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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
    :C0025598    a    :CTDrugName.

    #Alpha Glucoside Inhabitor
    :C1299007    a    :CTDrugName.

   :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.

   :C0031495   a    :CTDrugName.

   #non-steroidal anti-inflammatory preparations (not sure)
   :C0003211  a    :CTDrugName.

   #clopidogrel, anti-patelet agent
   :C0070166   a    :CTDrugName.

   :C0033209    a    :CTDrugName.

   :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
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)
Sodium estrone sulfate(C0304783)
Beclomethasone Dipropionate(C0004906)
Betamethasone acetate(C0005310)
Betamethasone benzoate(C0005311)
Topical form betamethasone(C0358518)
betamethasone sodium phosphate(C0700603)
Augmented betamethasone dipropionate(C0718926)
Betamethasone valerate(C0750848)
dexamethasone acetate(C0057598)
Dexamethasone sodium phosphate(C0113286)
Dexamethasone ophthalmic preparation(C0304706)
Dexamethasone phosphate(C0770565)
halobetasol propionate(C0098735)
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)
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.