HCLS/ClinicalObservationsInteroperability/DrugMapping.html
Mappings From Clinical Trial Eligibility Drug Information to Prescription in Patient Data Using Drug Ontology
When checking a patient's eligibility for a given CT, we need to run a query in SPARQL8.html, which specifies drugs in terms of "class of drugs" (i.e alpha glucisudase inhibitors).
In patient medical records, we find drug prescription information in terms of brand names and packaging information (NDC Code).
Samson Tu and colleagues have constructed a drug ontology. Below are some excerpts of this Drug Ontology
Drug Ontology By Stanford
Drug Ontology is developed by the nosology project at Stanford Center for Biomedical Informatics Research. This project seeks to discover new therapeutic uses and adverse effects of drugs by finding diseases that have gene expression profiles similar to those of the known indications and adverse effects of drugs. The objectives of the Drug Ontology are:
- defines a core set of concepts and relationships that allow us to integrate information from multiple sources,
- provides classification services along multiple axes,
- provides links to external sources so that data not in the ontology can be queried from these sources.
The following diagram depicts top level concepts and relationship in Drug Ontology
See also the attached presentation Using Drug Ontology to Bridge Clinical Trial Eligibility and Patient Record
Derive Weight Reduction Class From Drug Ontology
One type of drugs identified in CT#8 is for control weight. There is no such class in Drug Ontology. However, there exists relationship between a drug to the clinical finding "Obese" via a property "may_treat".
Using the following simply rules, we get a list of drugs that can be used for controlling weight.
@prefix owl: <http://www.w3.org/2002/07/owl#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . @prefix : <http://www.owl-ontologies.com/DrugOntology.owl#> . #check all drugs that "may_treat obese" {?A rdfs:subClassOf ?B; rdfs:label ?D. ?B a owl:Restriction; owl:onProperty :may_treat; owl:someValuesFrom :C0028754} => {?D a :WeightLoseDrug}.
The results are a list of drugs that are used for weight reduction purposes. Note: this is not a complete list because of this ESW's restrictions on displaying certain words. The complete list can be found in this N3 file Media:HCLS$$ClinicalObservationsInteroperability$$DrugMapping.html$CT2DOMappingWL.n3
"Benzphetamine" a :WeightLoseDrug. "Phenylpropanolamine Hydrochloride" a :WeightLoseDrug. "Dexfenfluramine" a :WeightLoseDrug. "Diethylpropion" a :WeightLoseDrug. "Fenfluramine" a :WeightLoseDrug. "Mazindol" a :WeightLoseDrug. "Methamphetamine" a :WeightLoseDrug. "Phenmetrazine" a :WeightLoseDrug. "Phenylpropanolamine" a :WeightLoseDrug. "phendimetrazine" a :WeightLoseDrug. "sibutramine" a :WeightLoseDrug. "orlistat" a :WeightLoseDrug. "SIBUTRAMINE HYDROCHLORIDE" a :WeightLoseDrug. "phendimetrazine tartrate" a :WeightLoseDrug. "Diethylpropion Hydrochloride" a :WeightLoseDrug. "Fenfluramine Hydrochloride" a :WeightLoseDrug. "Methamphetamine Hydrochloride" a :WeightLoseDrug. "Benzphetamine hydrochloride" a :WeightLoseDrug. "Dexfenfluramine Hydrochloride" a :WeightLoseDrug. "Phenmetrazine Hydrochloride" a :WeightLoseDrug. "PHENDIMETRAZINE HYDROCHLORIDE" a :WeightLoseDrug.
Drug Mapping for CT#8
For a drug entity in Clinical Trial #8, we first identify corresponding concept in Drug Ontology (uri). Then using the following rules, all sub-entities of this drug entity are recruited as drugs relevant to CT #8.
@prefix owl: <http://www.w3.org/2002/07/owl#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . @prefix : <http://www.owl-ontologies.com/DrugOntology.owl#> . #Drug Mentioned in CT 8 #metformin :C0025598 a :CTDrugName. #Alpha Glucoside Inhabitor :C1299007 a :CTDrugName. #Anticogulant :C0003280 a :CTDrugName. #although Asprin and Dipyridamole is not classified as "antocogulant", it is often used in such way :C000405 a :CTDrugName. :C0012582 a :CTDrugName. #Insulin secretagogue, in DrugOntology, it is called Sulfonylurea :C0038766 a :CTDrugName. #Therapy with rosiglitazone (Avandia) or pioglitazone (Actos), or extendin-4 (Byetta), :C0289313 a :CTDrugName. :C0071097 a :CTDrugName. :C1562104 a :CTDrugName. #corticosteroids and derivatives :C0582125 a :CTDrugName. #weightloss drugs #Peripherally acting antiobesity agent (orlist) and other drugs derived above :C0732646 a :CTDrugName. #Phenylpropanolamine :C0031495 a :CTDrugName. #non-steroidal anti-inflammatory preparations (not sure) :C0003211 a :CTDrugName. #clopidogrel, anti-patelet agent :C0070166 a :CTDrugName. #probenecid :C0033209 a :CTDrugName. #sulfinpyrazone :C0038742 a :CTDrugName. #uricosuric agent :C0041983 a :CTDrugName. #inference rule { ?A a :CTDrugName. ?B rdfs:subClassOf ?A. } => { ?B a :CTDrugName. }.
The reference result is a list of entities that relevant to drug classes/categories mentioned in CT#8, see the attached N3 file Media:HCLS$$ClinicalObservationsInteroperability$$DrugMapping.html$CT2DOMappingE.n3
Drug Ontology is accompanied by a database that contains source information, such as the corresponding rxNorm and Drug Bank IDs of a Drug Ontology concept. This table shows the mapping from CT#8 to rxNorm and Drug Bank Ids.
The mapping from rxnorm code to NDC code can be done via a rxNorm API, but it requires programming. The following NDC codes are obtained by query "active ingredients" using Common Data Hub services
Clinical Trial | Drug Ontology | RxNORM Code | Drug Bank Code |
Metformin | Metformin (C0025598) | 6809 | DB00331 |
Metformin hydrochloride(C0770893) | 235743 | ||
Alpha-glucoside inhibitor | Acarbose (C0050393) | 16681 | DB00284 |
miglitol (C0066535) | 30009 | DB00491 | |
Anticoagulant | Dipyridamole (C0012582) | 3521 | DB00975 |
argatroban (C0048470) | 15202 | DB00278 | |
Indanedione (C0304940) | |||
Pentosan Polysulfate (C0600296) | 155046 | DB00686 | |
Selective factor Xa inhibitor (C1272716) | |||
Phenindione (C0031406) | 8130 | DB00498 | |
anisindione (C0051919) | 17941 | DB01125 | |
Ancrod (C0002823) | |||
Heparin (C0019134) | 5224 | DB01109 | |
Heparinoids (C0019142) | |||
fondaparinux (C1098510) | |||
Hirudin and derivatives (C1320115) | |||
Direct thrombin inhibitor (C1532225) | |||
Dicumarol (C0005640) | 1598 | DB00266 | |
Phenprocoumon (C0031444) | 8150 | DB00946 | |
Coumarin anticoagulant (C0360596) | |||
Indanedione anticoagulant (C0360597) | |||
drotrecogin alfa (C1170000) | 352374 | DB00055 | |
Pentosan Polysulphate Sodium (C0524684) | 134413 | ||
Fondaparinux sodium (C1099664) | 322154 | DB00569 | |
Unfractionated heparin (C0019139) | |||
Heparin sodium (C0037513) | 9877 | ||
calcium heparin (C0054452) | 2044 | ||
HEPARIN, PORK (C0770546) | 235473 | ||
danaparoid (C0259507) | 78484 | ||
bivalirudin (C0168273) | 60819 | DB00006 | |
desirudin (C0378366) | 114934 | ||
lepirudin (C0772394) | 237057 | DB00001 | |
Acenocoumarol (C0000956) | 154 | DB01418 | |
Warfarin (C0043031) | 11289 | DB00682 | |
Enoxaparin (C0206460) | 67108 | DB01225 | |
Dalteparin (C0206461) | 67109 | ||
tinzaparin (C0216278) | 69646 | ||
reviparin (C0254215) | 75960 | ||
ardeparin (C0297269) | 87866 | DB00407 | |
certoparin (C0592532) | 152610 | ||
Danaparoid sodium (C0353453) | 103843 | ||
Warfarin Potassium (C0282378) | 82118 | ||
Warfarin Sodium (C0376218) | 114194 | ||
Enoxaparin sodium (C0724579) | 221095 | ||
Dalteparin Sodium (C0282471) | 82137 | ||
Tinzaparin sodium (C0354599) | 104466 | ||
Reviparin sodium (C0254216) | 75961 | ||
ardeparin sodium (C0297268) | 87865 | ||
Certoparin sodium (C0592534) | 152612 | ||
Insulin secretagogue | Sulfonylurea (C0038766) | ||
Acetohexamide (C0000992) | 173 | DB00414 | |
Chlorpropamide (C0008287) | 2404 | DB00672 | |
Glyburide (C0017628) | 4815 | ||
Gliclazide (C0017631) | 4816 | DB01120 | |
Glipizide (C0017642) | 4821 | DB01067 | |
Tolazamide (C0040372) | 10633 | DB00839 | |
Tolbutamide (C0040374) | 10635 | DB01124 | |
glimepiride (C0061323) | 25789 | DB00222 | |
gliquidone (C0061328) | 25793 | DB01251 | |
glibornuride (C0350998) | 102846 | ||
glymidine (C0351000) | 102848 | ||
First generation sulfonylurea (C1300197) | |||
Second generation sulfonylurea (C1300198) | |||
Tolbutamide sodium (C0724709) | 221173 | ||
rosiglitazone | rosiglitazone (C0289313) | 84108 | DB00412 |
Rosiglitazone maleate (C0795660) | 253198 | ||
pioglitazone | pioglitazone(C0071097) | 33738 | DB01132 |
Pioglitazone hydrochloride (C0872972) | 259319 | ||
extendin-4 (Byetta) | Incretin mimetic product(C1562104) | ||
exenatide (C0167117) | 60548 | DB01276 | |
probenecid | Probenecid (C0033209) | 8698 | DB01032 |
sulfinpyrazone | Sulfinpyrazone (C0038742) | 10205 | DB01138 |
uricosuric agent | Uricosuric agent (C0041983) | ||
Probenecid (C0033209) | 8698 | DB01032 | |
Sulfinpyrazone (C0038742) | 10205 | DB01138 | |
clopidogrel | clopidogrel (C0070166) | 32968 | DB00758 |
CLOPIDOGREL BISULFATE (C0772326) | |||
corticosteroids and derivatives | Corticosteroids and derivatives (C0582125) | ||
17-Ketogenic steroid (C0000163) | |||
17-Ketosteroid (C0000167) | |||
Deoxycorticosterone (C0011710) | 3256 | ||
Diflucortolone" (C0012227) | 3392 | ||
Glucocorticoid hormone (C0017710) | |||
deflazacort (C0057258) | 22396 | ||
tixocortol pivalate (C0076748) | 38336 | ||
Clobetasone (C0360518) | 108074 | ||
11-Deoxysteroid (C0522263) | |||
11-Oxycorticosteroid (C0522264) | |||
Fluorinated corticosteroid (C1285555) | |||
Mineralocorticoid agent (C1641843) | |||
Cortisone (C0010137) | 2878 | ||
Hydrocortisone (C0020268) | 5492 | DB00741 | |
Estrone (C0014942) | 4103 | DB00655 | |
11-Deoxy-17-ketosteroid (C0522262) | |||
deoxycortone pivalate (C0057420) | 22537 | ||
Desoxycorticosterone acetate (C0813203) | 25833 | ||
diflucortolone valerate (C0057994) | 23035 | ||
Beclomethasone (C0004905) | 1347 | DB00394 | |
Betamethasone (C0005308) | 1514 | DB00443 | |
Dexamethasone (C0011777) | 3264 | DB01234 | |
Flumethasone (C0016294) | 4458 | ||
Fluocinonide (C0016299) | 4462 | DB01047 | |
Fluorometholone(C0016351) | 4491 | DB00324 | |
Fluprednisolone(C0016369) | 4497 | ||
Flurandrenolone(C0016374) | 4500 | ||
Synthetic glucocorticoid(C0017711) | |||
Methylprednisolone(C0025815) | 6902 | DB00959 | |
Paramethasone(C0030454) | 7910 | DB01384 | |
prednisolone(C0032950) | 8638 | DB00860 | |
Prednisone(C0032952) | 8640 | DB00635 | |
Triamcinolone(C0040864) 10759 | DB00620 | ||
amcinonide(C0051556) | 17652 | DB00288 | |
flunisolide(C0060501) | 25120 | DB00180 | |
meprednisone(C0065967) | 29523 | ||
prednicarbate(C0071836) | 34369 | DB01130 | |
Fluclorolone(C0360537) | 108091 | ||
FLUPREDNIDENE(C0771950) | 236650 | ||
Loteprednol(C0772364) | 237027 | ||
clobetasone butyrate(C0055896) | 21246 | ||
Pregnenolone(C0373704) | 114052 | ||
cortisone acetate(C0056391) | 21655 | DB01380 | |
Clioquinol(C0021978) | 5942 | DB04815 | |
hydrocortisone 17-butyrate 21-propionate(C0063076) | |||
hydrocortisone acetate(C0063077) | |||
hydrocortisone valerate(C0063079) | |||
Hydrocortisone butyrate(C0352536) | |||
hydrocortisone cypionate(C0612688) | |||
Hydrocortisone sodium phosphate(C0770559) | |||
Hydrocortisone sodium succinate(C0770560) | |||
estropipate(C0071108) | |||
Sodium estrone sulfate(C0304783) | |||
Androstenedione(C0002860) | |||
dehydroepiandrosterone(C0011185) | |||
Beclomethasone Dipropionate(C0004906) | |||
Betamethasone acetate(C0005310) | |||
Betamethasone benzoate(C0005311) | |||
betamethasone-17,21-dipropionate(C0053523) | |||
Topical form betamethasone(C0358518) | |||
betamethasone sodium phosphate(C0700603) | |||
Augmented betamethasone dipropionate(C0718926) | |||
Betamethasone valerate(C0750848) | |||
Desoximetasone(C0011707) | |||
dexamethasone acetate(C0057598) | |||
Dexamethasone sodium phosphate(C0113286) | |||
Dexamethasone ophthalmic preparation(C0304706) | |||
Dexamethasone phosphate(C0770565) | |||
Desonide(C0011705) | |||
Budesonide(C0054201) | |||
clocortolone(C0055899) | |||
halobetasol propionate(C0098735) | |||
rimexolone(C0140594) | |||
Alclometasone(C0360534) | |||
ciclesonide(C0907850) | |||
Synthetic glucocorticoid, chlorinated(C1289953) | |||
methylprednisolone acetate(C0600901) | |||
6 alpha-Methylprednisolone Sodium Hemisuccinate(C0700546) | |||
paramethasone acetate(C0070073) | |||
prednisolone acetate(C0071839) | |||
prednisolone tebutate(C0071844) | |||
Prednisolone sodium phosphate(C0138273) | |||
Prednisolone ophthalmic preparation(C0304711) | |||
Triamcinolone Acetonide(C0040866) | |||
triamcinolone diacetate(C0040867) | |||
triamcinolone hexacetonide(C0077004) | |||
Parenteral form triamcinolone(C0360581) | |||
Fluclorolone acetonide(C0352474) | |||
loteprednol etabonate(C0126177) | |||
fluticasone(C0082607) | |||
Mometasone(C0360564) | |||
Clobetasol(C0008992) | |||
Fludrocortisone(C0016280) | |||
Fluocortolone(C0016301) | |||
Halcinonide(C0018513) | |||
fluocinolone(C0060507) | |||
Diflorasone(C0304612) | |||
clocortolone pivalate(C0055900) | |||
alclometasone dipropionate(C0051113) | |||
Fluticasone propionate(C0117996) | |||
mometasone furoate(C0066700) | |||
Mometasone furoate monohydrate(C0594488) | |||
Clobetasol Propionate(C0055895) | |||
fludrocortisone 21-acetate(C0616274) | |||
Fluocortolone Caproate(C0016302) | |||
Fluocortolone Pivalate(C0016304) | |||
Fluocinolone Acetonide(C0016298) | |||
diflorasone diacetate(C0057992) | |||
Weight reduce drugs | orlistat (C0076275) | 37925 | DB01083 |
Methamphetamine (C0025611) | 6816 | DB01577 |
A list of Non-steroidal anti-inflammatory drugs from Drug Ontology
"Non-steroidal anti-inflammatory agent" :hasID :C0003211. "Aminopyrine" :hasID :C0002586. "Apazone" :hasID :C0003524. "benorilate" :hasID :C0005011. "Benzydamine" :hasID :C0005099. "Diclofenac" :hasID :C0012091. "Dipyrone" :hasID :C0012586. "Fenoprofen" :hasID :C0015837. "Flurbiprofen" :hasID :C0016377. "Ibuprofen" :hasID :C0020740. "Indomethacin" :hasID :C0021246. "Ketoprofen" :hasID :C0022635. "Sodium Meclofenamate" :hasID :C0025041. "Meclofenamic Acid" :hasID :C0025042. "Mefenamic Acid" :hasID :C0025152. "Naproxen" :hasID :C0027396. "Nefopam" :hasID :C0027556. "Oxyphenbutazone" :hasID :C0030078. "Phenylbutazone" :hasID :C0031463. "Piroxicam" :hasID :C0031990. "salicylate" :hasID :C0036075. "Salicylate product" :hasID :C0036077. "Sulindac" :hasID :C0038792. "Suprofen" :hasID :C0038878. "Tolmetin" :hasID :C0040377. "aceclofenac" :hasID :C0050403. "acemetacin" :hasID :C0050409. "balsalazide" :hasID :C0052940. "bromfenac" :hasID :C0054094. "carprofen" :hasID :C0054827. "lornoxicam" :hasID :C0055477. "Etodolac" :hasID :C0059865. "fenbufen" :hasID :C0060156. "flunixin" :hasID :C0060502. "morazone" :hasID :C0066795. "orgotein" :hasID :C0069638. "oxaprozin" :hasID :C0069739. "Ketorolac" :hasID :C0073631. "tenoxicam" :hasID :C0076096. "tiaprofenic acid" :hasID :C0076653. "tolfenamic acid" :hasID :C0076799. "zomepirac" :hasID :C0078840. "Dexketoprofen" :hasID :C0772505. "Mefenamate" :hasID :C0806919. "Felbinac" :hasID :C0877860. "nepafenac" :hasID :C0961209. "Meclofenamate" :hasID :C1289957. "Propionic acid derivative anti-inflammatory agent" :hasID :C1626403. "Para-aminophenol derivative anti-inflammatory agent" :hasID :C1690486. "Benzydamine Hydrochloride" :hasID :C0282070. "Diclofenac Potassium" :hasID :C0282131. "Diclofenac Sodium" :hasID :C0700583. "Fenoprofen Calcium" :hasID :C0887323. "Flurbiprofen sodium" :hasID :C0304658. "Indomethacin sodium trihydrate" :hasID :C0813196. "Naproxen sodium" :hasID :C0546873. "Nefopam Hydrochloride" :hasID :C0015820. "piroxicam-beta-cyclodextrin" :hasID :C0209263. "Aluminum aspirin" :hasID :C0002370. "Aminosalicylic Acid" :hasID :C0002590. "Aspirin" :hasID :C0004057. "Diflunisal" :hasID :C0012228. "salicylamide" :hasID :C0036071. "Sulfasalazine" :hasID :C0036078. "Sodium Salicylate" :hasID :C0037549. "aloxiprin" :hasID :C0051254. "choline salicylate" :hasID :C0055573. "olsalazine" :hasID :C0069454. "Salsalate" :hasID :C0073983. "trolamine salicylate" :hasID :C0077376. "Magnesium Salicylate" :hasID :C0126789. "mesalamine" :hasID :C0127615. "Thiosalicylate" :hasID :C0304346. "Acetyl salicylate" :hasID :C0304348. "diethylamine salicylate" :hasID :C0610988. "Choline Magnesium Trisalicyclate" :hasID :C0719064. "Salicin extract" :hasID :C0874039. "Tolmetin Sodium" :hasID :C0087097. "Bromfenac sodium" :hasID :C0107211. "flunixin meglumine" :hasID :C0060503. "Ketorolac Tromethamine" :hasID :C0064326. "Zomepirac sodium" :hasID :C0149477. "Acetaminophen" :hasID :C0000970. "Aminosalicylic sodium" :hasID :C0301336. "Buffered aspirin" :hasID :C0718687. "Olsalazine sodium" :hasID :C0353940. "Sodium thiosalicylate" :hasID :C0304347.