cgreich
commented
5 years ago @noahgengel:
Yeah. There are a few problems with them:
- Most of them are Measurements, but so unspecific that you cannot use them for analytics. Essentially they all are "Measurement of something, with no result provided". You can't map that junk to anything useful. Take R76.8: "Other specified abnormal immunological findings in serum" - what use case will this record fulfill?
- Some of them are artifacts to get reimbursed, such as V72.62 "LABORATORY EXAMINATION ORDERED AS PART OF A ROUTINE GENERAL MEDICAL EXAMINATION". For analytics completely useless.
Your Local codes just need to be mapped:
- FLOW CYTOMETRY, CD4 AND CD8: I assume that is in blood for HIV, is it not? How about http://athena.ohdsi.org/search-terms/terms/40768448
- FLOW CYTOMETRY, CD4: Same thing. http://athena.ohdsi.org/search-terms/terms/40768447
- FLOW CYTOMETRY, PNH: http://athena.ohdsi.org/search-terms/terms/40758294
- FLOW CYTOMETRY T,B,NK LYMPHOCYTE COUNTS (with the flow cytometry it seems like there are obstacles when it comes to all of the combinations of cell types): http://athena.ohdsi.org/search-terms/terms/40768449. However, this is a panel. It's B-cell, T-cell and NK cell counts using surface markers. You need to write three separate MEASUREMENT records and put the results into the respective tests.
- EMG / NCS Testing (current codes list EMG and NCS separately; parent of both codes is too vague): Understood. But what does the record actually say? One or the other? Again, pretty useless for analytics. You can't look for patients that "maybe" have had one of two tests, and you have no idea what the result refers to. Junk code.
- CHEM 7 PANEL (HISTORICAL): NOTE - The current best fit for this in the 'Measurement' domain is 3041230. This ID, however, does not include sodium in the panel: It's a panel. So, you would need to write out the individual tests anyway. Because the MEASUREMENT table can only give results for one test at a time.
- PAIN MANAGEMENT PROFILE: What's that? Drug in urine testing for pain and addiction management? Again, you need to cut this panel into pieces anyway.
Hope this helps. Keep it coming. BTW: The Forum is probably the better place for this generic debate.
noahgengel
Hello,
After some investigation, Zoey and I (both from CUMC) found that many sites struggled to map some of their local concepts to 'standard' concepts because no equivalent exists in the standard vocabulary. To document these gaps in the language, we wanted to list the nonstandard concepts that have no corresponding standard mapping:
ICD10/ICD10CM: R76.8: Other specified abnormal immunological findings in serum R78.9: Finding of unspecified substance, not normally found in blood R74.8: Abnormal levels of other serum enzymes R74.9: Abnormal serum enzyme level, unspecified R76.9: Abnormal immunological finding in serum unspecified R77.8: Other specified abnormalities of plasma proteins (NOTE: we found standard concepts that were unidirectional. In other words, we found a measurement for 'low' plasma proteins but not 'high' or 'general abnormal' plasma proteins). R77.9: Abnormality of plasma protein, unspecified Z51.81: THERAPEUTIC DRUG LEVEL MONITOR R97.8: Other abnormal tumor markers R77.0: Abnormality of albumin (NOTE: there are some standard concepts relating to albumin abnormalities but these are too specific) Z68.54: BMI PEDIATRIC GREAT THAN OR EQUAL TO 95% FOR AGE Z6851: BMI PEDIATRIC, LESS THAN 5TH PERCENTILE FOR AGE Z72.61: Antibody Response Examination V72.32: Encounter for Papanicolaou cervical smear to confirm findings of recent normal smear following initial abnormal smear Z13.79: ECT FOR OT SCREEN FOR GENETC&CHROMSOML ANOMALITY R77.1: Abnormality of Globulin (NOTE: there are specific abnormalities listed as standard concepts) V72.63: Pre-Procedural Laboratory Examination V72.62:LABORATORY EXAMINATION ORDERED AS PART OF A ROUTINE GENERAL MEDICAL EXAMINATION Z0283: ENCOUNTER FOR BLOOD-ALCOHOL AND BLOOD-DRUG TEST (NOTE: we have been normally classifying 'encounters' as procedures rather than measurements) Z0182:ENCOUNTER FOR ALLERGY TESTING Z0142:ECT FOR CERV SMR - CNFRM NORM SMR FOL INI AB Z0184:ENCOUNTER FOR ANTIBODY RESPONSE EXAMINATION
ICD9/ICD9CM: 790.6: OTHER ABNORMAL BLOOD CHEMISTRY 795.79: Other and unspecified nonspecific immunological findings 790.5: Other nonspecific abnormal serum enzyme levels 792.9: OTHER NONSPECIFIC ABNORMAL FINDINGS IN BODY 794.2: NONSPECIFIC ABNORMAL RESULTS OF PULMONARY FUNCTION STUDY 796.0: NONSPECIFIC ABNORMAL TOXICOLOGICAL FINDINGS 795.08: UNSATISFACTORY CERVICAL CYTOLOGY SMEAR 791.7: OTHER CELLS AND CASTS IN URINE
Local Vocabulary (not on Athena):
We recognize that this is a long list and that not all of these codes will warrant the creation of a new standard concept but thought it would not hurt to document everything we saw here. We also recognize that some of these codes technically have standard concepts in Athena but, after inspection, realized that the 'standard' mapping leaves out crucial information (e.g. going from abnormal findings to a general measurement.)
Please let either of us know if you have any questions or concerns.
Thank you, Noah Engel