Standardizing procedures (call for non-US based collaborators)

Vojtech_Huser · November 18, 2014, 12:24pm

I am working on an analysis that uses CDM schema and in order to make it final, I need to analyze procedural data.

In OHDSI, we emphasize SNOMED, LOINC and RxNorm/ATC that help us standardize diagnoses, labs and medications. However, we need some good common terminology to express
procedures. I would like to find collaborators that would be willing to look at their top 10 procedures found in their CDM-shaped repository.

I would be interested to hear perspective of any non-US data OMOP CDM implementers, how
they currently represent, for example, Gynecologic Examination, Chest X-ray (2 views), Electrocardiogram (with interpretation and report) or Pre-surgery evaluation ( in their PROCEDURE_OCCURRENCE table)

Please email me to vojtech.huser at nih.gov if interested in collaborating about analysis of Procedures. (I am hoping to get some insights into procedures coming from non-US data repositories).
If you are familiar with work on top2000 LOINC codes, I need a similar set (just top 20 is enough) for procedures.

Vojtech

rwpark · November 18, 2014, 2:05pm

I am willing to join your project.
Although I emailed you, I copy some of them for open communication.

–
I am willing to join your project.
As you see, the mapping for procedure in our data is not complete yet.
In Korea, we use EDI (Electronic Data Interchange) code for procedures of radiology, pathology , anesthesia, and we use ICD9-CM for surgery.
The EDI code is a Korean standard code for reimbursement.
Would you let me know what kind of procedures you want to know?

wstephens · November 18, 2014, 8:08pm

Vojtech,

I’ll be heading to London in early 2015 to ETL a small data set into CDM 4 for a rare disease research network. This is the first of several non-US deployments for this network. We’ll be doing the same in Sweden, Poland, Italy, Israel and Australia. I’m happy to share what we learn through this process.

Bill

rwpark · November 19, 2014, 2:24am

Vojtech,

We are now calculating the frequency table for all the procedures in sequence in our 20 year of EMR data.
We categorized the procedures into 4 domains: surgery, anesthesia, radiology and pathology.
We will use our own local Korean codes for the frequency table, and will add flag whether they are mapped to OMOP vocabulary or not.
It will not take a long time.

rwpark · November 19, 2014, 12:07pm

Here is top 100 procedures in pathology and radiology in order.
I hope Korean character appear correct in your brower although you may not understand it:
LOCAL_EXAM_CODE LOCAL_EXAM_NAME MAPPING_CODE MAPPING_EXAM_NAME TOTAL_COUNT
XG210102 Chest AP¶ SNOMED-CT Plain chest X-ray 2864511
XG240103 Abd. Supine & Erect SNOMED-CT Plain X-ray abdomen 326459
C5501001 작은조직검사(<5CM) SNOMED-CT Histopathology test 235382
C5920002 자궁질도말 세포병리검사 CPT-4 Cytopathology, cervical or vaginal (any reporting system); requiring interpretation by physician (List separately in addition to code for technical service) 184406
XHA47503 C-T Abd.Routine c Contrast SNOMED-CT Computed tomography of abdomen and pelvis with contrast 174920
XG250101 K. U. B. SNOMED-CT Plain X-ray abdomen 165466
XG240101 Abd. Supine SNOMED-CT Plain X-ray abdomen 149424
HU001230 U/S Abd.Routine SNOMED-CT Ultrasonography of abdomen 144176
XG210113 Chest PA & LT Lat. SNOMED-CT Plain chest X-ray 111715
XG970101 Standard Panoramic View SNOMED-CT Plain X-ray facial sinuses 107292
HU001227 U/S Breast SNOMED-CT Ultrasonography of breast 97204
XHA45101 C-T Brain Routin SNOMED-CT Computed tomography of brain perfusion 96271
C5911001 Biopsy 1-3개 SNOMED-CT Histopathology test 91196
XHA47102 C-T Brain Angio c Contrast SNOMED-CT Computed tomography of brain perfusion 77052
C5916001 절편이필요한조직및장기적출술,Blocks6개이하 SNOMED-CT Histopathology test 73993
XHA46403 C-T Chest c Contrast SNOMED-CT Computed tomography of thorax and abdomen with contrast 69677
CX541001 액상 자궁경부 세포병리검사 CPT-4 Cytopathology, fluids, washings or brushings, except cervical or vaginal; smears with interpretation 69046
C5511001 Frozen Biopsy (Pathology) CPT-4 Pathology consultation during surgery 65738
XG120103 PNS Series SNOMED-CT Plain X-ray guided wire localization of breast lesion 65106
C5941001 흡인 세포병리검사(Cell Block 미포함) CPT-4 Cytopathology, fluids, washings or brushings, except cervical or vaginal; smears with interpretation 57401
XHE20101 MR Brain Routin c Contrast SNOMED-CT MRI of brain 57292
XG440104 T-L Spine AP & Lat. SNOMED-CT Plain x-ray 47058
XG110110 Skull AP & RT Lat. SNOMED-CT Plain film of head 46516
XG410104 C-Spine AP & Lat. SNOMED-CT Plain x-ray 44650
C5931014 액상 흡인 세포병리검사 CPT-4 Cytopathology, fluids, washings or brushings, except cervical or vaginal; smears with interpretation 38405
XG510101 Pelvis AP SNOMED-CT Plain X-ray ischium 37432
XG120101 Skull Water’s SNOMED-CT Plain film of head 36387
CX541102 액상 소변 세포병리 검사 CPT-4 Cytopathology, fluids, washings or brushings, except cervical or vaginal; smears with interpretation 36229
XG460104 L-S Spine AP & Lat. SNOMED-CT Plain x-ray 34088
XG520101 Both Hip AP in one Film SNOMED-CT Plain X-ray ischium 33995
XHA47508 C-T Liver c Contrast Dynamic SNOMED-CT Computed tomography of liver with contrast 33352
XHA46102 C-T Brain Routin c Contrast SNOMED-CT Computed tomography of brain perfusion 32420
XHA47105 C-T Brain 3D s SNOMED-CT Computed tomography of brain perfusion 30717
HU001245 U/S Transvaginal SNOMED-CT Ultrasonography 30075
XG720109 Both Knee AP & Lat. SNOMED-CT Plain x-ray 29000
C5912001 Biopsy 4-6개 SNOMED-CT Histopathology test 28971
XG770121 Both Patella Merchant View SNOMED-CT Plain x-ray 28815
XG720108 LT Knee AP & Lat. SNOMED-CT Plain x-ray 28248
XG720107 RT Knee AP & Lat. SNOMED-CT Plain x-ray 28189
XG100101 Nasal Bone Routine SNOMED-CT Plain X-ray facial sinuses 28070
XG410111 C-Spine Open Mouth SNOMED-CT Plain x-ray 27522
XG330103 Both Shoulder AP SNOMED-CT Plain x-ray 26944
C5920001 Pap Smear, Cervix CPT-4 Cytopathology, cervical or vaginal (any reporting system); requiring interpretation by physician (List separately in addition to code for technical service) 26110
XHA47408 C-T Coronary Angio 3D c Contrast SNOMED-CT Computed tomography of thorax and abdomen with contrast 26007
XG410103 C-Spine Lat. SNOMED-CT Plain x-ray 25431
XG460114 L-S Spine Series & Flex,Ext. SNOMED-CT Plain x-ray 24770
XG430104 T-Spine AP & Lat. SNOMED-CT Plain x-ray 24498
XHA46301 C-T Neck c Contrast SNOMED-CT Computed tomography of head and neck with contrast 24304
HU001208 U/S Neck SNOMED-CT Ultrasonography of head and neck 24072
XG050102 Orbit PA SNOMED-CT Plain film of head 24012
XG210112 Chest PA & RT Lat. SNOMED-CT Plain chest X-ray 23751
XG450104 L-Spine AP & Lat. SNOMED-CT Plain x-ray 23064
XG180103 Neck AP & Lat. SNOMED-CT Plain film of neck 22860
XG720131 Both Knee AP & Lat (Standing) SNOMED-CT Plain x-ray 22644
XG490101 Whole Spine AP & Lat (Standing) SNOMED-CT Plain X-ray ischium 22283
XG210104 Chest LT Lat. SNOMED-CT Plain chest X-ray 21931
XG200101 Zygomatic Arch SNOMED-CT Plain film of neck 21449
XG760103 Scanogram Leg with wt bearing> 6세 SNOMED-CT Fluoroscopy 21294
XHA45201 C-T Orbit SNOMED-CT Computed tomography of orbits 21167
HA454101 C-T Chest s (Low dose) SNOMED-CT Computed tomography of thorax and abdomen with contrast 20852
HU001201 U/S Brain Routine SNOMED-CT Ultrasonography for midline shift of brain 20712
HA010902 Fluoroscopy c Contrast(QGIF) SNOMED-CT Plain x-ray 20357
XG120104 PNS Water’s View SNOMED-CT Plain film of neck 20157
HU001244 U/S Transrectal SNOMED-CT Ultrasonography by transrectal approach 19953
XG420107 Swimmer’s View SNOMED-CT Plain x-ray 19877
XG730107 RT Tibia AP & Lat. SNOMED-CT Plain x-ray 19314
XHE11101 MR L-Spine c Cont. SNOMED-CT MRI of thoracolumbar spine 19211
XG730108 LT Tibia AP & Lat. SNOMED-CT Plain x-ray 18670
XG460103 L-S Spine Lat. SNOMED-CT Plain x-ray 18592
XG210103 Chest RT Lat. SNOMED-CT Plain chest X-ray 18555
XHE40102 MR Brain s (Limi) SNOMED-CT MRI of brain 18489
XG620108 LT Elbow AP & Lat. SNOMED-CT Plain x-ray 18211
XG110111 Skull AP & LT Lat. SNOMED-CT Plain film of head 18003
XG710108 LT Femur AP & Lat. SNOMED-CT Plain x-ray 17919
XG710107 RT Femur AP & Lat. SNOMED-CT Plain x-ray 17843
XG640108 LT Wrist AP & Lat. SNOMED-CT Plain x-ray 17838
C5956152 HPV DNA(Hybrid Capture) CPT-4 Infectious agent detection by nucleic acid (DNA or RNA); papillomavirus, human, direct probe technique 17820
XG410113 C-Spine Series & Flex,Ext. SNOMED-CT Plain X-ray ischium 17727
XG640107 RT Wrist AP & Lat. SNOMED-CT Plain x-ray 17282
XHE13504 MR Brain(Limi+MRA) s SNOMED-CT MRI of brain 16985
XG110108 Skull Town’s SNOMED-CT Plain film of head 16774
XHA45204 C-T OMU SNOMED-CT Computed tomography of head and neck 16760
XG650112 Both Hand AP & Obl. SNOMED-CT Plain x-ray 16621
XG720103 Both Knee AP SNOMED-CT Plain x-ray 16320
XHA47504 C-T Abdomen 3D c Contrast SNOMED-CT Computed tomography of abdomen and pelvis with contrast 16050
XHE10101 MR Brain s SNOMED-CT MRI of brain 15876
XHA47404 C-T Chest 3D c Contrast SNOMED-CT Computed tomography of thorax and abdomen with contrast 15753
XHA45206 C-T Facial SNOMED-CT Computed tomography of head and neck 15542
XG620107 RT Elbow AP & Lat. SNOMED-CT Plain x-ray 15522
XHA47509 C-T Pancreas c Contrast Dynamic SNOMED-CT Computed tomography of pancreas with contrast 15437
XG450116 L-Spine series & Flex,Ext. SNOMED-CT Plain x-ray 15404
XHA45105 C-T Temporal Bone SNOMED-CT Computed tomography of head and neck 15384
XG330110 RT Shoulder Axial SNOMED-CT Plain x-ray 14941
XG410101 C-Spine Series SNOMED-CT Plain film of head 14884
XG750109 BT Foot AP & Lat. SNOMED-CT Plain x-ray 14745
XG750130 Both foot AP/Obl/Lat SNOMED-CT Plain x-ray 14291
HU001243 U/S Kidney SNOMED-CT Ultrasonography of abdomen and urinary system 14211
XG350101 Rib Series SNOMED-CT Plain chest X-ray 13323
XG330111 LT Shoulder Axial SNOMED-CT Plain x-ray 13115

rwpark · November 19, 2014, 12:10pm

Here is top 100 Lab tests in order:

LOCAL_EXAM_CODE LOCAL_EXAM_NAME MAPPING_CODE MAPPING_EXAM_NAME TOTAL_COUNT
B1010001 Hemoglobin LOINC Hemoglobin [Mass/volume] in Blood 1949631
B1010001 Hemoglobin LOINC Hemoglobin [Mass/volume] in Blood 1949631
B2580001 ALT (GPT) LOINC Alanine aminotransferase [Enzymatic activity/volume] in Serum or Plasma 1896582
B2570001 AST (GOT) LOINC Aspartate aminotransferase [Enzymatic activity/volume] in Serum or Plasma 1895848
C3750001 Creatinine LOINC Creatinine [Mass/volume] in Peritoneal dialysis fluid 1574378
C3750001 Creatinine LOINC Creatinine [Mass/volume] in Serum or Plasma 1574378
C3711001 Glucose (AC) LOINC Glucose [Mass/volume] in Serum or Plasma 1466001
B1020001 Hematocrit LOINC Hematocrit [Volume Fraction] of Blood 1431160
B1020001 Hematocrit LOINC Hematocrit [Volume Fraction] of Blood 1431160
B2710001 r-GT LOINC Gamma glutamyl transferase [Enzymatic activity/volume] in Semen 1348920
B1530002 aPTT LOINC Activated partial thromboplastin time (aPTT) in Platelet poor plasma by Coagulation assay 1323280
C3730001 BUN LOINC Urea nitrogen [Mass/volume] in Serum or Plasma 1308141
C2243002 CRP LOINC C reactive protein [Mass/volume] in Serum or Plasma 1129048
B1060001 Platelet LOINC Platelets [#/volume] in Blood 1085791
C3797001 Magnesium LOINC Magnesium [Mass/volume] in Serum or Plasma 1079292
B1050001 WBC LOINC Leukocytes [#/volume] in Blood 1079166
B1030001 ESR LOINC Erythrocyte sedimentation rate 1069668
C2411001 T.Cholesterol LOINC Cholesterol [Mass/volume] in Serum or Plasma 969546
C3720001 T.Bilirubin LOINC Bilirubin.total [Mass/volume] in Serum or Plasma 952066
C3796001 Ionized Calcium LOINC Calcium.ionized [Mass/volume] in Serum or Plasma 900523
C2210001 Albumin LOINC Albumin [Mass/volume] in Serum or Plasma 884862
C2443001 Triglyceride LOINC Triglyceride [Mass/volume] in Pleural fluid 873952
C2443001 Triglyceride LOINC Triglyceride [Mass/volume] in Serum or Plasma 873952
C2420001 HDL-Cholesterol LOINC Cholesterol in HDL [Mass/volume] in Serum or Plasma 781569
B4144004 Culture(Blood/Fluid) LOINC Bacteria identified in Blood by Culture 752365
C2200001 T.Protein LOINC Protein [Mass/volume] in Serum or Plasma 726237
C3792001 Potassium LOINC Potassium [Moles/volume] in Serum or Plasma 716458
C3791001 Sodium LOINC Sodium [Moles/volume] in Serum or Plasma 713278
B2602001 Alk.Phosphatase LOINC Alkaline phosphatase [Enzymatic activity/volume] in Serum or Plasma 622046
B2630001 Creatine Kinase LOINC Creatine kinase [Enzymatic activity/volume] in Serum or Plasma 610205
B2590001 Lactate Dehydrogenase LOINC Lactate dehydrogenase [Enzymatic activity/volume] in Semen 598911
B2640001 CK-MB LOINC Creatine kinase.MB [Mass/volume] in Serum or Plasma 536855
C3793001 Chloride LOINC Chloride [Moles/volume] in Serum or Plasma 535290
C3795001 Calcium LOINC Calcium [Mass/volume] in Serum or Plasma 438484
B4120001 AFB Stain LOINC Bacteria identified in Sputum by Culture 437674
C3794001 In. Phosphorus LOINC Phosphate [Mass/volume] in Serum or Plasma 436391
B4143002 Culture(Genital/Urinary) LOINC Bacteria identified in Urine by Culture 431171
C3721001 D.Bilirubin LOINC Bilirubin.direct [Mass/volume] in Serum or Plasma 430467
B4052001 AFB Culture LOINC Bacteria identified in Sputum by Culture 429348
C4600001 VDRL Serum(정성) LOINC Reagin Ab [Presence] in Serum by VDRL 426048
C3812001 T.CO2 LOINC Carbon dioxide, total [Moles/volume] in Serum or Plasma 415704
C4712001 Anti-HIV I/II LOINC HIV 1 Ab [Presence] in Serum 413809
C3780001 Uric acid LOINC Urate [Mass/volume] in Serum or Plasma 409674
B2611001 Amylase LOINC Amylase [Enzymatic activity/volume] in Serum or Plasma 391055
C4903001 RF(정량) LOINC Rheumatoid factor [Units/volume] in Serum 369928
C3825001 HbA1C LOINC HBA1 gene.c.G223C [Presence] in Blood by Molecular genetics method 362016
C3750002 Creatinine LOINC Creatinine [Mass or Moles/volume] in Urine 350865
B0651001 Occult Blood LOINC Occult blood panel in Stool 344290
C2430001A LDL-Cholesterol LOINC Cholesterol in LDL [Mass/volume] in Serum or Plasma 323910
B2010001 ABO Grouping LOINC ABO group [Type] in Blood 317895
B2010001 ABO Grouping LOINC ABO group [Type] in Blood 317895
B2021001 Rh(D) Typing LOINC ABO and Rh group [Type] in Serum or Plasma from Blood product unit 316565
B2021001 Rh(D) Typing LOINC ABO and Rh group [Type] in Blood 316565
C4802001 HBs Ag LOINC Hepatitis B virus e Ag [Presence] in Serum 293110
C4812001 Anti-HBs LOINC Hepatitis B virus surface Ab [Presence] in Serum 286566
C3941001 Troponin T hs LOINC Troponin T.cardiac [Mass/volume] in Serum or Plasma 272664
C2200002 Protein LOINC Protein [Mass/volume] in Urine 243371
C4872001 Anti-HCV LOINC Hepatitis C virus Ab [Presence] in Serum 218794
C3850001 Lactic Acid LOINC Lactate [Moles/volume] in Blood 180140
C3360001 TSH(진단검사의학과) LOINC Thyroid stimulating immunoglobulins [Units/volume] in Serum 179779
B4149001 Culture(Miscellaneous) LOINC Bacteria identified in Catheter tip by Culture 158765
C3340001 Free T4(진단검사의학과) LOINC Thyroxine (T4) free [Mass/volume] in Serum or Plasma 155984
B2621001 Lipase LOINC Lipase [Enzymatic activity/volume] in Serum or Plasma 146371
C2243001 hs-CRP LOINC C reactive protein [Mass/volume] in Serum or Plasma by High sensitivity method 145096
B1601001 Fibrinogen LOINC Fibrinogen [Mass/volume] in Platelet poor plasma by Coagulation assay 127381
C4962107 Homocysteine LOINC Homocysteine [Moles/volume] in Serum or Plasma 120849
C3711006 Blood PC120 min LOINC Glucose [Mass/volume] in Serum or Plasma --2 hours post XXX challenge 117526
B0260001 Urine HCG LOINC Choriogonadotropin (pregnancy test) [Presence] in Urine 117409
C2520002 Ferritin LOINC Ferritin [Mass/volume] in Serum or Plasma 115225
C4212001 AFP LOINC Alpha-1-Fetoprotein [Mass/volume] in Serum or Plasma 113206
B4141005 Culture(Respiratory) LOINC Bacteria identified in Sputum by Respiratory culture 112478
C4220001 CEA LOINC Carcinoembryonic Ag [Mass/volume] in Serum or Plasma 109313
B1040001 RBC LOINC Erythrocytes [#/volume] in Blood 109173
B0010009 Urine Specific Gravity LOINC Specific gravity of Urine 100386
B1081001 Reticulocyte Count LOINC Reticulocytes/100 erythrocytes in Blood 94213
B0010010 Urine pH LOINC pH of Urine 90336
B0010005 Urine Blood LOINC Blood [Presence] in Urine by Visual 88698
C3870001 Ammonia LOINC Ammonia [Moles/volume] in Blood 88018
C3796002 Ionized Calcium(artery) LOINC Calcium.ionized [Mass/volume] in Arterial blood 87055
C3796002 Ionized Calcium(artery) LOINC Calcium.ionized [Mass/volume] in Arterial blood 87055
C3791004 Sodium(artery) LOINC Sodium [Moles/volume] in Arterial blood 86366
C3791004 Sodium(artery) LOINC Sodium [Moles/volume] in Arterial blood 86366
C3792004 Potassium(artery) LOINC Potassium [Moles/volume] in Arterial blood 86235
C3792004 Potassium(artery) LOINC Potassium [Moles/volume] in Arterial blood 86235
C3793004 Chloride(artery) LOINC Chloride [Moles/volume] in Arterial blood 86039
C3793004 Chloride(artery) LOINC Chloride [Moles/volume] in Arterial blood 86039
B0010003 Urine Protein LOINC Protein [Presence] in Urine 85739
C3850004 Lactic acid(artery) LOINC Lactate [Moles/volume] in Arterial blood 84502
C3850004 Lactic acid(artery) LOINC Lactate [Moles/volume] in Arterial blood 84502
C4633001 ASO LOINC Streptolysin O Ab [Units/volume] in Serum 84448
C3290001 T3(진단검사의학과) LOINC Triiodothyronine (T3) [Mass/volume] in Serum or Plasma 83598
C3800001 Osmolality LOINC Osmolality of Serum or Plasma 83341
C3800001 Osmolality LOINC Osmolality of Urine 83341
B0010004 Urine Glucose LOINC Glucose [Presence] in Urine 82714
C2310062 D2 Dermatophagoides farinae IgE LOINC Dermatophagoides sp IgE Ab [Units/volume] in Serum 82285
C2310062 D2 Dermatophagoides farinae IgE LOINC Dermatophagoides sp IgE Ab [Units/volume] in Serum 82285
B0010007 Urine Ketone LOINC Ketones [Presence] in Urine 79444
B1612001 FDP LOINC Fibrin+Fibrinogen fragments [Mass/volume] in Platelet poor plasma 77994
B1070001 Eosinophil Count LOINC Eosinophils [#/volume] in Blood 77949
B0010002 Urine Urobilinogen LOINC Urobilinogen [Mass/volume] in Urine 77188

Vojtech_Huser · November 19, 2014, 12:59pm

Thank you for those who responded. In terms of what procedures I want to focus: The larger context for the work is to describe what happens to a archetypical patient. For example a typical 45yo may have a lipid profile done, perhaps an eye exame and if woman, most likely a gynecological exam. In terms of CPT codes (but the focus should be on SNOMED) - in US there are codes for Proc-Claim-Visit (ER visit, code or level 3 outpatient visit) or Proc-Claim-Lab (Lipid panel) or Proc-Action (ECG 12 leads)

Vojtech_Huser · February 23, 2016, 6:05pm

Dear all,
this a renewed call for potential collaborators. We are looking into common terminology for procedures. In order to do that, we need to know what procedures you currently record in your data. If you are willing to become co-author of this study and contribute data, we need you to run and share with me (by email) CSV file with 100 rows (top 100 procedures in your dataset by count).

Use the following query to generate it

select procedure_concept_id, count(*) as freq
from procedure_occurrence
order by freq desc
limit 100

Vojtech_Huser · July 20, 2016, 6:48pm

Just to post an update - this effort is slowly progressing.

We have just recruited one more site.

Also, ICD10PCS was recently added into OMOP CDM Vocabulary.

Vojtech_Huser · January 25, 2018, 3:36pm

I am pleased to update that the study will be getting data from one more country (Czech republic) (inpatient procedural data only). Maybe the OHDSI Europe group will also have more input on this at some point.

Dymshyts · March 13, 2018, 5:45pm

We want to inform that OHDSI-vocabulary team is working on Procedure consolidation which results in building of mappings (if concepts are equal) and hierarchical relationship between HCPCS, CPT4, OPCS4, ICD10PCS, ICD9PCS, SNOMED and LOINC.
SNOMED and LOINC are used as a core vocabularies.
SNOMED has comprehensive hierarchy and attributes relationships, LOINC has standardized list of measurements and lab-test.
As a result you’ll be able to find HCPCS, CPT4, OPCS4, ICD10PCS, ICD9PCS concepts as a descendants of SNOMED or LOINC concepts.
And if your protocol has a concept set defined through HCPCS, CPT4, OPCS4, ICD10PCS, ICD9PCS you’ll be able to find cross-ontology equivalents and not miss any patient data eventually.

Christian_Reich · March 13, 2018, 7:29pm

@Dymshyts:

This looks like a very laudable activity with tons of good use cases, like @Evan_Minty’s surgery outcomes, but also smells of very hard work. Should we call it Hephaistos, the Greek God of blacksmiths, metalworking, carpenters, craftsmen, artisans, sculptors, metallurgy, fire, and volcanoes?

Vojtech_Huser · April 6, 2018, 2:17pm

Here is a small update on procedure standardization.

Looking at mapping from ICD-10-PCS to SNOMED CT - it seems that the map will not be similar to maps for drugs or diagnoses. E.g., for drugs - the ‘Maps to’ relationship is essentially an exact match.

It may be important to think about how to handle broad-to-narrow and narrow-to-broad in general in Athena.

We observe that SCT as target terminology is not granular enough. So instead of ‘exact-match-maps-to’ - the only relationship from ICD10PCS to SCT we will have to settle for (in some cases) is ‘narrowICD10PCS-to-broadSNOMEDCT’. (or open the pandora box of postcoordinated expression appearing in procedure_concept_id (which, from analyst point of view) may not be an option in the foreseeable future. (due to no good subsumption reasoning software that would be nicely baked into SQL).

Dymshyts · May 9, 2018, 11:08am

You are totally right. - most of the relationships (or even all of them) will be

And it’s not hard to keep them in Athena - we just use “Is a” relationship_id,
and then the users will be able to see these relationships both in the “Hierarchy” (as it make hierarchy) and “Related Concepts” tabs

Vojtech_Huser · July 6, 2018, 2:43pm

I am please to say that initial work on the Czech republic procedures has started.

We are still looking for contributors from other countries. Please reply here.

from other work:
In fact, we hope to get a very large sample to generate high priority procedures which we plan to pitch to SNOMED International. (ThemisProc network study)

Work on ICD10PCS mapping confirms that SNOMED CT is not granural enough in many cases. In 56% of cases, an ICD10PCS code can be only mapped to SCT expression (postcoordination) because pre-coordinated term does not exist in SCT.

Vojtech_Huser · March 7, 2019, 4:16pm

The narrow-to-broad mapping is also present in Diagnoses. See discussion here: https://github.com/OHDSI/Vocabulary-v5.0/issues/203.

Vojtech_Huser · April 24, 2020, 1:19pm

Ad granularity discussion: SNOMED browser for UK now includes classification map. If OPCS-4 has more granular term, it gets added to SNOMED (inside UK extension).

Perhaps the same approach can be taked by CPT4 and ICD-10 PCS and using US SNOMED extension. It shows that UK is indeed focused on a single terminology (as their plan from 2016 says) (see https://hscic.kahootz.com/gf2.ti/f/762498/32410181.2/PPTX/-/SNOMED_CT_awareness_for_clinical_coders_v1.0_PASSWORD_PROTECTED.pptx)

See example here

Vojtech_Huser · June 22, 2020, 2:09pm

This project is still living. We are looking for more nordic countries possibly using NOMESCO https://en.wikipedia.org/wiki/NOMESCO#NOMESCO_Procedures

Thanks to @Javier there is one more country now represented. @Nicole_Pratt - any chance you have now better Australian Proc data ? Also COVID triggered more interest in procedures. We may be shooting for OHDSI symposium abstract and a paper. If you have procedure data (e.g., Germany, France), please reply here or email me.