Open turbomam opened 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.
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
TURBO_0010147
) 0 to 'measurement datum' obo:IAO_0000109
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 |
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 |
Please provide a short list of exemplar measurement types that need to be classified.