A 2013 workshop: vaccine and drug ontology studies (VDOS 2013)

The 2013 “Vaccine and Drug Ontology Studies” (VDOS 2013) international workshop series focuses on vaccine- and drug-related ontology modeling and applications. Drugs and vaccines have contributed to dramatic improvements in public health worldwide. Over the last decade, tremendous efforts have been made in the biomedical ontology community to ontologically represent various areas associated with vaccines and drugs – extending existing clinical terminology systems such as SNOMED, RxNorm, NDF-RT, and MedDRA, as well as developing new models such as Vaccine Ontology. The VDOS workshop series provides a platform for discussing innovative solutions as well as the challenges in the development and applications of biomedical ontologies for representing and analyzing drugs and vaccines, their administration, host immune responses, adverse events, and other related topics. The six full-length papers included in this thematic issue focuses on three main areas: (i) ontology development and representation, (ii) ontology mapping, maintaining and auditing, and (iii) ontology applications

RECOMED: A Comprehensive Pharmaceutical Recommendation System

A comprehensive pharmaceutical recommendation system was designed based on the patients and drugs features extracted from Drugs.com and Druglib.com. First, data from these databases were combined, and a dataset of patients and drug information was built. Secondly, the patients and drugs were clustered, and then the recommendation was performed using different ratings provided by patients, and importantly by the knowledge obtained from patients and drug specifications, and considering drug interactions. To the best of our knowledge, we are the first group to consider patients conditions and history in the proposed approach for selecting a specific medicine appropriate for that particular user. Our approach applies artificial intelligence (AI) models for the implementation. Sentiment analysis using natural language processing approaches is employed in pre-processing along with neural network-based methods and recommender system algorithms for modeling the system. In our work, patients conditions and drugs features are used for making two models based on matrix factorization. Then we used drug interaction to filter drugs with severe or mild interactions with other drugs. We developed a deep learning model for recommending drugs by using data from 2304 patients as a training set, and then we used data from 660 patients as our validation set. After that, we used knowledge from critical information about drugs and combined the outcome of the model into a knowledge-based system with the rules obtained from constraints on taking medicine.Comment: 39 pages, 14 figures, 13 table

Desenvolvimento e análise de um sistema de recomendação para sugestão de artigos médicos no internamento do Hospital da Luz Lisboa

The internet advances have led to an increase of data and information availability. This overload of information tends to compromise the capacity to manage and filter the available data. In the health domain, the increasing digitalization in healthcare led to a substantial rise of the recorded data. Various recommendation systems (RS) have been developed to help healthcare professionals integrate all information and make efficient and effective decisions. Here, a preliminary RS based on collaborative filtering is proposed to reduce the time that healthcare professionals spend in registering medical items consumed during patients’ hospitalization. For that purpose, the RS was built to perform suggestions of the medical items and respective quantities needed in the first day of hospitalization of a patient. Data regarding the diagnostics, surgical procedures and medical item records associated to surgeries of inpatients during a period of one year in Hospital da Luz Lisboa was filtered, restructured, and analysed (N = 5088 surgeries) for the construction of the RS. A 75-25% split of the data was considered with a 4-fold cross-validation procedure applied on the train set to tune the hyperparameters settings for the algorithm. The RS was then tested and evaluated regarding its overall performance in terms of accuracy, classification performance, and coverage. The same measures were applied to assess the quality of the recommendations for each medical specialty of the hospital. Furthermore, the trust of healthcare professionals in the RS was also assessed. A moderate overall performance was achieved (precision = 0.608, recall = 0.729, F1-Measure = 0.663, RMSE = 6.901) and the quality of the algorithm’s recommendations varied between medical specialties. Additionally, the algorithm presented higher values of precision, recall and F1-Measure in the predictions of the most frequently registered medical items in the test set, which corresponded to approximately 85% of the consumptions in the first day of hospitalization. Regarding the coverage of the RS, approximately 80% of the medical items used in the test set were never recommended by the algorithm, corresponding to only 5.57% of the consumptions. Lastly, although in the point of view of hospital’s nurses there is some trust in the RS results, several suggestions were given for further improvements of the algorithm. Despite the limitations of the RS, the observed results represent a starting point for the development of a tool that can support healthcare professionals of Hospital da Luz Lisboa in registering medical items needed during inpatients’ hospitalization.Os avanços da internet têm aumentado a quantidade de informação disponível, pelo que o seu excesso tende a dificultar a capacidade de gestão e filtragem da mesma. Este fenómeno pode ser observado no domínio da saúde onde a digitalização dos serviços médicos levou a um aumento substancial dos dados registados nos hospitais. Com o intuito de ajudar os profissionais de saúde a integrar toda a informação e, assim, realizarem decisões eficientes e efetivas, vários sistemas de recomendação (SR) foram desenvolvidos. Neste projeto, propõe-se um SR preliminar baseado em filtragem colaborativa para reduzir o tempo despendido pelos profissionais de saúde do Hospital da Luz Lisboa no registo de artigos médicos consumidos durante o período de internamento de doentes. Para isso, o SR foi desenvolvido de modo a formular recomendações relativamente aos artigos médicos e respetivas quantidades necessárias para o primeiro dia de internamento de um doente. A construção do SR teve por base os diagnósticos, procedimentos cirúrgicos e registos de consumos de artigos médicos associados a propostas cirúrgicas de doentes que foram internados no período de um ano no Hospital da Luz Lisboa. O conjunto de dados foi filtrado, reestruturado e analisado (N = 5088 propostas cirúrgicas), para posteriormente ser dividido em conjuntos de treino e de teste (75-25%). Foi aplicada uma 4-fold cross-validation sobre o conjunto de treino para a afinação dos hiperparâmetros do algoritmo, sendo o SR foi testado e avaliado relativamente às suas recomendações a nível global e em cada especialidade médica do hospital em termos de accuracy, classification performance e coverage. Foi igualmente avaliado o grau de confiança no SR por parte dos profissionais de saúde do hospital. O SR apresentou uma performance global razoável (precisão = 0.608, sensibilidade = 0.729, F1 = 0.663, RMSE = 6.901) e demonstrou diferentes níveis de qualidade de recomendações dependendo da especialidade médica. Os melhores valores de precisão, sensibilidade e F1 foram observados nas previsões dos artigos médicos mais frequentemente registados, que correspondem a cerca de 85% dos consumos feitos no primeiro dia de internamento dos doentes do conjunto de teste. O algoritmo nunca sugeriu aproximadamente 80% dos artigos médicos utilizados no conjunto de teste, no entanto, estes apenas correspondiam 5.57% dos consumos totais. Por fim, e embora do ponto de vista dos enfermeiros do hospital haja alguma confiança nos resultados do SR, foram dadas sugestões para futuros ajustes do algoritmo. Não obstante as limitações do SR, os resultados obtidos representam um ponto de partida para o desenvolvimento de uma ferramenta de apoio aos profissionais de saúde do Hospital da Luz nos registos dos artigos médicos necessários durante o internamento de doentes.Mestrado em Estatística Médic

Computational Advances in Drug Safety: Systematic and Mapping Review of Knowledge Engineering Based Approaches

Drug Safety (DS) is a domain with significant public health and social impact. Knowledge Engineering (KE) is the Computer Science discipline elaborating on methods and tools for developing “knowledge-intensive” systems, depending on a conceptual “knowledge” schema and some kind of “reasoning” process. The present systematic and mapping review aims to investigate KE-based approaches employed for DS and highlight the introduced added value as well as trends and possible gaps in the domain. Journal articles published between 2006 and 2017 were retrieved from PubMed/MEDLINE and Web of Science® (873 in total) and filtered based on a comprehensive set of inclusion/exclusion criteria. The 80 finally selected articles were reviewed on full-text, while the mapping process relied on a set of concrete criteria (concerning specific KE and DS core activities, special DS topics, employed data sources, reference ontologies/terminologies, and computational methods, etc.). The analysis results are publicly available as online interactive analytics graphs. The review clearly depicted increased use of KE approaches for DS. The collected data illustrate the use of KE for various DS aspects, such as Adverse Drug Event (ADE) information collection, detection, and assessment. Moreover, the quantified analysis of using KE for the respective DS core activities highlighted room for intensifying research on KE for ADE monitoring, prevention and reporting. Finally, the assessed use of the various data sources for DS special topics demonstrated extensive use of dominant data sources for DS surveillance, i.e., Spontaneous Reporting Systems, but also increasing interest in the use of emerging data sources, e.g., observational healthcare databases, biochemical/genetic databases, and social media. Various exemplar applications were identified with promising results, e.g., improvement in Adverse Drug Reaction (ADR) prediction, detection of drug interactions, and novel ADE profiles related with specific mechanisms of action, etc. Nevertheless, since the reviewed studies mostly concerned proof-of-concept implementations, more intense research is required to increase the maturity level that is necessary for KE approaches to reach routine DS practice. In conclusion, we argue that efficiently addressing DS data analytics and management challenges requires the introduction of high-throughput KE-based methods for effective knowledge discovery and management, resulting ultimately, in the establishment of a continuous learning DS system