Drugs That Interact With Colchicine Via Inhibition of Cytochrome P450 3A4 and P-Glycoprotein: A Signal Detection Analysis Using a Database of Spontaneously Reported Adverse Events (FAERS).

BACKGROUND: Colchicine has a narrow therapeutic index. Its toxicity can be increased due to concomitant exposure to drugs inhibiting its metabolic pathway; these are cytochrome P450 3A4 (CYP3A4) and P-glycoprotein (P-gp). OBJECTIVE: To examine clinical outcomes associated with colchicine drug interactions using the spontaneous reports of the US Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS). METHODS: We conducted a disproportionality analysis using FAERS data from January 2004 through June 2020. The reporting odds ratio (ROR) and observed-to-expected ratio (O/E) with shrinkage for adverse events related to colchicine's toxicity (ie, rhabdomyolysis/myopathy, agranulocytosis, hemorrhage, acute renal failure, hepatic failure, arrhythmias, torsade de pointes/QT prolongation, and cardiac failure) were compared between FAERS reports. RESULTS: A total of 787 reports included the combined mention of colchicine, an inhibitor of both CYP3A4 and P-gp drug, and an adverse event of interest. Among reports that indicated the severity, 61% mentioned hospitalization and 24% death. A total of 37 ROR and 34 O/E safety signals involving colchicine and a CYP3A4/P-gp inhibitor were identified. The strongest ROR signal was for colchicine + atazanavir and rhabdomyolysis/myopathy (ROR = 35.4, 95% CI: 12.8-97.6), and the strongest O/E signal was for colchicine + atazanavir and agranulocytosis (O/E = 3.79, 95% credibility interval: 3.44-4.03). CONCLUSION AND RELEVANCE: This study identifies numerous safety signals for colchicine and CYP3A4/P-gp inhibitor drugs. Avoiding the interaction or monitoring for toxicity in patients when co-prescribing colchicine and these agents is highly recommended.

Developing a Knowledge Graph for Pharmacokinetic Natural Product-Drug Interactions.

BACKGROUND: Pharmacokinetic natural product-drug interactions (NPDIs) occur when botanical or other natural products are co-consumed with pharmaceutical drugs. With the growing use of natural products, the risk for potential NPDIs and consequent adverse events has increased. Understanding mechanisms of NPDIs is key to preventing or minimizing adverse events. Although biomedical knowledge graphs (KGs) have been widely used for drug-drug interaction applications, computational investigation of NPDIs is novel. We constructed NP-KG as a first step toward computational discovery of plausible mechanistic explanations for pharmacokinetic NPDIs that can be used to guide scientific research. METHODS: We developed a large-scale, heterogeneous KG with biomedical ontologies, linked data, and full texts of the scientific literature. To construct the KG, biomedical ontologies and drug databases were integrated with the Phenotype Knowledge Translator framework. The semantic relation extraction systems, SemRep and Integrated Network and Dynamic Reasoning Assembler, were used to extract semantic predications (subject-relation-object triples) from full texts of the scientific literature related to the exemplar natural products green tea and kratom. A literature-based graph constructed from the predications was integrated into the ontology-grounded KG to create NP-KG. NP-KG was evaluated with case studies of pharmacokinetic green tea- and kratom-drug interactions through KG path searches and meta-path discovery to determine congruent and contradictory information in NP-KG compared to ground truth data. We also conducted an error analysis to identify knowledge gaps and incorrect predications in the KG. RESULTS: The fully integrated NP-KG consisted of 745,512 nodes and 7,249,576 edges. Evaluation of NP-KG resulted in congruent (38.98% for green tea, 50% for kratom), contradictory (15.25% for green tea, 21.43% for kratom), and both congruent and contradictory (15.25% for green tea, 21.43% for kratom) information compared to ground truth data. Potential pharmacokinetic mechanisms for several purported NPDIs, including the green tea-raloxifene, green tea-nadolol, kratom-midazolam, kratom-quetiapine, and kratom-venlafaxine interactions were congruent with the published literature. CONCLUSION: NP-KG is the first KG to integrate biomedical ontologies with full texts of the scientific literature focused on natural products. We demonstrate the application of NP-KG to identify known pharmacokinetic interactions between natural products and pharmaceutical drugs mediated by drug metabolizing enzymes and transporters. Future work will incorporate context, contradiction analysis, and embedding-based methods to enrich NP-KG. NP-KG is publicly available at https://doi.org/10.5281/zenodo.6814507. The code for relation extraction, KG construction, and hypothesis generation is available at https://github.com/sanyabt/np-kg.

Causal feature selection using a knowledge graph combining structured knowledge from the biomedical literature and ontologies: A use case studying depression as a risk factor for Alzheimer's disease.

BACKGROUND: Causal feature selection is essential for estimating effects from observational data. Identifying confounders is a crucial step in this process. Traditionally, researchers employ content-matter expertise and literature review to identify confounders. Uncontrolled confounding from unidentified confounders threatens validity, conditioning on intermediate variables (mediators) weakens estimates, and conditioning on common effects (colliders) induces bias. Additionally, without special treatment, erroneous conditioning on variables combining roles introduces bias. However, the vast literature is growing exponentially, making it infeasible to assimilate this knowledge. To address these challenges, we introduce a novel knowledge graph (KG) application enabling causal feature selection by combining computable literature-derived knowledge with biomedical ontologies. We present a use case of our approach specifying a causal model for estimating the total causal effect of depression on the risk of developing Alzheimer's disease (AD) from observational data. METHODS: We extracted computable knowledge from a literature corpus using three machine reading systems and inferred missing knowledge using logical closure operations. Using a KG framework, we mapped the output to target terminologies and combined it with ontology-grounded resources. We translated epidemiological definitions of confounder, collider, and mediator into queries for searching the KG and summarized the roles played by the identified variables. We compared the results with output from a complementary method and published observational studies and examined a selection of confounding and combined role variables in-depth. RESULTS: Our search identified 128 confounders, including 58 phenotypes, 47 drugs, 35 genes, 23 collider, and 16 mediator phenotypes. However, only 31 of the 58 confounder phenotypes were found to behave exclusively as confounders, while the remaining 27 phenotypes played other roles. Obstructive sleep apnea emerged as a potential novel confounder for depression and AD. Anemia exemplified a variable playing combined roles. CONCLUSION: Our findings suggest combining machine reading and KG could augment human expertise for causal feature selection. However, the complexity of causal feature selection for depression with AD highlights the need for standardized field-specific databases of causal variables. Further work is needed to optimize KG search and transform the output for human consumption.

Early prediction of Alzheimer's disease and related dementias using real-world electronic health records.

INTRODUCTION: This study aims to explore machine learning (ML) methods for early prediction of Alzheimer's disease (AD) and related dementias (ADRD) using the real-world electronic health records (EHRs). METHODS: A total of 23,835 ADRD and 1,038,643 control patients were identified from the OneFlorida+ Research Consortium. Two ML methods were used to develop the prediction models. Both knowledge-driven and data-driven approaches were explored. Four computable phenotyping algorithms were tested. RESULTS: The gradient boosting tree (GBT) models trained with the data-driven approach achieved the best area under the curve (AUC) scores of 0.939, 0.906, 0.884, and 0.854 for early prediction of ADRD 0, 1, 3, or 5 years before diagnosis, respectively. A number of important clinical and sociodemographic factors were identified. DISCUSSION: We tested various settings and showed the predictive ability of using ML approaches for early prediction of ADRD with EHRs. The models can help identify high-risk individuals for early informed preventive or prognostic clinical decisions.

A Pharmacovigilance Study of Adverse Drug Reactions Reported for Cardiovascular Disease Medications Approved Between 2012 and 2017 in the United States Food and Drug Administration Adverse Event Reporting System (FAERS) Database.

PURPOSE: Between 2012 and 2017, the FDA approved 29 therapies for a cardiovascular disease (CVD) indication. Due to the limited literature on patient safety outcomes for recently approved CVD medications, this study investigated adverse drug reports (ADRs) reported in the FDA Adverse Event Reporting System (FAERS). METHODS: A disproportionality analysis of spontaneously reported ADR was conducted. Reports in FAERS from Quarter 1, 2012, through Quarter 1, 2019, were compiled, allowing a 2-year buffer following drug approval in 2017. Top 10 reported ADRs and reporting odds ratios (ROR; confidence interval (CI)), a measure of disproportionality, were analyzed and compared to drugs available prior to 2012 as appropriate. RESULTS: Of 7,952,147 ADR reports, 95,016 (1.19%) consisted of reports for newly approved CVD medications. For oral anticoagulants, apixaban had significantly lower reports for anemia and renal failure compared to dabigatran and rivaroxaban but greater reports for neurological signs/symptoms, and arrhythmias. Evaluating heart failure drugs, sacubitril/valsartan had greater reports for acute kidney injury, coughing, potassium imbalances, and renal impairment but notably, lower for angioedema compared to lisinopril. Assessing familial hypercholesterolemia drugs, alirocumab had greater reports for joint-related-signs/symptoms compared to other agents in this category. A newer pulmonary arterial hypertension treatment, selexipag, had greater reports of reporting for bone/joint-related-signs/symptoms but riociguat had greater reports for hemorrhages and vascular hypotension. CONCLUSION: Pharmacovigilance studies allow an essential opportunity to evaluate the safety profile of CVD medications in clinical practice. Additional research is needed to evaluate these reported safety concerns for recently approved CVD medications.

Using computable knowledge mined from the literature to elucidate confounders for EHR-based pharmacovigilance.

INTRODUCTION: Drug safety research asks causal questions but relies on observational data. Confounding bias threatens the reliability of studies using such data. The successful control of confounding requires knowledge of variables called confounders affecting both the exposure and outcome of interest. However, causal knowledge of dynamic biological systems is complex and challenging. Fortunately, computable knowledge mined from the literature may hold clues about confounders. In this paper, we tested the hypothesis that incorporating literature-derived confounders can improve causal inference from observational data. METHODS: We introduce two methods (semantic vector-based and string-based confounder search) that query literature-derived information for confounder candidates to control, using SemMedDB, a database of computable knowledge mined from the biomedical literature. These methods search SemMedDB for confounders by applying semantic constraint search for indications treated by the drug (exposure) and that are also known to cause the adverse event (outcome). We then include the literature-derived confounder candidates in statistical and causal models derived from free-text clinical notes. For evaluation, we use a reference dataset widely used in drug safety containing labeled pairwise relationships between drugs and adverse events and attempt to rediscover these relationships from a corpus of 2.2 M NLP-processed free-text clinical notes. We employ standard adjustment and causal inference procedures to predict and estimate causal effects by informing the models with varying numbers of literature-derived confounders and instantiating the exposure, outcome, and confounder variables in the models with dichotomous EHR-derived data. Finally, we compare the results from applying these procedures with naive measures of association (χ2 and reporting odds ratio) and with each other. RESULTS AND CONCLUSIONS: We found semantic vector-based search to be superior to string-based search at reducing confounding bias. However, the effect of including more rather than fewer literature-derived confounders was inconclusive. We recommend using targeted learning estimation methods that can address treatment-confounder feedback, where confounders also behave as intermediate variables, and engaging subject-matter experts to adjudicate the handling of problematic covariates.

A New Data Repository for Pharmacokinetic Natural Product-Drug Interactions: From Chemical Characterization to Clinical Studies.

There are many gaps in scientific knowledge about the clinical significance of pharmacokinetic natural product-drug interactions (NPDIs) in which the natural product (NP) is the precipitant and a conventional drug is the object. The National Center for Complimentary and Integrative Health created the Center of Excellence for NPDI Research (NaPDI Center) (www.napdi.org) to provide leadership and guidance on the study of pharmacokinetic NPDIs. A key contribution of the Center is the first user-friendly online repository that stores and links pharmacokinetic NPDI data across chemical characterization, metabolomics analyses, and pharmacokinetic in vitro and clinical experiments (repo.napdi.org). The design is expected to help researchers more easily arrive at a complete understanding of pharmacokinetic NPDI research on a particular NP. The repository will also facilitate multidisciplinary collaborations, as the repository links all of the experimental data for a given NP across the study types. The current work describes the design of the repository, standard operating procedures used to enter data, and pharmacokinetic NPDI data that have been entered to date. To illustrate the usefulness of the NaPDI Center repository, more details on two high-priority NPs, cannabis and kratom, are provided as case studies. SIGNIFICANCE STATEMENT: The data and knowledge resulting from natural product-drug interaction (NPDI) studies is distributed across a variety of information sources, rendering difficulties to find, access, and reuse. The Center of Excellence for NPDI Research addressed these difficulties by developing the first user-friendly online repository that stores data from in vitro and clinical pharmacokinetic NPDI experiments and links them with study data from chemical characterization and metabolomics analyses of natural products that are also stored in the repository.

Testing the face validity and inter-rater agreement of a simple approach to drug-drug interaction evidence assessment.

Low concordance between drug-drug interaction (DDI) knowledge bases is a well-documented concern. One potential cause of inconsistency is variability between drug experts in approach to assessing evidence about potential DDIs. In this study, we examined the face validity and inter-rater reliability of a novel DDI evidence evaluation instrument designed to be simple and easy to use. METHODS: A convenience sample of participants with professional experience evaluating DDI evidence was recruited. Participants independently evaluated pre-selected evidence items for 5 drug pairs using the new instrument. For each drug pair, participants labeled each evidence item as sufficient or insufficient to establish the existence of a DDI based on the evidence categories provided by the instrument. Participants also decided if the overall body of evidence supported a DDI involving the drug pair. Agreement was computed both at the evidence item and drug pair levels. A cut-off of ≥ 70% was chosen as the agreement threshold for percent agreement, while a coefficient > 0.6 was used as the cut-off for chance-corrected agreement. Open ended comments were collected and coded to identify themes related to the participants' experience using the novel approach. RESULTS: The face validity of the new instrument was established by two rounds of evaluation involving a total of 6 experts. Fifteen experts agreed to participate in the reliability assessment, and 14 completed the study. Participant agreement on the sufficiency of 22 of the 34 evidence items (65%) did not exceed the a priori agreement threshold. Similarly, agreement on the sufficiency of evidence for 3 of the 5 drug pairs (60%) was poor. Chance-corrected agreement at the drug pair level further confirmed the poor interrater reliability of the instrument (Gwet's AC1 = 0.24, Conger's Kappa = 0.24). Participant comments suggested several possible reasons for the disagreements including unaddressed subjectivity in assessing an evidence item's type and study design, an infeasible separation of evidence evaluation from the consideration of clinical relevance, and potential issues related to the evaluation of DDI case reports. CONCLUSIONS: Even though the key findings were negative, the study's results shed light on how experts approach DDI evidence assessment, including the importance situating evidence assessment within the context of consideration of clinical relevance. Analysis of participant comments within the context of the negative findings identified several promising future research directions including: novel computer-based support for evidence assessment; formal evaluation of a more comprehensive evidence assessment approach that requires consideration of specific, explicitly stated, clinical consequences; and more formal investigation of DDI case report assessment instruments.

A Conceptual Framework to Study the Implementation of Clinical Decision Support Systems (BEAR): Literature Review and Concept Mapping.

BACKGROUND: The implementation of clinical decision support systems (CDSSs) as an intervention to foster clinical practice change is affected by many factors. Key factors include those associated with behavioral change and those associated with technology acceptance. However, the literature regarding these subjects is fragmented and originates from two traditionally separate disciplines: implementation science and technology acceptance. OBJECTIVE: Our objective is to propose an integrated framework that bridges the gap between the behavioral change and technology acceptance aspects of the implementation of CDSSs. METHODS: We employed an iterative process to map constructs from four contributing frameworks-the Theoretical Domains Framework (TDF); the Consolidated Framework for Implementation Research (CFIR); the Human, Organization, and Technology-fit framework (HOT-fit); and the Unified Theory of Acceptance and Use of Technology (UTAUT)-and the findings of 10 literature reviews, identified through a systematic review of reviews approach. RESULTS: The resulting framework comprises 22 domains: agreement with the decision algorithm; attitudes; behavioral regulation; beliefs about capabilities; beliefs about consequences; contingencies; demographic characteristics; effort expectancy; emotions; environmental context and resources; goals; intentions; intervention characteristics; knowledge; memory, attention, and decision processes; patient-health professional relationship; patient's preferences; performance expectancy; role and identity; skills, ability, and competence; social influences; and system quality. We demonstrate the use of the framework providing examples from two research projects. CONCLUSIONS: We proposed BEAR (BEhavior and Acceptance fRamework), an integrated framework that bridges the gap between behavioral change and technology acceptance, thereby widening the view established by current models.

Identifying Common Methods Used by Drug Interaction Experts for Finding Evidence About Potential Drug-Drug Interactions: Web-Based Survey.

BACKGROUND: Preventing drug interactions is an important goal to maximize patient benefit from medications. Summarizing potential drug-drug interactions (PDDIs) for clinical decision support is challenging, and there is no single repository for PDDI evidence. Additionally, inconsistencies across compendia and other sources have been well documented. Standard search strategies for complete and current evidence about PDDIs have not heretofore been developed or validated. OBJECTIVE: This study aimed to identify common methods for conducting PDDI literature searches used by experts who routinely evaluate such evidence. METHODS: We invited a convenience sample of 70 drug information experts, including compendia editors, knowledge-base vendors, and clinicians, via emails to complete a survey on identifying PDDI evidence. We created a Web-based survey that included questions regarding the (1) development and conduct of searches; (2) resources used, for example, databases, compendia, search engines, etc; (3) types of keywords used to search for the specific PDDI information; (4) study types included and excluded in searches; and (5) search terms used. Search strategy questions focused on 6 topics of the PDDI information-(1) that a PDDI exists; (2) seriousness; (3) clinical consequences; (4) management options; (5) mechanism; and (6) health outcomes. RESULTS: Twenty participants (response rate, 20/70, 29%) completed the survey. The majority (17/20, 85%) were drug information specialists, drug interaction researchers, compendia editors, or clinical pharmacists, with 60% (12/20) having >10 years' experience. Over half (11/20, 55%) worked for clinical solutions vendors or knowledge-base vendors. Most participants developed (18/20, 90%) and conducted (19/20, 95%) search strategies without librarian assistance. PubMed (20/20, 100%) and Google Scholar (11/20, 55%) were most commonly searched for papers, followed by Google Web Search (7/20, 35%) and EMBASE (3/20, 15%). No respondents reported using Scopus. A variety of subscription and open-access databases were used, most commonly Lexicomp (9/20, 45%), Micromedex (8/20, 40%), Drugs@FDA (17/20, 85%), and DailyMed (13/20, 65%). Facts and Comparisons was the most commonly used compendia (8/20, 40%). Across the 6 attributes of interest, generic drug name was the most common keyword used. Respondents reported using more types of keywords when searching to identify the existence of PDDIs and determine their mechanism than when searching for the other 4 attributes (seriousness, consequences, management, and health outcomes). Regarding the types of evidence useful for evaluating a PDDI, clinical trials, case reports, and systematic reviews were considered relevant, while animal and in vitro data studies were not. CONCLUSIONS: This study suggests that drug interaction experts use various keyword strategies and various database and Web resources depending on the PDDI evidence they are seeking. Greater automation and standardization across search strategies could improve one's ability to identify PDDI evidence. Hence, future research focused on enhancing the existing search tools and designing recommended standards is needed.

Information needs for making clinical recommendations about potential drug-drug interactions: a synthesis of literature review and interviews.

BACKGROUND: Drug information compendia and drug-drug interaction information databases are critical resources for clinicians and pharmacists working to avoid adverse events due to exposure to potential drug-drug interactions (PDDIs). Our goal is to develop information models, annotated data, and search tools that will facilitate the interpretation of PDDI information. To better understand the information needs and work practices of specialists who search and synthesize PDDI evidence for drug information resources, we conducted an inquiry that combined a thematic analysis of published literature with unstructured interviews. METHODS: Starting from an initial set of relevant articles, we developed search terms and conducted a literature search. Two reviewers conducted a thematic analysis of included articles. Unstructured interviews with drug information experts were conducted and similarly coded. Information needs, work processes, and indicators of potential strengths and weaknesses of information systems were identified. RESULTS: Review of 92 papers and 10 interviews identified 56 categories of information needs related to the interpretation of PDDI information including drug and interaction information; study design; evidence including clinical details, quality and content of reports, and consequences; and potential recommendations. We also identified strengths/weaknesses of PDDI information systems. CONCLUSIONS: We identified the kinds of information that might be most effective for summarizing PDDIs. The drug information experts we interviewed had differing goals, suggesting a need for detailed information models and flexible presentations. Several information needs not discussed in previous work were identified, including temporal overlaps in drug administration, biological plausibility of interactions, and assessment of the quality and content of reports. Richly structured depictions of PDDI information may help drug information experts more effectively interpret data and develop recommendations. Effective information models and system designs will be needed to maximize the utility of this information.

Use of Telemedicine to Enhance Pharmacist Services in the Nursing Facility.

OBJECTIVE: To conduct a systematic literature review to determine what telemedicine services are provided by pharmacists and the impact of these services in the nursing facility setting. DATA SOURCES: MEDLINE®, Scopus®, and Embase® databases. STUDY SELECTION: The terms "telemedicine" or "telehealth" were combined by "and" with the terms "pharmacist" or "pharmacy" to identify pharmacists' use of telemedicine. Also, "telepharmacy" was added as a search term. The initial search yielded 322 results. These abstracts were reviewed by two individuals independently, for selection of articles that discussed telemedicine and involvement of a pharmacist, either as the primary user of the service or as part of an interprofessional health care team. Those abstracts discussing the pharmacist service for purpose of dispensing or product preparation were excluded. DATA EXTRACTION: A description of pharmacists' services provided and the impact on resident care. DATA SYNTHESIS: Only three manuscripts met inclusion criteria. One was a narrative proposition of the benefits of using telemedicine by senior care pharmacists. Two published original research studies indirectly assessed the pharmacists' use of telemedicine in the nursing facility through an anticoagulation program and an osteoporosis management service. Both services demonstrated improvement in patient care. CONCLUSION: There is a general paucity of practice-related research to demonstrate potential benefits of pharmacists' services incorporating telemedicine. Telemedicine may be a resource-efficient approach to enhance pharmacist services in the nursing facility and improve resident care.

Physician Perceptions of Consultant Pharmacist Services Associated with an Intervention for Adverse Drug Events in the Nursing Facility.

OBJECTIVE: To assess the importance and performance of consultant pharmacist services delivered before and after an intervention to detect and manage adverse drug events among nursing facility residents. DESIGN: Before and after intervention survey of physicians participating in a randomized, controlled trial. SETTING: Four nonprofit, academically affiliated nursing facilities. PARTICIPANTS: Attending physicians providing nursing facility care who were randomized to intervention or control groups. INTERVENTIONS: Within the intervention arm, consultant pharmacists provided academic detailing in which trained health care professionals visit practicing physicians in their offices and present the most up-to-date clinical information. Physicians responded to alerts from a medication monitoring system, adjudicated system alerts for adverse drug events (ADEs), and provided structured recommendations about ADE management. MAIN OUTCOME MEASURES: We compared physicians' assessments of the importance and performance of consultant pharmacist services before and after the trial intervention in the intervention and control groups. RESULTS: In the intervention group, ratings of importance increased for all 24 survey questions, and 5 of the changes were statistically significant (P < 0.05). In the control group, ratings of importance increased for 16 questions, and none of the changes were statistically significant. In the intervention group, ratings of performance increased for all 24 questions, and 20 of the changes were statistically significant. In the control group, ratings of performance increased for 16 questions, and none of the changes was statistically significant. CONCLUSION: A multifaceted, consultant pharmacist-led intervention comprising academic detailing, computerized decision support, and structured communication framework can improve physicians' assessment of importance and performance of consultant pharmacist services. ABBREVIATIONS: ADE = Adverse drug event, M = Statistically significant mean, RCT = Randomized controlled trial, SBAR = Situation, Background, Discussion, Recommendation, SD = Standard deviation.

The Matter in Extreme Conditions instrument at the Linac Coherent Light Source.

The LCLS beam provides revolutionary capabilities for studying the transient behavior of matter in extreme conditions. The particular strength of the Matter in Extreme Conditions instrument is that it combines the unique LCLS beam with high-power optical laser beams, and a suite of dedicated diagnostics tailored for this field of science. In this paper an overview of the beamline, the capabilities of the instrumentation, and selected highlights of experiments and commissioning results are presented.

Toward a complete dataset of drug-drug interaction information from publicly available sources.

Although potential drug-drug interactions (PDDIs) are a significant source of preventable drug-related harm, there is currently no single complete source of PDDI information. In the current study, all publically available sources of PDDI information that could be identified using a comprehensive and broad search were combined into a single dataset. The combined dataset merged fourteen different sources including 5 clinically-oriented information sources, 4 Natural Language Processing (NLP) Corpora, and 5 Bioinformatics/Pharmacovigilance information sources. As a comprehensive PDDI source, the merged dataset might benefit the pharmacovigilance text mining community by making it possible to compare the representativeness of NLP corpora for PDDI text extraction tasks, and specifying elements that can be useful for future PDDI extraction purposes. An analysis of the overlap between and across the data sources showed that there was little overlap. Even comprehensive PDDI lists such as DrugBank, KEGG, and the NDF-RT had less than 50% overlap with each other. Moreover, all of the comprehensive lists had incomplete coverage of two data sources that focus on PDDIs of interest in most clinical settings. Based on this information, we think that systems that provide access to the comprehensive lists, such as APIs into RxNorm, should be careful to inform users that the lists may be incomplete with respect to PDDIs that drug experts suggest clinicians be aware of. In spite of the low degree of overlap, several dozen cases were identified where PDDI information provided in drug product labeling might be augmented by the merged dataset. Moreover, the combined dataset was also shown to improve the performance of an existing PDDI NLP pipeline and a recently published PDDI pharmacovigilance protocol. Future work will focus on improvement of the methods for mapping between PDDI information sources, identifying methods to improve the use of the merged dataset in PDDI NLP algorithms, integrating high-quality PDDI information from the merged dataset into Wikidata, and making the combined dataset accessible as Semantic Web Linked Data.

Utilizing the Wikidata system to improve the quality of medical content in Wikipedia in diverse languages: a pilot study.

BACKGROUND: Wikipedia is an important source of medical information for both patients and medical professionals. Given its wide reach, improving the quality, completeness, and accessibility of medical information on Wikipedia could have a positive impact on global health. OBJECTIVE: We created a prototypical implementation of an automated system for keeping drug-drug interaction (DDI) information in Wikipedia up to date with current evidence about clinically significant drug interactions. Our work is based on Wikidata, a novel, graph-based database backend of Wikipedia currently in development. METHODS: We set up an automated process for integrating data from the Office of the National Coordinator for Health Information Technology (ONC) high priority DDI list into Wikidata. We set up exemplary implementations demonstrating how the DDI data we introduced into Wikidata could be displayed in Wikipedia articles in diverse languages. Finally, we conducted a pilot analysis to explore if adding the ONC high priority data would substantially enhance the information currently available on Wikipedia. RESULTS: We derived 1150 unique interactions from the ONC high priority list. Integration of the potential DDI data from Wikidata into Wikipedia articles proved to be straightforward and yielded useful results. We found that even though the majority of current English Wikipedia articles about pharmaceuticals contained sections detailing contraindications, only a small fraction of articles explicitly mentioned interaction partners from the ONC high priority list. For 91.30% (1050/1150) of the interaction pairs we tested, none of the 2 articles corresponding to the interacting substances explicitly mentioned the interaction partner. For 7.21% (83/1150) of the pairs, only 1 of the 2 associated Wikipedia articles mentioned the interaction partner; for only 1.48% (17/1150) of the pairs, both articles contained explicit mentions of the interaction partner. CONCLUSIONS: Our prototype demonstrated that automated updating of medical content in Wikipedia through Wikidata is a viable option, albeit further refinements and community-wide consensus building are required before integration into public Wikipedia is possible. A long-term endeavor to improve the medical information in Wikipedia through structured data representation and automated workflows might lead to a significant improvement of the quality of medical information in one of the world's most popular Web resources.

Pharmacogenomic knowledge representation, reasoning and genome-based clinical decision support based on OWL 2 DL ontologies.

BACKGROUND: Every year, hundreds of thousands of patients experience treatment failure or adverse drug reactions (ADRs), many of which could be prevented by pharmacogenomic testing. However, the primary knowledge needed for clinical pharmacogenomics is currently dispersed over disparate data structures and captured in unstructured or semi-structured formalizations. This is a source of potential ambiguity and complexity, making it difficult to create reliable information technology systems for enabling clinical pharmacogenomics. METHODS: We developed Web Ontology Language (OWL) ontologies and automated reasoning methodologies to meet the following goals: 1) provide a simple and concise formalism for representing pharmacogenomic knowledge, 2) finde errors and insufficient definitions in pharmacogenomic knowledge bases, 3) automatically assign alleles and phenotypes to patients, 4) match patients to clinically appropriate pharmacogenomic guidelines and clinical decision support messages and 5) facilitate the detection of inconsistencies and overlaps between pharmacogenomic treatment guidelines from different sources. We evaluated different reasoning systems and test our approach with a large collection of publicly available genetic profiles. RESULTS: Our methodology proved to be a novel and useful choice for representing, analyzing and using pharmacogenomic data. The Genomic Clinical Decision Support (Genomic CDS) ontology represents 336 SNPs with 707 variants; 665 haplotypes related to 43 genes; 22 rules related to drug-response phenotypes; and 308 clinical decision support rules. OWL reasoning identified CDS rules with overlapping target populations but differing treatment recommendations. Only a modest number of clinical decision support rules were triggered for a collection of 943 public genetic profiles. We found significant performance differences across available OWL reasoners. CONCLUSIONS: The ontology-based framework we developed can be used to represent, organize and reason over the growing wealth of pharmacogenomic knowledge, as well as to identify errors, inconsistencies and insufficient definitions in source data sets or individual patient data. Our study highlights both advantages and potential practical issues with such an ontology-based approach.

Long-Term Outcomes Associated With ß-Lactam Allergies.

Importance: ß-lactam (BL) allergies are the most common drug allergy worldwide, but most are reported in error. BL allergies are also well-established risk factors for adverse drug events and antibiotic-resistant infections during inpatient health care encounters, but the understanding of the long-term outcomes of patients with BL allergies remains limited. Objective: To evaluate the long-term clinical outcomes of patients with BL allergies. Design, Setting, and Participants: This longitudinal retrospective cohort study was conducted at a single regional health care system in western Pennsylvania. Electronic health records were analyzed for patients who had an index encounter with a diagnosis of sepsis, pneumonia, or urinary tract infection between 2007 and 2008. Patients were followed-up until death or the end of 2018. Data analysis was performed from January 2022 to January 2024. Exposure: The presence of any BL class antibiotic in the allergy section of a patient's electronic health record, evaluated at the earliest occurring observed health care encounter. Main Outcomes and Measures: The primary outcome was all-cause mortality, derived from the Social Security Death Index. Secondary outcomes were defined using laboratory and microbiology results and included infection with methicillin-resistant Staphylococcus aureus (MRSA), Clostridium difficile, or vancomycin-resistant Enterococcus (VRE) and severity and occurrence of acute kidney injury (AKI). Generalized estimating equations with a patient-level panel variable and time exposure offset were used to evaluate the odds of occurrence of each outcome between allergy groups. Results: A total of 20 092 patients (mean [SD] age, 62.9 [19.7] years; 12 231 female [60.9%]), of whom 4211 (21.0%) had BL documented allergy and 15 881 (79.0%) did not, met the inclusion criteria. A total of 3513 patients (17.5%) were Black, 15 358 (76.4%) were White, and 1221 (6.0%) were another race. Using generalized estimating equations, documented BL allergies were not significantly associated with the odds of mortality (odds ratio [OR], 1.02; 95% CI, 0.96-1.09). BL allergies were associated with increased odds of MRSA infection (OR, 1.44; 95% CI, 1.36-1.53), VRE infection (OR, 1.18; 95% CI, 1.05-1.32), and the pooled rate of the 3 evaluated antibiotic-resistant infections (OR, 1.33; 95% CI, 1.30-1.36) but were not associated with C difficile infection (OR, 1.04; 95% CI, 0.94-1.16), stage 2 and 3 AKI (OR, 1.02; 95% CI, 0.96-1.10), or stage 3 AKI (OR, 1.06; 95% CI, 0.98-1.14). Conclusions and Relevance: Documented BL allergies were not associated with the long-term odds of mortality but were associated with antibiotic-resistant infections. Health systems should emphasize accurate allergy documentation and reduce unnecessary BL avoidance.

Broadening the capture of natural products mentioned in FAERS using fuzzy string-matching and a Siamese neural network.

Increased sales of natural products (NPs) in the US and growing safety concerns highlight the need for NP pharmacovigilance. A challenge for NP pharmacovigilance is ambiguity when referring to NPs in spontaneous reporting systems. We used a combination of fuzzy string-matching and a neural network to reduce this ambiguity. Our aim is to increase the capture of reports involving NPs in the US Food and Drug Administration Adverse Event Reporting System (FAERS). For this, we utilized Gestalt pattern-matching (GPM) and Siamese neural network (SM) to identify potential mentions of NPs of interest in 389,386 FAERS reports with unmapped drug names. A team of health professionals refined the candidates identified in the previous step through manual review and annotation. After candidate adjudication, GPM identified 595 unique NP names and SM 504. There was little overlap between candidates identified by each (Non-overlapping: GPM 347, SM 248). We identified a total of 686 novel NP names from FAERS reports. Including these names in the FAERS collection yielded 3,486 additional reports mentioning NPs.