Better and more use of labs in future OHDSI studies

Vojtech_Huser · September 24, 2019, 2:16pm

I want to post my response to email discussion on the forum.

The topic is that LOINC is too granular and measurements are not nicely ready for analysis across the network.

Few points:

LOINC parts are important and having them in Athena is important (described here )
current parts structure imported into Athena comes from LOINC to SNOMED map and that is not optimal. Using raw LOINC file would be better.
LOINC groupings may be helpfull (this already is in Athena)
in ThemisConcept study - we did observe SNOMED CT being used for lab, but its use was not winning over LOINC.
some measurement reasoning may have to left to be tackled by analyst (and not during ETL) at study design time. E.g., the study (not CDM) will deal with the fact that analysis can take advantage of glucose in 12 hour urine somehow (if ideally I would want to have glucose in 24 hour urine)
-ThemisConcept study (and Anna’s ConceptPrevalence study) both try to produce network level insights into what the network is using as concepts in measurements tables
even if LOINC is too granular (but maybe for a good reason), the first step is to have same unit for that granular LOINC code. ETL help for folks to achieve that is here sandbox/unitmorph at master · OHDSI/sandbox · GitHub (so directly convertable LOINC codes will be made beautiful this way)
if we want to group “equivalent LOINC” (not convertible but close enough), LOINC groups may be best. I know that LOINC admins would in fact welcome submissions of new grouping concepts (and I hope to submit some for HIV-related LOINC tests). That way the burden of maintenance is not on us but shifted to the SDO (Regenstrief in this case) (which is our mantra)
This concept is a good parent term to see LOINC groups http://athena.ohdsi.org/search-terms/terms/40652445 (it has 724 lab LOINC groups under it)

exhibits and links

Example of loinc group http://athena.ohdsi.org/search-terms/terms/40656148

snomed codes in ThemisConcept results

github.com

vojtechhuser/ThemisConcepts/blob/55451169e1e4bd0f70a0044dcfccb351def018e4/extras/results2019/S3-units-with-tests.csv

n,perc50,concept_name.x.x,concept_code.y,concept_name.y,vocabulary_id.x,concept_code.x,concept_id,unit_concept_id,mean_ratio,perc03,perc25,perc75,perc97,concept_name.x.y,QualUnitCnt,allQualUnits,allQualUnitsNs,allQualUnitsMedians
8,0.9999956039484079,Body weight,kg,kilogram,LOINC,29463-7,3025315,9529,0.8290906149260063,0.3320376307663496,0.8095032451052463,1,1,Body weight,1,kg,8,1
6,0.7690050356558193,Free/Total PSA serum/plasme,%,percent,LOINC,12841-3,3001784,8554,0.7404531319870096,0.46084926973505497,0.5183731418311397,0.9490239641883594,0.9974515271383179,Free/Total PSA serum/plasme,2,"%,No matching concept","6,2","0.77,0.42"
6,0.8317017850017665,Chloride serum/plasma,mmol/L,millimole per liter,LOINC,2075-0,3014576,8753,0.7960298404827612,0.4610171571426566,0.7140121475734879,0.9714814194351182,0.9998421652758807,Chloride serum/plasma,1,mmol/L,6,0.83
6,0.8179854635409587,Neutrophils %,%,percent,LOINC,26511-6,3018010,8554,0.6951194946149425,0.184538952999284,0.45595872061586235,0.9925423835671543,0.9997873672655914,Neutrophils %,1,%,6,0.82
6,0.8256031818386919,Sodium serum/plasma,mmol/L,millimole per liter,LOINC,2951-2,3019550,8753,0.7944763088132315,0.4620162376053024,0.7131738753371352,0.9708180151786082,0.9998432485930977,Sodium serum/plasma,1,mmol/L,6,0.83
6,0.9990202851829741,Triglyceride [Mass/volume] in Serum or Plasma,mg/dL,milligram per deciliter,LOINC,2571-8,3022192,8840,0.8476546192250868,0.27157998279348783,0.9492869471120895,0.9999991441977969,0.9999998716395594,Triglyceride [Mass/volume] in Serum or Plasma,1,mg/dL,6,1
6,0.8126850722852145,Potassium serum/plasma,mmol/L,millimole per liter,LOINC,2823-3,3023103,8753,0.7898245711468658,0.461015816352302,0.706518135055525,0.9701955636267603,0.9998451219081494,Potassium serum/plasma,1,mmol/L,6,0.81
6,0.9999969549989445,Body height,cm,centimeter,LOINC,8302-2,3036277,8582,0.7153770723075636,0.14613426187036904,0.35959917399947217,1,1,Body height,3,"cm,[in_us],m","6,2,2","1,1,1"
6,1,Body mass index,kg/m2,kilogram per square meter,LOINC,39156-5,3038553,9531,0.9042811552203951,0.5118338916240148,1,1,1,Body mass index,2,"kg/m2,No matching concept","6,2","1,0.79"
5,0.8613936406527865,Sodium [Moles/volume] in Blood,mmol/L,millimole per liter,LOINC,2947-0,3000285,8753,0.7061584159809379,0.3908747129714049,0.394448458574181,0.8845625966521499,0.986147511598258,Sodium [Moles/volume] in Blood,1,mmol/L,5,0.86
5,0.905068621441899,Hemoglobin,g/dL,gram per deciliter,LOINC,718-7,3000963,8713,0.6332379558404369,0.054773305038693654,0.2320586531555261,0.9984644743092701,0.9998157369171125,Hemoglobin,2,"g/dL,g/L","5,2","0.91,0.98"
5,0.950479586300874,Carcinoembryonic Ag [Mass/volume] in Serum or Plasma,ng/mL,nanogram per milliliter,LOINC,2039-6,3003785,8842,0.7732400729766253,0.13588196734436422,0.9047034262556797,0.9799908878337519,0.9975846391000502,Carcinoembryonic Ag [Mass/volume] in Serum or Plasma,1,ng/mL,5,0.95
5,0.8622029877817432,Potassium [Moles/volume] in Blood,mmol/L,millimole per liter,LOINC,6298-4,3005456,8753,0.6604355453018437,0.18968111015911118,0.3904070045949924,0.887258336850992,0.986471000422119,Potassium [Moles/volume] in Blood,1,mmol/L,5,0.86
5,1,Cholesterol in HDL [Mass/volume] in Serum or Plasma,mg/dL,milligram per deciliter,LOINC,2085-9,3007070,8840,0.9914280308978233,0.963365711945165,0.9985758210595493,1,1,Cholesterol in HDL [Mass/volume] in Serum or Plasma,1,mg/dL,5,1
5,0.8449506500088017,Carbon dioxide serum/plasma,mmol/L,millimole per liter,LOINC,2028-9,3015632,8753,0.862403251719998,0.776537739596991,0.7962351858773902,0.900880341312586,0.984672195298873,Carbon dioxide serum/plasma,1,mmol/L,5,0.84
5,0.999840706,Creatinine [Mass/volume] in Urine,mg/dL,milligram per deciliter,LOINC,2161-8,3017250,8840,0.9791151799307982,0.9423054940434632,0.9551861531211173,1,1,Creatinine [Mass/volume] in Urine,1,mg/dL,5,1
5,0.7285027605958626,Chloride [Moles/volume] in Blood,mmol/L,millimole per liter,LOINC,2069-3,3018572,8753,0.6762867043530328,0.15216327792390033,0.663902634746556,0.9066474880655712,0.9887976985678686,Chloride [Moles/volume] in Blood,1,mmol/L,5,0.73
5,0.912336901154493,Cholesterol [Mass/volume] in Serum or Plasma,mg/dL,milligram per deciliter,LOINC,2093-3,3027114,8840,0.7076729508567896,0.19535973679555163,0.4678220709978537,1,1,Cholesterol [Mass/volume] in Serum or Plasma,1,mg/dL,5,0.91
5,0.999704180683687,Direct bilirubin serum/plasma,mg/dL,milligram per deciliter,LOINC,1968-7,3027597,8840,0.9973820225408945,0.9899672721137823,0.9987293010322483,0.999704181,0.9999645017200001,Direct bilirubin serum/plasma,1,mg/dL,5,1

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Vojtech_Huser · September 25, 2019, 8:23pm

Anna made a relevant point in another thread.
She said:

Apart from that, there is a problem with SNOMED and LOINC being two standard vocabs for measurements with no connections between them. Improve LOINC representation in OMOP Vocabulary (Athena) (link parts to lab tests) - #6 by aostropolets

her diagram

It is an interesting problem of two SDOs: SNOMED International and Regenstrief. It would be good to consult an expert who knows the current status of the collaboration. See SNOMED International – LOINC (what is new in 2018 and 2019).