Towards new information resources for public health: From WordNet to MedicalWordNet

In the last two decades, WORDNET has evolved as the most comprehensive computational lexicon of general English. In this article, we discuss its potential for supporting the creation of an entirely new kind of information resource for public health, viz. MEDICAL WORDNET. This resource is not to be conceived merely as a lexical extension of the original WORDNET to medical terminology; indeed, there is already a considerable degree of overlap between WORDNET and the vocabulary of medicine. Instead, we propose a new type of repository, consisting of three large collections of (1) medically relevant word forms, structured along the lines of the existing Princeton WORDNET; (2) medically validated propositions, referred to here as medical facts, which will constitute what we shall call MEDICAL FACTNET; and (3) propositions reflecting laypersons’ medical beliefs, which will constitute what we shall call the MEDICAL BELIEFNET. We introduce a methodology for setting up the MEDICAL WORDNET. We then turn to the discussion of research challenges that have to be met in order to build this new type of information resource

Exploiting the UMLS Metathesaurus for extracting and categorizing concepts representing signs and symptoms to anatomically related organ systems

AbstractObjectiveTo develop a method to exploit the UMLS Metathesaurus for extracting and categorizing concepts found in clinical text representing signs and symptoms to anatomically related organ systems. The overarching goal is to classify patient reported symptoms to organ systems for population health and epidemiological analyses.Materials and methodsUsing the concepts’ semantic types and the inter-concept relationships as guidance, a selective portion of the concepts within the UMLS Metathesaurus was traversed starting from the concepts representing the highest level organ systems. The traversed concepts were chosen, filtered, and reviewed to obtain the concepts representing clinical signs and symptoms by blocking deviations, pruning superfluous concepts, and manual review. The mapping process was applied to signs and symptoms annotated in a corpus of 750 clinical notes.ResultsThe mapping process yielded a total of 91,000 UMLS concepts (with approximately 300,000 descriptions) possibly representing physical and mental signs and symptoms that were extracted and categorized to the anatomically related organ systems. Of 1864 distinct descriptions of signs and symptoms found in the 750 document corpus, 1635 of these (88%) were successfully mapped to the set of concepts extracted from the UMLS. Of 668 unique concepts mapped, 603 (90%) were correctly categorized to their organ systems.ConclusionWe present a process that facilitates mapping of signs and symptoms to their organ systems. By providing a smaller set of UMLS concepts to use for comparing and matching patient records, this method has the potential to increase efficiency of information extraction pipelines

Health Effects Associated With Electronic Cigarette Use: Automated Mining of Online Forums.

BACKGROUND:Our previous infodemiological study was performed by manually mining health-effect data associated with electronic cigarettes (ECs) from online forums. Manual mining is time consuming and limits the number of posts that can be retrieved. OBJECTIVE:Our goal in this study was to automatically extract and analyze a large number (>41,000) of online forum posts related to the health effects associated with EC use between 2008 and 2015. METHODS:Data were annotated with medical concepts from the Unified Medical Language System using a modified version of the MetaMap tool. Of over 1.4 million posts, 41,216 were used to analyze symptoms (undiagnosed conditions) and disorders (physician-diagnosed terminology) associated with EC use. For each post, sentiment (positive, negative, and neutral) was also assigned. RESULTS:Symptom and disorder data were categorized into 12 organ systems or anatomical regions. Most posts on symptoms and disorders contained negative sentiment, and affected systems were similar across all years. Health effects were reported most often in the neurological, mouth and throat, and respiratory systems. The most frequently reported symptoms and disorders were headache (n=939), coughing (n=852), malaise (n=468), asthma (n=916), dehydration (n=803), and pharyngitis (n=565). In addition, users often reported linked symptoms (eg, coughing and headache). CONCLUSIONS:Online forums are a valuable repository of data that can be used to identify positive and negative health effects associated with EC use. By automating extraction of online information, we obtained more data than in our prior study, identified new symptoms and disorders associated with EC use, determined which systems are most frequently adversely affected, identified specific symptoms and disorders most commonly reported, and tracked health effects over 7 years

Medical Informatics

Information technology has been revolutionizing the everyday life of the common man, while medical science has been making rapid strides in understanding disease mechanisms, developing diagnostic techniques and effecting successful treatment regimen, even for those cases which would have been classified as a poor prognosis a decade earlier. The confluence of information technology and biomedicine has brought into its ambit additional dimensions of computerized databases for patient conditions, revolutionizing the way health care and patient information is recorded, processed, interpreted and utilized for improving the quality of life. This book consists of seven chapters dealing with the three primary issues of medical information acquisition from a patient's and health care professional's perspective, translational approaches from a researcher's point of view, and finally the application potential as required by the clinicians/physician. The book covers modern issues in Information Technology, Bioinformatics Methods and Clinical Applications. The chapters describe the basic process of acquisition of information in a health system, recent technological developments in biomedicine and the realistic evaluation of medical informatics

Utilizing Consumer Health Posts for Pharmacovigilance: Identifying Underlying Factors Associated with Patients’ Attitudes Towards Antidepressants

Non-adherence to antidepressants is a major obstacle to antidepressants therapeutic benefits, resulting in increased risk of relapse, emergency visits, and significant burden on individuals and the healthcare system. Several studies showed that non-adherence is weakly associated with personal and clinical variables, but strongly associated with patients’ beliefs and attitudes towards medications. The traditional methods for identifying the key dimensions of patients’ attitudes towards antidepressants are associated with some methodological limitations, such as concern about confidentiality of personal information. In this study, attempts have been made to address the limitations by utilizing patients’ self report experiences in online healthcare forums to identify underlying factors affecting patients attitudes towards antidepressants. The data source of the study was a healthcare forum called “askapatients.com”. 892 patients’ reviews were randomly collected from the forum for the four most commonly prescribed antidepressants including Sertraline (Zoloft) and Escitalopram (Lexapro) from SSRI class, and Venlafaxine (Effexor) and duloxetine (Cymbalta) from SNRI class. Methodology of this study is composed of two main phases: I) generating structured data from unstructured patients’ drug reviews and testing hypotheses concerning attitude, II) identification and normalization of Adverse Drug Reactions (ADRs), Withdrawal Symptoms (WDs) and Drug Indications (DIs) from the posts, and mapping them to both The UMLS and SNOMED CT concepts. Phase II also includes testing the association between ADRs and attitude. The result of the first phase of this study showed that “experience of adverse drug reactions”, “perceived distress received from ADRs”, “lack of knowledge about medication’s mechanism”, “withdrawal experience”, “duration of usage”, and “drug effectiveness” are strongly associated with patients attitudes. However, demographic variables including “age” and “gender” are not associated with attitude. Analysis of the data in second phase of the study showed that from 6,534 identified entities, 73% are ADRs, 12% are WDs, and 15 % are drug indications. In addition, psychological and cognitive expressions have higher variability than physiological expressions. All three types of entities were mapped to 811 UMLS and SNOMED CT concepts. Testing the association between ADRs and attitude showed that from twenty-one physiological ADRs specified in the ASEC questionnaire, “dry mouth”, “increased appetite”, “disorientation”, “yawning”, “weight gain”, and “problem with sexual dysfunction” are associated with attitude. A set of psychological and cognitive ADRs, such as “emotional indifference” and “memory problem were also tested that showed significance association between these types of ADRs and attitude. The findings of this study have important implications for designing clinical interventions aiming to improve patients\u27 adherence towards antidepressants. In addition, the dataset generated in this study has significant implications for improving performance of text-mining algorithms aiming to identify health related information from consumer health posts. Moreover, the dataset can be used for generating and testing hypotheses related to ADRs associated with psychiatric mediations, and identifying factors associated with discontinuation of antidepressants. The dataset and guidelines of this study are available at https://sites.google.com/view/pharmacovigilanceinpsychiatry/hom

Supporting Clinical Decision Making in Cancer Care Delivery

Background: Cancer treatment and management require complicated clinical decision making to provide the highest quality of care for an individual patient. This is facilitated in part with ever-increasing availability of medications and treatments but hindered due to barriers such as access to care, cost of medications, clinician knowledge, and patient preferences or clinical factors. Although guidelines for cancer treatment and many symptoms have been developed to inform clinical practice, implementation of these guidelines into practice is often delayed or does not occur. Informatics-based approaches, such as clinical decision support, may be an effective tool to improve guideline implementation by delivering patient-specific and evidence-based knowledge to the clinician at the point of care to allow shared decision making with a patient and their family. The large amount of data in the electronic health record can be utilized to develop, evaluate, and implement automated approaches; however, the quality of the data must first be examined and evaluated. Methods: This dissertation addresses gaps the literature about clinical decision making for cancer care delivery. Specifically, following an introduction and review of the literature for relevant topics to this dissertation, the researcher presents three studies. In Study One, the researcher explores the use of clinical decision support in cancer therapeutic decision making by conducting a systematic review of the literature. In Study Two, the researcher conducts a quantitative study to describe the rate of guideline concordant care provided for prevention of acute chemotherapy-induced nausea and vomiting (CINV) and to identify predictors of receiving guideline concordant care. In Study Three, the researcher conducts a mixed-methods study to evaluate the completeness, concordance, and heterogeneity of clinician documentation of CINV. The final chapter of this dissertation is comprised of key findings of each study, the strengths and limitations, clinical and research implications, and future research. Results: In Study One, the systematic review, the researcher identified ten studies that prospectively studied clinical decision support systems or tools in a cancer setting to guide therapeutic decision making. There was variability in these studies, including study design, outcomes measured, and results. There was a trend toward benefit, both in process and patient-specific outcomes. Importantly, few studies were integrated into the electronic health record. In Study Two, of 180 patients age 26 years or less, 36% received guideline concordant care as defined by pediatric or adult guidelines, as appropriate. Factors associated with receiving guideline concordant care included receiving a cisplatin-based regimen, being treated in adult oncology compared to pediatric oncology, and solid tumor diagnosis. In Study Three, of the 127 patient records reviewed for the documentation of chemotherapy-induced nausea and vomiting, 75% had prescriber assessment documented and 58% had nursing assessment documented. Of those who had documented assessments by both prescriber and nurse, 72% were in agreement of the presence/absence of chemotherapy-induced nausea and vomiting. After mapping the concept through the United Medical Language System and developing a post-coordinated expression to identify chemotherapy-induced nausea and vomiting in the text, 85% of prescriber documentation and 100% of nurse documentation could be correctly categorized as present/absent. Further descriptors of the symptoms, such as severity or temporality, however, were infrequently reported. Conclusion: In summary, this dissertation provides new knowledge about decision making in cancer care delivery. Specifically, in Study One the researcher describes that clinical decision support, one potential implementation strategy to improve guideline concordant care, is understudied or under published but a promising potential intervention. In Study Two, I identified factors that were associated with receipt of guideline concordant care for CINV, and these should be further explored to develop interventions. Finally, in Study Three, I report on the limitations of the data quality of CINV documentation in the electronic health record. Future work should focus on validating these results on a multi-institutional level

Exploiting semantics for improving clinical information retrieval

Clinical information retrieval (IR) presents several challenges including terminology mismatch and granularity mismatch. One of the main objectives in clinical IR is to fill the semantic gap among the queries and documents and going beyond keywords matching. To address these issues, in this study we attempt to use semantic information to improve the performance of clinical IR systems by representing queries in an expressive and meaningful context. In this study we propose query context modeling to improve the effectiveness of clinical IR systems. To model query contexts we propose two novel approaches to modeling medical query contexts. The first approach concerns modeling medical query contexts based on mining semantic-based AR for improving clinical text retrieval. The query context is derived from the rules that cover the query and then weighted according to their semantic relatedness to the query concepts. In our second approach we model a representative query context by developing query domain ontology. To develop query domain ontology we extract all the concepts that have semantic relationship with the query concept(s) in UMLS ontologies. Query context represents concepts extracted from query domain ontology and weighted according to their semantic relatedness to the query concept(s). The query context is then exploited in the patient records query expansion and re-ranking for improving clinical retrieval performance. We evaluate this approach on the TREC Medical Records dataset. Results show that our proposed approach significantly improves the retrieval performance compare to classic keyword-based IR model