BackgroundAs one of the serious public health issues, vaccination refusal has been attracting more and more attention, especially for newly approved human papillomavirus (HPV) vaccines. Understanding public opinion towards HPV vaccines, especially concerns on social media, is of significant importance for HPV vaccination promotion.MethodsIn this study, we leveraged a hierarchical machine learning based sentiment analysis system to extract public opinions towards HPV vaccines from Twitter. English tweets containing HPV vaccines-related keywords were collected from November 2, 2015 to March 28, 2016. Manual annotation was done to evaluate the performance of the system on the unannotated tweets corpus. Followed time series analysis was applied to this corpus to track the trends of machine-deduced sentiments and their associations with different days of the week.ResultsThe evaluation of the unannotated tweets corpus showed that the micro-averaging F scores have reached 0.786. The learning system deduced the sentiment labels for 184,214 tweets in the collected unannotated tweets corpus. Time series analysis identified a coincidence between mainstream outcome and Twitter contents. A weak trend was found for “Negative” tweets that decreased firstly and began to increase later; an opposite trend was identified for “Positive” tweets. Tweets that contain the worries on efficacy for HPV vaccines showed a relative significant decreasing trend. Strong associations were found between some sentiments (“Positive”, “Negative”, “Negative-Safety” and “Negative-Others”) with different days of the week.ConclusionsOur efforts on sentiment analysis for newly approved HPV vaccines provide us an automatic and instant way to extract public opinion and understand the concerns on Twitter. Our approaches can provide a feedback to public health professionals to monitor online public response, examine the effectiveness of their HPV vaccination promotion strategies and adjust their promotion plans.Electronic supplementary materialThe online version of this article (doi:10.1186/s12911-017-0469-6) contains supplementary material, which is available to authorized users.

BackgroundTimely understanding of public perceptions allows public health agencies to provide up-to-date responses to health crises such as infectious diseases outbreaks. Social media such as Twitter provide an unprecedented way for the prompt assessment of the large-scale public response.ObjectiveThe aims of this study were to develop a scheme for a comprehensive public perception analysis of a measles outbreak based on Twitter data and demonstrate the superiority of the convolutional neural network (CNN) models (compared with conventional machine learning methods) on measles outbreak-related tweets classification tasks with a relatively small and highly unbalanced gold standard training set.MethodsWe first designed a comprehensive scheme for the analysis of public perception of measles based on tweets, including 3 dimensions: discussion themes, emotions expressed, and attitude toward vaccination. All 1,154,156 tweets containing the word “measles” posted between December 1, 2014, and April 30, 2015, were purchased and downloaded from DiscoverText.com. Two expert annotators curated a gold standard of 1151 tweets (approximately 0.1% of all tweets) based on the 3-dimensional scheme. Next, a tweet classification system based on the CNN framework was developed. We compared the performance of the CNN models to those of 4 conventional machine learning models and another neural network model. We also compared the impact of different word embeddings configurations for the CNN models: (1) Stanford GloVe embedding trained on billions of tweets in the general domain, (2) measles-specific embedding trained on our 1 million measles related tweets, and (3) a combination of the 2 embeddings.ResultsCohen kappa intercoder reliability values for the annotation were: 0.78, 0.72, and 0.80 on the 3 dimensions, respectively. Class distributions within the gold standard were highly unbalanced for all dimensions. The CNN models performed better on all classification tasks than k-nearest neighbors, naïve Bayes, support vector machines, or random forest. Detailed comparison between support vector machines and the CNN models showed that the major contributor to the overall superiority of the CNN models is the improvement on recall, especially for classes with low occurrence. The CNN model with the 2 embedding combination led to better performance on discussion themes and emotions expressed (microaveraging F1 scores of 0.7811 and 0.8592, respectively), while the CNN model with Stanford embedding achieved best performance on attitude toward vaccination (microaveraging F1 score of 0.8642).ConclusionsThe proposed scheme can successfully classify the public’s opinions and emotions in multiple dimensions, which would facilitate the timely understanding of public perceptions during the outbreak of an infectious disease. Compared with conventional machine learning methods, our CNN models showed superiority on measles-related tweet classification tasks with a relatively small and highly unbalanced gold standard. With the success of these tasks, our...

Abstract Objective The goal of this study is to develop a robust Time Event Ontology (TEO), which can formally represent and reason both structured and unstructured temporal information. Materials and Methods Using our previous Clinical Narrative Temporal Relation Ontology 1.0 and 2.0 as a starting point, we redesigned concept primitives (clinical events and temporal expressions) and enriched temporal relations. Specifically, 2 sets of temporal relations (Allen’s interval algebra and a novel suite of basic time relations) were used to specify qualitative temporal order relations, and a Temporal Relation Statement was designed to formalize quantitative temporal relations. Moreover, a variety of data properties were defined to represent diversified temporal expressions in clinical narratives. Results TEO has a rich set of classes and properties (object, data, and annotation). When evaluated with real electronic health record data from the Mayo Clinic, it could faithfully represent more than 95% of the temporal expressions. Its reasoning ability was further demonstrated on a sample drug adverse event report annotated with respect to TEO. The results showed that our Java-based TEO reasoner could answer a set of frequently asked time-related queries, demonstrating that TEO has a strong capability of reasoning complex temporal relations. Conclusion TEO can support flexible temporal relation representation and reasoning. Our next step will be to apply TEO to the natural language processing field to facilitate automated temporal information annotation, extraction, and timeline reasoning to better support time-based clinical decision-making.

BackgroundKnowledge engineering for ontological knowledgebases is resource and time intensive. To alleviate these issues, especially for novices, automated tools from the natural language domain can assist in the development process of ontologies. We focus towards the development of ontologies for the public health domain and use patient-centric sources from MedlinePlus related to HPV-causing cancers.MethodsThis paper demonstrates the use of a lightweight open information extraction (OIE) tool to derive accurate knowledge triples that can lead to the seeding of an ontological knowledgebase. We developed a custom application, which interfaced with an information extraction software library, to help facilitate the tasks towards producing knowledge triples from textual sources.ResultsThe results of our efforts generated accurate extractions ranging from 80–89% precision. These triples can later be transformed to OWL/RDF representation for our planned ontological knowledgebase.ConclusionsOIE delivers an effective and accessible method towards the development ontologies.

BackgroundToday, there is an increasing need to centralize and standardize electronic health data within clinical research as the volume of data continues to balloon. Domain-specific common data elements (CDEs) are emerging as a standard approach to clinical research data capturing and reporting. Recent efforts to standardize clinical study CDEs have been of great benefit in facilitating data integration and data sharing. The importance of the temporal dimension of clinical research studies has been well recognized; however, very few studies have focused on the formal representation of temporal constraints and temporal relationships within clinical research data in the biomedical research community. In particular, temporal information can be extremely powerful to enable high-quality cancer research.ObjectiveThe objective of the study was to develop and evaluate an ontological approach to represent the temporal aspects of cancer study CDEs.MethodsWe used CDEs recorded in the National Cancer Institute (NCI) Cancer Data Standards Repository (caDSR) and created a CDE parser to extract time-relevant CDEs from the caDSR. Using the Web Ontology Language (OWL)–based Time Event Ontology (TEO), we manually derived representative patterns to semantically model the temporal components of the CDEs using an observing set of randomly selected time-related CDEs (n=600) to create a set of TEO ontological representation patterns. In evaluating TEO’s ability to represent the temporal components of the CDEs, this set of representation patterns was tested against two test sets of randomly selected time-related CDEs (n=425).ResultsIt was found that 94.2% (801/850) of the CDEs in the test sets could be represented by the TEO representation patterns.ConclusionsIn conclusion, TEO is a good ontological model for representing the temporal components of the CDEs recorded in caDSR. Our representative model can harness the Semantic Web reasoning and inferencing functionalities and present a means for temporal CDEs to be machine-readable, streamlining meaningful searches.