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PennTURBO / semantic-engine

TURBO semantic engine (Drivetrain). Transforms source-dependent RDF data into a source-independent, semantically rich RDF model.
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Coarse class buckets for measurements, like procedures? #33

Open turbomam opened 4 years ago

cstoeckert commented 4 years ago

Please provide a short list of exemplar measurement types that need to be classified.

turbomam commented 4 years ago

Does this help?

Note that I have only instantiated scalar measurements so far. There are a lot of smoking status datums, but that would require a categorical datum/value specification solution. Pain severity 1-10 could probably be handled as scalar or categorical.

turbomam commented 4 years ago

Right now, I'm only instantiating Synthea/OMOP measurements for which we have already determined the corresponding OBO class or have already created a TURBO class. See below.

We could leave it like that, or

  1. I think I could also instantiate all other kinds of OMOP measurements as generic measurement datums by assigning the OMOP concept ID (TURBO_0010147) 0 to 'measurement datum' obo:IAO_0000109
  2. We could try to bucket the measurements like we did for procedures

What has been classified already?

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
select *
where 
{
    graph <https://raw.githubusercontent.com/PennTURBO/Turbo-Ontology/master/ontologies/turbo_merged.owl> {
        ?OboMeasDat rdfs:subClassOf* obo:IAO_0000109 ;
                          <http://transformunify.org/ontologies/TURBO_0010147> ?OmopConceptId ;
                          rdfs:label ?l .
    }
}
OboMeasDat OmopConceptId l
http://www.ebi.ac.uk/efo/EFO_0004340 3038553 body mass index
http://purl.obolibrary.org/obo/IAO_0000408 3036277 length measurement datum
http://purl.obolibrary.org/obo/IAO_0000414 3025315 mass measurement datum
http://purl.obolibrary.org/obo/HTN_00000000 3012888 diastolic blood pressure measurement datum
http://purl.obolibrary.org/obo/HTN_00000001 3004249 systolic blood pressure measurement datum
http://transformunify.org/ontologies/TURBO_0010153 8840 blood glucose measurement datum
http://transformunify.org/ontologies/TURBO_0010154 3004410 Hemoglobin with A1c glycosylation percentage datum

What measurements does Synthea/OMOP include?

concept_name count Already classified
Pain severity - 0-10 verbal numeric rating [Score] - Reported 12701
BP systolic 10657 http://purl.obolibrary.org/obo/HTN_00000001
BP diastolic 10657 http://purl.obolibrary.org/obo/HTN_00000000
Body height 10484 http://purl.obolibrary.org/obo/IAO_0000408
Body weight 10484 http://purl.obolibrary.org/obo/IAO_0000414
Tobacco smoking status NHIS 10484
Body mass index 9137 http://www.ebi.ac.uk/efo/EFO_0004340
Chloride [Moles/volume] in Blood 4710
Urea nitrogen [Mass/volume] in Blood 4710
Potassium [Moles/volume] in Blood 4710
Calcium [Mass/volume] in Blood 4710
Creatinine [Mass/volume] in Blood 4710
Sodium [Moles/volume] in Blood 4710
Glucose [Mass/volume] in Blood 4710 http://transformunify.org/ontologies/TURBO_0010153
Carbon dioxide, total [Moles/volume] in Blood 4710
Glomerular filtration rate/1.73 sq M.predicted [Volume Rate/Area] in Serum, Plasma or Blood by Creatinine-based formula (MDRD) 4370
Triglyceride [Mass/volume] in Serum or Plasma 3882
Cholesterol in LDL [Mass/volume] in Serum or Plasma by Direct assay 3882
Cholesterol in HDL [Mass/volume] in Serum or Plasma 3882
Cholesterol [Mass/volume] in Serum or Plasma 3882
Hemoglobin A1c (Glycated) 3446 http://transformunify.org/ontologies/TURBO_0010154
Hemoglobin 2245
MCH [Entitic mass] by Automated count 2231
Erythrocytes [#/volume] in Blood by Automated count 2231
Platelet distribution width [Entitic volume] in Blood by Automated count 2231
Platelets [#/volume] in Blood by Automated count 2231
Hematocrit [Volume Fraction] of Blood by Automated count 2231
MCV [Entitic volume] by Automated count 2231
Leukocytes [#/volume] in Blood by Automated count 2231
Erythrocyte distribution width [Entitic volume] by Automated count 2231
MCHC [Mass/volume] by Automated count 2231
Platelet mean volume [Entitic volume] in Blood by Automated count 2231
Microalbumin/Creatinine [Mass Ratio] in Urine 1484
Albumin serum/plasma 1218
Aspartate aminotransferase serum/plasma 1218
Globulin [Mass/volume] in Serum by calculation 1218
Alkaline phosphatase serum/plasma 1218
Protein serum/plasma 1218
Alanine aminotransferase serum/plasma 1218
Total Bilirubin serum/plasma 1216
Weight difference [Mass difference] --pre dialysis - post dialysis 1214
Oral temperature 868
Appearance of Urine 770
Hemogram, automated, with RBC, WBC, Hgb, Hct, Indices, Platelet count, and manual WBC differential 661
Standard pregnancy test 520
Nitrite [Presence] in Urine by Test strip 385
Protein [Presence] in Urine by Test strip 385
Specific gravity of Urine by Test strip 385
Glucose [Presence] in Urine by Test strip 385
Leukocyte esterase [Presence] in Urine by Test strip 385
Ketones [Mass/volume] in Urine by Test strip 385
Hemoglobin [Presence] in Urine by Test strip 385
Glucose urine dipstick 385
Color of Urine 385
Bilirubin.total [Presence] in Urine by Test strip 385
Ketones urine dipstick 385
Clarity of Urine 385
Protein [Mass/volume] in Urine by Test strip 385
Bilirubin.total [Mass/volume] in Urine by Test strip 385
pH of Urine by Test strip 385
Hepatitis B surface antigen measurement 337
Syphilis infectious titer test 337
Skin test for tuberculosis, Tine test 337
Chlamydia antigen test 337
HIV antigen test 337
Urine protein test 337
Gonorrhea infection titer test 337
Urine screening test for diabetes 337
Blood group typing 337
Urine culture 337
Hepatitis C antibody, confirmatory test 337
Measurement of Varicella-zoster virus antibody 337
Throat culture 327
Alpha-fetoprotein test - antenatal 324
Urine screening for glucose 324
FEV1/FVC 316
Spirometry 316
Streptococcus pneumoniae group B antigen assay 306
Measurement of respiratory function 267
Cardiac ejection fraction 170
Are you covered by health insurance or some other kind of health care plan [PhenX] 140
History of Hospitalizations+Outpatient visits Narrative 140
HIV status 140
Sexual orientation 140
PSA serum/plasma 121
Physical findings of Prostate 121
Cat dander IgE Ab [Units/volume] in Serum 83
Cow milk IgE Ab [Units/volume] in Serum 83
Honey bee IgE Ab [Units/volume] in Serum 83
Shrimp IgE Ab [Units/volume] in Serum 83
Soybean IgE Ab [Units/volume] in Serum 83
Walnut IgE Ab [Units/volume] in Serum 83
Wheat IgE Ab [Units/volume] in Serum 83
Cladosporium herbarum IgE Ab [Units/volume] in Serum 83
Codfish IgE Ab [Units/volume] in Serum 83
Common Ragweed IgE Ab [Units/volume] in Serum 83
American house dust mite IgE Ab [Units/volume] in Serum 83
Egg white IgE Ab [Units/volume] in Serum 83
Latex IgE Ab [Units/volume] in Serum 83
White Oak IgE Ab [Units/volume] in Serum 83
Peanut IgE Ab [Units/volume] in Serum 83
DXA Radius and Ulna [T-score] Bone density 82
Antenatal RhD antibody screening 57
Hemoglobin.gastrointestinal.lower [Presence] in Stool by Immunoassay --1st specimen 55
Polyp size greatest dimension 55
NT proBNP serum/plasma 53
US Guidance for biopsy of Prostate 22
Hematocrit 14
Percentage area affected by eczema Trunk [PhenX] 8
Percentage area affected by eczema Lower extremity - bilateral [PhenX] 8
Percentage area affected by eczema Head and Neck [PhenX] 8
Percentage area affected by eczema Upper extremity - bilateral [PhenX] 8
Thyroxine (T4) free [Mass/volume] in Serum or Plasma 4
Thyrotropin [Units/volume] in Serum or Plasma 4
Carbon dioxide serum/plasma 2
Red blood cell (RBC) count 2
Calcium serum/plasma serum/plasma 2
Platelet count 2
Sodium serum/plasma 2
Potassium serum/plasma 2
Erythrocyte distribution width [Ratio] 2
Glucose lab 2
MCV 2
Creatinine serum/plasma 2
Urea nitrogen serum/plasma 2
Anion gap serum/plasma 2
White Blood cell (WBC) count (leukocyte) 2
Chloride serum/plasma 2
Physical findings of Abdomen by Palpation 2
Bilirubin.total [Mass/volume] in Blood 2
Mental health Outpatient Note 1