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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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LOINC base URI = http://purl.bioontology.org/ontology/LNC/ #56

Closed turbomam closed 4 years ago

turbomam commented 4 years ago

when instantiated with umls2rdf or downloaded from bioportal

OMOP calls the vocabulary LOINC..., so Mark's current Acorn directives construct URIs like http://purl.bioontology.org/ontology/LOINC/8462-4

That will resolve over the web, but not in a local triplestore

turbomam commented 4 years ago

How often do TURBO entities from Synthea/OMOP mention LOINC?

t l ostr count
ontologies:TURBO_0010404 provenance data item SNOMEDCT 2599
obo:HTN_00000000 diastolic blood pressure measurement datum LOINC 898
obo:IAO_0000408 length measurement datum LOINC 898
obo:IAO_0000414 mass measurement datum LOINC 898
obo:HTN_00000001 systolic blood pressure measurement datum LOINC 898
efo:EFO_0004340 body mass index LOINC 845
obo:PDRO_0000024 drug prescription RXNORM 751
obo:OGMS_0000073 diagnosis SNOMEDCT 689
ontologies:TURBO_0010154 Hemoglobin with A1c glycosylation percentage datum LOINC 349 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
select 
#distinct 
?t ?l ?ostr (count(?s) as ?count)
where 
{
    ?s a ?t ;
       <http://purl.obolibrary.org/obo/IAO_0000142> ?o .
    optional {
        ?t rdfs:label ?l 
    }
    bind(strbefore(strafter(str(?o),"http://purl.bioontology.org/ontology/"), "/") as ?ostr)
    filter(lang(?l) = "en" || lang(?l) = "")
}
group by ?t ?l ?ostr 
order by desc(count(?s) )

This doesn't include measurements that weren't instantiated because they weren't mapped in the TURBO ontology. Those might be even more enriched for LOINC.

measurement_source_concept_id concept_name vocabulary_id count
43055141 Pain severity - 0-10 verbal numeric rating [Score] - Reported LOINC 12701
3012888 Diastolic blood pressure LOINC 10657
3004249 Systolic blood pressure LOINC 10657
3036277 Body height LOINC 10484
3025315 Body weight LOINC 10484
43054909 Tobacco smoking status LOINC 10484
3038553 Body mass index (BMI) [Ratio] LOINC 9137
765467 Documentation of current medications SNOMED 4755
3005456 Potassium [Moles/volume] in Blood LOINC 4710
3014094 Carbon dioxide, total [Moles/volume] in Blood LOINC 4710
3051825 Creatinine [Mass/volume] in Blood LOINC 4710
3018572 Chloride [Moles/volume] in Blood LOINC 4710
3000285 Sodium [Moles/volume] in Blood LOINC 4710
3004295 Urea nitrogen [Mass/volume] in Blood LOINC 4710
3000483 Glucose [Mass/volume] in Blood LOINC 4710
3032503 Calcium [Mass/volume] in Blood LOINC 4710
3030354 Glomerular filtration rate/1.73 sq M.predicted [Volume Rate/Area] in Serum or Plasma by Creatinine-based formula (MDRD) LOINC 4370
3007070 Cholesterol in HDL [Mass/volume] in Serum or Plasma LOINC 3882
3009966 Cholesterol in LDL [Mass/volume] in Serum or Plasma by Direct assay LOINC 3882
3027114 Cholesterol [Mass/volume] in Serum or Plasma LOINC 3882
3022192 Triglyceride [Mass/volume] in Serum or Plasma LOINC 3882
3004410 Hemoglobin A1c/Hemoglobin.total in Blood LOINC 3446
4168236 Evaluation of uterine fundal height SNOMED 2921
4075363 Auscultation of the fetal heart SNOMED 2921
3000963 Hemoglobin [Mass/volume] in Blood LOINC 2245
3024929 Platelets [#/volume] in Blood by Automated count LOINC 2231
3023599 MCV [Entitic volume] by Automated count LOINC 2231
3000905 Leukocytes [#/volume] in Blood by Automated count LOINC 2231
3012030 MCH [Entitic mass] by Automated count LOINC 2231
3043111 Platelet mean volume [Entitic volume] in Blood by Automated count LOINC 2231
3023314 Hematocrit [Volume Fraction] of Blood by Automated count LOINC 2231
3020416 Erythrocytes [#/volume] in Blood by Automated count LOINC 2231
3009744 MCHC [Mass/volume] by Automated count LOINC 2231
3015182 Erythrocyte distribution width [Entitic volume] by Automated count LOINC 2231
3002736 Platelet distribution width [Entitic volume] in Blood by Automated count LOINC 2231
4107731 Subcutaneous immunotherapy SNOMED 1512
3001802 Microalbumin/Creatinine [Mass Ratio] in Urine LOINC 1484
4295880 Intramuscular injection SNOMED 1425
3027970 Globulin [Mass/volume] in Serum by calculation LOINC 1218
3006923 Alanine aminotransferase [Enzymatic activity/volume] in Serum or Plasma LOINC 1218
3024561 Albumin [Mass/volume] in Serum or Plasma LOINC 1218
3020630 Protein [Mass/volume] in Serum or Plasma LOINC 1218
3035995 Alkaline phosphatase [Enzymatic activity/volume] in Serum or Plasma LOINC 1218
3013721 Aspartate aminotransferase [Enzymatic activity/volume] in Serum or Plasma LOINC 1218
3024128 Bilirubin.total [Mass/volume] in Serum or Plasma LOINC 1216
4146536 Renal dialysis SNOMED 1215
44786664 Weight difference [Mass difference] --pre dialysis - post dialysis LOINC 1214
3006322 Oral temperature LOINC 868
4240345 Physical examination SNOMED 850
3007876 Appearance of Urine LOINC 770
4078793 Direct current cardioversion SNOMED 705
4015052 Hemogram, automated, with RBC, WBC, Hgb, Hct, Indices, Platelet count, and manual WBC differential SNOMED 661
4091461 Standard pregnancy test SNOMED 520
4060626 Ultrasound scan for fetal viability SNOMED 520
4064377 Depression screening SNOMED 513
45766298 Combined chemotherapy and radiation therapy SNOMED 475
4249893 Colonoscopy SNOMED 470
3000330 Specific gravity of Urine by Test strip LOINC 385
3021601 Nitrite [Presence] in Urine by Test strip LOINC 385
3022621 pH of Urine by Test strip LOINC 385
3006513 Bilirubin.total [Mass/volume] in Urine by Test strip LOINC 385
3024629 Glucose [Mass/volume] in Urine by Test strip LOINC 385
3014051 Protein [Presence] in Urine by Test strip LOINC 385
3005897 Protein [Mass/volume] in Urine by Test strip LOINC 385
3035350 Ketones [Presence] in Urine by Test strip LOINC 385
3011397 Hemoglobin [Presence] in Urine by Test strip LOINC 385
3023539 Ketones [Mass/volume] in Urine by Test strip LOINC 385
3000348 Leukocyte esterase [Presence] in Urine by Test strip LOINC 385
3018834 Bilirubin.total [Presence] in Urine by Test strip LOINC 385
3027162 Color of Urine LOINC 385
3009261 Glucose [Presence] in Urine by Test strip LOINC 385
3008204 Clarity of Urine LOINC 385
4168615 Hepatitis B surface antigen measurement SNOMED 337
4014117 Gonorrhea infection titer test SNOMED 337
4018595 Measurement of Varicella-zoster virus antibody SNOMED 337
4018603 Hepatitis C antibody, confirmatory test SNOMED 337
4024509 Urine culture SNOMED 337
4041881 Urine protein test SNOMED 337
4061811 Rubella screening SNOMED 337
4258677 Blood group typing SNOMED 337
4102154 Skin test for tuberculosis, Tine test SNOMED 337
4234541 Cytopathology procedure, preparation of smear, genital source SNOMED 337
4136494 HIV antigen test SNOMED 337
4149631 Chlamydia antigen test SNOMED 337
4151408 Syphilis infectious titer test SNOMED 337
4191851 Urine screening test for diabetes SNOMED 337
40481948 Detection of chromosomal aneuploidy in prenatal amniotic fluid specimen using FISH screening technique SNOMED 334
4024958 Throat culture SNOMED 327
4078285 Alpha-fetoprotein test - antenatal SNOMED 324
4150653 Fetal anatomy study SNOMED 324
4149386 Urine screening for glucose SNOMED 324
4163708 Vaccination for diphtheria, pertussis, and tetanus SNOMED 324
3011505 FEV1/FVC LOINC 316
0 No matching concept None 316
4133840 Spirometry SNOMED 316
4304821 Streptococcus pneumoniae group B antigen assay SNOMED 306
4052083 Measurement of respiratory function SNOMED 267
40623280 Parturition SNOMED 262
4134565 Hearing examination SNOMED 231
4043071 Cognitive and behavioral therapy SNOMED 204
4276519 Extraction of wisdom tooth SNOMED 190
4163872 Plain chest X-ray SNOMED 173
4125906 Suture open wound SNOMED 172
3027172 Left ventricular Ejection fraction LOINC 170
4057420 Catheter ablation of tissue of heart SNOMED 167
4275113 Insertion of intrauterine contraceptive device SNOMED 148
4199458 Passive immunization SNOMED 143
4210433 Information gathering SNOMED 140
3037141 Abuse Status [OMAHA] LOINC 140
40766240 Are you covered by health insurance or some other kind of health care plan [PhenX] LOINC 140
40758406 HIV status LOINC 140
3051031 History of Hospitalizations+Outpatient visits Narrative LOINC 140
46235214 Sexual orientation LOINC 140
42869557 Housing status LOINC 140
4170947 Bone immobilization SNOMED 129
3014902 Physical findings of Prostate LOINC 121
4254766 Digital examination of rectum SNOMED 121
3013603 Prostate specific Ag [Mass/volume] in Serum or Plasma LOINC 121
4035793 Pulmonary rehabilitation SNOMED 118
4302270 Pregnancy termination care SNOMED 111
37018340 Induced termination of pregnancy SNOMED 110
4015590 Counseling for termination of pregnancy SNOMED 110
40771960 Cause of death [US Standard Certificate of Death] LOINC 108
4151422 Sputum examination SNOMED 106
4059978 Insertion of subcutaneous contraceptive SNOMED 95
4311671 Episiotomy SNOMED 87
4238715 Removal of intrauterine device SNOMED 87
3001247 Common Ragweed IgE Ab [Units/volume] in Serum LOINC 83
3019406 Latex IgE Ab [Units/volume] in Serum LOINC 83
42869860 Total score [MMSE] LOINC 83
3006451 Walnut IgE Ab [Units/volume] in Serum LOINC 83
3005136 Cladosporium herbarum IgE Ab [Units/volume] in Serum LOINC 83
3027231 Wheat IgE Ab [Units/volume] in Serum LOINC 83
3015076 Soybean IgE Ab [Units/volume] in Serum LOINC 83
3001488 Cow milk IgE Ab [Units/volume] in Serum LOINC 83
3020655 Honey bee IgE Ab [Units/volume] in Serum LOINC 83
3000876 Codfish IgE Ab [Units/volume] in Serum LOINC 83
3012494 Peanut IgE Ab [Units/volume] in Serum LOINC 83
3006734 White Oak IgE Ab [Units/volume] in Serum LOINC 83
3023430 Cat dander IgE Ab [Units/volume] in Serum LOINC 83
4191853 Allergy screening test SNOMED 83
3014599 Egg white IgE Ab [Units/volume] in Serum LOINC 83
3021226 Shrimp IgE Ab [Units/volume] in Serum LOINC 83
3036780 American house dust mite IgE Ab [Units/volume] in Serum LOINC 83
3049273 DXA Radius and Ulna [T-score] Bone density LOINC 82
4195803 Bone density scan SNOMED 82
4150970 Medical induction of labor SNOMED 68
4166761 Rectal polypectomy SNOMED 66
4186930 Replacement of intrauterine contraceptive device SNOMED 59
4078199 Epidural anesthesia SNOMED 57
4060266 Antenatal RhD antibody screening SNOMED 57
4199276 Removal of subcutaneous contraceptive SNOMED 56
3030315 Polyp size greatest dimension LOINC 55
40761014 Hemoglobin.gastrointestinal.lower [Presence] in Stool by Immunoassay --1st specimen LOINC 55
37393315 Faecal occult blood test SNOMED 55
4335825 Transthoracic echocardiography SNOMED 53
3029187 Natriuretic peptide.B prohormone N-Terminal [Mass/volume] in Serum or Plasma LOINC 53
4047491 Radiography of humerus SNOMED 51
4139064 Admission to orthopedic department SNOMED 49
44805732 Reinsertion of subcutaneous contraceptive SNOMED 43
4015701 Cesarean section SNOMED 42
4202451 Percutaneous mechanical thrombectomy of portal vein using fluoroscopic guidance SNOMED 41
4058899 Plain X-ray of clavicle SNOMED 36
4117038 Bilateral tubal ligation SNOMED 34
4243062 Radiography of wrist SNOMED 33
4024289 Radiography of ankle SNOMED 33
4293740 Injection of tetanus antitoxin SNOMED 27
4127260 Augmentation of labor SNOMED 24
4252419 Radiologic examination of knee SNOMED 24
4197460 Injection of epinephrine SNOMED 23
4278515 Biopsy of prostate SNOMED 22
3051673 US Guidance for biopsy of Prostate LOINC 22
4336464 Coronary artery bypass graft SNOMED 21
4216130 Percutaneous coronary intervention SNOMED 21
4128031 Instrumental delivery SNOMED 20
4181917 Electroencephalogram SNOMED 19
44783196 Surgical manipulation of joint of knee SNOMED 19
40619801 Premature birth of newborn SNOMED 16
3009542 Hematocrit [Volume Fraction] of Blood LOINC 14
4145310 Pelvis X-ray SNOMED 13
4326177 Medication Reconciliation SNOMED 12
4037675 Brief general examination SNOMED 12
4187458 Review of systems SNOMED 12
40492359 Insertion of biventricular implantable cardioverter defibrillator SNOMED 10
4062501 Asthma screening SNOMED 9
44784284 Magnetic resonance imaging for measurement of brain volume SNOMED 9
4302356 CT of chest and abdomen SNOMED 9
4181781 Partial resection of colon SNOMED 9
40769194 Percentage area affected by eczema Lower extremity - bilateral [PhenX] LOINC 8
40769179 Percentage area affected by eczema Head and Neck [PhenX] LOINC 8
40769184 Percentage area affected by eczema Upper extremity - bilateral [PhenX] LOINC 8
40769189 Percentage area affected by eczema Trunk [PhenX] LOINC 8
4010253 Nasal sinus endoscopy SNOMED 8
4235738 Prostatectomy SNOMED 7
4294513 Biopsy of colon SNOMED 5
4198190 Appendectomy SNOMED 5
40493226 Excision of fallopian tube and surgical removal of ectopic pregnancy SNOMED 5
4139065 Admission to trauma surgery department SNOMED 5
4330583 Vasectomy SNOMED 5
3009201 Thyrotropin [Units/volume] in Serum or Plasma LOINC 4 
select
    m.measurement_source_concept_id,
    c.concept_name,
--  m.*,
 c.vocabulary_id,
    count(1)
from
    cdm_synthea10.measurement m
join cdm_synthea10.concept c on
    m.measurement_source_concept_id = c.concept_id
group by
    m.measurement_source_concept_id,
    c.concept_name,
 c.vocabulary_id 
order by
    count(1) desc
turbomam commented 4 years ago

see #32