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Known Issues in Vocabularies

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Masha Khitrun edited this page Mar 18, 2024 · 15 revisions

Vocabulary 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 the 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 in 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. We've missed a small part of the deStandardization/mapping of historical and vaccine administration concepts (and probably some other groups). It mostly happens due to discrepancies in the 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 v20240229 40 HCPCS codes appear to be reused:
The list of the reused concepts
concept_id HCPCS code Old HCPCS name New HCPCS name Reused code effective date
40664450 CS Item or service related, in whole or in part, to an illness, injury, or condition that was caused by or exacerbated by the effects, direct or indirect, of the 2010 oil spill in the gulf of mexico, including but not limited to subsequent clean-up activi... Cost-sharing waived for specified covid-19 testing-related services that result in and order for or administration of a covid-19 test and/or used for cost-sharing waived preventive services furnished via telehealth in rural health clinics and federally qualified health centers during the covid-19 public health emergency 2020-03-01
40217479 A4560 Pessary Neuromuscular electrical stimulator (nmes), disposable, replacement only 2023-04-01
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 2023-01-01
44782059 G0031 PET IMAGING PREV PET MULTPLE Palliative care services given to patient any time during the measurement period 2022-01-01
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 2022-01-01
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 2022-01-01
44782062 G0034 PET FOLLOW SPECT 76865 SINGL Patients receiving palliative care during the measurement period 2022-01-01
44782063 G0035 PET FOLLOW SPECT 78465 MULT Patient has any emergency department encounter during the performance period with place of service indicator 23 2022-01-01
44782064 G0036 PET FOLLOW CORNRY ANGIO SING Patient or care partner decline assessment 2022-01-01
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 2022-01-01
44782066 G0038 PET FOLLOW MYOCARD PERF SING Clinician determines patient does not require referral 2022-01-01
44782067 G0039 PET FOLLOW MYOCARD PERF MULT Patient not referred, reason not otherwise specified 2022-01-01
44782068 G0040 PET FOLLOW STRESS ECHO SINGL Patient already receiving physical/occupational/speech/recreational therapy during the measurement period 2022-01-01
44782069 G0041 PET FOLLOW STRESS ECHO MULT Patient and/or care partner decline referral 2022-01-01
44782070 G0042 PET FOLLOW VENTRICULOGM SING Referral to physical, occupational, speech, or recreational therapy 2022-01-01
44782071 G0043 PET FOLLOW VENTRICULOGM MULT Patients with mechanical prosthetic heart valve 2022-01-01
44782072 G0044 PET FOLLOWING REST ECG SINGL Patients with moderate or severe mitral stenosis 2022-01-01
44782073 G0045 PET FOLLOWING REST ECG MULT Clinical follow-up and mrs score assessed at 90 days following endovascular stroke intervention 2022-01-01
44782074 G0046 PET FOLLOW STRESS ECG SINGL Clinical follow-up and mrs score not assessed at 90 days following endovascular stroke intervention 2022-01-01
44782075 G0047 PET FOLLOW STRESS ECG MULT Pediatric patient with minor blunt head trauma and pecarn prediction criteria are not assessed 2022-01-01
40217731 G0050 Residual urine by ultrasound Patients with a catheter that have limited life expectancy 2022-01-01
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 2023-01-01
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 2023-01-01
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) 2022-05-11
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) 2022-05-11
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) 2022-05-11
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) 2022-05-11
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) 2022-05-11
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) 2022-05-11
2617394 G0316 ESRD related svs 1vis/12-19y Prolonged hospital inpatient or observation care evaluation and management service(s) beyond the total time for the primary service (when the primary service has been selected using time on the date of the primary service); each additional 15 minutes by the physician or qualified healthcare professional, with or without direct patient contact (list separately in addition to cpt codes 99223, 99233, and 99236 for hospital inpatient or observation care evaluation and management services). (do not report g0316 on the same date of service as other prolonged services for evaluation and management 99358, 99359, 99418, 99415, 99416). (do not report g0316 for any time unit less than 15 minutes) 2023-01-01
2617395 G0317 END STAGE RENAL DISEASE (ESRD) RELATED SERVICES DURING THE COURSE OF TREATMENT, FOR PATIENTS 20 YEARS OF AGE AND OVER; WITH 4 OR MORE FACE-TO-FACE PHYSICIAN VISITS PER MONTH Prolonged nursing facility evaluation and management service(s) beyond the total time for the primary service (when the primary service has been selected using time on the date of the primary service); each additional 15 minutes by the physician or qualified healthcare professional, with or without direct patient contact (list separately in addition to cpt codes 99306, 99310 for nursing facility evaluation and management services). (do not report g0317 on the same date of service as other prolonged services for evaluation and management 99358, 99359, 99418). (do not report g0317 for any time unit less than 15 minutes) 2023-01-01
2617396 G0318 END STAGE RENAL DISEASE (ESRD) RELATED SERVICES DURING THE COURSE OF TREATMENT, FOR PATIENTS 20 YEARS OF AGE AND OVER; WITH 2 OR 3 FACE-TO-FACE PHYSICIAN VISITS PER MONTH Prolonged home or residence evaluation and management service(s) beyond the total time for the primary service (when the primary service has been selected using time on the date of the primary service); each additional 15 minutes by the physician or qualified healthcare professional, with or without direct patient contact (list separately in addition to cpt codes 99345, 99350 for home or residence evaluation and management services). (do not report g0318 on the same date of service as other prolonged services for evaluation and management 99358, 99359, 99417). (do not report g0318 for any time unit less than 15 minutes) 2023-01-01
2617398 G0320 END STAGE RENAL DISEASE (ESRD) RELATED SERVICES FOR HOME DIALYSIS PATIENTS PER FULL MONTH; FOR PATIENTS UNDER TWO YEARS OF AGE TO INCLUDE MONITORING FOR ADEQUACY OF NUTRITION, ASSESSMENT OF GROWTH AND DEVELOPMENT, AND COUNSELING OF PARENTS Home health services furnished using synchronous telemedicine rendered via a real-time two-way audio and video telecommunications system 2023-01-01
2617399 G0321 END STAGE RENAL DISEASE (ESRD) RELATED SERVICES FOR HOME DIALYSIS PATIENTS PER FULL MONTH; FOR PATIENTS TWO TO ELEVEN YEARS OF AGE TO INCLUDE MONITORING FOR ADEQUACY OF NUTRITION, ASSESSMENT OF GROWTH AND DEVELOPMENT, AND COUNSELING OF PARENTS Home health services furnished using synchronous telemedicine rendered via telephone or other real-time interactive audio-only telecommunications system 2023-01-01
2617400 G0322 END STAGE RENAL DISEASE (ESRD) RELATED SERVICES FOR HOME DIALYSIS PATIENTS PER FULL MONTH; FOR PATIENTS TWELVE TO NINETEEN YEARS OF AGE TO INCLUDE MONITORING FOR ADEQUACY OF NUTRITION, ASSESSMENT OF GROWTH AND DEVELOPMENT, AND COUNSELING OF PARENTS The collection of physiologic data digitally stored and/or transmitted by the patient to the home health agency (i.e., remote patient monitoring) 2023-01-01
2617401 G0323 END STAGE RENAL DISEASE (ESRD) RELATED SERVICES FOR HOME DIALYSIS PATIENTS PER FULL MONTH; FOR PATIENTS TWENTY YEARS OF AGE AND OLDER Care management services for behavioral health conditions, at least 20 minutes of clinical psychologist or clinical social worker time, per calendar month. (these services include the following required elements: initial assessment or follow-up monitoring, including the use of applicable validated rating scales; behavioral health care planning in relation to behavioral/psychiatric health problems, including revision for patients who are not progressing or whose status changes; facilitating and coordinating treatment such as psychotherapy, coordination with and/or referral to physicians and practitioners who are authorized by medicare to prescribe medications and furnish e/m services, counseling and/or psychiatric consultation; and continuity of care with a designated member of the care team) 2023-01-01
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 2021-07-01
2718911 J9350 Injection, topotecan, 4 mg (Deprecated) Injection, mosunetuzumab-axgb, 1 mg 2023-07-01
2718383 J1440 Injection, filgrastim (g-csf), 300 mcg (Deprecated) Fecal microbiota, live - jslm, 1 ml 2023-07-01
2718917 J9380 Vincristine sulfate, 5 mg (Deprecated) Injection, teclistamab-cqyv, 0.5 mg 2023-07-01

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

HCPCS code ‘J9321, Injection, pemetrexed (sandoz) not therapeutically equivalent to j9305, 10 mg’ was added on 2023-07-01 and subsequently deleted as a duplicate of code J9297. On 2024-01-01 this concept code was reused and assigned with another description: ‘‘J9321, Injection, epcoritamab-bysp, 0.16 mg’. As the previous concept code was initially added by mistake as duplicative and deleted by the source in the scope of the same source version, we assumed that it was not widely presented in the raw data and that new brand-specific concept code would be more actively used. In this case, we do not preserve the old code description as an exception to our general logic.

  1. The idea of mapping 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.
  2. In 2014 concepts belonging to HCPCS Class (which essentially were Berenson-Eggers Type of Service (BETOS) codes) were dropped from the sources and subsequently deprecated, thus currently HCPCS doesn’t have any internal hierarchy in Athena. The idea is being discussed to use Restructured BETOS Classification System for the creation of a new HCPCS hierarchy.
  3. Our aim is to build a unique hierarchy of Procedures with HCPCS concepts being embedded into the hierarchy of SNOMED/OMOP Extension. This work is being made manually and at the moment is only partially completed:
source_vocabulary_id number of concepts without hierarchical relationships to SNOMED/OMOP Ext number of concepts in hierarchy target_vocabulary_id
HCPCS 9366 1426 OMOP Extension/SNOMED

*This number does not include Modifiers and Classification concepts

  1. HCPCS concepts that represent Medical Specialties are to be mapped to the respective domain and deStandardized.
  2. The problem of CPT4/HCPCS Modifiers reorganization is under discussion.

CPT4

  1. Our aim is to build a unique hierarchy of Procedures with CPT4 concepts being embedded into the hierarchy of SNOMED/OMOP Extension. This work is being made manually and at the moment is only partially completed:
source_vocabulary_id number of concepts without hierarchical relationships to SNOMED/OMOP Ext* number of concepts in hierarchy target_vocabulary_id
CPT4 100 4310 OMOP Extension/SNOMED

*This number does not include Modifiers and Classification concepts

  1. Currently we have some concerns in building hierarchical relationships between some CPT4 concepts which essentially are procedures performed on a cadaver, i.e. organ retrieval operations from a cadaver donor, and SNOMED/OMOP Extension. At the moment there is a quite short list of specific concepts for organ-retrieval operations on donors in SNOMED, that’s why some CPT4 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 4021529 Abdominal hysterectomy SNOMED
Is a 606749 Removal of organ from cadaver SNOMED

Since source concepts are used in the 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). The idea of hierarchy creation for procedures performed on a cadaver is being discussed to allow distinguishing such concepts in the course of Data Analysis.

  1. Domains of CPT4 are currently assigned according to specific patterns, defined with help of regexp expressions, and according to the domains of target Standard concepts that the respective CPT4 concepts are mapped to. This approach leads to imprecise domain assignment. Our aim is to change the logic and assign domains manually to CPT4 Hierarchy Concepts and propagate them down to the descendants and save the domain assignment according to mapping.

  2. CPT4 concepts that represent Medical Specialties are to be mapped to the respective domain and deStandardized.

  3. The problem of CPT4/HCPCS Modifiers reorganization is under discussion.

  4. The CPT Editorial Panel approves new Vaccine and Immunization codes and releases them to the AMA website quarterly or sometimes even monthly. These changes often are not captured by our releases of CPT4 OMOP vocabulary, as we take UMLS as a source, and it’s updated bi-annually. Besides, the newly introduced stable cadence of bi-annual OHDSI Vocabulary releases limits our ability to add codes on requests. It may pose a problem for CDM users, who need these codes for their research. The Vocabulary Team usually includes such concepts in the nearest scheduled CPT4 release (see Roadmap) on request. We recommend adding the necessary codes to the local CDMs in case of urgent need.

  5. In CPT4 deprecated by the source concepts are excluded from the internal CPT4 hierarchy. They appear to be ‘orphans’ with no hierarchical relationships or mapping. They should be assigned proper links to SNOMED/OMOP ext/etc.

VANDF

  1. Nearly 30% of VANDF mappings, related to solutions of all kinds (topical solution, injectable solution, etc.) are incorrect. These mappings are coming directly from the source data. VANDF and target RxNorm concepts differ in the amount of ingredients and concentration of the ingredients. We have found no differences in ingredients between VANDF and RxNorm concepts. Therefore, mappings may be used for the drug_exposure population, unless drug dosages are a prime question of the study. The examples of the mappings are represented below:
VANDF concept_code VANDF concept_name Relationship_id RxNorm concept_code RxNorm concept_name
4003882 CEPHAPIRIN NA 20GM/VIL INJ Maps to 313899 cephapirin 417 MG/ML Injectable Solution
4004136 GENTAMICIN SO4 10MG/ML (PF) INJ Maps to 1870676 2 ML gentamicin 10 MG/ML Injection
4004199 MEPIVACAINE HCL 3% INJ Maps to 1305263 1.7 ML mepivacaine hydrochloride 30 MG/ML Cartridge
4004573 MEZLOCILLIN NA 1GM/VIL INJ Maps to 311689 mezlocillin 250 MG/ML Injectable Solution
4004574 MEZLOCILLIN NA 2GM/VIL INJ Maps to 311689 mezlocillin 250 MG/ML Injectable Solution
4005823 DOPAMINE HCL 80MG/ML INJ Maps to 1743953 5 ML dopamine hydrochloride 80 MG/ML Injection
4006008 MANNITOL 100MG/ML INJ Maps to 1791395 500 ML mannitol 100 MG/ML Injection
4007046 RANITIDINE HCL 150MG GRANULES,EFFERVSC Maps to 827179 ranitidine 1 MG/ML Oral Solution
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