score not assessed at 90 days following endovascular stroke intervention
44782075	G0047	PET FOLLOW STRESS ECG MULT	Pediatric patient with minor blunt head trauma and pecarn prediction criteria are not assessed
40217731	G0050	Residual urine by ultrasound	Patients with a catheter that have limited life expectancy
2617386	G0308	ESRD related svc 4+mo < 2yrs	Creation of subcutaneous pocket with insertion of 180 day implantable interstitial glucose sensor, including system activation and patient training
2617387	G0309	ESRD related svc 2-3mo <2yrs	Removal of implantable interstitial glucose sensor with creation of subcutaneous pocket at different anatomic site and insertion of new 180 day implantable sensor, including system activation
2617388	G0310	ESRD related svc 1 vst <2yrs	Immunization counseling by a physician or other qualified health care professional when the vaccine(s) is not administered on the same date of service, 5 to 15 mins time (this code is used for medicaid billing purposes)
2617389	G0311	ESRD related svs 4+mo 2-11yr	Immunization counseling by a physician or other qualified health care professional when the vaccine(s) is not administered on the same date of service, 16-30 mins time (this code is used for medicaid billing purposes)
2617390	G0312	ESRD relate svs 2-3 mo 2-11y	Immunization counseling by a physician or other qualify ed health care professional when the vaccine(s) is not administered on the same date of service for ages under 21, 5 to 15 mins time (this code is used for medicaid billing purposes)
2617391	G0313	ESRD related svs 1 mon 2-11y	Immunization counseling by a physician or other qualified health care professional when the vaccine(s) is not administered on the same date of service for ages under 21, 16-30 mins time (this code is used for medicaid billing purposes)
2617392	G0314	ESRD related svs 4+ mo 12-19	Immunization counseling by a physician or other qualified health care professional for covid-19, ages under 21, 16-30 mins time (this code is used for the medicaid early and periodic screening, diagnostic, and treatment benefit (epsdt)
2617393	G0315	ESRD related svs 2-3mo/12-19	Immunization counseling by a physician or other qualified health care professional for covid-19, ages under 21, 5-15 mins time (this code is used for the medicaid early and periodic screening, diagnostic, and treatment benefit (epsdt)
2617405	G0327	END STAGE RENAL DISEASE (ESRD) RELATED SERVICES LESS THAN FULL MONTH, PER DAY; FOR PATIENTS TWENTY YEARS OF AGE AND OVER	Colorectal cancer screening; blood-based biomarker

Unless the code reuse handling approach is implemented in OMOP, we preserve reused codes with old semantics.

2. The idea about mapping of the concepts associated with death of a patient to the CDM table ‘Death’ is now being discussed in the Community and has not been addressed yet.

3. Our aim is to build a unique hierarchy of Procedures with CPT4/HCPCS concepts being embedded into the hierarchy of SNOMED. This work is being made manually and at the moment is only partially completed:

source_vocabulary_id	number of concepts in hierarchy	target_vocabulary_id
CPT4	9	OMOP Extension
CPT4	631	SNOMED
HCPCS	10	OMOP Extension
HCPCS	1986	SNOMED

4. Currently we have some concerns in building hierarchical relationships between some CPT4/HCPCS concepts which essentially are procedures performed on a cadaver, i.e. organ retrieval operations from cadaver donor, and SNOMED/OMOP Extension. At the moment in SNOMED there is a quite short list of specific concepts for organ-retrieval operations on donor, that’s why some CPT4/HCPCS concepts have become descendants of ordinary organ excision performed without organ-saving technique:

1389598	Donor hysterectomy (including cold preservation); open, from cadaver donor	CPT4	Is a	Abdominal hysterectomy	SNOMED
			Is a	Removal of organ from cadaver	SNOMED

Since source concepts are used in health data of a donor, in the course of Data Analysis the question may arise whether the death resulted from the organ excision (e.g. hysterectomy). Unfortunately, at the moment we don’t have a better decision, but we keep watching for new SNOMED/OMOP Extension concepts for procedures performed on a cadaver.