Automatic Determination of Anti-Coagulation Status with NDF-RT
Total Page：16
File Type：pdf, Size：1020Kb
Proceedings of the 13th ISMB'2010 SIG meeting "Bio-ontologies" 2010:140-143. Automatic determination of anticoagulation status with NDF-RT Olivier Bodenreider*1, Fleur Mougin2 and Anita Burgun3 1 National Library of Medicine, Bethesda, Maryland, USA 2 LESIM, INSERM U897, ISPED, University Victor Segalen Bordeaux 2, France 3 INSERM U936, EA3888, School of Medicine, University of Rennes 1, IFR 140, France ABSTRACT tients at home, as it requires parenteral administration Objectives: To determine the anti-coagulation status of pa- (intravenous or subcutaneous route). tients, based on the list of medications they have been pre- From the perspective of clinical pharmacology, clopido- scribed, using the publicly available resource NDF-RT (Na- grel and warfarin are active moieties, while platelet aggre- tional Drug File Reference Terminology). Methods: We ex- gation inhibitors and anticoagulants are pharmacologic plored the legacy VA classes and we refined the definition of classes. Classes are typically established in reference to external pharmacologic classes (EXT) in NDF-RT in order to some of the properties of the active moiety, with respect to enable inferences by a description logic classifier. Results: chemistry, physiology, metabolism and therapeutic intent Of the 9 patients with a positive anticoagulation status, the (Carter, et al., 2006). For example, the classes platelet ag- VA class approach identified only 6, while the EXT approach gregation inhibitors and anticoagulants refer to the physi- identified 8. Conclusions: This preliminary experiment illu- ologic effect of drugs decreasing platelet aggregation and strates the benefits of using a refined definition of external coagulation, respectively. In contrast, the class cardiac gly- pharmacologic classes in NDF-RT. Further investigation is coside refers to the chemical structure of drugs such as di- needed. Supplementary figure: Representation of the drug goxin, while the class antianginal refers to the therapeutic clopidogrel in NDF-RT, available at: properties of some drugs on angina pectoris. Some classes http://mor.nlm.nih.gov/pubs/supp/2010-bioonto-ob/index.html. are also defined in reference to several properties, e.g., ni- trate vasodilator, referring to both the chemical structure of 1 INTRODUCTION nitrates and their relaxing action on the musculature of Patients suffering from heart failure are increasingly treated blood vessels (physiologic effect). with implantable cardioverter defibrillators (ICD) and bene- The main objective of this study is to determine the anti- fit from home monitoring. In this context of telecardiology, coagulation status of patients from the AKENATON ICDs send remote alerts about arrhythmic episodes to phy- project, based on the list of medications they have been pre- sicians, who have to determine their emergency level. The scribed. A secondary objective is to evaluate the extent to objective of the French AKENATON project is to integrate which the publicly available resource NDF-RT (National the data transmitted by the ICDs with their clinical context, Drug File Reference Terminology) provides appropriate in order to improve alert management (AKENATON, 2010; classes and drug-class membership relations to support such Burgun, et al., 2010). For example, in case of atrial fibrilla- a use case. tion, the thromboembolic risk depends on the medications taken by the patient. The formation of a clot in the heart is a 2 BACKGROUND complex process that involves platelets and multiple sub- The National Drug File Reference Terminology (NDF-RT) stances called clotting factors. is a resource developed by the Department of Veterans Af- Medications that prevent blood clots from occurring in- fairs (VA) Veterans Health Administration, as an extension clude platelet aggregation inhibitors and anticoagulants of the VA National Drug File (Lincoln, et al., 2004). Like (Weimar, et al., 2009). Platelet aggregation inhibitors, such other modern biomedical terminologies, NDF-RT was de- as clopidogrel, work by decreasing the ability of platelets to veloped using description logics and is available in several aggregate. Aspirin also makes platelets less likely to form formats, including XML and OWL. The version used in this blood clots. Oral anticoagulants, such as warfarin, decrease study is the latest OWL version available, dated September the body’s ability to form blood clots by blocking the for- 1, 2009, downloaded from the NCI website1. This version mation of vitamin K-dependent clotting factors. Another covers 1751 active moieties (level = ingredient) and 4695 anticoagulant, heparin, is less likely to be prescribed to pa- clinical drugs (level = VA product). Two independent kinds of drug classes are represented in NDF-RT: legacy VA * To whom correspondence should be addressed. 1 ftp://ftp1.nci.nih.gov/pub/cacore/EVS/NDF-RT/ 1 O. Bodenreider et al. classes and “external pharmacologic classes” defined in cardioverter defibrillators. The list of medications for each reference to some of the properties of the active moiety. patient was extracted manually from the text of the records, Legacy VA classes are simply listed as parents of clinical yielding a total of 46 medications (3.6 per patient on aver- drugs (“VA Products”). For example, the drug CLOPIDO- age). Medication names were mapped manually to generic GREL BISULFATE 75MG TAB is a subclass of PLATELET ingredient names. This step was necessary, because of loca- AGGREGATION INHIBITORS. There are 485 such VA lized brand names (e.g., Lasilix in France vs. Lasix in the classes, organized in a shallow hierarchy. The set of VA U.S. for furosemide). A total of 23 unique ingredient names classes forms a classification system, i.e., accommodates were identified. Ingredients were mapped to NDF-RT iden- virtually any drug through residual classes (e.g., BLOOD tifiers automatically through the RxNav API (Peters and PRODUCTS, OTHER). In most cases, a clinical drug is as- Bodenreider, 2008). In four cases, no NDF-RT correspon- sociated with one and only one class. No relations are stated dence was found for the ingredient. In 3 of these cases, the between these classes and drug properties. corresponding ingredient was simply discarded, as it was External pharmacologic classes are defined in reference not central to our investigation (betahistine, an antivertigo to the properties of active moieties. A given class can reflect drug; trimetazidine, an anti-anginal agent; and zopiclone, a one property (e.g., Platelet Aggregation Inhibitor2, in refer- hypnotic agent). The remaining ingredient with no mapping ence to the physiologic effect Decreased Platelet Aggrega- to NDF-RT was the anticoagulant fluindione – prescribed in tion) or multiple properties (e.g., Antiarrhythmic, in refer- Europe, but not in the U.S. – to which we substituted a simi- ence to the therapeutic intent – both preventative and cura- lar drug, anisindione. Finally, in one case, the medication tive – expressed as may_prevent Arrhythmia and may_treat was expressed not as a clinical drug, but directly as a class Arrhythmia). There are 408 such external pharmacologic (Vitamin K Antagonist). classes, with no hierarchical organization. Although active 3.2 Establishing relations between ingredients moieties are also described in terms of similar properties (e.g., CLOPIDOGREL, in reference to the physiologic effect and external pharmacologic classes Decreased Platelet Aggregation), no relations are found Unlike for legacy VA classes, no relations are present in the between active moieties (ingredients) and external pharma- OWL version of NDF-RT between drugs and external cologic classes. Moreover, from the perspective of descrip- pharmacologic classes. Moreover, because the external tion logics (DL), because all concepts in NDF-RT are primi- pharmacologic classes are all primitive concepts, no such tive concepts (i.e., no necessary and sufficient conditions are relations can be inferred by a DL classifier. In order to sup- provided for external pharmacologic classes), no inferred port such inference, we modified the OWL version of NDF- relations can be computed automatically by a DL classifier RT in the following ways. between active moieties and external pharmacologic classes. Step 1. We transformed the primitive concepts for exter- In practice, CLOPIDOGREL and Platelet Aggregation Inhi- nal pharmacologic classes into defined classes by specifying bitor are not related – directly or through inference – in the a set of necessary and sufficient conditions for the class current OWL version of NDF-RT. (adding an owl:equivalentClass (≡) axiom). The re- Several groups have investigated various aspects of NDF- strictions based on has_TC are specific to external pharma- RT, including coverage (Brown, et al., 2004), representation cologic classes (providing links to high-level therapeutic of specific drug properties (Rosenbloom, et al., 2003), and class concepts) and not used in the ingredients. For this rea- fitness for purpose in applications, such as linkage to indica- son, they were left out of the necessary and sufficient condi- tions (Burton, et al., 2008) and detection of drug intolerance tions. (Schadow, 2009). Our present investigation of NDF-RT is Step 2. Because the therapeutic intent properties also performed in the context of an application. The specific may_treat and may_prevent are not always used consistently contribution of our study is to leverage (and improve) the in the ingredients compared to the external pharmacologic description logic