Closed turbomam closed 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
see #32
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