DEVO: an ontology to assist with dermoscopic feature standardization.

BACKGROUND: The utilization of dermoscopic analysis is becoming increasingly critical for diagnosing skin diseases by physicians and even artificial intelligence. With the expansion of dermoscopy, its vocabulary has proliferated, but the rapid evolution of the vocabulary of dermoscopy without standardized control is counterproductive. We aimed to develop a domain-specific ontology to formally represent knowledge for certain dermoscopic features. METHODS: The first phase involved creating a fundamental-level ontology that covers the fundamental aspects and elements in describing visualizations, such as shapes and colors. The second phase involved creating a domain ontology that harnesses the fundamental-level ontology to formalize the definitions of dermoscopic metaphorical terms. RESULTS: The Dermoscopy Elements of Visuals Ontology (DEVO) contains 1047 classes, 47 object properties, and 16 data properties. It has a better semiotic score compared to similar ontologies of the same domain. Three human annotators also examined the consistency, complexity, and future application of the ontology. CONCLUSIONS: The proposed ontology was able to harness the definitions of metaphoric terms by decomposing them into their visual elements. Future applications include providing education for trainees and diagnostic support for dermatologists, with the goal of generating responses to queries about dermoscopic features and integrating these features to diagnose skin diseases.

Toward a standard formal semantic representation of the model card report.

BACKGROUND: Model card reports aim to provide informative and transparent description of machine learning models to stakeholders. This report document is of interest to the National Institutes of Health's Bridge2AI initiative to address the FAIR challenges with artificial intelligence-based machine learning models for biomedical research. We present our early undertaking in developing an ontology for capturing the conceptual-level information embedded in model card reports. RESULTS: Sourcing from existing ontologies and developing the core framework, we generated the Model Card Report Ontology. Our development efforts yielded an OWL2-based artifact that represents and formalizes model card report information. The current release of this ontology utilizes standard concepts and properties from OBO Foundry ontologies. Also, the software reasoner indicated no logical inconsistencies with the ontology. With sample model cards of machine learning models for bioinformatics research (HIV social networks and adverse outcome prediction for stent implantation), we showed the coverage and usefulness of our model in transforming static model card reports to a computable format for machine-based processing. CONCLUSIONS: The benefit of our work is that it utilizes expansive and standard terminologies and scientific rigor promoted by biomedical ontologists, as well as, generating an avenue to make model cards machine-readable using semantic web technology. Our future goal is to assess the veracity of our model and later expand the model to include additional concepts to address terminological gaps. We discuss tools and software that will utilize our ontology for potential application services.

"Down the Rabbit Hole" of Vaccine Misinformation on YouTube: Network Exposure Study.

BACKGROUND: Social media platforms such as YouTube are hotbeds for the spread of misinformation about vaccines. OBJECTIVE: The aim of this study was to explore how individuals are exposed to antivaccine misinformation on YouTube based on whether they start their viewing from a keyword-based search or from antivaccine seed videos. METHODS: Four networks of videos based on YouTube recommendations were collected in November 2019. Two search networks were created from provaccine and antivaccine keywords to resemble goal-oriented browsing. Two seed networks were constructed from conspiracy and antivaccine expert seed videos to resemble direct navigation. Video contents and network structures were analyzed using the network exposure model. RESULTS: Viewers are more likely to encounter antivaccine videos through direct navigation starting from an antivaccine video than through goal-oriented browsing. In the two seed networks, provaccine videos, antivaccine videos, and videos containing health misinformation were all found to be more likely to lead to more antivaccine videos. CONCLUSIONS: YouTube has boosted the search rankings of provaccine videos to combat the influence of antivaccine information. However, when viewers are directed to antivaccine videos on YouTube from another site, the recommendation algorithm is still likely to expose them to additional antivaccine information.

Visualized Emotion Ontology: a model for representing visual cues of emotions.

BACKGROUND: Healthcare services, particularly in patient-provider interaction, often involve highly emotional situations, and it is important for physicians to understand and respond to their patients' emotions to best ensure their well-being. METHODS: In order to model the emotion domain, we have created the Visualized Emotion Ontology (VEO) to provide a semantic definition of 25 emotions based on established models, as well as visual representations of emotions utilizing shapes, lines, and colors. RESULTS: As determined by ontology evaluation metrics, VEO exhibited better machine-readability (z=1.12), linguistic quality (z=0.61), and domain coverage (z=0.39) compared to a sample of cognitive ontologies. Additionally, a survey of 1082 participants through Amazon Mechanical Turk revealed that a significantly higher proportion of people agree than disagree with 17 out of our 25 emotion images, validating the majority of our visualizations. CONCLUSION: From the development, evaluation, and serialization of the VEO, we have defined a set of 25 emotions using OWL that linked surveyed visualizations to each emotion. In the future, we plan to use the VEO in patient-facing software tools, such as embodied conversational agents, to enhance interactions between patients and providers in a clinical environment.

Developing a computational representation of human physical activity and exercise using open ontology-based approach: a Tai Chi use case.

Many studies have examined the impact of exercise and other physical activities in influencing the health outcomes of individuals. These physical activities entail an intricate sequence and series of physical anatomy, physiological movement, movement of the anatomy, etc. To better understand how these components interact with one another and their downstream impact on health outcomes, there needs to be an information model that conceptualizes all entities involved. In this study, we introduced our early development of an ontology model to computationally describe human physical activities and the various entities that compose each activity. We developed an open-sourced biomedical ontology called the Kinetic Human Movement Ontology that reused OBO Foundry terminologies and encoded in OWL2. We applied this ontology in modeling and linking a specific Tai Chi movement. The contribution of this work could enable modeling of information relating to human physical activity, like exercise, and lead towards information standardization of human movement for analysis. Future work will include expanding our ontology to include more expressive information and completely modeling entire sets of movement from human physical activity.

Dermoscopy Differential Diagnosis Explorer (D3X) Ontology to Aggregate and Link Dermoscopic Patterns to Differential Diagnoses: Development and Usability Study.

BACKGROUND: Dermoscopy is a growing field that uses microscopy to allow dermatologists and primary care physicians to identify skin lesions. For a given skin lesion, a wide variety of differential diagnoses exist, which may be challenging for inexperienced users to name and understand. OBJECTIVE: In this study, we describe the creation of the dermoscopy differential diagnosis explorer (D3X), an ontology linking dermoscopic patterns to differential diagnoses. METHODS: Existing ontologies that were incorporated into D3X include the elements of visuals ontology and dermoscopy elements of visuals ontology, which connect visual features to dermoscopic patterns. A list of differential diagnoses for each pattern was generated from the literature and in consultation with domain experts. Open-source images were incorporated from DermNet, Dermoscopedia, and open-access research papers. RESULTS: D3X was encoded in the OWL 2 web ontology language and includes 3041 logical axioms, 1519 classes, 103 object properties, and 20 data properties. We compared D3X with publicly available ontologies in the dermatology domain using a semiotic theory-driven metric to measure the innate qualities of D3X with others. The results indicate that D3X is adequately comparable with other ontologies of the dermatology domain. CONCLUSIONS: The D3X ontology is a resource that can link and integrate dermoscopic differential diagnoses and supplementary information with existing ontology-based resources. Future directions include developing a web application based on D3X for dermoscopy education and clinical practice.

The spread of COVID-19 vaccine information in Arabic on YouTube: A network exposure study.

Objective: The Arabic-speaking world had the lowest vaccine rates worldwide. The region's increasing reliance on social media as a source of COVID-19 information coupled with the increasing popularity of YouTube in the Middle East and North Africa region begs the question of what COVID-19 vaccine content is available in Arabic on YouTube. Given the platform's reputation for being a hotbed for vaccine-related misinformation in English, this study explored the COVID-19 vaccine-related content an individual is likely to be exposed to on YouTube when using keyword-based search or redirected to YouTube from another platform from an anti-vaccine seed video in Arabic. Methods: Only using the Arabic language, four networks of videos based on YouTube's recommendations were created in April 2021. Two search networks were created based on Arabic pro-vaccine and anti-vaccine keywords, and two seed networks were created from conspiracy theory and anti-vaccine expert seed videos. The network exposure model was used to examine the video contents and network structures. Results: Results show that users had a low chance of being exposed to anti-vaccine content in Arabic compared to the results of a previous study of YouTube content in English. Of the four networks, only the anti-vaccine expert network had a significant likelihood of exposing the user to more anti-vaccine videos. Implications were discussed. Conclusion: YouTube deserves credit for its efforts to clean up and limit anti-vaccine content exposure in Arabic on its platform, but continuous evaluations of the algorithm functionality are warranted.

Application of an ontology for model cards to generate computable artifacts for linking machine learning information from biomedical research.

Model card reports provide a transparent description of machine learning models which includes information about their evaluation, limitations, intended use, etc. Federal health agencies have expressed an interest in model cards report for research studies using machine-learning based AI. Previously, we have developed an ontology model for model card reports to structure and formalize these reports. In this paper, we demonstrate a Java-based library (OWL API, FaCT++) that leverages our ontology to publish computable model card reports. We discuss future directions and other use cases that highlight applicability and feasibility of ontology-driven systems to support FAIR challenges.

Dental EHR-infused Persona Ontologies to Enrich Dental Dialogue Interaction of Agents.

The quality of patient-provider communication can predict the healthcare outcomes in patients, and therefore, training dental providers to handle the communication effort with patients is crucial. In our previous work, we developed an ontology model that can standardize and represent patient-provider communication, which can later be integrated in conversational agents as tools for dental communication training. In this study, we embark on enriching our previous model with an ontology of patient personas to portray and express types of dental patient archetypes. The Ontology of Patient Personas that we developed was rooted in terminologies from an OBO Foundry ontology and dental electronic health record data elements. We discuss how this ontology aims to enhance the aforementioned dialogue ontology and future direction in executing our model in software agents to train dental students.

Towards an ontology-based medication conversational agent for PrEP and PEP.

HIV (human immunodeficiency virus) can damage a human's immune system and cause Acquired Immunodeficiency Syndrome (AIDS) which could lead to severe outcomes, including death. While HIV infections have decreased over the last decade, there is still a significant population where the infection permeates. PrEP and PEP are two proven preventive measures introduced that involve periodic dosage to stop the onset of HIV infection. However, the adherence rates for this medication is low in part due to the lack of information about the medication. There exist several communication barriers that prevent patient-provider communication from happening. In this work, we present our ontology-based method for automating the communication of this medication that can be deployed for live conversational agents for PrEP and PEP. This method facilitates a model of automated conversation between the machine and user can also answer relevant questions.

NET-EXPO: A Gephi Plugin Towards Social Network Analysis of Network Exposure for Unipartite and Bipartite Graphs.

Social network analysis (SNA) concerns itself in studying network structures in relation to individuals' behavior. Individuals may be influenced by their network members in their behavior, and thus past researchers have developed computational methods that allow us to measure the extent to which individuals are exposed to members with certain behavior within one's social network, and that be correlated with their own behavior. Some of these methods include network exposure model, affiliation exposure model, and decomposed network exposure models. We developed a Gephi plugin that computes and visualizes these various kinds of network exposure models called NET-EXPO. We experimented with NET-EXPO on some social network datasets to demonstrate its pragmatic use in social network research. This plugin has the potential to equip researchers with a tool to compute network exposures in a user friendly way and simplify the process to compute and visualize the network data.

Designing an Ontology for Emotion-driven Visual Representations.

Emotions influence our perceptions and decisions and are often felt more strongly in situations related to healthcare. Therefore, it is important to understand how both providers and patients express their emotions in face-to-face scenarios. An ontology is a way to represent domain concepts and the relationships between them in a polyarchical manner. We have created an ontological model called the Visualized Emotion Ontology (VEO) that expresses the semantic definitions and visualizations of 25 emotions based on published research. With VEO, we can augment patient-facing software tools, like embodied conversational agents, to improve patient-provider interaction in clinical environments.